using ModelingToolkit
using OrdinaryDiffEq, DiffEqCallbacks
using Plots
using CSV
using DataFrames
using Dates
using CaMKIIModel
using CaMKIIModel: second, μM
Plots.default(lw=1.5)ROS effects
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) 8.926502 seconds (23.29 M allocations: 1.224 GiB, 2.36% gc time, 90.19% compilation time)retcode: Success
Interpolation: 3rd order Hermite
t: 4019-element Vector{Float64}:
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3.4517766411484665
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⋮
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u: 4019-element Vector{Vector{Float64}}:
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⋮
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prob2 = remake(prob, p=[sys.ROS => 0.1μM])
@time sol2 = solve(prob2, alg; callback) 0.920238 seconds (63.27 k allocations: 208.038 MiB, 11.14% gc time)retcode: Success
Interpolation: 3rd order Hermite
t: 4019-element Vector{Float64}:
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⋮
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u: 4019-element Vector{Vector{Float64}}:
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⋮
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[151362.40315333926, 13431.05892960409, -70.10161714072797, 0.13478294893696188, 0.13478325487688592, 0.1347835614396127, 0.1347838686976125, 0.13478417672628637, 0.13478448560411557, 0.13478479541282054 … 0.001174205774785441, 0.0016063612392441043, 0.002486532941516183, 0.0015842287273537604, 0.9997310237639004, 0.9997290512889963, 0.006428037481650419, 783.0047063629532, 782.6741631568799, 0.0018757671135336876]
[151406.62434878098, 13386.965138502435, -70.01850741882363, 0.13422996720047692, 0.13423026631111062, 0.13423056615569012, 0.13423086680754737, 0.1342311683429796, 0.1342314708414007, 0.13423177438550152 … 0.0011894303887176486, 0.0016163142191269301, 0.002501934916894105, 0.0016032570495331491, 0.9997261418803839, 0.9997241530147133, 0.006464463403179324, 782.2462919952438, 781.9243369434565, 0.0018290343462134598]
[151453.0632770309, 13340.661567046856, -69.93029457539885, 0.13365570753819137, 0.13365599754487992, 0.1336562883678799, 0.13365658008038048, 0.13365687275853003, 0.1336571664815876, 0.1336574613320827 … 0.0012057983815949476, 0.0016269448841401395, 0.0025183857108780827, 0.0016236975512667596, 0.9997208281021642, 0.9997188571416543, 0.006503350163092712, 781.4248482052263, 781.1117204902667, 0.0017808883290139025]
[151469.10599508276, 13324.665891674314, -69.89958935312049, 0.13345897605266832, 0.13345926268983752, 0.13345955016769007, 0.1334598385592453, 0.13346012794047482, 0.1334604183904534, 0.13346070999151852 … 0.0012115413836495288, 0.001630661156493646, 0.002524136944550219, 0.0016308723776175197, 0.9997189531991868, 0.9997169899201898, 0.00651694016171944, 781.1360311597318, 780.8259048088499, 0.0017645029323400737]ROS (H2O2) 0.5uM
prob3 = remake(prob, p=[sys.ROS => 0.5μM])
@time sol3 = solve(prob3, alg; callback) 1.139676 seconds (63.31 k allocations: 208.344 MiB, 22.74% gc time)retcode: Success
Interpolation: 3rd order Hermite
t: 4019-element Vector{Float64}:
0.0
0.019333123284852018
0.09098129546759268
0.20735582943986758
0.45611910276868917
1.047256292840759
2.0342667657226547
3.4517766411489377
6.73379242391375
12.450117081024938
⋮
152229.668379067
156693.01110375646
162137.25596277026
168220.05331925137
175684.1621984258
183498.26432090864
192274.69276273437
202819.53195738627
205000.0
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]
[150952.7504077194, 13838.375711519551, -68.79732946186226, 0.1211319185255175, 0.1211301421535992, 0.12113000811850358, 0.12113000037367234, 0.12113000001389383, 0.12113000000038378, 0.12113000000000405 … 0.2608055799112056, 0.009769882842069916, 0.001879826176081169, 0.09242766669618695, 0.2215639938807744, 0.9660018276402699, 0.007020208561323646, 829.9999654017583, 829.9994975880693, 0.002598565959029538]
[150952.75062244057, 13838.374513299192, -68.81607005265553, 0.12115248970210647, 0.12113624253259858, 0.12113143375871602, 0.12113027926811751, 0.12113004704056851, 0.12113000693481112, 0.12113000089551408 … 0.26078941009382306, 0.009769459049732313, 0.001878904244651442, 0.09241901973901424, 0.2215787945110049, 0.9660085993318799, 0.00702008986027517, 829.9998348635061, 829.9976422525165, 0.0025933105246816854]
[150952.7509740238, 13838.372555328333, -68.84681913285227, 0.12118951551963694, 0.12115723910142132, 0.12114109135582982, 0.12113403405679991, 0.12113131833063846, 0.12113038966346883, 0.12113010483012127 … 0.2607638707001999, 0.009768805322556195, 0.0018766436937193184, 0.09240497563401104, 0.22160283236040595, 0.9660195931792828, 0.007017234889558553, 829.9996133960318, 829.9946506157202, 0.002584947833510376]
[150952.7517373371, 13838.368384399068, -68.91207316777847, 0.12125418995384041, 0.12120713813483533, 0.12117519662647316, 0.1211549441109046, 0.12114295934422183, 0.12113633873395532, 0.12113292110288301 … 0.2607122383588733, 0.00976754294689657, 0.0018699196262940544, 0.0923749578279845, 0.2216542075240971, 0.9660430731013478, 0.0070030143052343865, 829.9990964774663, 829.9883445519497, 0.002567707801049976]
[150952.75361533565, 13838.358559292059, -69.06429960994141, 0.12136450208851983, 0.12130632552358438, 0.12125925929399752, 0.12122229800810433, 0.12119414515426226, 0.1211733598588045, 0.12115849269665879 … 0.26060507831375035, 0.009765228548607825, 0.0018505337694469342, 0.09230364339951613, 0.22177624785138977, 0.9660987611411453, 0.006946470397388732, 829.9976227528975, 829.9738229154025, 0.0025298083713906918]
[150952.75694915713, 13838.34240329337, -69.31024285744353, 0.12149196513254247, 0.12142927821043346, 0.12137426379919643, 0.12132672249013036, 0.12128628091507475, 0.12125242557826563, 0.12122454121844706 … 0.26047114911179464, 0.009763403076884485, 0.0018178174419014564, 0.09218462776986637, 0.2219798989175974, 0.9661914345949096, 0.006833754172875411, 829.9944193668179, 829.9509077855928, 0.002474807978215882]
[150952.76215620188, 13838.319723120678, -69.64637448767446, 0.12162015426876963, 0.12155743299711912, 0.12149988983034511, 0.12144759471003602, 0.12140052118634274, 0.12135855488207918, 0.12132150441596085 … 0.2603648729749554, 0.00976504655280048, 0.0017738156907532085, 0.09201383579531924, 0.22227216398019903, 0.9663239343003682, 0.006675512062656691, 829.9883533251192, 829.9205247545176, 0.002410689396481114]
[150952.77598869594, 13838.2694938995, -70.3506378865745, 0.12180447948880602, 0.1217476844353238, 0.12169340184085987, 0.12164180995533581, 0.12159304920072049, 0.12154722283384203, 0.12150439833798572 … 0.2604150766754201, 0.009786689200123865, 0.0016855899094922052, 0.09161908329520757, 0.22294828828976596, 0.966628695781256, 0.0063550397136777625, 829.9689941817725, 829.8589858006806, 0.002310655727734318]
[150952.80529264064, 13838.18882346682, -71.35304509818101, 0.1219637836440819, 0.1219193775332835, 0.12187579038290362, 0.12183318573340757, 0.12179171693004426, 0.1217515266716738, 0.12171274673876377 … 0.2610441780460306, 0.009873892913308365, 0.0015688568862425706, 0.09093422465365371, 0.22412560303273463, 0.967155451223036, 0.005926150085675941, 829.923524981244, 829.7704141396295, 0.0022289950402245053]
⋮
[151177.5980993207, 13615.453370126514, -70.44573834543321, 0.13702089704843468, 0.13702087757364084, 0.13702085295531424, 0.13702082309064229, 0.13702078787264227, 0.13702074718994864, 0.1370207009265871 … 0.0011131770383532844, 0.0015657870769716221, 0.002423751086816901, 0.001507598142252379, 0.9995547830962707, 0.9997484421326583, 0.006279371250897506, 784.8449238181372, 784.4802096989263, 0.0020448301294197727]
[151205.03598417286, 13588.035995577784, -70.39341088138066, 0.13673274132583893, 0.136732895962884, 0.13673304818191784, 0.1367331979668293, 0.13673334530084877, 0.136733490166514, 0.13673363254563464 … 0.00112232194319741, 0.0015718944501589048, 0.002433195616835611, 0.0015190704331408842, 0.999687738145029, 0.9997455790810663, 0.006301755412662899, 784.9919862779354, 784.6311823990416, 0.0020320089361796924]
[151237.75986518903, 13555.371490748064, -70.33247280165385, 0.13634740053466754, 0.13634765261927956, 0.13634790390132293, 0.13634815441499776, 0.1363484041958858, 0.13634865328102033, 0.13634890170896155 … 0.00113299254515042, 0.0015790326023814494, 0.0024442401824658773, 0.0015324893737585382, 0.9997301456758501, 0.9997422093364849, 0.006327922863482857, 784.8085405019236, 784.4535137053001, 0.002005449193395649]
[151273.380149257, 13519.836600603798, -70.26673060448118, 0.13590575282411063, 0.13590604665915662, 0.13590634049201958, 0.13590663438057235, 0.13590692838502635, 0.13590722256805066, 0.13590751699489872 … 0.0011446175865427724, 0.0015867698139152091, 0.002456211176358873, 0.0015470652229029617, 0.9997377628053504, 0.9997385273079582, 0.006356274292265693, 784.3927065966795, 784.0445517984208, 0.0019703233318538005]
[151315.77134176032, 13477.559244346083, -70.18840368846539, 0.13537097718663413, 0.13537128466560064, 0.135371592559394, 0.1353719009366889, 0.13537220986893667, 0.13537251943050674, 0.13537282969883685 … 0.001158583046947918, 0.001596035094479721, 0.0024705494336960724, 0.0015645910354670895, 0.9997357184902987, 0.999734073698319, 0.006390217698570697, 783.7665526660294, 783.4267996140948, 0.00192559510469377]
[151358.6447906545, 13434.806583900416, -70.10864235465442, 0.13483019080754075, 0.1348304971719486, 0.13483080414700774, 0.13483111180503518, 0.13483142022127176, 0.13483172947403166, 0.13483203964486032 … 0.0011729615039210981, 0.001605524198424321, 0.002485235283769428, 0.0015826299918434653, 0.9997314266114354, 0.9997294613744955, 0.006424967786165939, 783.067815006895, 782.7365344295829, 0.0018797711247857144]
[151405.0284895752, 13388.556398343191, -70.0215227935951, 0.13424982550942433, 0.13425012489997273, 0.13425042502099027, 0.1342507259457924, 0.13425102775065825, 0.13425133051498245, 0.1342516343214351 … 0.0011889215329410649, 0.0016159528187008525, 0.0025013741994334756, 0.0016025625757086037, 0.9997263208770492, 0.9997243321237557, 0.006463138217084981, 782.2740844758273, 781.9518225205945, 0.001830706160872507]
[151458.38250538096, 13335.357949703752, -69.92012537858207, 0.13359038775004053, 0.13359067665139435, 0.13359096637703705, 0.1335912570001161, 0.13359154859673603, 0.13359184124610946, 0.1335921350307172 … 0.0012076873871469751, 0.0016281752477340732, 0.0025202892519312413, 0.001626070201985845, 0.9997202085156732, 0.999718240182082, 0.006507848139662067, 781.329367112405, 781.0172372163787, 0.0017754417709193865]
[151469.10198081323, 13324.669921907891, -69.89959724546107, 0.13345902635865134, 0.1334593129723598, 0.13345960042704672, 0.13345988879574194, 0.1334601781544274, 0.1334604685821882, 0.1334607601613721 … 0.0012115058325973278, 0.0016306584080692144, 0.002524135532906223, 0.0016308705866936754, 0.9997189538410474, 0.9997169904224869, 0.006516937056444784, 781.1361067314048, 780.8259796394175, 0.001764507104782125]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")"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/ros-camkii.pdf"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")"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/ros-camkiiox.pdf"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")"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/ros-camkiip.pdf"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"])42-element Vector{Float64}:
0.02305850621757014
0.023225557529411765
0.023536003837902393
0.022995786588235295
0.023056161133316953
0.02236794743822152
0.02448575734900888
0.02631837493460871
0.029628792824062226
0.0306227531696316
⋮
0.02665056333747046
0.02525893438851731
0.024749347823716496
0.024158682609370527
0.023572491294117648
0.0240760416039372
0.023230166
0.023759599761907887
0.02369791084482974ros50 = 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"])42-element Vector{Float64}:
0.01579193843196981
0.015098907892605207
0.01579878654371588
0.015408311367567479
0.01575464714359121
0.015563615686070896
0.015839325542753135
0.01815890968670797
0.022420341690296358
0.026401360928455686
⋮
0.01970504059747541
0.018928610243134615
0.018308801083333333
0.017872510075561544
0.017135324764712814
0.016622042234321177
0.01699837223508933
0.01644948545788867
0.016236308371972322plot(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")"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/ros-exp.pdf"Runtime information
using InteractiveUtils
InteractiveUtils.versioninfo()Julia Version 1.12.4
Commit 01a2eadb047 (2026-01-06 16:56 UTC)
Build Info:
Official https://julialang.org release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 4 × Intel(R) Xeon(R) Platinum 8370C CPU @ 2.80GHz
WORD_SIZE: 64
LLVM: libLLVM-18.1.7 (ORCJIT, icelake-server)
GC: Built with stock GC
Threads: 4 default, 1 interactive, 4 GC (on 4 virtual cores)
Environment:
JULIA_CPU_TARGET = generic;icelake-server,clone_all;znver3,clone_all
JULIA_CONDAPKG_OFFLINE = true
JULIA_CONDAPKG_BACKEND = Null
JULIA_CI = true
LD_LIBRARY_PATH = /opt/hostedtoolcache/Python/3.14.2/x64/lib
JULIA_NUM_THREADS = autousing Pkg
Pkg.status()Project CaMKIIModel v0.7.0
Status `~/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/Project.toml`
[336ed68f] CSV v0.10.15
[a93c6f00] DataFrames v1.8.1
[459566f4] DiffEqCallbacks v4.11.0
[f6369f11] ForwardDiff v1.3.1
[682c06a0] JSON v1.3.0
[23fbe1c1] Latexify v0.16.10
[98b081ad] Literate v2.21.0
[2fda8390] LsqFit v0.15.1
⌅ [961ee093] ModelingToolkit v10.31.2
[77ba4419] NaNMath v1.1.3
[1dea7af3] OrdinaryDiffEq v6.105.0
[91a5bcdd] Plots v1.41.4
[2913bbd2] StatsBase v0.34.9
[9672c7b4] SteadyStateDiffEq v2.8.0
[ea8e919c] SHA v0.7.0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated`This notebook was generated using Literate.jl.