From c23120c0e52f0c67d13efd82f39b09f28d03bd1b Mon Sep 17 00:00:00 2001 From: Leandro Martinez Date: Fri, 20 Sep 2024 16:35:58 -0300 Subject: [PATCH] fix doc builds --- .github/workflows/CI.yml | 2 +- docs/Manifest.toml | 77 ++---- docs/make.jl | 4 + docs/src/pluto_notebooks/Manifest.toml | 46 +--- .../pluto_notebooks/{ => drafts}/sh3_tmao.jl | 0 docs/src/pluto_notebooks/proteinA_urea.jl | 76 ++---- docs/src/pluto_notebooks/proteinA_urea.md | 57 +++-- docs/src/pluto_notebooks/rnaset1_urea.jl | 66 ++--- docs/src/pluto_notebooks/rnaset1_urea.md | 52 ++-- docs/src/pluto_notebooks/sh3_tmao.md | 237 ------------------ 10 files changed, 132 insertions(+), 485 deletions(-) rename docs/src/pluto_notebooks/{ => drafts}/sh3_tmao.jl (100%) delete mode 100644 docs/src/pluto_notebooks/sh3_tmao.md diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index f4dae85..10583e5 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -40,7 +40,7 @@ jobs: - uses: actions/checkout@v3 - uses: julia-actions/setup-julia@v2 with: - version: 'pre' + version: '1.10' - run: | julia --project=docs -e ' import Pkg; Pkg.add("Documenter") diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 8876e2a..b058c46 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,6 +1,6 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.0-rc3" +julia_version = "1.10.5" manifest_format = "2.0" project_hash = "f24464e24f50c869c4c5b81eaeef23cca078ef04" @@ -32,7 +32,7 @@ version = "1.1.3" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.2" +version = "1.1.1" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] @@ -66,17 +66,15 @@ version = "7.16.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.11.0" [[deps.AtomsBase]] deps = ["LinearAlgebra", "PeriodicTable", "Printf", "Requires", "StaticArrays", "Unitful", "UnitfulAtomic"] -git-tree-sha1 = "0fa9318ceff45a514bd1dbed7563b32ae2cdb73f" +git-tree-sha1 = "aab46de4a22e3619fe0167a18019b94a65033bd7" uuid = "a963bdd2-2df7-4f54-a1ee-49d51e6be12a" -version = "0.4.1" +version = "0.4.2" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -version = "1.11.0" [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" @@ -236,7 +234,6 @@ version = "1.0.0" [[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -version = "1.11.0" [[deps.Dbus_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] @@ -265,7 +262,6 @@ version = "1.15.1" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] @@ -354,7 +350,6 @@ version = "4.4.4+1" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -version = "1.11.0" [[deps.FillArrays]] deps = ["LinearAlgebra"] @@ -426,7 +421,6 @@ version = "1.0.14+0" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -version = "1.11.0" [[deps.FuzzyCompletions]] deps = ["REPL"] @@ -557,7 +551,6 @@ version = "1.4.2" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -version = "1.11.0" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -651,7 +644,6 @@ version = "1.2.2" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" -version = "1.11.0" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -661,17 +653,16 @@ version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "8.6.0+0" +version = "8.4.0+0" [[deps.LibGit2]] deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -version = "1.11.0" [[deps.LibGit2_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.7.2+0" +version = "1.6.4+0" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] @@ -680,7 +671,6 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -version = "1.11.0" [[deps.Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -733,7 +723,6 @@ version = "2.40.1+0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -version = "1.11.0" [[deps.Literate]] deps = ["Base64", "IOCapture", "JSON", "REPL"] @@ -765,7 +754,6 @@ version = "0.3.28" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -version = "1.11.0" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] @@ -799,7 +787,6 @@ version = "1.1.1" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -version = "1.11.0" [[deps.MarkdownAST]] deps = ["AbstractTrees", "Markdown"] @@ -816,7 +803,7 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.6+0" +version = "2.28.2+1" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -831,7 +818,6 @@ version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" -version = "1.11.0" [[deps.MolSimToolkit]] deps = ["AtomsBase", "CellListMap", "Chemfiles", "DocStringExtensions", "EasyFit", "LaTeXStrings", "LinearAlgebra", "OffsetArrays", "PDBTools", "ProgressMeter", "ProteinSecondaryStructures", "Reexport", "StaticArrays", "Statistics", "StatsBase", "TestItems"] @@ -845,7 +831,7 @@ weakdeps = ["Plots"] [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2023.12.12" +version = "2023.1.10" [[deps.MsgPack]] deps = ["Serialization"] @@ -887,7 +873,7 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.27+1" +version = "0.3.23+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -976,13 +962,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.43.4+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.11.0" -weakdeps = ["REPL"] - - [deps.Pkg.extensions] - REPLExt = "REPL" +version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1066,7 +1048,6 @@ version = "2.3.2" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -version = "1.11.0" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] @@ -1111,9 +1092,9 @@ version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "1d587203cf851a51bf1ea31ad7ff89eff8d625ea" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.11.0" +version = "2.11.1" [deps.QuadGK.extensions] QuadGKEnzymeExt = "Enzyme" @@ -1122,14 +1103,12 @@ version = "2.11.0" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -version = "1.11.0" [[deps.Random]] deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -version = "1.11.0" [[deps.RecipesBase]] deps = ["PrecompileTools"] @@ -1202,7 +1181,6 @@ version = "1.4.5" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -version = "1.11.0" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] @@ -1217,13 +1195,12 @@ uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] @@ -1234,7 +1211,7 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -version = "1.11.0" +version = "1.10.0" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] @@ -1268,14 +1245,9 @@ uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" version = "1.4.3" [[deps.Statistics]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0" +deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.11.1" -weakdeps = ["SparseArrays"] - - [deps.Statistics.extensions] - SparseArraysExt = ["SparseArrays"] +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -1309,10 +1281,6 @@ git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" version = "0.3.4" -[[deps.StyledStrings]] -uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" -version = "1.11.0" - [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -1320,7 +1288,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "7.7.0+0" +version = "7.2.1+1" [[deps.TOML]] deps = ["Dates"] @@ -1353,7 +1321,6 @@ version = "0.1.1" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -version = "1.11.0" [[deps.TestItems]] git-tree-sha1 = "8621ba2637b49748e2dc43ba3d84340be2938022" @@ -1378,7 +1345,6 @@ version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -version = "1.11.0" [[deps.UnPack]] git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" @@ -1387,7 +1353,6 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -version = "1.11.0" [[deps.UnicodeFun]] deps = ["REPL"] @@ -1697,7 +1662,7 @@ version = "1.1.6+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.59.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] diff --git a/docs/make.jl b/docs/make.jl index 6cd9e65..d1273c5 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -30,6 +30,10 @@ makedocs( sitename = "PereiraMartinez2024.jl", format=Documenter.HTML(; mathengine=Documenter.MathJax3(), + size_threshold_ignore=[ + "pluto_notebooks/proteinA_urea.md", + "pluto_notebooks/rnaset1_urea.md", + ], ), pages = [ "Home" => "index.md", diff --git a/docs/src/pluto_notebooks/Manifest.toml b/docs/src/pluto_notebooks/Manifest.toml index e720f18..5747939 100644 --- a/docs/src/pluto_notebooks/Manifest.toml +++ b/docs/src/pluto_notebooks/Manifest.toml @@ -1,20 +1,18 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.0-rc3" +julia_version = "1.10.5" manifest_format = "2.0" project_hash = "33308c26aeaf88935c476becd75fdb6db775d1fc" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.2" +version = "1.1.1" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.11.0" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -version = "1.11.0" [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" @@ -52,12 +50,10 @@ version = "1.0.0" [[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -version = "1.11.0" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -version = "1.11.0" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -82,7 +78,6 @@ version = "0.10.13" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -version = "1.11.0" [[deps.FuzzyCompletions]] deps = ["REPL"] @@ -105,7 +100,6 @@ version = "0.9.5" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -version = "1.11.0" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -131,17 +125,16 @@ version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "8.6.0+0" +version = "8.4.0+0" [[deps.LibGit2]] deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -version = "1.11.0" [[deps.LibGit2_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.7.2+0" +version = "1.6.4+0" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] @@ -150,11 +143,9 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -version = "1.11.0" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -version = "1.11.0" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] @@ -176,7 +167,6 @@ version = "1.1.1" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -version = "1.11.0" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -187,11 +177,11 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.6+0" +version = "2.28.2+1" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2023.12.12" +version = "2023.1.10" [[deps.MsgPack]] deps = ["Serialization"] @@ -221,13 +211,9 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.6.3" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.11.0" -weakdeps = ["REPL"] - - [deps.Pkg.extensions] - REPLExt = "REPL" +version = "1.10.0" [[deps.Pluto]] deps = ["Base64", "Configurations", "Dates", "Downloads", "ExpressionExplorer", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "LoggingExtras", "MIMEs", "Malt", "Markdown", "MsgPack", "Pkg", "PlutoDependencyExplorer", "PrecompileSignatures", "PrecompileTools", "REPL", "RegistryInstances", "RelocatableFolders", "Scratch", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] @@ -261,17 +247,14 @@ version = "1.4.3" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -version = "1.11.0" [[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -version = "1.11.0" [[deps.Random]] deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -version = "1.11.0" [[deps.RegistryInstances]] deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"] @@ -297,7 +280,6 @@ version = "1.2.1" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -version = "1.11.0" [[deps.SimpleBufferStream]] git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" @@ -306,11 +288,6 @@ version = "1.2.0" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -version = "1.11.0" - -[[deps.StyledStrings]] -uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" -version = "1.11.0" [[deps.TOML]] deps = ["Dates"] @@ -337,7 +314,6 @@ version = "1.10.0" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -version = "1.11.0" [[deps.TranscodingStreams]] git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2" @@ -357,11 +333,9 @@ version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -version = "1.11.0" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -version = "1.11.0" [[deps.Zlib_jll]] deps = ["Libdl"] @@ -371,7 +345,7 @@ version = "1.2.13+1" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.59.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] diff --git a/docs/src/pluto_notebooks/sh3_tmao.jl b/docs/src/pluto_notebooks/drafts/sh3_tmao.jl similarity index 100% rename from docs/src/pluto_notebooks/sh3_tmao.jl rename to docs/src/pluto_notebooks/drafts/sh3_tmao.jl diff --git a/docs/src/pluto_notebooks/proteinA_urea.jl b/docs/src/pluto_notebooks/proteinA_urea.jl index bd8d26a..04179e2 100644 --- a/docs/src/pluto_notebooks/proteinA_urea.jl +++ b/docs/src/pluto_notebooks/proteinA_urea.jl @@ -7,6 +7,9 @@ using InteractiveUtils # ╔═╡ 96e27383-8c0b-4b95-b7fb-80bb97f390bb import Pkg +# ╔═╡ 0b04d8cc-36e6-4069-8f48-e2c4058f2839 +using Latexify + # ╔═╡ dff61cee-c2c4-41aa-8fc1-fbac08a67beb using Trapz @@ -189,8 +192,8 @@ md"The preferential interaction parameters of BpDA in urea, for the N and U stat # ╔═╡ 813427fb-7d88-44f3-b118-2d5b94031a50 ∂g₃∂g₂ = DataFrame( - "N" => [ 0.819482, 1.25926, 1.78542, 2.35528, 2.901680 ] / 184.4, - "U" => [0.469901, 1.43146, 2.24178, 2.71291, 3.41588 ] / 184.4, + "N" => [ 0.819482, 1.25926, 1.78542, 2.35528, 2.901680 ] / (M2/M3), + "U" => [0.469901, 1.43146, 2.24178, 2.71291, 3.41588 ] / (M2/M3), ) # ╔═╡ 4d8bfae0-2eda-462b-a9ec-c0082097305d @@ -293,6 +296,7 @@ PLUTO_PROJECT_TOML_CONTENTS = """ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" EasyFit = "fde71243-0cda-4261-b7c7-4845bd106b21" LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" +Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" MolSimToolkit = "054db54f-6694-444d-9bbb-e9ecdbfe77be" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" @@ -304,6 +308,7 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" DataFrames = "~1.6.1" EasyFit = "~0.6.6" LaTeXStrings = "~1.3.1" +Latexify = "~0.16.5" MolSimToolkit = "~1.18.1" Plots = "~1.40.8" PlutoUI = "~0.7.60" @@ -315,9 +320,9 @@ Unitful = "~1.21.0" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.0-rc3" +julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "55045c72e7af5ece6a3c7703cf8f35843f41b634" +project_hash = "462273a7e4f1e29a79507a57ad862077f68deb15" [[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] @@ -343,7 +348,7 @@ version = "1.1.3" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.2" +version = "1.1.1" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] @@ -377,7 +382,6 @@ version = "7.16.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.11.0" [[deps.AtomsBase]] deps = ["LinearAlgebra", "PeriodicTable", "Printf", "Requires", "StaticArrays", "Unitful", "UnitfulAtomic"] @@ -387,7 +391,6 @@ version = "0.4.2" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -version = "1.11.0" [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" @@ -541,7 +544,6 @@ version = "1.0.0" [[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -version = "1.11.0" [[deps.Dbus_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] @@ -570,7 +572,6 @@ version = "1.15.1" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] @@ -643,7 +644,6 @@ version = "4.4.4+1" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -version = "1.11.0" [[deps.FillArrays]] deps = ["LinearAlgebra"] @@ -715,7 +715,6 @@ version = "1.0.14+0" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -version = "1.11.0" [[deps.GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] @@ -810,7 +809,6 @@ version = "1.4.2" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -version = "1.11.0" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -904,17 +902,16 @@ version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "8.6.0+0" +version = "8.4.0+0" [[deps.LibGit2]] deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -version = "1.11.0" [[deps.LibGit2_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.7.2+0" +version = "1.6.4+0" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] @@ -923,7 +920,6 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -version = "1.11.0" [[deps.Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -976,7 +972,6 @@ version = "2.40.1+0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -version = "1.11.0" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] @@ -996,7 +991,6 @@ version = "0.3.28" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -version = "1.11.0" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] @@ -1024,7 +1018,6 @@ version = "0.5.13" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -version = "1.11.0" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1035,7 +1028,7 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.6+0" +version = "2.28.2+1" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1050,7 +1043,6 @@ version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" -version = "1.11.0" [[deps.MolSimToolkit]] deps = ["AtomsBase", "CellListMap", "Chemfiles", "DocStringExtensions", "EasyFit", "LaTeXStrings", "LinearAlgebra", "OffsetArrays", "PDBTools", "ProgressMeter", "ProteinSecondaryStructures", "Reexport", "StaticArrays", "Statistics", "StatsBase", "TestItems"] @@ -1064,7 +1056,7 @@ weakdeps = ["Plots"] [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2023.12.12" +version = "2023.1.10" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1100,7 +1092,7 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.27+1" +version = "0.3.23+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1189,13 +1181,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.43.4+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.11.0" -weakdeps = ["REPL"] - - [deps.Pkg.extensions] - REPLExt = "REPL" +version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1262,7 +1250,6 @@ version = "2.3.2" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -version = "1.11.0" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] @@ -1318,14 +1305,12 @@ version = "2.11.1" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -version = "1.11.0" [[deps.Random]] deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -version = "1.11.0" [[deps.RecipesBase]] deps = ["PrecompileTools"] @@ -1392,7 +1377,6 @@ version = "1.4.5" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -version = "1.11.0" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] @@ -1413,7 +1397,6 @@ version = "1.2.0" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] @@ -1424,7 +1407,7 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -version = "1.11.0" +version = "1.10.0" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] @@ -1458,14 +1441,9 @@ uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" version = "1.4.3" [[deps.Statistics]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0" +deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.11.1" -weakdeps = ["SparseArrays"] - - [deps.Statistics.extensions] - SparseArraysExt = ["SparseArrays"] +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -1499,10 +1477,6 @@ git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" version = "0.3.4" -[[deps.StyledStrings]] -uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" -version = "1.11.0" - [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -1510,7 +1484,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "7.7.0+0" +version = "7.2.1+1" [[deps.TOML]] deps = ["Dates"] @@ -1543,7 +1517,6 @@ version = "0.1.1" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -version = "1.11.0" [[deps.TestItems]] git-tree-sha1 = "42fd9023fef18b9b78c8343a4e2f3813ffbcefcb" @@ -1573,7 +1546,6 @@ version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -version = "1.11.0" [[deps.UnPack]] git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" @@ -1582,7 +1554,6 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -version = "1.11.0" [[deps.UnicodeFun]] deps = ["REPL"] @@ -1892,7 +1863,7 @@ version = "1.1.6+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.59.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] @@ -1924,6 +1895,7 @@ version = "1.4.1+1" # ╟─19208b6e-7039-11ef-2685-c9fd57102877 # ╟─77c25151-8673-4ec1-9687-80f1fceb4e5c # ╟─6f3ec99b-15b1-4014-b146-09e29864382c +# ╠═0b04d8cc-36e6-4069-8f48-e2c4058f2839 # ╟─8293f49a-57a1-49b5-a2da-95a43b4cd097 # ╟─1ca88373-114c-464d-aaac-9f3b25893820 # ╟─90ad306d-163e-4fb3-a00e-6b86c32900f9 diff --git a/docs/src/pluto_notebooks/proteinA_urea.md b/docs/src/pluto_notebooks/proteinA_urea.md index 5c9443d..83e619c 100644 --- a/docs/src/pluto_notebooks/proteinA_urea.md +++ b/docs/src/pluto_notebooks/proteinA_urea.md @@ -25,8 +25,8 @@

BdpA transfer free energy to urea

@@ -47,6 +47,9 @@

Experimental data for urea aqueous solutions (28\(^\circ\)C):

+
using Latexify
+ +
m₃γ₃ρ₀
10.0 mol kg^-11.00.997 g mL^-1
20.51 mol kg^-10.961.0084 g mL^-1
31.05 mol kg^-10.9241.016 g mL^-1
42.2 mol kg^-10.8591.0298 g mL^-1
@@ -54,7 +57,7 @@

The data above is used to compute the \((\partial\ln\gamma_3/\partial m_3)\) quantity. For that we need to create first a plot:

- +

The shape of the plot suggests that a quadratic fit will capture precisely the trend:

@@ -64,15 +67,15 @@ Equation: y = ax^2 + bx + c -With: a = 0.005647775953714212 kg^2 mol^-2 - b = -0.0813806205226127 kg mol^-1 - c = -0.00022283020608271598 +With: a = 0.005647775958546127 kg^2 mol^-2 + b = -0.08138062053425879 kg mol^-1 + c = -0.00022283020256378232 Pearson correlation coefficient, R = 0.9999787191515569 mol kg^-1 -Average square residue = 1.3341140148131078e-7 +Average square residue = 1.3341140148130794e-7 -Predicted Y: ypred = [-0.00022283020608271598, -0.04025796014705413, ...] -residues = [-0.00022283020608271598, 0.0005640343732010375, ...] +Predicted Y: ypred = [-0.00022283020256378232, -0.040257960148217926, ...] +residues = [-0.00022283020256378232, 0.0005640343720372393, ...] ----------------------------------------------- @@ -88,10 +91,10 @@ residues = [-0.00022283020608271598, 0.0005640343732010375, ...] 
4-element Vector{Quantity{Float64, 𝐌 𝐍^-1, Unitful.FreeUnits{(kg, mol^-1), 𝐌 𝐍^-1, nothing}}}:
-  -0.0813806205226127 kg mol^-1
- -0.07561988904982421 kg mol^-1
- -0.06952029101981286 kg mol^-1
- -0.05653040632627017 kg mol^-1
+ -0.08138062053425879 kg mol^-1 + -0.07561988905654174 kg mol^-1 + -0.06952029102131192 kg mol^-1 + -0.05653040631665583 kg mol^-1 
urea_data
m₃γ₃ρ₀∂lnγ₃∂m₃
10.0 mol kg^-11.00.997 g mL^-1-0.0813806 kg mol^-1
20.51 mol kg^-10.961.0084 g mL^-1-0.0756199 kg mol^-1
31.05 mol kg^-10.9241.016 g mL^-1-0.0695203 kg mol^-1
42.2 mol kg^-10.8591.0298 g mL^-1-0.0565304 kg mol^-1
@@ -100,7 +103,7 @@ residues = [-0.00022283020608271598, 0.0005640343732010375, ...]

We also obtain an expression for the density as a function of the concentration, in mol/L:

- +

Where the fit is:

@@ -110,15 +113,15 @@ residues = [-0.00022283020608271598, 0.0005640343732010375, ...] Equation: y = ax^2 + bx + c -With: a = -0.003148583771408349 g L^2 mL^-1 mol^-2 - b = 0.021417043071873296 g L mL^-1 mol^-1 - c = 0.9973483095725536 g mL^-1 +With: a = -0.003148583771714299 g L^2 mL^-1 mol^-2 + b = 0.02141704307263717 g L mL^-1 mol^-1 + c = 0.9973483095723117 g mL^-1 -Pearson correlation coefficient, R = 0.9988889736362447 g mol mL^-1 L^-1 -Average square residue = 3.1548945450689946e-7 g^2 mL^-2 +Pearson correlation coefficient, R = 0.9988889736362446 g mol mL^-1 L^-1 +Average square residue = 3.154894545069039e-7 g^2 mL^-2 -Predicted Y: ypred = [0.9973483095725536 g mL^-1, 1.0075299894243765 g mL^-1, ...] -residues = [0.00034830957255360673 g mL^-1, -0.0008700105756234144 g mL^-1, ...] +Predicted Y: ypred = [0.9973483095723117 g mL^-1, 1.0075299894244465 g mL^-1, ...] +residues = [0.00034830957231168913 g mL^-1, -0.0008700105755534704 g mL^-1, ...] ----------------------------------------------- @@ -173,10 +176,10 @@ residues = [0.00034830957255360673 g mL^-1, -0.0008700105756234144 g mL^-1, ...]

The preferential interaction parameters of BpDA in urea, for the N and U states, are (converted from mol/mol to g/g):

-
NU
10.004444050.00254827
20.006828960.0077628
30.009682320.0121572
40.01277270.0147121
50.01573580.0185243
+
NU
10.007271680.00416967
20.01117410.0127021
30.01584290.0198925
40.02089960.024073
50.02574810.0303108
- +

And using the gas constant in kcal/(K mol), and the temperature in K:

@@ -200,22 +203,22 @@ residues = [0.00034830957255360673 g mL^-1, -0.0008700105756234144 g mL^-1, ...]

Applying this equation to the three possible sets of parameters for the three concentrations studied in the paper, we get:

-
NU
1-3.13441 kcal kg mol^-2-1.73368 kcal kg mol^-2
2-2.25181 kcal kg mol^-2-2.54811 kcal kg mol^-2
3-2.17549 kcal kg mol^-2-2.59841 kcal kg mol^-2
4-2.08904 kcal kg mol^-2-2.38334 kcal kg mol^-2
5-2.05609 kcal kg mol^-2-2.38867 kcal kg mol^-2
+
NU
1-5.12875 kcal kg mol^-2-2.83677 kcal kg mol^-2
2-3.68459 kcal kg mol^-2-4.16942 kcal kg mol^-2
3-3.55969 kcal kg mol^-2-4.25171 kcal kg mol^-2
4-3.41825 kcal kg mol^-2-3.89981 kcal kg mol^-2
5-3.36433 kcal kg mol^-2-3.90852 kcal kg mol^-2

Now we can plot those values as function of the concentration of urea:

- +

The shaded areas are, qualitatively, the transfer free energy of each state up to each concentration.

The plot shows that at very low concentrations, the native state has a lower transfer free energy to urea than the denatured state. Thus, at this low concentration, the native state is stabilized in urea relative to the denatured state.

At higher urea concentrations the integral associated to the denatured state becomes progressively more negative, thus the denatured state is stabilized relative to the native state upon transfer to a urea solution.

Integrating these curves provides a qualitative measure of the free energy of transfer in each case:

-
-0.9089462489528358 kcal mol^-1
+
-1.4872863073264493 kcal mol^-1
-
-0.9603877794163389 kcal mol^-1
+
-1.571458813648106 kcal mol^-1

Implying the the denatured state is slightly more favorably transfered to a 0.5 mol/L aqueous urea solution than the native state. The difference probably increases with increasing urea concentration.

diff --git a/docs/src/pluto_notebooks/rnaset1_urea.jl b/docs/src/pluto_notebooks/rnaset1_urea.jl index cfc692c..c35ec2d 100644 --- a/docs/src/pluto_notebooks/rnaset1_urea.jl +++ b/docs/src/pluto_notebooks/rnaset1_urea.jl @@ -316,9 +316,9 @@ Unitful = "~1.21.0" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.0-rc3" +julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "55045c72e7af5ece6a3c7703cf8f35843f41b634" +project_hash = "8064f1599bc652ca467eba54f4ff185763673168" [[deps.AbstractPlutoDingetjes]] deps = ["Pkg"] @@ -344,7 +344,7 @@ version = "1.1.3" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.2" +version = "1.1.1" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] @@ -378,7 +378,6 @@ version = "7.16.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.11.0" [[deps.AtomsBase]] deps = ["LinearAlgebra", "PeriodicTable", "Printf", "Requires", "StaticArrays", "Unitful", "UnitfulAtomic"] @@ -388,7 +387,6 @@ version = "0.4.2" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -version = "1.11.0" [[deps.BitFlags]] git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" @@ -542,7 +540,6 @@ version = "1.0.0" [[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -version = "1.11.0" [[deps.Dbus_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] @@ -571,7 +568,6 @@ version = "1.15.1" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] @@ -644,7 +640,6 @@ version = "4.4.4+1" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -version = "1.11.0" [[deps.FillArrays]] deps = ["LinearAlgebra"] @@ -716,7 +711,6 @@ version = "1.0.14+0" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -version = "1.11.0" [[deps.GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] @@ -811,7 +805,6 @@ version = "1.4.2" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -version = "1.11.0" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -905,17 +898,16 @@ version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "8.6.0+0" +version = "8.4.0+0" [[deps.LibGit2]] deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -version = "1.11.0" [[deps.LibGit2_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.7.2+0" +version = "1.6.4+0" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] @@ -924,7 +916,6 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -version = "1.11.0" [[deps.Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -977,7 +968,6 @@ version = "2.40.1+0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -version = "1.11.0" [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] @@ -997,7 +987,6 @@ version = "0.3.28" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -version = "1.11.0" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] @@ -1025,7 +1014,6 @@ version = "0.5.13" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -version = "1.11.0" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1036,7 +1024,7 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.6+0" +version = "2.28.2+1" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -1051,7 +1039,6 @@ version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" -version = "1.11.0" [[deps.MolSimToolkit]] deps = ["AtomsBase", "CellListMap", "Chemfiles", "DocStringExtensions", "EasyFit", "LaTeXStrings", "LinearAlgebra", "OffsetArrays", "PDBTools", "ProgressMeter", "ProteinSecondaryStructures", "Reexport", "StaticArrays", "Statistics", "StatsBase", "TestItems"] @@ -1065,7 +1052,7 @@ weakdeps = ["Plots"] [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2023.12.12" +version = "2023.1.10" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1101,7 +1088,7 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.27+1" +version = "0.3.23+4" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -1190,13 +1177,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.43.4+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.11.0" -weakdeps = ["REPL"] - - [deps.Pkg.extensions] - REPLExt = "REPL" +version = "1.10.0" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1263,7 +1246,6 @@ version = "2.3.2" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -version = "1.11.0" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] @@ -1319,14 +1301,12 @@ version = "2.11.1" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -version = "1.11.0" [[deps.Random]] deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -version = "1.11.0" [[deps.RecipesBase]] deps = ["PrecompileTools"] @@ -1393,7 +1373,6 @@ version = "1.4.5" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -version = "1.11.0" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] @@ -1414,7 +1393,6 @@ version = "1.2.0" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] @@ -1425,7 +1403,7 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -version = "1.11.0" +version = "1.10.0" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] @@ -1459,14 +1437,9 @@ uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" version = "1.4.3" [[deps.Statistics]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0" +deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.11.1" -weakdeps = ["SparseArrays"] - - [deps.Statistics.extensions] - SparseArraysExt = ["SparseArrays"] +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -1500,10 +1473,6 @@ git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" version = "0.3.4" -[[deps.StyledStrings]] -uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" -version = "1.11.0" - [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -1511,7 +1480,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "7.7.0+0" +version = "7.2.1+1" [[deps.TOML]] deps = ["Dates"] @@ -1544,7 +1513,6 @@ version = "0.1.1" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -version = "1.11.0" [[deps.TestItems]] git-tree-sha1 = "42fd9023fef18b9b78c8343a4e2f3813ffbcefcb" @@ -1574,7 +1542,6 @@ version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -version = "1.11.0" [[deps.UnPack]] git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" @@ -1583,7 +1550,6 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -version = "1.11.0" [[deps.UnicodeFun]] deps = ["REPL"] @@ -1893,7 +1859,7 @@ version = "1.1.6+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.59.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] diff --git a/docs/src/pluto_notebooks/rnaset1_urea.md b/docs/src/pluto_notebooks/rnaset1_urea.md index e42b871..e3f2305 100644 --- a/docs/src/pluto_notebooks/rnaset1_urea.md +++ b/docs/src/pluto_notebooks/rnaset1_urea.md @@ -25,8 +25,8 @@

RNaseT1 transfer free energy to urea

@@ -54,7 +54,7 @@

The data above is used to compute the \((\partial\ln\gamma_3/\partial m_3)\) quantity. For that we need to create first a plot:

- +

The shape of the plot suggests that a quadratic fit will capture precisely the trend:

@@ -64,15 +64,15 @@ Equation: y = ax^2 + bx + c -With: a = 0.005647775945604377 kg^2 mol^-2 - b = -0.08138062050306537 kg mol^-1 - c = -0.00022283021198975627 +With: a = 0.0056477759579218806 kg^2 mol^-2 + b = -0.08138062053275442 kg mol^-1 + c = -0.00022283020301808176 -Pearson correlation coefficient, R = 0.9999787191515568 mol kg^-1 -Average square residue = 1.334114014813098e-7 +Pearson correlation coefficient, R = 0.9999787191515569 mol kg^-1 +Average square residue = 1.334114014813093e-7 -Predicted Y: ypred = [-0.00022283021198975627, -0.0402579601451014, ...] -residues = [-0.00022283021198975627, 0.0005640343751537671, ...] +Predicted Y: ypred = [-0.00022283020301808176, -0.04025796014806736, ...] +residues = [-0.00022283020301808176, 0.0005640343721878063, ...] ----------------------------------------------- @@ -88,10 +88,10 @@ residues = [-0.00022283021198975627, 0.0005640343751537671, ...] 
urea_data[:, :∂lnγ₃∂m₃] = ∂lnγ₃∂m₃.(urea_data[!,:m₃])
4-element Vector{Quantity{Float64, 𝐌 𝐍^-1, Unitful.FreeUnits{(kg, mol^-1), 𝐌 𝐍^-1, nothing}}}:
- -0.08138062050306537 kg mol^-1
- -0.07561988903854891 kg mol^-1
- -0.06952029101729618 kg mol^-1
- -0.05653040634240611 kg mol^-1
+ -0.08138062053275442 kg mol^-1 + -0.0756198890556741 kg mol^-1 + -0.06952029102111848 kg mol^-1 + -0.056530406317898144 kg mol^-1 
urea_data
m₃γ₃ρ₀∂lnγ₃∂m₃
10.0 mol kg^-11.00.997 g mL^-1-0.0813806 kg mol^-1
20.51 mol kg^-10.961.0084 g mL^-1-0.0756199 kg mol^-1
31.05 mol kg^-10.9241.016 g mL^-1-0.0695203 kg mol^-1
42.2 mol kg^-10.8591.0298 g mL^-1-0.0565304 kg mol^-1
@@ -100,7 +100,7 @@ residues = [-0.00022283021198975627, 0.0005640343751537671, ...]

We also obtain an expression for the density as a function of the concentration, in mol/L:

- +

Where the fit is:

@@ -110,15 +110,15 @@ residues = [-0.00022283021198975627, 0.0005640343751537671, ...] Equation: y = ax^2 + bx + c -With: a = -0.003148583766844562 g L^2 mL^-1 mol^-2 - b = 0.021417043060545628 g L mL^-1 mol^-1 - c = 0.997348309576051 g mL^-1 +With: a = -0.0031485837687515316 g L^2 mL^-1 mol^-2 + b = 0.021417043065280902 g L mL^-1 mol^-1 + c = 0.9973483095745871 g mL^-1 -Pearson correlation coefficient, R = 0.9988889736362446 g mol mL^-1 L^-1 -Average square residue = 3.1548945450687765e-7 g^2 mL^-2 +Pearson correlation coefficient, R = 0.9988889736362448 g mol mL^-1 L^-1 +Average square residue = 3.1548945450685753e-7 g^2 mL^-2 -Predicted Y: ypred = [0.997348309576051 g mL^-1, 1.0075299894232554 g mL^-1, ...] -residues = [0.0003483095760510313 g mL^-1, -0.0008700105767445176 g mL^-1, ...] +Predicted Y: ypred = [0.9973483095745871 g mL^-1, 1.0075299894237224 g mL^-1, ...] +residues = [0.0003483095745870912 g mL^-1, -0.0008700105762775578 g mL^-1, ...] ----------------------------------------------- @@ -176,7 +176,7 @@ residues = [0.0003483095760510313 g mL^-1, -0.0008700105767445176 g mL^-1, ...]
NU
10.02440.0247
20.03450.0542
30.06470.1445
- +

And using the gas constant in kcal/(K mol), and the temperature in K:

@@ -207,16 +207,16 @@ residues = [0.0003483095760510313 g mL^-1, -0.0008700105767445176 g mL^-1, ...]

Now we can plot those values as function of the concentration of urea:

- +

The shaded areas are, qualitatively, the transfer free energy of each state up to each concentration.

The plot shows that at very low concentrations, the native state has a lower transfer free energy to urea than the denatured state. Thus, at this low concentration, the native state is stabilized in urea relative to the denatured state.

At higher urea concentrations the integral associated to the denatured state becomes progressively more negative, thus the denatured state is stabilized relative to the native state upon transfer to a urea solution.

Integrating these curves provides a qualitative measure of the free energy of transfer in each case:

-
-5.350177937007998 kcal mol^-1
+
-5.350177937045624 kcal mol^-1
-
-8.720979559176175 kcal mol^-1
+
-8.720979559284727 kcal mol^-1

Implying the the denatured state is more favorably transfered to a 0.5 mol/L aqueous urea solution than the native state.

diff --git a/docs/src/pluto_notebooks/sh3_tmao.md b/docs/src/pluto_notebooks/sh3_tmao.md deleted file mode 100644 index c0af0ed..0000000 --- a/docs/src/pluto_notebooks/sh3_tmao.md +++ /dev/null @@ -1,237 +0,0 @@ -```@raw html - - - - - -

Computing the free energy of transfer

- - -``` -## Aqueous solutions of TMAO -```@raw html -
-
- - -

In Lin & Timasheff (Biochemistry 1994, 13, 12695), the activity coefficients (\(\gamma_3\)) of TMAO in aqueous solutions and the corresponding densities are provided. The data provided is that of \(\gamma_3\) as a function of the concentration \(m_3\) (in mol/kg):

- - -

Properties of aqueous solutions of TMAO

- - -

Experimental data for TMAO aqueous solutions (28\(^\circ\)C):

- - -
m₃γ₃ρ₀
10.0 mol kg^-11.00.996232 g mL^-1
20.25 mol kg^-10.9921.0029 g mL^-1
30.52 mol kg^-10.9651.0034 g mL^-1
41.08 mol kg^-10.8831.0058 g mL^-1
- - -

The data above is used to compute the \((\partial\ln\gamma_3/\partial m_3)\) quantity. For that we need to create first a plot:

- - - - - -

The shape of the plot suggests that a quadratic fit will capture precisely the trend:

- - -
------------------- Quadratic Fit -------------
-
-Equation: y = ax^2 + bx + c
-
-With: a = -0.08735756774224473
-      b = -0.021843040321997204
-      c = 0.0008238495482700726
-
-Pearson correlation coefficient, R = 0.9996329404972704
-Average square residue = 1.7896632180819053e-6
-
-Predicted Y: ypred = [0.0008238495482700726, -0.010096758516119523, ...]
-residues = [0.0008238495482700726, -0.0020645868188552564, ...]
-
------------------------------------------------
-
- - -

The derivative of the logarithmic of the activity coefficient as a function of the molality is, then, the derivative of the above quadratic fit:

- -
∂lnγ₃∂m₃(m₃) = (2 * tmao_fit.a * ustrip(m₃) + tmao_fit.b) / (oneunit(m₃))
-
∂lnγ₃∂m₃ (generic function with 1 method)
- - -

Which can be computed for the concentrations given in Table 2 of the article, and do not agree quantitatively, but follow the same trend:

- -
tmao_data[:, :∂lnγ₃∂m₃] = ∂lnγ₃∂m₃.(tmao_data[!,:m₃])
-
4-element Vector{Quantity{Float64, 𝐌 𝐍^-1, Unitful.FreeUnits{(kg, mol^-1), 𝐌 𝐍^-1, nothing}}}:
- -0.021843040321997204 kg mol^-1
-  -0.06552182419311957 kg mol^-1
-  -0.11269491077393173 kg mol^-1
-  -0.21053538664524585 kg mol^-1
- -
tmao_data
-
m₃γ₃ρ₀∂lnγ₃∂m₃
10.0 mol kg^-11.00.996232 g mL^-1-0.021843 kg mol^-1
20.25 mol kg^-10.9921.0029 g mL^-1-0.0655218 kg mol^-1
30.52 mol kg^-10.9651.0034 g mL^-1-0.112695 kg mol^-1
41.08 mol kg^-10.8831.0058 g mL^-1-0.210535 kg mol^-1
- - -``` -## RNaseT1 in TMAO (validation) -```@raw html -
-
- - -

With the data above, we can proceed to using equation 5 of Lin and Timasheff:

$$\left(\frac{\partial\mu_2}{\partial m_3}\right)_{T,P,m_2} = --\left(\frac{\partial g_3}{\partial g_2}\right)_{T,P,\mu_3} -\left(\frac{RTM_2}{M_3}\right) -\left(\frac{1}{m_3}+\frac{\partial\ln \gamma_3}{\partial m_3}\right)$$

- - -

where, in the case of TMAO (species 3) and SH3 (solute, species 2) we have:

- - -
75.10966 g mol^-1
- - -
11200 g mol^-1
- - -

Preferential interaction parameters

- - -

The preferential interaction parameters obtained for the native state, in our simulations, as a function of the TMAO concentration, are:

- - -
3-element Vector{Float64}:
-  0.0008
- -0.0096
- -0.045
- - -

And using the gas constant in cal/(K mol):

- - -
1.98720425864083 cal K^-1 mol^-1
- - -

We can define Eq. 5 of the article (written above), as a function of the preferential interactions, molar mass of the cossolvent, and ∂lnγ₃∂m₃:

- -
∂μ₃∂m₃(∂g₃∂g₂, m₃, ∂lnγ₃∂m₃,M2,M3) = 
-    -(∂g₃∂g₂) * (R * (28+273)u"K" * M2 / M3) * (1/m₃ + ∂lnγ₃∂m₃)
-
∂μ₃∂m₃ (generic function with 1 method)
- - -

Applying this equation to the three possible sets of parameters for the three concentrations studied in the paper, we get:

- -
v1 = ∂μ₃∂m₃(∂g₃∂g₂[1], 0.25u"mol/kg", tmao_data[2,:∂lnγ₃∂m₃],M2,M3)
-
-280.74262676331807 cal kg mol^-2
- -
v2 = ∂μ₃∂m₃(∂g₃∂g₂[2], 0.52u"mol/kg", tmao_data[3,:∂lnγ₃∂m₃],M2,M3)
-
1550.1463082069981 cal kg mol^-2
- -
v3 = ∂μ₃∂m₃(∂g₃∂g₂[3], 1.08u"mol/kg", tmao_data[4,:∂lnγ₃∂m₃],M2,M3)
-
2871.355316488171 cal kg mol^-2
- - -

The values above are reasonably consistent with the reported -283, 1495 and 2973 cal/mol\(^2\) of the paper.

- - -

Now we can plot those values as function of the concentration of TMAO:

- - - - - -

And this plot corresponds to Figure 4 of the article (open squares).

- - -

The line above was, then fitted by a line:

- - -
------------------- Linear Fit -------------
-
-Equation: y = ax + b
-
-With: a = 3580.4894443289654
-      b = -827.7154912311368
-
-Pearson correlation coefficient, R = 0.9576301503006615
-Average square residue = 138549.27734964484
-
-Predicted Y: ypred = [67.4068698511046, 1034.1390198199251, ...]
-residues = [348.1494966144227, -516.007288387073, ...]
-
---------------------------------------------
-
- - -

And we have, now the integral of this line computed from zero to each concentration:

- -
int(m₃, fit) = (fit.a/2)*ustrip(m₃)^2 + fit.b*ustrip(m₃)
-
int (generic function with 1 method)
- -
int(tmao_data[2,:m₃], tmao_fit2)
-
-95.03857767250402
- -
int(tmao_data[3,:m₃], tmao_fit2)
-
53.67011743308507
- -
int(tmao_data[4,:m₃], tmao_fit2)
-
1194.2087134030248
- - -

This last value is the one corresponding to the 1197 cal/mol reported for 1M TMAO in Table 5 of the article.

- - -

Packages used

- -
using MolSimToolkit
- - -
using DataFrames
- - -
using Unitful
- - -
using Plots
- - -
using LaTeXStrings
- - -
using EasyFit
- - -
begin
-    using PlutoUI
-    TableOfContents()
-end
- - - -``` -