From 44d4a9f6a888327403bcdf347c13e69070f4ed79 Mon Sep 17 00:00:00 2001 From: "atiyah.elsheikh" Date: Wed, 30 Jun 2021 13:19:12 +0200 Subject: [PATCH] Release 1.1.2 (#41) * Removing duplicate implementations in several package.mo files (#40) * removing duplicate implementations in package.mo * remove duplicate implementations in package.mo * removing duplicate implementations from package.mo * remove duplicate implementation from package.mo * release 1.1.2 * release notes V1.1.2 --- BioChem/Examples/package.mo | 3590 ----------------- BioChem/Math/package.mo | 112 +- BioChem/Reactions/Activation/package.mo | 113 +- BioChem/Reactions/BiSubstrate/package.mo | 110 +- BioChem/Reactions/FastEquilibrium/package.mo | 253 +- BioChem/Reactions/Hill/package.mo | 82 +- .../Reactions/HyperbolicModifier/package.mo | 39 +- BioChem/Reactions/Inhibition/package.mo | 180 +- .../MassAction/Irreversible/BiBi/package.mo | 31 - .../MassAction/Irreversible/BiTri/package.mo | 31 - .../MassAction/Irreversible/BiUni/package.mo | 31 - .../MassAction/Irreversible/TriBi/package.mo | 31 - .../MassAction/Irreversible/TriTri/package.mo | 31 - .../MassAction/Irreversible/TriUni/package.mo | 31 - .../MassAction/Irreversible/UniBi/package.mo | 47 - .../MassAction/Irreversible/UniTri/package.mo | 31 - .../MassAction/Irreversible/UniUni/package.mo | 31 - .../MassAction/Reversible/BiBi/package.mo | 225 +- .../MassAction/Reversible/BiTri/package.mo | 177 +- .../MassAction/Reversible/BiUni/package.mo | 225 +- .../MassAction/Reversible/TriBi/package.mo | 225 +- .../MassAction/Reversible/TriTri/package.mo | 225 +- .../MassAction/Reversible/TriUni/package.mo | 225 +- .../MassAction/Reversible/UniBi/package.mo | 225 +- .../MassAction/Reversible/UniTri/package.mo | 225 +- .../MassAction/Reversible/UniUni/package.mo | 225 +- .../MassAction/Reversible/package.mo | 841 ---- BioChem/Reactions/MichaelisMenten/package.mo | 58 - BioChem/Substances/package.order | 2 +- BioChem/UsersGuide/ReleaseNotes.mo | 2 +- BioChem/package.mo | 2 +- README.md | 4 +- 32 files changed, 26 insertions(+), 7634 deletions(-) diff --git a/BioChem/Examples/package.mo b/BioChem/Examples/package.mo index f62e5e1..41d6229 100644 --- a/BioChem/Examples/package.mo +++ b/BioChem/Examples/package.mo @@ -3,3596 +3,6 @@ within BioChem; package Examples "Some examples of BioChem models" extends Modelica.Icons.ExamplesPackage; - model InsulinSignaling_Sedaghat "Metabolic insulin signaling pathway in rat adipocytes" - extends BioChem.Compartments.Compartment; - Substances.Substance irPMembIns(c.start = 0) "Phosphorylated insulin receptor at plasma membrane, one insulin bound" annotation( - Placement(transformation(origin = {10, 30}, extent = {{-10, -10}, {10, 10}}))); - Reactions.MassAction.Irreversible.UniUni.Uui uui(k1 = 2500 / 60) annotation( - Placement(transformation(origin = {-10, 30}, extent = {{-10, -10}, {10, 10}}))); - Substances.Substance irInt(c.start = 1 / 10000000000000.0) "Internal IR" annotation( - Placement(transformation(origin = {-70, -50}, extent = {{-10, -10}, {10, 10}}))); - Substances.Substance irPIntIns(c.start = 0) "Internal phosphorylated insulin receptor, one insulin" annotation( - Placement(transformation(origin = {-34, -10}, extent = {{-10, -10}, {10, 10}}))); - Substances.Substance irPInt2Ins(c.start = 0) "Internal phosphorylated insulin receptor, two insulin bound" annotation( - Placement(transformation(origin = {-4, -10}, extent = {{-10, -10}, {10, 10}}))); - Reactions.MassAction.Irreversible.UniUni.Uui uui2(k1 = 0.461 / 60) annotation( - Placement(transformation(origin = {-38, -50}, extent = {{-10, -10}, {10, 10}}, rotation = 180))); - Reactions.MassAction.Reversible.BiUni.Bur bur2(k1 = 60000000 / 60, k2 = 100 * 0.2 / 60) annotation( - Placement(transformation(origin = {30, 50}, extent = {{-10, -10}, {10, 10}}))); - Reactions.MassAction.Reversible.BiUni.Bur bur1(k2 = 0.2 / 60, k1 = 60000000 / 60) annotation( - Placement(transformation(origin = {-54, 50}, extent = {{-10, -10}, {10, 10}}))); - Reactions.MassAction.Reversible.UniUni.Uur uur5(k2 = 0.003 / 60, k1 = 0.003 / 9 / 60) annotation( - Placement(transformation(origin = {-70, -10}, extent = {{-10, -10}, {10, 10}}, rotation = 270))); - Reactions.MassAction.Reversible.UniUni.Uur uur3(k1 = 0.00021 / 60, k2 = 0.0021 / 60) annotation( - Placement(transformation(origin = {20, 10}, extent = {{-10, -10}, {10, 10}}))); - Reactions.MassAction.Irreversible.UniUni.Uui uui1(k1 = 0.461 / 60) annotation( - Placement(transformation(origin = {-51.5948, -30}, extent = {{-10, -10}, {10, 10}}, rotation = 180))); - Reactions.MassAction.Irreversible.UniUni.Uui uui3(k1 = 0.2 / 60) annotation( - Placement(transformation(origin = {-50, 20}, extent = {{-10, -10}, {10, 10}}, rotation = 180))); - Substances.Substance Insulin(c.start = 1 / 10000000) "Insulin" annotation( - Placement(transformation(origin = {-70, 70}, extent = {{-10, -10}, {10, 10}}))); - Reactions.MassAction.Reversible.UniUni.Uur uur2(k1 = 0.00021 / 60, k2 = 0.0021 / 60) annotation( - Placement(transformation(origin = {-17.5, 10}, extent = {{-10, -10}, {10, 10}}))); - Substances.Substance irMembIns(c.start = 0) "Insulin receptor at plasma membrane, one insulin bound" annotation( - Placement(transformation(origin = {-30, 30}, extent = {{-10, -10}, {10, 10}}))); - Substances.Substance irMemb(c.start = 9 / 10000000000000.0) annotation( - Placement(transformation(origin = {-70, 30}, extent = {{-10, -10}, {10, 10}}))); - Substances.Substance irPMemb2Ins(c.start = 0) "Phosphorylated insulin receptor at plasma membrane, two insulin bound" annotation( - Placement(transformation(origin = {50, 30}, extent = {{-10, -10}, {10, 10}}))); - Interfaces.Nodes.SubstanceConnector sInsulin "Connector for insulin" annotation( - Placement(transformation(origin = {0.0, 100.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = 180), iconTransformation(origin = {-0.0, 115.0}, extent = {{-15.0, -15.0}, {15.0, 15.0}}, rotation = 180))); - equation - connect(sInsulin, Insulin.n1) annotation( - Line(points = {{0.0, 100.0}, {0.0, 70.04}, {-70.0, 70.0}}, smooth = Smooth.Bezier)); - connect(irPInt2Ins.n1, uur3.s1) annotation( - Line(points = {{-4, -10}, {-4.267, 10.24}, {8.75, 10}}, smooth = Smooth.Bezier)); - connect(uur5.p1, irInt.n1) annotation( - Line(points = {{-70, -21.25}, {-70, -50}})); - connect(bur2.s2, irPMembIns.n1) annotation( - Line(points = {{18.75, 45}, {10, 46.2}, {10, 30}}, smooth = Smooth.Bezier)); - connect(uui3.s1, irPIntIns.n1) annotation( - Line(points = {{-38.75, 20}, {-37.5, 18.75}, {-34, 11.25}, {-34, -10}}, smooth = Smooth.Bezier)); - connect(uui1.p1, irInt.n1) annotation( - Line(points = {{-62.8448, -30}, {-70.27, -29.87}, {-70, -50}}, smooth = Smooth.Bezier)); - connect(uui1.s1, irPIntIns.n1) annotation( - Line(points = {{-40.3448, -30}, {-34, -30}, {-34, -10}}, smooth = Smooth.Bezier)); - connect(uui2.s1, irPInt2Ins.n1) annotation( - Line(points = {{-26.75, -50}, {-4.07, -50.04}, {-4, -10}}, smooth = Smooth.Bezier)); - connect(uui.p1, irPMembIns.n1) annotation( - Line(points = {{1.25, 30}, {10, 30}})); - connect(irInt.n1, uui2.p1) annotation( - Line(points = {{-70, -50}, {-49.25, -50}})); - connect(Insulin.n1, bur1.s1) annotation( - Line(points = {{-70, 70}, {-70.07, 54.05}, {-65.25, 55}}, smooth = Smooth.Bezier)); - connect(Insulin.n1, bur2.s1) annotation( - Line(points = {{-70, 70}, {-30, 69.99}, {-7.5, 54.62}, {18.75, 55}}, smooth = Smooth.Bezier)); - connect(uur2.p1, irPMembIns.n1) annotation( - Line(points = {{-6.25, 10}, {0, 10}, {10, 30}}, smooth = Smooth.Bezier)); - connect(irPIntIns.n1, uur2.s1) annotation( - Line(points = {{-34, -10}, {-34, 10}, {-28.75, 10}}, smooth = Smooth.Bezier)); - connect(irMembIns.n1, uui.s1) annotation( - Line(points = {{-30, 30}, {-21.25, 30}})); - connect(bur1.p1, irMembIns.n1) annotation( - Line(points = {{-42.75, 50}, {-30, 50}, {-30, 30}}, smooth = Smooth.Bezier)); - connect(irMemb.n1, uui3.p1) annotation( - Line(points = {{-70, 30}, {-69.7, 20.2}, {-61.25, 20}}, smooth = Smooth.Bezier)); - connect(irMemb.n1, bur1.s2) annotation( - Line(points = {{-70, 30}, {-70.07, 46.2}, {-65.25, 45}}, smooth = Smooth.Bezier)); - connect(uur5.s1, irMemb.n1) annotation( - Line(points = {{-70, 1.25}, {-70, 30}})); - connect(bur2.p1, irPMemb2Ins.n1) annotation( - Line(points = {{41.25, 50}, {50.01, 50}, {50, 30}}, smooth = Smooth.Bezier)); - connect(uur3.p1, irPMemb2Ins.n1) annotation( - Line(points = {{31.25, 10}, {50, 10}, {50, 30}}, smooth = Smooth.Bezier)); - annotation( - Documentation(info = " -

InsulinSignaling

-

- A model of the first steps of a metabolic insulin signaling pathway.
- Based on the model by Sedaghat et al. (2002).

- A. Sedaghat, R, A. Sherman, and J. Quon, Michael.
- A mathematical model of metabolic insulin signaling.
- American Journal of Physiology - Endocrinology and Metabolism, 283:1048-1101, Jul 2002. -

- ", revisions = ""), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Ellipse(lineColor = {85, 170, 255}, fillColor = {0, 0, 255}, fillPattern = FillPattern.Sphere, extent = {{-100.43, -91.42}, {100.02, 19.94}}), Line(points = {{0.0, 110.0}, {0.0, -34.05}, {25.0, -52.36}}, color = {170, 0, 0})})); - end InsulinSignaling_Sedaghat; - - model Glycolysis "Glycolysis" - extends BioChem.Compartments.Compartment; - Reactions.MassAction.Irreversible.UniUni.Uui uui1 annotation( - Placement(transformation(origin = {1.83964e-13, -3.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = 270))); - Substances.Substance PEP1(c.start = 0) "Phosphoenol pyruvate" annotation( - Placement(transformation(origin = {2.96307e-12, -108.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -270))); - Reactions.MassAction.Irreversible.UniUni.Uui uui4 annotation( - Placement(transformation(origin = {1.19682e-13, -123.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -90))); - Reactions.MassAction.Reversible.UniUni.Uur uur2 annotation( - Placement(transformation(origin = {1.1291e-13, -63.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -270))); - Substances.Substance G13BP(c.start = 0) "Glycerate-1,3-bisphosphate" annotation( - Placement(transformation(origin = {1.16462e-13, -18.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -270))); - Reactions.MassAction.Reversible.UniUni.Uur uur(k1 = 1) annotation( - Placement(transformation(origin = {1.13798e-13, 93.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -90))); - Reactions.MassAction.Reversible.UniUni.Uur uur1 annotation( - Placement(transformation(origin = {1.17351e-13, 18.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}))); - Reactions.MassAction.Irreversible.UniBi.Ubi ubi annotation( - Placement(transformation(origin = {1.60982e-14, 33.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = 270))); - Reactions.MassAction.Irreversible.UniUni.Uui uui3 annotation( - Placement(transformation(origin = {-6.3094e-13, -93.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = 270))); - Substances.Substance G2P1(c.start = 0) "Glycerate-2-phosphate" annotation( - Placement(transformation(origin = {1.03362e-13, -78.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -630))); - Reactions.MassAction.Irreversible.UniUni.Uui uui2 annotation( - Placement(transformation(origin = {1.14242e-13, -33.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -90))); - Substances.Substance GA3P(c.start = 0) "Glycerate-3-phosphate" annotation( - Placement(transformation(origin = {1.06248e-13, -48.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -270))); - Reactions.MassAction.Irreversible.UniUni.Uui uui5(k1 = 1) annotation( - Placement(transformation(origin = {1.03287e-11, 123.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -90))); - Reactions.MassAction.Irreversible.UniUni.Uui uui annotation( - Placement(transformation(origin = {1.91513e-13, 63.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -90))); - Substances.Substance Pyruvate(c.start = 0) annotation( - Placement(transformation(origin = {1.19571e-13, -138.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -360))); - Substances.Substance Glucose(c.start = 1) "Glucose" annotation( - Placement(transformation(origin = {3.32706e-16, 139.222}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -270))); - Substances.Substance G6P(c.start = 0) "Glucose-6-phosphate" annotation( - Placement(transformation(origin = {1.13798e-13, 108.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -270))); - Substances.Substance F6P(c.start = 0) "Fructose-6-phosphate" annotation( - Placement(transformation(origin = {2.39286e-12, 78.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -630))); - Substances.Substance F16BP(c.start = 0) "Fructose-1,6-bisphosphate" annotation( - Placement(transformation(origin = {1.13354e-13, 48.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}, rotation = -270))); - Substances.Substance G3P(c.start = 0) "Glyceraldehyde-3-phosphate" annotation( - Placement(transformation(origin = {-15, 18.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}))); - Substances.Substance DHAP(c.start = 0) "Dihydroxyacetone phosphate" annotation( - Placement(transformation(origin = {15, 18.75}, extent = {{-7.5, -7.5}, {7.5, 7.5}}))); - BioChem.Interfaces.Nodes.SubstanceConnector sGlucose annotation( - Placement(transformation(origin = {0.0, 147.5}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = 180), iconTransformation(origin = {0.0, 115.0}, extent = {{-15.0, -15.0}, {15.0, 15.0}}, rotation = 180))); - Interfaces.Nodes.SubstanceConnector sPyruvate annotation( - Placement(transformation(origin = {-22.5, -147.5}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {-27.5, -112.5}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); - Interfaces.Nodes.SubstanceConnector sPyruvate4 annotation( - Placement(transformation(origin = {22.5, -147.5}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {27.5, -112.5}, extent = {{-12.5, -12.5}, {12.5, 12.5}}))); - equation - connect(Pyruvate.n1, sPyruvate4) annotation( - Line(points = {{0.0, -138.75}, {22.5, -139.4}, {22.5, -147.5}}, smooth = Smooth.Bezier)); - connect(sPyruvate, Pyruvate.n1) annotation( - Line(points = {{-22.5, -147.5}, {-22.5, -138.8}, {0.0, -138.75}}, smooth = Smooth.Bezier)); - connect(sGlucose, Glucose.n1) annotation( - Line(points = {{0.0, 147.5}, {0.0, 139.222}})); - connect(GA3P.n1, uur2.p1) annotation( - Line(points = {{1.06248e-13, -48.75}, {1.12893e-13, -55.3125}})); - connect(uur2.s1, G2P1.n1) annotation( - Line(points = {{1.12893e-13, -72.1875}, {1.03362e-13, -78.75}})); - connect(uui3.p1, PEP1.n1) annotation( - Line(points = {{-6.30923e-13, -102.188}, {2.96307e-12, -108.75}})); - connect(uui1.p1, G13BP.n1) annotation( - Line(points = {{1.83981e-13, -12.1875}, {1.16462e-13, -18.75}})); - connect(uui2.p1, GA3P.n1) annotation( - Line(points = {{1.14259e-13, -42.1875}, {1.06248e-13, -48.75}})); - connect(G2P1.n1, uui3.s1) annotation( - Line(points = {{1.03362e-13, -78.75}, {-6.30957e-13, -85.3125}})); - connect(PEP1.n1, uui4.s1) annotation( - Line(points = {{2.96307e-12, -108.75}, {1.19665e-13, -115.312}})); - connect(G13BP.n1, uui2.s1) annotation( - Line(points = {{1.16462e-13, -18.75}, {1.14225e-13, -25.3125}})); - connect(uui4.p1, Pyruvate.n1) annotation( - Line(points = {{1.19699e-13, -132.188}, {1.19571e-13, -138.75}})); - connect(Glucose.n1, uui5.s1) annotation( - Line(points = {{3.32706e-16, 139.222}, {1.03287e-11, 132.188}})); - connect(uui5.p1, G6P.n1) annotation( - Line(points = {{1.03287e-11, 115.312}, {1.13798e-13, 108.75}})); - connect(G6P.n1, uur.s1) annotation( - Line(points = {{1.13798e-13, 108.75}, {1.13815e-13, 102.188}})); - connect(F6P.n1, uui.s1) annotation( - Line(points = {{2.39286e-12, 78.75}, {1.91496e-13, 72.1875}})); - connect(uur.p1, F6P.n1) annotation( - Line(points = {{1.13815e-13, 85.3125}, {2.39286e-12, 78.75}})); - connect(F16BP.n1, ubi.s1) annotation( - Line(points = {{1.13354e-13, 48.75}, {1.60815e-14, 42.1875}})); - connect(uui.p1, F16BP.n1) annotation( - Line(points = {{1.9153e-13, 55.3125}, {1.13354e-13, 48.75}})); - connect(ubi.p2, G3P.n1) annotation( - Line(points = {{-3.75, 25.3125}, {-15, 26.25}, {-15, 18.75}}, smooth = Smooth.Bezier)); - connect(G3P.n1, uui1.s1) annotation( - Line(points = {{-15, 18.75}, {-7.5, 11.25}, {1.138e-13, 7.719}, {1.83947e-13, 4.6875}}, smooth = Smooth.Bezier)); - connect(uur1.s1, G3P.n1) annotation( - Line(points = {{-8.4375, 18.75}, {-15, 18.75}})); - connect(ubi.p1, DHAP.n1) annotation( - Line(points = {{3.75, 25.3125}, {15, 26.25}, {15, 18.75}}, smooth = Smooth.Bezier)); - connect(DHAP.n1, uur1.p1) annotation( - Line(points = {{15, 18.75}, {8.4375, 18.75}})); - annotation( - Documentation(info = " -

Glycolysis

-

- A simple glycolysis model. - The parameter values in this model are arbitrarily chosen, - to obtain a fully functional model, realistic parameter values must be used. -

- ", revisions = ""), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Line(points = {{0, 100}, {0, 25}, {-25, 0}, {0, -25}, {0, -75}, {-25, -100}}), Line(points = {{0, 25}, {25, 0}, {-25, 0}}), Line(points = {{0, -75}, {25, -100}})}), - Diagram(coordinateSystem(extent = {{-105, 148.5}, {105, -148.5}}, preserveAspectRatio = true, grid = {10, 10}))); - end Glycolysis; - - model EnzMM "An enzymatic reaction with Michaelis-Menten kinetics" - extends BioChem.Compartments.Compartment; - Substances.Substance F6P(c.start = 2) "Fructose-6-phosphate" annotation( - Placement(transformation(origin = {10, 10}, extent = {{-10, -10}, {10, 10}}))); - Reactions.MichaelisMenten.Uur uur(vF = 1.5, KmS = 0.1, KmP = 0.05) annotation( - Placement(transformation(origin = {-10, 10}, extent = {{-10, -10}, {10, 10}}))); - Substances.Substance G6P(c.start = 1) "Glucose-6-phosphate" annotation( - Placement(transformation(origin = {-30, 10}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(uur.p1, F6P.n1) annotation( - Line(points = {{1.25, 10}, {10, 10}})); - connect(G6P.n1, uur.s1) annotation( - Line(points = {{-30, 10}, {-21.25, 10}})); - annotation( - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - annotation( - Documentation(info = " -

EnzMM

- -

- An enzymatic reaction with Michaelis-Menten kinetics. - The parameter values in this model are arbitrarily chosen, - to obtain a fully functional model, realistic parameter values must be used. -

- ", revisions = ""), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Ellipse(fillColor = {170, 0, 0}, fillPattern = FillPattern.Solid, extent = {{-100, -25}, {-50, 25}}), Ellipse(fillColor = {0, 85, 0}, fillPattern = FillPattern.Solid, extent = {{50, -25}, {100, 25}}), Line(points = {{-50, 0}, {50, 0}}, arrow = {Arrow.Open, Arrow.Open}, arrowSize = 30)})); - end EnzMM; - - package GMO "Goldbeter1991_MinMitOscil" - extends BioChem.Icons.Example; - - model cell "cell" - extends BioChem.Compartments.MainCompartment(V(start = 1)); - import BioChem.Math.*; - import BioChem.Constants.*; - - model C_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end C_; - - model M_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end M_; - - model X_ - extends BioChem.Substances.Substance; - end X_; - - model reaction1_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real vi = 0.025; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * vi; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end reaction1_; - - model reaction2_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real kd = 0.01; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = s1.c * cell_V * kd; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end reaction2_; - - model reaction3_ - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real vd = 0.25; - parameter Real Kd = 0.02; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = s1.c * cell_V * vd * m1.c * (s1.c + Kd) ^ (-1); - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end reaction3_; - - model reaction4_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real K1 = 0.005; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - Real V1; - equation - rr = cell_V * (1 + (-1) * p1.c) * V1 * (K1 + (-1) * p1.c + 1) ^ (-1); - annotation( - __MathCore(RDF = " - - - - - - - - - - ")); - end reaction4_; - - model reaction5_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real V2 = 1.5; - parameter Real K2 = 0.005; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * s1.c * V2 * (K2 + s1.c) ^ (-1); - annotation( - __MathCore(RDF = " - - - - - - - - - - ")); - end reaction5_; - - model reaction6_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real K3 = 0.005; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - Real V3; - equation - rr = cell_V * V3 * (1 + (-1) * p1.c) * (K3 + (-1) * p1.c + 1) ^ (-1); - end reaction6_; - - model reaction7_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real K4 = 0.005; - parameter Real V4 = 0.5; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * V4 * s1.c * (K4 + s1.c) ^ (-1); - end reaction7_; - - inner Real cell_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - BioChem.Examples.GMO.cell.C_ C(c(start = 0.01)) "Cyclin" annotation( - Placement(transformation(origin = {80.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - BioChem.Examples.GMO.cell.M_ M(c(start = 0.01)) "CDC-2 Kinase" annotation( - Placement(transformation(origin = {-70.0, 70.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - BioChem.Examples.GMO.cell.X_ X(c(start = 0.01)) "Cyclin Protease" annotation( - Placement(transformation(origin = {50.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Real V1 "V1"; - Real V3 "V3"; - parameter Real VM1 = 3 "VM1"; - parameter Real VM3 = 1 "VM3"; - parameter Real Kc = 0.5 "Kc"; - BioChem.Substances.AmbientSubstance ambientSubstance annotation( - Placement(transformation(origin = {-10.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - BioChem.Examples.GMO.cell.reaction1_ reaction1 "creation of cyclin" annotation( - Placement(transformation(origin = {50.0, 40.0}, extent = {{-10.0, 10.0}, {10.0, -10.0}}))); - BioChem.Examples.GMO.cell.reaction2_ reaction2 "default degradation of cyclin" annotation( - Placement(transformation(origin = {30.0, -60.0}, extent = {{-10.0, 10.0}, {10.0, -10.0}}, rotation = 180))); - BioChem.Examples.GMO.cell.reaction3_ reaction3 "cdc2 kinase triggered degration of cyclin" annotation( - Placement(transformation(origin = {50.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - BioChem.Examples.GMO.cell.reaction4_ reaction4(V1 = V1) "activation of cdc2 kinase" annotation( - Placement(transformation(origin = {-70.0, 40.0}, extent = {{10.0, -10.0}, {-10.0, 10.0}}, rotation = 270))); - BioChem.Examples.GMO.cell.reaction5_ reaction5 "deactivation of cdc2 kinase" annotation( - Placement(transformation(origin = {-30.0, 70.0}, extent = {{-10.0, 10.0}, {10.0, -10.0}}))); - BioChem.Examples.GMO.cell.reaction6_ reaction6(V3 = V3) "activation of cyclin protease" annotation( - Placement(transformation(origin = {10.0, -37.8911}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Examples.GMO.cell.reaction7_ reaction7 "deactivation of cyclin protease" annotation( - Placement(transformation(origin = {20.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - equation - connect(X.n1, reaction7.s1) annotation( - Line(origin = {43.75, -16.6667}, points = {{6.25, -13.3333}, {6.25, 6.6667}, {-12.5, 6.6667}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, reaction7.p1) annotation( - Line(origin = {-3.75, 3.3333}, points = {{-6.25, 26.6667}, {-6.25, -13.3333}, {12.5, -13.3333}}, smooth = Smooth.Bezier)); - connect(X.n1, reaction6.p1) annotation( - Line(origin = {30.5633, -33.9455}, points = {{19.4367, 3.9455}, {-5.0617, 3.9455}, {-5.0617, -3.9455}, {-9.3133, -3.9455}}, smooth = Smooth.Bezier)); - connect(X.n1, reaction3.m1) annotation( - Line(origin = {50.0, -14.5}, points = {{0.0, -15.5}, {0.0, 15.5}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, reaction6.s1) annotation( - Line(origin = {-7.0833, -15.2607}, points = {{-2.9167, 45.2607}, {-2.9167, -22.6304}, {5.8333, -22.6304}}, smooth = Smooth.Bezier)); - connect(M.n1, reaction4.p1) annotation( - Line(origin = {-70.0, 60.625}, points = {{0.0, 9.375}, {0.0, -9.375}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, reaction4.s1) annotation( - Line(origin = {-39.2, 27.5494}, points = {{29.2, 2.4506}, {16.2, 2.4506}, {16.2, -3.0509}, {-30.8, -3.0509}, {-30.8, 1.2006}}, smooth = Smooth.Bezier)); - connect(M.n1, reaction5.s1) annotation( - Line(origin = {-55.625, 70.0}, points = {{-14.375, 0.0}, {14.375, 0.0}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, reaction5.p1) annotation( - Line(origin = {-12.9167, 56.6667}, points = {{2.9167, -26.6667}, {2.9167, 13.3333}, {-5.8333, 13.3333}}, smooth = Smooth.Bezier)); - connect(C.n1, reaction2.s1) annotation( - Line(origin = {67.0833, -40.0}, points = {{12.9167, 40.0}, {12.9167, -20.0}, {-25.8333, -20.0}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, reaction2.p1) annotation( - Line(origin = {-50.4167, -20.9454}, points = {{40.4167, 50.9454}, {-9.5833, -30.588}, {69.1667, -39.0546}}, smooth = Smooth.Bezier)); - connect(C.n1, reaction1.p1) annotation( - Line(origin = {73.75, 26.6667}, points = {{6.25, -26.6667}, {6.25, 13.3333}, {-12.5, 13.3333}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, reaction1.s1) annotation( - Line(origin = {24.4367, 35.0}, points = {{-34.4367, -5.0}, {10.0617, -5.0}, {10.0617, 5.0}, {14.3133, 5.0}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, reaction3.p1) annotation( - Line(origin = {24.4367, 20.0}, points = {{-34.4367, 10.0}, {10.0617, 10.0}, {10.0617, -10.0}, {14.3133, -10.0}}, smooth = Smooth.Bezier)); - connect(C.n1, reaction3.s1) annotation( - Line(origin = {68.0633, 5.0}, points = {{11.9367, -5.0}, {-2.5617, -5.0}, {-2.5617, 5.0}, {-6.8133, 5.0}}, smooth = Smooth.Bezier)); - V1 = C.c * VM1 * (C.c + Kc) ^ (-1); - V3 = M.c * VM3; - annotation( - __MathCore(RDF = " - - - - - - - - "), - Documentation(info = " -

A Simple Mitotic Oscillator

- -This example is a modelica version of the model presented in - -A minimal cascade model for the miotic oscillator involving cyclin and cdc2 kinase by Goldbeter A. (Proc. Nati. Acad. Sci. USA -Vol. 88, pp. 9107-9111, October 1991 -Cell Biology.) - -

Abstract

-A minimal model for the mitotic oscillator is presented. The model, built on recent experimental advances, is based on the cascade of post-translational modification that modulates the activity of cdc2 kinase during the cell cycle. The model pertains to the situation encountered in early amphibian embryos, where the accumulation of cyclin suffices to trigger the onset of mitosis. In the first cycle of the bicyclic cascade model, cyclin promotes the activation of cdc2 kinase through reversible dephosphorylation, and in the second cycle, cdc2 kinase activates a cyclin protease by reversible phosphorylation. That cyclin activates cdc2 kinase while the kinase triggers the degradation of cyclin has suggested that oscillations may originate from such a negative feedback loop [Félix, M. A., Labbé, J. C., Dorée, M., Hunt, T. & Karsenti, E. (1990) Nature (London) 346, 379-382]. This conjecture is corroborated by the model, which indicates that sustained oscillations of the limit cycle type can arise in the cascade, provided that a threshold exists in the activation of cdc2 kinase by cyclin and in the activation of cyclin proteolysis by cdc2 kinase. The analysis shows how miototic oscillations may readily arise from time lags associated with these thresholds and from the delayed negative feedback provided by cdc2-induced cyclin degradation. A mechanism for the origin of the thresholds is proposed in terms of the phenomenon of zero-order ultrasensitivity previously described for biochemical systems regulated by covalent modification. - -

Simulations

-The simulation results are shown in the - Figure 1. This plot corresponds to Fig 3 of the paper (Goldbeter 1991). - - -\"Fig1: - -", revisions = ""), - experiment(StartTime = 0.0, StopTime = 100, NumberOfIntervals = -1, Algorithm = "dassl", Tolerance = 1e-06)); - end cell; - annotation( - __MathCore(RDF = " - - - - - - Shapiro - Bruce - - bshapiro@jpl.nasa.gov - - NASA Jet Propulsion Laboratory - - - - - - 2005-02-06T23:39:40Z - - - 2008-08-21T11:31:07Z - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ")); - annotation( - Documentation(info = " -

A Simple Mitotic Oscillator

- -This example is a modelica version of the model presented in - -A minimal cascade model for the miotic oscillator involving cyclin and cdc2 kinase by Goldbeter A. (Proc. Nati. Acad. Sci. USA -Vol. 88, pp. 9107-9111, October 1991 -Cell Biology.) - -
-
- -See -cell - for more documentation and simulation results. -", revisions = "")); - end GMO; - - package centralMetabolism - extends BioChem.Icons.Example; - - model cytosol "cytosol" - extends BioChem.Compartments.Compartment(V(start = 2)); - - model DHAP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end DHAP_; - - model G3P_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end G3P_; - - model NADH_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end NADH_; - - model FDP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end FDP_; - - model PYR_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end PYR_; - - model ADP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end ADP_; - - model IMP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end IMP_; - - model ATP_ - extends BioChem.Substances.SignalSubstance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end ATP_; - - model AMP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end AMP_; - - model LAC_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end LAC_; - - model NAD_ - extends BioChem.Substances.SignalSubstance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end NAD_; - - model CP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end CP_; - - model Cr_ - extends BioChem.Substances.SignalSubstance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Cr_; - - model GLY_ - extends BioChem.Substances.BoundarySubstance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end GLY_; - - model PN_ - extends BioChem.Substances.SignalSubstance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end PN_; - - model G6P_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end G6P_; - - model F6P_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end F6P_; - - model jda_ - extends BioChem.Interfaces.Reactions.Uur(nS1 = cytosol_V / bamp, nP1 = cytosol_V); - parameter Real KmAMP = 0.3; - parameter Real KmIMP = 3.54545; - parameter Real KcatDA = 121; - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real bamp; - equation - rr = KcatDA * s1.c / (KmAMP + s1.c) - 0.01 * p1.c / (KmIMP + p1.c); - end jda_; - - model vgpdh_ - extends BioChem.Interfaces.Reactions.Bbi(nS1 = 2 * cytosol_V / badp); - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real KcatGPDH = 78595.6; - parameter Real KmGPDH = 0.0369; - parameter Real KmADP = 1.4; - parameter Real KmPN = 120; - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real badp; - equation - rr = KcatGPDH * s2.c * s1.c * m1.c / ((KmGPDH + s2.c) * (s1.c + KmADP) * (m1.c + KmPN)); - end vgpdh_; - - model vpfk_ - extends BioChem.Interfaces.Reactions.Ubi(nP2 = cytosol_V / badp); - parameter Real n_sbml = 2; - parameter Real KcatPFK = 400; - parameter Real KmF6P = 3.49515; - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real badp; - equation - rr = KcatPFK * s1.c ^ n_sbml / (KmF6P + s1.c ^ n_sbml); - end vpfk_; - - model vald_ - extends BioChem.Interfaces.Reactions.Uui(nP1 = 2); - parameter Real kt; - parameter Real ka1 = 0.01; - parameter Real ka2 = 1.65; - parameter Real ka3 = 3000; - parameter Real ka4 = 0.125; - parameter Real ka5 = 340; - parameter Real ka6 = 14000000.0; - parameter Real ka7 = 56000; - equation - rr = (ka7 * s1.c - ka6 * p1.c * kt * p1.c) / (ka1 + ka2 * p1.c + s1.c + ka3 * p1.c * s1.c + ka4 * kt * p1.c + ka5 * p1.c * kt * p1.c); - end vald_; - - model vldh_ - extends BioChem.Interfaces.Reactions.Bui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real kia = 0.00245; - parameter Real kmb = 0.137; - parameter Real kip = 7.3; - parameter Real kmq = 0.1; - parameter Real kiq = 0.5; - parameter Real k1ib = 0.1; - parameter Real kmp = 1; - parameter Real kma = 0.00844; - parameter Real kib = 0.228; - parameter Real kf = 458; - parameter Real kr = 135; - parameter Real e0 = 8; - equation - rr = e0 * (s2.c * s1.c * kf / (kia * kmb) - kr * p1.c * m1.c / (kiq * kmp)) / (s2.c / kia + s2.c * s1.c / (kia * kmb) + s2.c * s1.c * p1.c / (kia * kip * kmb) + s2.c * kmq * p1.c / (kia * kiq * kmp) + (1 + s1.c / k1ib) * (1 + s1.c * kma / (kia * kmb) + kmq * p1.c / (kiq * kmp)) + m1.c / kiq + s1.c * kma * m1.c / (kia * kiq * kmb) + p1.c * m1.c / (kiq * kmp) + s1.c * p1.c * m1.c / (kib * kiq * kmp)); - end vldh_; - - model vpdh_ - extends BioChem.Interfaces.Reactions.Bui(nS2 = cytosol_V / badp, nP1 = 3.67); - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real KmPYR = 0.5; - parameter Real KcatPDH = 1; - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real badp; - equation - rr = KcatPDH * s1.c * m1.c / ((s1.c + KmPYR) * (m1.c + 0.1)); - end vpdh_; - - model jak_ - extends BioChem.Interfaces.Reactions.Uur(nS1 = cytosol_V / bamp, nP1 = 2 * cytosol_V / badp); - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real KcatAK = 150000; - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real bamp; - input Real badp; - equation - rr = KcatAK * (m1.c * s1.c - p1.c * p1.c) / (1 + s1.c / 0.1 + p1.c / 0.1 + m1.c * (10 + s1.c / 0.01) + p1.c * (10 + p1.c / 0.01 + s1.c / 3.49)); - end jak_; - - model vgph_ - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.MultipleModifiers(dimM = 3); - parameter Real kh; - parameter Real KcatGPH = 248; - input Real bamp; - equation - rr = KcatGPH * m[3].c * (0.002 + m[2].c + m[1].c / bamp) / ((0.014 + m[2].c + m[1].c / bamp) * (8 * (0.01 + m[2].c + m[1].c / bamp) / (0.002 + m[2].c + m[1].c / bamp) + m[3].c)); - end vgph_; - - model jatpase_ - extends BioChem.Interfaces.Reactions.Uui(nP1 = cytosol_V / badp); - parameter Real KcatATPase = 370 "I am unsure about this value"; - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real badp; - equation - rr = KcatATPase * s1.c / (s1.c + 0.05); - end jatpase_; - - model jck_ - extends BioChem.Interfaces.Reactions.Bbi(nP1 = cytosol_V / badp); - parameter Real KcatCK = 1970; - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real badp; - equation - rr = KcatCK * (20 * s1.c * s2.c / 10.85 - 29.333 * p1.c * p2.c / 0.1) / (1 + s2.c / 34.9 + p2.c / 0.8 + s1.c * (1.43 + s2.c / 10.85) + p1.c * (16.7 + p2.c / 0.1 + s2.c / 2.1)); - end jck_; - - inner Real cytosol_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - centralMetabolism.cytosol.NADH_ NADH(c(start = 0.00406177)) "NADH" annotation( - Placement(transformation(origin = {100.0, -20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.FDP_ FDP(c(start = 0.0999758)) "Fructose 1,6-diphosphate" annotation( - Placement(transformation(origin = {-19.7747, -40.109}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.PYR_ PYR(c(start = 0.148871)) "Pyruvate" annotation( - Placement(transformation(origin = {100.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - centralMetabolism.cytosol.ADP_ ADP(c(start = 0.0695775)) "ADP" annotation( - Placement(transformation(origin = {-19.7747, -20.109}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.IMP_ IMP(c(start = 0.650608)) "IMP" annotation( - Placement(transformation(origin = {-120.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - centralMetabolism.cytosol.ATP_ ATP(c(start = 12.7913) = atp) "ATP" annotation( - Placement(transformation(origin = {-10.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -720))); - centralMetabolism.cytosol.AMP_ AMP(c(start = 0.000398124)) "AMP" annotation( - Placement(transformation(origin = {-120.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - centralMetabolism.cytosol.LAC_ LAC(c(start = 4.34299)) "Lactate" annotation( - Placement(transformation(origin = {140.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.NAD_ NAD(c(start = 0.695938) = nad) "NAD" annotation( - Placement(transformation(origin = {120.0, -60.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -450))); - centralMetabolism.cytosol.CP_ CP(c(start = 28.2621)) "Phosphocreatine" annotation( - Placement(transformation(origin = {-80.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - centralMetabolism.cytosol.Cr_ Cr(c(start = 25.7379) = cr) "Creatine" annotation( - Placement(transformation(origin = {-80.0, 50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - centralMetabolism.cytosol.GLY_ GLY(c(start = 1)) "Glycogen" annotation( - Placement(transformation(origin = {-140.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.PN_ PN(c = pn) "Inorganic phosphate" annotation( - Placement(transformation(origin = {80.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - centralMetabolism.cytosol.G6P_ G6P(c(start = 0.603855 / (1 + kh))) "Glucose 6-phosphate" annotation( - Placement(transformation(origin = {-100.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.F6P_ F6P(c(start = 0.603855 * kh / (1 + kh))) "Fructose 6-phosphate" annotation( - Placement(transformation(origin = {-60.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -360))); - centralMetabolism.cytosol.jda_ jda(bamp = bamp) "jda" annotation( - Placement(transformation(origin = {-120.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - centralMetabolism.cytosol.vpfk_ vpfk(badp = badp) "vpfk" annotation( - Placement(transformation(origin = {-40.0, -30.0}, extent = {{-10.0, 10.0}, {10.0, -10.0}}))); - centralMetabolism.cytosol.vldh_ vldh "vldh" annotation( - Placement(transformation(origin = {120.0, -30.0}, extent = {{-10.0, 10.0}, {10.0, -10.0}}))); - centralMetabolism.cytosol.vpdh_ vpdh(badp = badp) "vpdh" annotation( - Placement(transformation(origin = {120.0, -90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.jak_ jak(bamp = bamp, badp = badp) "jak" annotation( - Placement(transformation(origin = {10.0, 30.0}, extent = {{10.0, -10.0}, {-10.0, 10.0}}, rotation = 90))); - centralMetabolism.cytosol.vgph_ vgph(bamp = bamp, kh = kh) "vgph" annotation( - Placement(transformation(origin = {-120.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.jatpase_ jatpase(badp = badp) "jatpase" annotation( - Placement(transformation(origin = {-40.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - centralMetabolism.cytosol.jck_ jck(badp = badp) "jck" annotation( - Placement(transformation(origin = {-70.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - BioChem.Interfaces.Nodes.SubstanceConnector node_LAC annotation( - Placement(transformation(origin = {140.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {125.0384, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.mitochondria mitochondria(badp = badp) annotation( - Placement(transformation(origin = {100.0, 40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - input Real bamp; - input Real badp; - input Real pn; - input Real atp; - input Real cr; - input Real nad; - parameter Real kh; - parameter Real kt; - BioChem.Reactions.FastEquilibrium.Uuf vH6P(kP1 = kh) "Fast equilibrium reaction for the compound of G6P and F6P" annotation( - Placement(transformation(origin = {-80.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.vald_ vald(kt = kt) "vald" annotation( - Placement(transformation(origin = {0.2253, -40.109}, extent = {{-10.0, 10.0}, {10.0, -10.0}}))); - centralMetabolism.cytosol.DHAP_ DHAP(c.start = 0.07427 / (1 + kt)) annotation( - Placement(transformation(origin = {20.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.G3P_ G3P(c.start = 0.07427 * kt / (1 + kt)) annotation( - Placement(transformation(origin = {60.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.cytosol.vgpdh_ vgpdh_1(badp = badp) annotation( - Placement(transformation(origin = {80.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Reactions.FastEquilibrium.Uuf vT3P(kS1 = 1, kP1 = kt) "Fast equilibrium reaction for the compound of G6P and F6P" annotation( - Placement(transformation(origin = {40.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - equation - connect(PN.n1, vgph.m[3]) annotation( - Line(origin = {-43.1831, -17.0363}, points = {{123.1831, 7.0363}, {23.1831, 13.8613}, {-53.1252, -3.9637}, {-76.8169, -3.9637}}, smooth = Smooth.Bezier)); - connect(vgpdh_1.m1, PN.n1) annotation( - Line(origin = {80.0, -15.5}, points = {{0.0, -5.5}, {0.0, 5.5}}, smooth = Smooth.Bezier)); - connect(PYR.n1, vgpdh_1.p2) annotation( - Line(origin = {94.1667, -38.3333}, points = {{5.8333, -1.6667}, {-2.9167, -1.6667}, {-2.9167, 3.3333}}, smooth = Smooth.Bezier)); - connect(PYR.n1, vpdh.s1) annotation( - Line(origin = {99.5833, -70.0}, points = {{0.4167, 30.0}, {-9.5833, -15.0}, {9.1667, -15.0}}, smooth = Smooth.Bezier)); - connect(vldh.s1, PYR.n1) annotation( - Line(origin = {105.8333, -38.3333}, points = {{2.9167, 3.3333}, {2.9167, -1.6667}, {-5.8333, -1.6667}}, smooth = Smooth.Bezier)); - connect(vT3P.s1, DHAP.n1) annotation( - Line(origin = {24.375, -40.0}, points = {{4.375, 0.0}, {-4.375, 0.0}})); - connect(vT3P.p1, G3P.n1) annotation( - Line(origin = {55.625, -40.0}, points = {{-4.375, 0.0}, {4.375, 0.0}})); - connect(vald.p1, DHAP.n1) annotation( - Line(origin = {14.3169, -40.0363}, points = {{-2.8416, -0.0727}, {-2.8416, 0.0363}, {5.6831, 0.0363}})); - connect(ADP.n1, mitochondria.node_ADP) annotation( - Line(origin = {29.9388, 18.5441}, points = {{-49.7135, -38.6531}, {-14.7833, -28.5441}, {4.222, 16.7428}, {57.4791, 16.7428}}, smooth = Smooth.Bezier)); - connect(ADP.n1, vpdh.s2) annotation( - Line(origin = {31.3122, -73.3958}, points = {{-51.0869, 53.2868}, {-21.3122, -1.1347}, {9.2453, -24.5854}, {77.4378, -21.6042}}, smooth = Smooth.Bezier)); - connect(G3P.n1, vgpdh_1.s2) annotation( - Line(origin = {62.9167, -36.6667}, points = {{-2.9167, -3.3333}, {-2.9167, 1.6667}, {5.8333, 1.6667}}, smooth = Smooth.Bezier)); - connect(vgph.p1, G6P.n1) annotation( - Line(origin = {-105.8333, -30.0}, points = {{-2.9167, 0.0}, {-2.9167, 0.0}, {5.8333, 0.0}}, smooth = Smooth.Bezier)); - connect(jatpase.s1, ATP.n1) annotation( - Line(origin = {-30.0, 27.0833}, points = {{-10.0, -5.8333}, {-10.0, 2.9167}, {20.0, 2.9167}}, smooth = Smooth.Bezier)); - connect(jck.p1, ADP.n1) annotation( - Line(origin = {-63.2582, -1.5662}, points = {{-1.7418, 20.3162}, {-1.7418, 1.5662}, {43.4835, -18.5428}}, smooth = Smooth.Bezier)); - connect(FDP.n1, vald.s1) annotation( - Line(origin = {-16.8581, -40.109}, points = {{-2.9166, 0.0}, {-2.9167, 0.0}, {5.8334, 0.0}}, smooth = Smooth.Bezier)); - connect(vgpdh_1.p1, NADH.n1) annotation( - Line(origin = {94.1667, -21.6667}, points = {{-2.9167, -3.3333}, {-2.9167, 1.6667}, {5.8333, 1.6667}}, smooth = Smooth.Bezier)); - connect(vpdh.p1, mitochondria.node_NADHm) annotation( - Line(origin = {128.4604, -19.1758}, points = {{2.7896, -70.8242}, {21.5396, -70.8242}, {19.4827, 64.1758}, {-15.8864, 64.1758}}, smooth = Smooth.Bezier)); - connect(ADP.n1, jak.p1) annotation( - Line(origin = {-4.8874, -4.2701}, points = {{-14.8873, -15.8389}, {0.2923, -3.5556}, {14.8874, 7.589}, {14.8874, 23.0201}}, smooth = Smooth.Bezier)); - connect(NAD.n1, vldh.m1) annotation( - Line(origin = {120.0, -49.5}, points = {{0.0, -10.5}, {0.0, 10.5}}, smooth = Smooth.Bezier)); - connect(Cr.n1, jck.s2) annotation( - Line(origin = {-78.3333, 44.1667}, points = {{-1.6667, 5.8333}, {-1.6667, -2.9167}, {3.3333, -2.9167}}, smooth = Smooth.Bezier)); - connect(IMP.n1, vgph.m[1]) annotation( - Line(origin = {-120.0, -17.3333}, points = {{0.0, 7.3333}, {0.0, -3.6667}, {0.0, -3.6667}}, smooth = Smooth.Bezier)); - connect(ATP.n1, jak.m1) annotation( - Line(origin = {-6.3333, 30.0}, points = {{-3.6667, 0.0}, {-3.6667, 0.0}, {7.3333, 0.0}}, smooth = Smooth.Bezier)); - connect(jck.p2, CP.n1) annotation( - Line(origin = {-76.6667, 12.9167}, points = {{1.6667, 5.8333}, {1.6667, -2.9167}, {-3.3333, -2.9167}}, smooth = Smooth.Bezier)); - connect(AMP.n1, jak.s1) annotation( - Line(origin = {-30.0, 71.6841}, points = {{-90.0, -41.6841}, {-90.0, -1.6841}, {40.0, -1.6841}, {40.0, -30.4341}}, smooth = Smooth.Bezier)); - connect(jatpase.p1, ADP.n1) annotation( - Line(origin = {-33.2582, -13.8227}, points = {{-6.7418, 12.5727}, {-6.7418, 5.6243}, {13.4835, -6.2863}}, smooth = Smooth.Bezier)); - connect(FDP.n1, vpfk.p1) annotation( - Line(origin = {-22.6914, -36.7756}, points = {{2.9167, -3.3334}, {-5.8333, -3.3334}, {-6.0586, 1.7756}}, smooth = Smooth.Bezier)); - connect(NAD.n1, vpdh.m1) annotation( - Line(origin = {120.0, -70.5}, points = {{0.0, 10.5}, {0.0, -10.5}}, smooth = Smooth.Bezier)); - connect(NADH.n1, mitochondria.node_NADH) annotation( - Line(origin = {108.7675, 7.2}, points = {{-8.7675, -27.2}, {-8.7675, -14.2}, {6.845, -14.2}, {6.845, 27.8}, {3.845, 27.8}}, smooth = Smooth.Bezier)); - connect(ATP.n1, mitochondria.node_ATP) annotation( - Line(origin = {32.2535, 41.25}, points = {{-42.2535, -11.25}, {-28.6502, 3.75}, {25.7571, 3.75}, {55.1466, 3.75}}, smooth = Smooth.Bezier)); - connect(F6P.n1, vpfk.s1) annotation( - Line(origin = {-57.0833, -30.0}, points = {{-2.9167, 0.0}, {-2.9167, 0.0}, {5.8333, 0.0}}, smooth = Smooth.Bezier)); - connect(vH6P.s1, G6P.n1) annotation( - Line(origin = {-115.625, -80.0}, points = {{24.375, 50.0}, {15.625, 50.0}}, smooth = Smooth.Bezier)); - connect(AMP.n1, vgph.m[2]) annotation( - Line(origin = {-170.5636, 9.014}, points = {{50.5636, 20.986}, {20.5636, 0.986}, {50.5636, -30.014}}, smooth = Smooth.Bezier)); - connect(IMP.n1, jda.p1) annotation( - Line(origin = {-120.0, -4.1667}, points = {{0.0, -5.8333}, {0.0, 2.9167}, {0.0, 2.9167}}, smooth = Smooth.Bezier)); - connect(ADP.n1, vpfk.p2) annotation( - Line(origin = {-22.6914, -23.4423}, points = {{2.9167, 3.3333}, {-5.8333, 3.3333}, {-6.0586, -1.5577}}, smooth = Smooth.Bezier)); - connect(vgpdh_1.s1, ADP.n1) annotation( - Line(origin = {8.8565, -22.5545}, points = {{59.8935, -2.4455}, {-15.6312, -2.4455}, {-15.6312, 2.4455}, {-28.6312, 2.4455}}, smooth = Smooth.Bezier)); - connect(vH6P.p1, F6P.n1) annotation( - Line(origin = {-65.8333, -30.0}, points = {{-2.9167, 0.0}, {-2.9167, 0.0}, {5.8333, 0.0}}, smooth = Smooth.Bezier)); - connect(LAC.n1, node_LAC) annotation( - Line(origin = {140.0, -16.6667}, points = {{0.0, -13.3333}, {0.0, 6.6667}, {0.0, 6.6667}}, smooth = Smooth.Bezier)); - connect(ATP.n1, jck.s1) annotation( - Line(origin = {-43.0, 45.9685}, points = {{33.0, -15.9685}, {33.0, 6.2028}, {-22.0, 6.2028}, {-22.0, -1.7185}, {-22.0, -4.7185}}, smooth = Smooth.Bezier)); - connect(AMP.n1, jda.s1) annotation( - Line(origin = {-120.0, 24.1667}, points = {{0.0, 5.8333}, {0.0, -2.9167}, {0.0, -2.9167}}, smooth = Smooth.Bezier)); - connect(vldh.s2, NADH.n1) annotation( - Line(origin = {105.8333, -21.6667}, points = {{2.9167, -3.3333}, {2.9167, 1.6667}, {-5.8333, 1.6667}}, smooth = Smooth.Bezier)); - connect(LAC.n1, vldh.p1) annotation( - Line(origin = {137.0833, -30.0}, points = {{2.9167, 0.0}, {2.9167, 0.0}, {-5.8333, 0.0}}, smooth = Smooth.Bezier)); - connect(GLY.n1, vgph.s1) annotation( - Line(origin = {-137.0833, -30.0}, points = {{-2.9167, 0.0}, {-2.9167, 0.0}, {5.8333, 0.0}}, smooth = Smooth.Bezier)); - annotation( - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-148.5, -105.0}, {148.5, 105.0}}, preserveAspectRatio = true, grid = {10, 10})), - Documentation(info = "

Cytosol

- -\"Fig1: -

Fig. 1. Scheme of glycolysis and coupled processes simulated in the model: consumption and synthesis of ATP and transformation of reducing equivalents of NADH. The relevant equations, which account for stoicheiometry of the ATP production, are given in Supplementary materials. One molecule of ATP is consumed per molecule of fructose 6-phosphate in the phosphofructokinase reaction; two molecules of ATP per molecule of triose phospate (four molecules per hexose molecule) are then produced on the way to pyruvate; 2.5 molecules of ATP are produced when one molecule of NADH is oxidized. Cytosolic NADH is produced in the reaction of glyceraldehyde-3-phosphate dehydrogenase and consumed when pyruvate is transformed to lactate. In mitochondria one molecule of NADH is produced in the pyruvate dehydrogenase reaction and then three NADH molecules and one FADH2 molecule in the tricarboxylate cycle. Abbreviations: AK, adenylate kinase (EC 2.7.4.3); CK, creatine kinase (EC 2.7.3.2); CP, phosphocreatine; Cr, creatine; F6P, fructose 6-phosphate; FBP, fructose 1,6-bisphosphate; G6P, glucose 6-phosphate; GAPDH, glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12); -GPh, glycogen phosphorylase (EC 2.4.1.1); Lac, lactate; LDH, lactate dehydrogenase (EC 1.1.1.27); PFK, phosphofructokinase (EC 2.7.1.11); GPI, glucose phosphate isomerase (EC 5.3.1.9.); Pyr, pyruvate. Subscripts: m, mitochondrial; c, cytosolic.

", revisions = "")); - end cytosol; - - model extra_cellular - extends BioChem.Compartments.MainCompartment(V(start = 2)); - - model LACext_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end LACext_; - - model vef_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real VmaxEF = 15; - parameter Real KmLAC = 26.8483; - equation - rr = VmaxEF * s1.c / (KmLAC + s1.c); - end vef_; - - centralMetabolism.cytosol cytosol(bamp = bamp, badp = badp, kh = kh, pn = pn, atp = atp, kt = kt, nad = nad, cr = cr) annotation( - Placement(transformation(origin = {1.221, -0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.extra_cellular.vef_ vef "vef" annotation( - Placement(transformation(origin = {40.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -360))); - centralMetabolism.extra_cellular.LACext_ LACext(c.start = 0) "Lactate" annotation( - Placement(transformation(origin = {70.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - inner Real default_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - inner Real cytosol_V = cytosol.V "Variable used to make the compartment volume of inner compartments accessible. Do not edit."; - parameter Real iv1 = 0.603855; - parameter Real iv2 = 0.0999758; - parameter Real iv3 = 0.07427; - parameter Real iv4 = 0.148871; - parameter Real iv5 = 4.34299; - parameter Real iv6 = 0.00406177; - parameter Real iv7 = 1.72073e-05; - parameter Real iv8 = 0.0695775; - parameter Real iv9 = 28.2621; - parameter Real iv10 = 0.000398124; - parameter Real iv11 = 0.650608; - parameter Real nv19 = 1; - parameter Real nv20 = 1.14947; - parameter Real kamp = 0.00841471; - parameter Real k2amp = 200; - parameter Real kadp = 0.05; - parameter Real k2adp = 84.7376; - parameter Real tan = 27.5 ""; - parameter Real tcr = 54; - parameter Real kt = 0.085; - parameter Real kh = 0.2; - parameter Real PNt = 139.117; - Real adpt; - Real ampt; - Real atp; - Real atpt; - Real badp; - Real bamp; - Real pn; - Real cr; - Real nad; - equation - connect(vef.p1, LACext.n1) annotation( - Line(origin = {60.625, 0.0}, points = {{-9.375, 0.0}, {9.375, -0.0}})); - connect(cytosol.node_LAC, vef.s1) annotation( - Line(origin = {21.2374, -0.0}, points = {{-7.5126, 0.0}, {7.5126, -0.0}})); - badp = k2adp * kadp / (kadp + cytosol.ADP.c); - adpt = cytosol.ADP.c * badp; - atpt = tan - adpt - ampt - cytosol.IMP.c; - ampt = cytosol.AMP.c * bamp; - atp = atpt / cytosol.V; - pn = (PNt - atpt * 3 - adpt * 2 - ampt - cytosol.CP.c * 2 - cytosol.IMP.c - (cytosol.G6P.c + cytosol.F6P.c + cytosol.FDP.c * 2 + cytosol.G3P.c + cytosol.DHAP.c) * cytosol.V) / cytosol.V; - bamp = k2amp * kamp / (kamp + cytosol.AMP.c); - nad = 0.7 - cytosol.NADH.c; - cr = tcr - cytosol.CP.c; - annotation( - Diagram(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10})), - Documentation(info = "

Energy metabolism of human muscle

-

The model simulates the processes of utilization of energy stored in the form of glycogen. This is the main energy supply of working muscle. The pathway includes glycolytic and TCA cycle reactions stoichiometrically connected with synthesis ATP, which is used mainly for mechanical work (ATPase). The biochemical scheme of the simulated processes is shown in Figure 1.

- -\"Fig1: -

Fig. 1. Scheme of glycolysis and coupled processes simulated in the model: consumption and synthesis of ATP and transformation of reducing equivalents of NADH. The relevant equations, which account for stoicheiometry of the ATP production, are given in Supplementary materials. One molecule of ATP is consumed per molecule of fructose 6-phosphate in the phosphofructokinase reaction; two molecules of ATP per molecule of triose phospate (four molecules per hexose molecule) are then produced on the way to pyruvate; 2.5 molecules of ATP are produced when one molecule of NADH is oxidized. Cytosolic NADH is produced in the reaction of glyceraldehyde-3-phosphate dehydrogenase and consumed when pyruvate is transformed to lactate. In mitochondria one molecule of NADH is produced in the pyruvate dehydrogenase reaction and then three NADH molecules and one FADH2 molecule in the tricarboxylate cycle. Abbreviations: AK, adenylate kinase (EC 2.7.4.3); CK, creatine kinase (EC 2.7.3.2); CP, phosphocreatine; Cr, creatine; F6P, fructose 6-phosphate; FBP, fructose 1,6-bisphosphate; G6P, glucose 6-phosphate; GAPDH, glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12); -GPh, glycogen phosphorylase (EC 2.4.1.1); Lac, lactate; LDH, lactate dehydrogenase (EC 1.1.1.27); PFK, phosphofructokinase (EC 2.7.1.11); GPI, glucose phosphate isomerase (EC 5.3.1.9.); Pyr, pyruvate. Subscripts: m, mitochondrial; c, cytosolic.

-

This model was used to study the biochemical effects of training programmes, consisted of 14 training sessions either with 24 (short period, SP) or 72 h (long period, LP) intervals between the individual sessions (Parra et al., 2000). In this example the analysed data included the change in enzyme activities after both tytes of training as Table 1 shows.

- -

Table 1
- Measured enzyme activity in biobpsy before and after training (Parra et al. 2000).

-\"Tab1: -

Moreover, the concentrations of metabolites at rest and after 30s of maximal intensity exercise were measured before and after accomplishing the training programs. The measured metabolites are adenine nucleotides and the forms of creatine (Table 2) and intermediates of glycolysis (Table 3).

- -

Table 2

-\"Tab2: -

The model simulates the experimental data as an example in Figure 2 shows. The switch from rest to maximal intensity exercise in the model simulation induced by the change of only one parameter, increase of ATPase activity; stimulation of all the metabolic fluxes is a result of activation by the products of ATP hydrolysis.

-

-The simulation have shown that after short periods of training the glycolytic flux at rest was three times higher than it had been before training, whereas during exercise the flux and energy consumption remained the same as before training. Long periods of training had less effect on the glycolytic flux at rest, but increased it in response to exercise, increasing the contribution of oxidative phosphorylation. -This model and data analysis are described in (Selivanov VA, de Atauri P, Centelles JJ, Cadefau J, Parra J, Cussó R, Carreras J, Cascante M. (2008) The changes in the energy metabolism of human muscle induced by training. J Theor Biol. 252, 402-410) -

- -

Table 3

-\"Tab3: -

- -\"Fig2: -

Fig. 2. Time-courses of high-energy phophates and glycolytic intermediates during 30s of maximal exercise before training. Points with error bars are experimental metabolite concentrations at rest and after 30s of excersise. For simulation at the beginning of excersise (time=0), ATPase activity increased from 3.2 to 200 mM min-1. Other parameters are given in Table 1 and Supplementary materials. Abbrevetaions are given in Fig. 1,

-

Simulations

-

The time scale of the model is minutes, so it simulates 0.5 min of maximal intensity exercise. The model produces the same results as seen from experiments.

-

If simulated for more than 0.5 minutes the model has numerical problems. In real life a person cannot maintain maximal intensity exercise, then fatigue comes and the intensity decreases. So, steady state at maximal intensity does not exist in real life either.

- ", revisions = ""), - __MathCore(RDF = ""), - experiment(StartTime = 0.0, StopTime = 0.5, Algorithm = "dassl", Tolerance = 1e-05)); - end extra_cellular; - - model mitochondria - extends BioChem.Compartments.Compartment(V.start = 2); - - model NADH_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end NADH_; - - model NAD_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end NAD_; - - model jox_ - extends BioChem.Interfaces.Reactions.Bbi(nS1 = 2.5 * cytosol_V / badp); - outer Real cytosol_V "Variable used to access the volume of an outer compartment. Do not edit."; - Real badp; - equation - rr = 10000 * s1.c * s2.c / ((0.01 + s1.c) * (0.15 + s2.c)); - end jox_; - - model vn_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real VmaxN = 10.8347; - parameter Real KmNADH = 0.216694; - equation - rr = VmaxN * s1.c / (KmNADH + s1.c); - end vn_; - - centralMetabolism.mitochondria.NADH_ NADHm(c.start = 0) "NADH" annotation( - Placement(transformation(origin = {-20.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.mitochondria.NAD_ NADm(c.start = 0) "NAD" annotation( - Placement(transformation(origin = {20.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.mitochondria.jox_ jox(badp = badp) "jox" annotation( - Placement(transformation(origin = {-0.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Interfaces.Nodes.SubstrateConnector node_ADP annotation( - Placement(transformation(origin = {-20.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {-125.8208, -47.131}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Interfaces.Nodes.SubstanceConnector node_NADHm annotation( - Placement(transformation(origin = {-30.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {125.7398, 50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - centralMetabolism.mitochondria.vn_ vn "vn" annotation( - Placement(transformation(origin = {-50.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Interfaces.Nodes.SubstrateConnector node_NADH annotation( - Placement(transformation(origin = {-80.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {126.1247, -50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Interfaces.Nodes.ProductConnector node_ATP annotation( - Placement(transformation(origin = {20.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {-125.999, 50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Real badp; - equation - connect(jox.p1, NADm.n1) annotation( - Line(origin = {14.1667, 8.3333}, points = {{-2.9167, -3.3333}, {-2.9167, 1.6667}, {5.8333, 1.6667}}, smooth = Smooth.Bezier)); - connect(NADHm.n1, node_NADHm) annotation( - Line(origin = {-29.831, -9.3231}, points = {{9.831, -0.6769}, {-0.169, -0.6769}, {-0.169, -20.6769}}, smooth = Smooth.Bezier)); - connect(vn.p1, NADHm.n1) annotation( - Line(origin = {-29.375, -10.0}, points = {{-9.375, 0.0}, {9.375, 0.0}})); - connect(NADHm.n1, jox.s2) annotation( - Line(origin = {-14.1667, -8.3333}, points = {{-5.8333, -1.6667}, {2.9167, -1.6667}, {2.9167, 3.3333}}, smooth = Smooth.Bezier)); - connect(jox.p2, node_ATP) annotation( - Line(origin = {17.0833, -6.6667}, points = {{-5.8333, 1.6667}, {2.9167, 1.6667}, {2.9167, -3.3333}})); - connect(jox.s1, node_ADP) annotation( - Line(origin = {-14.1667, 8.3333}, points = {{2.9167, -3.3333}, {2.9167, 1.6667}, {-5.8333, 1.6667}}, smooth = Smooth.Bezier)); - connect(vn.s1, node_NADH) annotation( - Line(origin = {-70.625, -10.0}, points = {{9.375, 0.0}, {-9.375, 0.0}})); - annotation( - Diagram(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}))); - end mitochondria; - end centralMetabolism; - - package CircadianOscillator "Weimann2004_CircadianOscillator" - extends BioChem.Icons.Example; - - model Container - extends BioChem.Compartments.MainCompartment(V(start = 1)); - import BioChem.Math.*; - import BioChem.Constants.*; - BioChem.Examples.CircadianOscillator.Nucleus nucleus(k3t = k3t, k3d = k3d, k6t = k6t, k6d = k6d, k6a = k6a, k7a = k7a, k7d = k7d) annotation( - Placement(transformation(origin = {-30.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Cytoplasm cytoplasm(trans_per2_cry = trans_per2_cry, k1d = k1d, k2b = k2b, q = q, k2d = k2d, k2t = k2t, trans_Bmal1 = trans_Bmal1, k4d = k4d, k5b = k5b, k5d = k5d, k5t = k5t) annotation( - Placement(transformation(origin = {21.5395, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - inner Real Nucleus_V = nucleus.V "Variable used to make the compartment volume of inner compartments accessible. Do not edit."; - inner Real Cytoplasm_V = cytoplasm.V "Variable used to make the compartment volume of inner compartments accessible. Do not edit."; - inner Real Container_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - Real trans_per2_cry(start = 0); - parameter Real v1b = 9; - parameter Real c_sbml = 0.01; - parameter Real k1b = 1; - parameter Real k1i = 0.56; - parameter Real hill_coeff = 8; - Real trans_Bmal1(start = 0); - parameter Real v4b = 3.6; - parameter Real r_sbml = 3; - parameter Real k4b = 2.16; - Real y5_y6_y7(start = 3.05); - parameter Real k1d = 0.12; - parameter Real k2b = 0.3; - parameter Real q = 2; - parameter Real k2d = 0.05; - parameter Real k2t = 0.24; - parameter Real k3t = 0.02; - parameter Real k3d = 0.12; - parameter Real k4d = 0.75; - parameter Real k5b = 0.24; - parameter Real k5d = 0.06; - parameter Real k5t = 0.45; - parameter Real k6t = 0.06; - parameter Real k6d = 0.12; - parameter Real k6a = 0.09; - parameter Real k7a = 0.003; - parameter Real k7d = 0.09; - equation - connect(cytoplasm.y5_node, nucleus.y5_node) annotation( - Line(origin = {-4.2302, -19.0}, points = {{14.7697, 0.0}, {-14.7697, 0.0}})); - connect(nucleus.y6_node, cytoplasm.y6_node) annotation( - Line(origin = {-4.2302, -1.0}, points = {{-14.7697, 0.0}, {14.7697, 0.0}})); - connect(cytoplasm.y2_node, nucleus.y2_node) annotation( - Line(origin = {-4.2302, -7.0}, points = {{14.7697, 0.0}, {-14.7697, 0.0}})); - connect(nucleus.y3_node, cytoplasm.y3_node) annotation( - Line(origin = {-4.2302, -13.0}, points = {{-14.7697, 0.0}, {14.7697, 0.0}})); - trans_per2_cry = v1b * (nucleus.y7.c + c_sbml) / (k1b * (1 + (nucleus.y3.c / k1i) ^ hill_coeff) + nucleus.y7.c + c_sbml); - trans_Bmal1 = v4b * nucleus.y3.c ^ r_sbml / (k4b ^ r_sbml + nucleus.y3.c ^ r_sbml); - y5_y6_y7 = cytoplasm.y5.c + nucleus.y6.c + nucleus.y7.c; - annotation( - Documentation(info = " -

Circadian Oscillator

- -This example is the modelica version of the model presented in -Modeling feedback loops of the Mammalian circadian oscillator by -Becker-Weimann S, Wolf J, Herzel H, Kramer A. (Biophysical Journal Volume 87 November 2004 3023-3034) - -

Abstract

-The suprachiasmatic nucleus governs daily variations of physiology and behavior in mammals. Within single neurons, interlocked transcriptional/translational feedback loops generate circadian rhythms on the molecular level. We present a mathematical model that reflects the essential features of the mammalian circadian oscillator to characterize the differential roles of negative and positive feedback loops. The oscillations that are obtained have a 24-h period and are robust toward parameter variations even when the positive feedback is replaced by a constantly expressed activator. This demonstrates the crucial role of the negative feedback for rhythm generation. Moreover, it explains the rhythmic phenotype of Rev-erbalpha-/- mutant mice, where a positive feedback is missing. The interplay of negative and positive feedback reveals a complex dynamics. In particular, the model explains the unexpected rescue of circadian oscillations in Per2Brdm1/Cry2-/- double-mutant mice (Per2Brdm1 single-mutant mice are arrhythmic). Here, a decrease of positive feedback strength associated with mutating the Per2 gene is compensated by the Cry2-/- mutation that simultaneously decreases the negative feedback strength. Finally, this model leads us to a testable prediction of a molecular and behavioral phenotype: circadian oscillations should be rescued when arrhythmic Per2Brdm1 mutant mice are crossed with Rev- erbalpha -/- mutant mice. - -

Simulations

-The simulation results are shown in the - Figure 1. This plot corresponds to Fig 3A from the paper (Becker-Weimann, 2004). - - -\"Fig1: - -", revisions = ""), - experiment(StartTime = 0, StopTime = 150, NumberOfIntervals = -1, Algorithm = "dassl", Tolerance = 1e-06)); - end Container; - - model Nucleus "Nucleus" - extends BioChem.Compartments.Compartment(V(start = 1)); - import BioChem.Math.*; - import BioChem.Constants.*; - - model y3_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end y3_; - - model y6_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end y6_; - - model y7_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end y7_; - - model per2_cry_nuclear_export_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Nucleus_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k3t; - equation - rr = Nucleus_V * k3t * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end per2_cry_nuclear_export_; - - model nuclear_per2_cry_complex_degradation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Nucleus_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k3d; - equation - rr = Nucleus_V * k3d * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end nuclear_per2_cry_complex_degradation_; - - model BMAL1_nuclear_export_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Nucleus_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k6t; - equation - rr = Nucleus_V * k6t * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end BMAL1_nuclear_export_; - - model nuclear_BMAL1_degradation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Nucleus_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k6d; - equation - rr = Nucleus_V * k6d * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end nuclear_BMAL1_degradation_; - - model BMAL1_activation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Nucleus_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k6a; - equation - rr = Nucleus_V * k6a * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end BMAL1_activation_; - - model BMAL1_deactivation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Nucleus_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k7a; - equation - rr = Nucleus_V * k7a * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end BMAL1_deactivation_; - - model Active_BMAL1_degradation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Nucleus_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k7d; - equation - rr = Nucleus_V * k7d * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Active_BMAL1_degradation_; - - inner Real Nucleus_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - BioChem.Examples.CircadianOscillator.Nucleus.y3_ y3(c(start = 1.1)) "PER2_CRY_complex_nucleus" annotation( - Placement(transformation(origin = {70.0, -50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - BioChem.Examples.CircadianOscillator.Nucleus.y6_ y6(c(start = 1)) "BMAL1_nucleus" annotation( - Placement(transformation(origin = {-10.0, 50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - BioChem.Examples.CircadianOscillator.Nucleus.y7_ y7(c(start = 1.05)) "Active BMAL1" annotation( - Placement(transformation(origin = {-45.6104, -16.1148}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - BioChem.Interfaces.Nodes.SubstanceConnector y3_node annotation( - Placement(transformation(origin = {90.0, -60.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - parameter Real k3t; - BioChem.Interfaces.Nodes.SubstanceConnector y2_node annotation( - Placement(transformation(origin = {90.0, 60.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Examples.CircadianOscillator.Nucleus.per2_cry_nuclear_export_ per2_cry_nuclear_export(k3t = k3t) "per2_cry_nuclear_export" annotation( - Placement(transformation(origin = {68.1433, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - BioChem.Substances.AmbientSubstance ambientSubstance annotation( - Placement(transformation(origin = {10.0, -50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - parameter Real k3d; - BioChem.Examples.CircadianOscillator.Nucleus.nuclear_per2_cry_complex_degradation_ nuclear_per2_cry_complex_degradation(k3d = k3d) "nuclear_per2_cry_complex_degradation" annotation( - Placement(transformation(origin = {40.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - BioChem.Interfaces.Nodes.SubstanceConnector y6_node annotation( - Placement(transformation(origin = {90.0, 90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, 90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - parameter Real k6t; - BioChem.Interfaces.Nodes.SubstanceConnector y5_node annotation( - Placement(transformation(origin = {90.0, -90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, -90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Nucleus.BMAL1_nuclear_export_ BMAL1_nuclear_export(k6t = k6t) "BMAL1_nuclear_export" annotation( - Placement(transformation(origin = {-80.0, 20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - parameter Real k6d; - BioChem.Examples.CircadianOscillator.Nucleus.nuclear_BMAL1_degradation_ nuclear_BMAL1_degradation(k6d = k6d) "nuclear_BMAL1_degradation" annotation( - Placement(transformation(origin = {10.0, 10.0}, extent = {{10.0, -10.0}, {-10.0, 10.0}}, rotation = 90))); - parameter Real k6a; - Nucleus.BMAL1_activation_ BMAL1_activation(k6a = k6a) "BMAL1_activation" annotation( - Placement(transformation(origin = {-30.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - parameter Real k7a; - Nucleus.BMAL1_deactivation_ BMAL1_deactivation(k7a = k7a) "BMAL1_deactivation" annotation( - Placement(transformation(origin = {-61.7118, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - parameter Real k7d; - BioChem.Examples.CircadianOscillator.Nucleus.Active_BMAL1_degradation_ Active_BMAL1_degradation(k7d = k7d) "Active_BMAL1_degradation" annotation( - Placement(transformation(origin = {-30.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - equation - connect(y3.n1, nuclear_per2_cry_complex_degradation.s1) annotation( - Line(origin = {58.0633, -45.0}, points = {{11.9367, -5.0}, {-2.5617, -5.0}, {-2.5617, 5.0}, {-6.8133, 5.0}}, smooth = Smooth.Bezier)); - connect(y3.n1, per2_cry_nuclear_export.s1) annotation( - Line(origin = {69.0717, -15.5633}, points = {{0.9283, -34.4367}, {0.9283, 10.0617}, {-0.9284, 10.0617}, {-0.9284, 14.3133}}, smooth = Smooth.Bezier)); - connect(y3.n1, y3_node) annotation( - Line(origin = {76.6667, -56.6667}, points = {{-6.6667, 6.6667}, {-6.6667, -3.3333}, {13.3333, -3.3333}}, smooth = Smooth.Bezier)); - connect(y7.n1, BMAL1_activation.p1) annotation( - Line(origin = {-35.2035, -11.1599}, points = {{-10.4069, -4.9549}, {5.2035, -4.9549}, {5.2035, 9.9099}}, smooth = Smooth.Bezier)); - connect(y7.n1, Active_BMAL1_degradation.s1) annotation( - Line(origin = {-44.1569, -32.0383}, points = {{-1.4535, 15.9235}, {-1.4535, -7.9617}, {2.9069, -7.9617}}, smooth = Smooth.Bezier)); - connect(y7.n1, BMAL1_deactivation.s1) annotation( - Line(origin = {-56.3447, -11.1599}, points = {{10.7343, -4.9549}, {-5.3671, -4.9549}, {-5.3671, 9.9099}}, smooth = Smooth.Bezier)); - connect(y6.n1, BMAL1_deactivation.p1) annotation( - Line(origin = {-44.4745, 40.4167}, points = {{34.4745, 9.5833}, {-17.2373, 9.5833}, {-17.2373, -19.1667}}, smooth = Smooth.Bezier)); - connect(y6.n1, BMAL1_activation.s1) annotation( - Line(origin = {-20.0, 30.5633}, points = {{10.0, 19.4367}, {10.0, -5.0617}, {-10.0, -5.0617}, {-10.0, -9.3133}}, smooth = Smooth.Bezier)); - connect(y6.n1, nuclear_BMAL1_degradation.s1) annotation( - Line(origin = {0.0, 30.5633}, points = {{-10.0, 19.4367}, {-10.0, -5.0617}, {10.0, -5.0617}, {10.0, -9.3133}}, smooth = Smooth.Bezier)); - connect(y6.n1, BMAL1_nuclear_export.s1) annotation( - Line(origin = {-56.6667, 43.75}, points = {{46.6667, 6.25}, {-23.3333, 6.25}, {-23.3333, -12.5}}, smooth = Smooth.Bezier)); - connect(y6.n1, y6_node) annotation( - Line(origin = {58.5, 70.0}, points = {{-68.5, -20.0}, {18.5, -20.0}, {18.5, 20.0}, {31.5, 20.0}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, nuclear_per2_cry_complex_degradation.p1) annotation( - Line(origin = {21.9367, -45.0}, points = {{-11.9367, -5.0}, {2.5617, -5.0}, {2.5617, 5.0}, {6.8133, 5.0}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, nuclear_BMAL1_degradation.p1) annotation( - Line(origin = {10.0, -25.625}, points = {{0.0, -24.375}, {0.0, 24.375}}, smooth = Smooth.Bezier)); - connect(BMAL1_nuclear_export.p1, y5_node) annotation( - Line(origin = {-23.3333, -57.0833}, points = {{-56.6667, 65.8333}, {-56.6667, -32.9167}, {113.3333, -32.9167}}, smooth = Smooth.Bezier)); - connect(per2_cry_nuclear_export.p1, y2_node) annotation( - Line(origin = {79.0717, 43.8125}, points = {{-10.9284, -22.5625}, {-10.9284, 3.1875}, {10.9283, 3.1875}, {10.9283, 16.1875}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, Active_BMAL1_degradation.p1) annotation( - Line(origin = {-9.4367, -45.0}, points = {{19.4367, -5.0}, {-5.0617, -5.0}, {-5.0617, 5.0}, {-9.3133, 5.0}}, smooth = Smooth.Bezier)); - end Nucleus; - - model Cytoplasm "Cytoplasm" - extends BioChem.Compartments.Compartment(V(start = 1)); - import BioChem.Math.*; - import BioChem.Constants.*; - - model y1_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - - - - - - - - ")); - end y1_; - - model y2_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end y2_; - - model y4_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - - - - - - - ")); - end y4_; - - model y5_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end y5_; - - model per2_cry_transcription_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real trans_per2_cry; - equation - rr = Cytoplasm_V * trans_per2_cry; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end per2_cry_transcription_; - - model per2_cry_mRNA_degradation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k1d; - equation - rr = Cytoplasm_V * k1d * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end per2_cry_mRNA_degradation_; - - model per2_cry_complex_formation_ - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k2b; - parameter Real q; - equation - rr = Cytoplasm_V * k2b * m1.c ^ q; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end per2_cry_complex_formation_; - - model cytoplasmic_per2_cry_complex_degradation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k2d; - equation - rr = Cytoplasm_V * k2d * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end cytoplasmic_per2_cry_complex_degradation_; - - model per2_cry_nuclear_import_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k2t; - equation - rr = Cytoplasm_V * k2t * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end per2_cry_nuclear_import_; - - model Bmal1_transcription_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - input Real trans_Bmal1; - equation - rr = Cytoplasm_V * trans_Bmal1; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Bmal1_transcription_; - - model Bmal1_mRNA_degradation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k4d; - equation - rr = Cytoplasm_V * k4d * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Bmal1_mRNA_degradation_; - - model BMAL1_translation_ - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k5b; - equation - rr = Cytoplasm_V * k5b * m1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end BMAL1_translation_; - - model cytoplasmic_BMAL1_degradation_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k5d; - equation - rr = Cytoplasm_V * k5d * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end cytoplasmic_BMAL1_degradation_; - - model BMAL1_nuclear_import_ - extends BioChem.Interfaces.Reactions.Uui; - outer Real Cytoplasm_V "Variable used to access the volume of an outer compartment. Do not edit."; - parameter Real k5t; - equation - rr = Cytoplasm_V * k5t * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end BMAL1_nuclear_import_; - - inner Real Cytoplasm_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - Cytoplasm.y1_ y1(c(start = 0.2)) "Per2 or Cry mRNA" annotation( - Placement(transformation(origin = {170.0, 60.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Cytoplasm.y2_ y2(c(start = 0)) "PER2_CRY_complex_cytoplasm" annotation( - Placement(transformation(origin = {140.0, -21.8298}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Cytoplasm.y4_ y4(c(start = 0.8)) "Bmal1 mRNA" annotation( - Placement(transformation(origin = {64.8293, -60.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Cytoplasm.y5_ y5(c(start = 1)) "BMAL1_cytoplasm" annotation( - Placement(transformation(origin = {20.0, 20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - BioChem.Substances.AmbientSubstance ambientSubstance annotation( - Placement(transformation(origin = {90.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - input Real trans_per2_cry; - Cytoplasm.per2_cry_transcription_ per2_cry_transcription(trans_per2_cry = trans_per2_cry) "per2_cry_transcription" annotation( - Placement(transformation(origin = {130.0, 50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - parameter Real k1d; - Cytoplasm.per2_cry_mRNA_degradation_ per2_cry_mRNA_degradation(k1d = k1d) "per2_cry_mRNA_degradation" annotation( - Placement(transformation(origin = {130.0, 70.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - parameter Real k2b; - parameter Real q; - Cytoplasm.per2_cry_complex_formation_ per2_cry_complex_formation(k2b = k2b, q = q) "per2_cry_complex_formation" annotation( - Placement(transformation(origin = {152.1486, 20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - parameter Real k2d; - Cytoplasm.cytoplasmic_per2_cry_complex_degradation_ cytoplasmic_per2_cry_complex_degradation(k2d = k2d) "cytoplasmic_per2_cry_complex_degradation" annotation( - Placement(transformation(origin = {120.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - parameter Real k2t; - BioChem.Interfaces.Nodes.SubstanceConnector y3_node annotation( - Placement(transformation(origin = {190.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Cytoplasm.per2_cry_nuclear_import_ per2_cry_nuclear_import(k2t = k2t) "per2_cry_nuclear_import" annotation( - Placement(transformation(origin = {180.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - BioChem.Interfaces.Nodes.SubstanceConnector y2_node annotation( - Placement(transformation(origin = {190.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - input Real trans_Bmal1; - Cytoplasm.Bmal1_transcription_ Bmal1_transcription(trans_Bmal1 = trans_Bmal1) "Bmal1_transcription" annotation( - Placement(transformation(origin = {74.9249, -23.3818}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - parameter Real k4d; - Cytoplasm.Bmal1_mRNA_degradation_ Bmal1_mRNA_degradation(k4d = k4d) "Bmal1_mRNA_degradation" annotation( - Placement(transformation(origin = {100.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - parameter Real k5b; - Cytoplasm.BMAL1_translation_ BMAL1_translation(k5b = k5b) "BMAL1_translation" annotation( - Placement(transformation(origin = {60.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - parameter Real k5d; - Cytoplasm.cytoplasmic_BMAL1_degradation_ cytoplasmic_BMAL1_degradation(k5d = k5d) "cytoplasmic_BMAL1_degradation" annotation( - Placement(transformation(origin = {60.0, 30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - parameter Real k5t; - BioChem.Interfaces.Nodes.SubstanceConnector y6_node annotation( - Placement(transformation(origin = {190.0, -90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, -90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Cytoplasm.BMAL1_nuclear_import_ BMAL1_nuclear_import(k5t = k5t) "BMAL1_nuclear_import" annotation( - Placement(transformation(origin = {50.0, -80.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -450))); - BioChem.Interfaces.Nodes.SubstanceConnector y5_node annotation( - Placement(transformation(origin = {190.0, 80.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, 90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - equation - connect(BMAL1_nuclear_import.p1, y6_node) annotation( - Line(origin = {128.8, -92.4506}, points = {{-78.8, 1.2006}, {-78.8, -3.0509}, {48.2, -3.0509}, {48.2, 2.4506}, {61.2, 2.4506}}, smooth = Smooth.Bezier)); - connect(y2.n1, y2_node) annotation( - Line(origin = {169.0149, -25.9149}, points = {{-29.0149, 4.0851}, {8.5, 4.0851}, {8.5, -4.0851}, {20.9851, -4.0851}}, smooth = Smooth.Bezier)); - connect(per2_cry_nuclear_import.p1, y3_node) annotation( - Line(origin = {183.3333, 27.0833}, points = {{-3.3333, -5.8333}, {-3.3333, 2.9167}, {6.6667, 2.9167}}, smooth = Smooth.Bezier)); - connect(y5.n1, y5_node) annotation( - Line(origin = {121.75, 70.0}, points = {{-101.75, -50.0}, {-41.75, 30.0}, {65.25, 10.0}, {68.25, 10.0}}, smooth = Smooth.Bezier)); - connect(y2.n1, per2_cry_nuclear_import.s1) annotation( - Line(origin = {166.6667, -14.9699}, points = {{-26.6667, -6.8599}, {13.3333, -6.8599}, {13.3333, 13.7199}}, smooth = Smooth.Bezier)); - connect(y1.n1, per2_cry_complex_formation.m1) annotation( - Line(origin = {167.0495, 33.3333}, points = {{2.9505, 26.6667}, {2.9505, -13.3333}, {-5.9009, -13.3333}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, per2_cry_complex_formation.s1) annotation( - Line(origin = {120.0594, 32.4506}, points = {{-30.0594, -2.4506}, {-17.0594, -2.4506}, {-17.0594, 3.0509}, {32.0892, 3.0509}, {32.0892, -1.2006}}, smooth = Smooth.Bezier)); - connect(y2.n1, per2_cry_complex_formation.p1) annotation( - Line(origin = {146.0743, -1.0207}, points = {{-6.0743, -20.8091}, {-6.0743, 5.5192}, {6.0743, 5.5192}, {6.0743, 9.7707}}, smooth = Smooth.Bezier)); - connect(y2.n1, cytoplasmic_per2_cry_complex_degradation.s1) annotation( - Line(origin = {130.0, -8.5207}, points = {{10.0, -13.3091}, {10.0, 3.0192}, {-10.0, 3.0192}, {-10.0, 7.2707}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, cytoplasmic_per2_cry_complex_degradation.p1) annotation( - Line(origin = {110.0, 27.0833}, points = {{-20.0, 2.9167}, {10.0, 2.9167}, {10.0, -5.8333}}, smooth = Smooth.Bezier)); - connect(y1.n1, per2_cry_transcription.p1) annotation( - Line(origin = {150.5633, 55.0}, points = {{19.4367, 5.0}, {-5.0617, 5.0}, {-5.0617, -5.0}, {-9.3133, -5.0}}, smooth = Smooth.Bezier)); - connect(y1.n1, per2_cry_mRNA_degradation.s1) annotation( - Line(origin = {150.5633, 65.0}, points = {{19.4367, -5.0}, {-5.0617, -5.0}, {-5.0617, 5.0}, {-9.3133, 5.0}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, per2_cry_mRNA_degradation.p1) annotation( - Line(origin = {99.5833, 56.6667}, points = {{-9.5833, -26.6667}, {-9.5833, 13.3333}, {19.1667, 13.3333}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, per2_cry_transcription.s1) annotation( - Line(origin = {106.872, 42.5}, points = {{-16.872, -12.5}, {-2.6325, -2.5}, {7.6265, 7.5}, {11.878, 7.5}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, BMAL1_translation.s1) annotation( - Line(origin = {83.75, 10.0}, points = {{6.25, 20.0}, {6.25, -10.0}, {-12.5, -10.0}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, Bmal1_mRNA_degradation.p1) annotation( - Line(origin = {95.0, -4.4367}, points = {{-5.0, 34.4367}, {-5.0, -10.0617}, {5.0, -10.0617}, {5.0, -14.3133}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, Bmal1_transcription.s1) annotation( - Line(origin = {82.4624, 0.5269}, points = {{7.5376, 29.4731}, {7.5376, -8.4072}, {-7.5375, -8.4072}, {-7.5375, -12.6587}}, smooth = Smooth.Bezier)); - connect(ambientSubstance.n1, cytoplasmic_BMAL1_degradation.p1) annotation( - Line(origin = {80.625, 30.0}, points = {{9.375, -0.0}, {-9.375, 0.0}}, smooth = Smooth.Bezier)); - connect(y5.n1, cytoplasmic_BMAL1_degradation.s1) annotation( - Line(origin = {39.4367, 25.0}, points = {{-19.4367, -5.0}, {5.0617, -5.0}, {5.0617, 5.0}, {9.3133, 5.0}}, smooth = Smooth.Bezier)); - connect(y5.n1, BMAL1_nuclear_import.s1) annotation( - Line(origin = {35.0, -44.4367}, points = {{-15.0, 64.4367}, {-15.0, -20.0617}, {15.0, -20.0617}, {15.0, -24.3133}}, smooth = Smooth.Bezier)); - connect(y5.n1, BMAL1_translation.p1) annotation( - Line(origin = {39.4367, 10.0}, points = {{-19.4367, 10.0}, {5.0617, 10.0}, {5.0617, -10.0}, {9.3133, -10.0}}, smooth = Smooth.Bezier)); - connect(y4.n1, BMAL1_translation.m1) annotation( - Line(origin = {62.4147, -24.2512}, points = {{2.4147, -35.7488}, {2.4147, 10.2487}, {-2.4147, 10.2487}, {-2.4147, 15.2512}}, smooth = Smooth.Bezier)); - connect(y4.n1, Bmal1_transcription.p1) annotation( - Line(origin = {69.8771, -43.0996}, points = {{-5.0478, -16.9004}, {-5.0478, 4.2163}, {5.0478, 4.2163}, {5.0478, 8.4678}}, smooth = Smooth.Bezier)); - connect(y4.n1, Bmal1_mRNA_degradation.s1) annotation( - Line(origin = {88.2764, -53.75}, points = {{-23.4471, -6.25}, {11.7236, -6.25}, {11.7236, 12.5}}, smooth = Smooth.Bezier)); - annotation( - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{0.0, -100.0}, {200.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}))); - end Cytoplasm; - annotation( - __MathCore(RDF = " - - - - - - Dharuri - Harish - - hdharuri@cds.caltech.edu - - California Institute of Technology - - - - - - 2008-04-16T11:56:13Z - - - 2008-08-20T18:28:56Z - - - - - - - - - - - - - - - - - - - - - - - - ")); - annotation( - Documentation(info = " -

Circadian Oscillator

- -This example is the modelica version of the model presented in -Modeling feedback loops of the Mammalian circadian oscillator by -Becker-Weimann S, Wolf J, Herzel H, Kramer A. (Biophysical Journal Volume 87 November 2004 3023-3034) - -
-
-See -Container - for more documentation and simulation results. -", revisions = "")); - end CircadianOscillator; - - package CellDivison "Tyson1991_CellCycle_6var" - extends BioChem.Icons.Example; - - model cell - extends BioChem.Compartments.MainCompartment(V(start = 1)); - import BioChem.Math.*; - import BioChem.Constants.*; - - model EmptySet_ - extends BioChem.Substances.BoundarySubstance; - end EmptySet_; - - model C2_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end C2_; - - model CP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end CP_; - - model M_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end M_; - - model pM_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end pM_; - - model Y_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Y_; - - model YP_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end YP_; - - model YT_ - extends BioChem.Substances.SignalSubstance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end YT_; - - model CT_ - extends BioChem.Substances.SignalSubstance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end CT_; - - model Reaction1_ - extends BioChem.Interfaces.Reactions.Ubi; - parameter Real k6 = 1; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * k6 * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - - - - - - ")); - end Reaction1_; - - model Reaction2_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k8notP = 1000000.0; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * s1.c * k8notP; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end Reaction2_; - - model Reaction3_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k9 = 1000; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * s1.c * k9; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end Reaction3_; - - model Reaction4_ - extends BioChem.Interfaces.Reactions.Bui; - parameter Real k3 = 200; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * s1.c * k3 * s2.c; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end Reaction4_; - - model Reaction5_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k5notP = 0; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * k5notP * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - - - - - - - - - ")); - end Reaction5_; - - model Reaction6_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k1aa = 0.015; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * k1aa; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Reaction6_; - - model Reaction7_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k2 = 0; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * k2 * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Reaction7_; - - model Reaction8_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k7 = 0.6; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * k7 * s1.c; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Reaction8_; - - model Reaction9_ - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real k4 = 180; - parameter Real k4prime = 0.018; - outer Real cell_V "Variable used to access the volume of an outer compartment. Do not edit."; - equation - rr = cell_V * s1.c * (k4prime + k4 * (p1.c / m1.c) ^ 2); - annotation( - __MathCore(RDF = " - - - - - - - - - - - - - - - - - ")); - end Reaction9_; - - inner Real cell_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - CellDivison.cell.EmptySet_ EmptySet(c(start = 0)) annotation( - Placement(transformation(origin = {10.0, 20.0}, extent = {{-10.0, 10.0}, {10.0, -10.0}}))); - CellDivison.cell.C2_ C2(c(start = 0)) "cdc2k" annotation( - Placement(transformation(origin = {20.0, 60.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - CellDivison.cell.CP_ CP(c(start = 0.75)) "cdc2k-P" annotation( - Placement(transformation(origin = {80.0, 60.0}, extent = {{-10.0, 10.0}, {10.0, -10.0}}, rotation = -90))); - CellDivison.cell.M_ M(c(start = 0)) "p-cyclin_cdc2" annotation( - Placement(transformation(origin = {-80.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - CellDivison.cell.pM_ pM(c(start = 0.25)) "p-cyclin_cdc2-p" annotation( - Placement(transformation(origin = {-10.0, -50.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - CellDivison.cell.Y_ Y(c(start = 0)) "cyclin" annotation( - Placement(transformation(origin = {20.0, -30.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - CellDivison.cell.YP_ YP(c(start = 0)) "p-cyclin" annotation( - Placement(transformation(origin = {-47.6389, -8.3553}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - CellDivison.cell.YT_ YT(c(start = 0)) "total_cyclin" annotation( - Placement(transformation(origin = {-70.0, 70.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - CellDivison.cell.CT_ CT(c(start = 0)) "total_cdc2" annotation( - Placement(transformation(origin = {-40.0, -60.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - CellDivison.cell.Reaction1_ Reaction1 "cyclin_cdc2k dissociation" annotation( - Placement(transformation(origin = {-70.0, 20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - CellDivison.cell.Reaction2_ Reaction2 "cdc2k phosphorylation" annotation( - Placement(transformation(origin = {50.0, 90.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - CellDivison.cell.Reaction3_ Reaction3 "cdc2k dephosphorylation" annotation( - Placement(transformation(origin = {50.0, 40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - CellDivison.cell.Reaction4_ Reaction4 "cyclin cdc2k-p association" annotation( - Placement(transformation(origin = {48.1433, -70.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - CellDivison.cell.Reaction5_ Reaction5 "deactivation of cdc2 kinase" annotation( - Placement(transformation(origin = {-45.4898, -80.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - CellDivison.cell.Reaction6_ Reaction6 "cyclin biosynthesis" annotation( - Placement(transformation(origin = {-7.8911, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - CellDivison.cell.Reaction7_ Reaction7 "default degradation of cyclin" annotation( - Placement(transformation(origin = {50.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - CellDivison.cell.Reaction8_ Reaction8 "cdc2 kinase triggered degration of cyclin" annotation( - Placement(transformation(origin = {-30.0, 20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - CellDivison.cell.Reaction9_ Reaction9 "activation of cdc2 kinase" annotation( - Placement(transformation(origin = {-40.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -180))); - equation - connect(CP.n1, Reaction2.p1) annotation( - Line(origin = {73.75, 80.0}, points = {{6.25, -20.0}, {6.25, 10.0}, {-12.5, 10.0}}, smooth = Smooth.Bezier)); - connect(C2.n1, Reaction2.s1) annotation( - Line(origin = {26.25, 80.0}, points = {{-6.25, -20.0}, {-6.25, 10.0}, {12.5, 10.0}}, smooth = Smooth.Bezier)); - connect(CP.n1, Reaction3.s1) annotation( - Line(origin = {73.75, 46.6667}, points = {{6.25, 13.3333}, {6.25, -6.6667}, {-12.5, -6.6667}}, smooth = Smooth.Bezier)); - connect(CP.n1, Reaction4.s1) annotation( - Line(origin = {66.5716, -26.9367}, points = {{13.4284, 86.9367}, {13.4284, -27.5617}, {-13.4284, -27.5617}, {-13.4284, -31.8133}}, smooth = Smooth.Bezier)); - connect(C2.n1, Reaction3.p1) annotation( - Line(origin = {26.25, 46.6667}, points = {{-6.25, 13.3333}, {-6.25, -6.6667}, {12.5, -6.6667}}, smooth = Smooth.Bezier)); - connect(C2.n1, Reaction1.p1) annotation( - Line(origin = {-36.9367, 42.5}, points = {{56.9367, 17.5}, {-17.5617, 17.5}, {-17.5617, -17.5}, {-21.8133, -17.5}}, smooth = Smooth.Bezier)); - connect(Y.n1, Reaction4.s2) annotation( - Line(origin = {31.5716, -49.4367}, points = {{-11.5716, 19.4367}, {-11.5716, -5.0617}, {11.5716, -5.0617}, {11.5716, -9.3133}}, smooth = Smooth.Bezier)); - connect(pM.n1, Reaction4.p1) annotation( - Line(origin = {18.4573, -70.4506}, points = {{-28.4573, 20.4506}, {-15.4573, 20.4506}, {-15.4573, -15.0509}, {29.686, -15.0509}, {29.686, -10.7994}}, smooth = Smooth.Bezier)); - connect(Y.n1, Reaction7.s1) annotation( - Line(origin = {40.0, -27.0833}, points = {{-20.0, -2.9167}, {10.0, -2.9167}, {10.0, 5.8333}}, smooth = Smooth.Bezier)); - connect(Y.n1, Reaction6.p1) annotation( - Line(origin = {1.4059, -27.0833}, points = {{18.5941, -2.9167}, {-9.297, -2.9167}, {-9.297, 5.8333}}, smooth = Smooth.Bezier)); - connect(M.n1, Reaction1.s1) annotation( - Line(origin = {-82.4506, -4.8}, points = {{2.4506, -25.2}, {2.4506, -12.2}, {-3.0509, -12.2}, {-3.0509, 24.8}, {1.2006, 24.8}}, smooth = Smooth.Bezier)); - connect(M.n1, Reaction5.s1) annotation( - Line(origin = {-72.2466, -63.3333}, points = {{-7.7534, 33.3333}, {-7.7534, -16.6667}, {15.5068, -16.6667}}, smooth = Smooth.Bezier)); - connect(M.n1, Reaction9.p1) annotation( - Line(origin = {-60.5633, -35.0}, points = {{-19.4367, 5.0}, {5.0617, 5.0}, {5.0617, -5.0}, {9.3133, -5.0}}, smooth = Smooth.Bezier)); - connect(pM.n1, Reaction5.p1) annotation( - Line(origin = {-18.0799, -70.0}, points = {{8.0799, 20.0}, {8.0799, -10.0}, {-16.1599, -10.0}}, smooth = Smooth.Bezier)); - connect(pM.n1, Reaction9.s1) annotation( - Line(origin = {-21.9367, -45.0}, points = {{11.9367, -5.0}, {-2.5617, -5.0}, {-2.5617, 5.0}, {-6.8133, 5.0}}, smooth = Smooth.Bezier)); - connect(CT.n1, Reaction9.m1) annotation( - Line(origin = {-40.0, -52.6667}, points = {{0.0, -7.3333}, {0.0, 3.6667}, {0.0, 3.6667}}, smooth = Smooth.Bezier)); - connect(EmptySet.n1, Reaction6.s1) annotation( - Line(origin = {1.0545, 8.0633}, points = {{8.9456, 11.9367}, {8.9456, -2.5617}, {-8.9456, -2.5617}, {-8.9456, -6.8133}}, smooth = Smooth.Bezier)); - connect(EmptySet.n1, Reaction7.p1) annotation( - Line(origin = {36.6667, 13.75}, points = {{-26.6667, 6.25}, {13.3333, 6.25}, {13.3333, -12.5}}, smooth = Smooth.Bezier)); - connect(EmptySet.n1, Reaction8.p1) annotation( - Line(origin = {-11.2, 28.4506}, points = {{21.2, -8.4506}, {8.2, -8.4506}, {8.2, 7.0509}, {-18.8, 7.0509}, {-18.8, 2.7994}}, smooth = Smooth.Bezier)); - connect(YP.n1, Reaction8.s1) annotation( - Line(origin = {-35.8796, -2.6535}, points = {{-11.7593, -5.7018}, {5.8796, -5.7018}, {5.8796, 11.4035}}, smooth = Smooth.Bezier)); - connect(YP.n1, Reaction1.p2) annotation( - Line(origin = {-51.3426, 7.2149}, points = {{3.7037, -15.5702}, {3.7037, 7.7851}, {-7.4074, 7.7851}}, smooth = Smooth.Bezier)); - YT.c = Y.c + YP.c + M.c + pM.c; - CT.c = C2.c + CP.c + M.c + pM.c; - annotation( - __MathCore(RDF = " - - - - - - - - "), - experiment(StartTime = 0.0, StopTime = 100, NumberOfIntervals = -1, Algorithm = "dassl", Tolerance = 1e-06), - Documentation(info = " -

CellDivision

-This example is a Modelica version of the model presented in Modeling the cell division cycle: cdc2 and cyclin interactions by John J. Tyson. (Proc. Nati. Acad. Sci. USA -Vol. 88, pp. 7328-7332, August 1991 -Cell Biology) - -

Abstract

-The proteins cdc2 and cyclin form a heterodimer -(maturation promoting factor) that controls the major -events of the cell cycle. A mathematical model for the interactions -of cdc2 and cyclin is constructed. Simulation and analysis -of the model show that the control system can operate in three -modes: as a steady state with high maturation promoting factor -activity, as a spontaneous oscillator, or as an excitable switch. -We associate the steady state with metaphase arrest in unfertilized -eggs, the spontaneous oscillations with rapid division -cycles in early embryos, and the excitable switch with growthcontrolled -division cycles typical of nonembryonic cells. - -

Simulations

- -The simulation results are shown in the - Figure 1. This plot corresponds to Fig 3A from the original publication (Tyson, 1991).
- - -\"Fig1: -", revisions = "")); - end cell; - annotation( - __MathCore(RDF = " - - - - - - Shapiro - Bruce - - bshapiro@jpl.nasa.gov - - NASA Jet Propulsion Laboratory - - - - - Chelliah - Vijayalakshmi - - viji@ebi.ac.uk - - EMBL-EBI - - - - - - 2005-02-08T18:28:27Z - - - 2008-08-21T11:31:54Z - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ")); - annotation( - Documentation(info = " -

CellDivision

-This example is a Modelica version of the model presented in Modeling the cell division cycle: cdc2 and cyclin interactions by John J. Tyson. (Proc. Nati. Acad. Sci. USA -Vol. 88, pp. 7328-7332, August 1991 -Cell Biology).

- -See -cell - for more documentation and simulation results. -", revisions = "")); - end CellDivison; - - package CaOscillations "Oxhamre2005_Ca_oscillation" - extends BioChem.Icons.Example; - - model Cytosol - extends BioChem.Compartments.MainCompartment(V(start = 1)); - import BioChem.Math.*; - import BioChem.Constants.*; - - model Ca_Cyt_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Ca_Cyt_; - - model Jpump_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real Fpump_0 = 2; - parameter Real Kpump = 0.1; - equation - rr = Fpump_0 * s1.c / (Kpump + s1.c); - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end Jpump_; - - Endoplasmic_Reticulum endoplasmicReticulum(p1_sbml = p1_sbml, p2_sbml = p2_sbml, p3_sbml = p3_sbml) annotation( - Placement(transformation(origin = {-28.4357, 20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - inner Real Cytosol_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - inner Real Endoplasmic_Reticulum_V = endoplasmicReticulum.V "Variable used to make the compartment volume of inner compartments accessible. Do not edit."; - Cytosol.Ca_Cyt_ Ca_Cyt(c(start = 0)) annotation( - Placement(transformation(origin = {-10.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Real n_sbml(start = 1); - parameter Real n0 = 1; - parameter Real kbN = 0.5; - parameter Real kappa = 5; - Real p1_sbml(start = 0); - parameter Real p11 = 0.2; - parameter Real p12 = 0.8; - parameter Real K1 = 5; - Real p2_sbml(start = 0); - parameter Real K2 = 0.7; - Real p3_sbml(start = 0.95); - parameter Real k31 = 0.5; - parameter Real K3 = 0.7; - Cytosol.Jpump_ Jpump annotation( - Placement(transformation(origin = {50.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - equation - connect(Ca_Cyt.n1, endoplasmicReticulum.Ca_Cyt_node) annotation( - Line(origin = {-29.2619, -10.8}, points = {{19.2619, -29.2}, {19.2619, -16.2}, {-14.175, -16.2}, {-14.175, 30.8}, {-10.1738, 30.8}}, smooth = Smooth.Bezier)); - connect(endoplasmicReticulum.CaER_node, Jpump.p1) annotation( - Line(origin = {27.5214, 13.75}, points = {{-44.9571, 6.25}, {22.4786, 6.25}, {22.4786, -12.5}}, smooth = Smooth.Bezier)); - connect(Ca_Cyt.n1, Jpump.s1) annotation( - Line(origin = {30.0, -33.75}, points = {{-40.0, -6.25}, {20.0, -6.25}, {20.0, 12.5}}, smooth = Smooth.Bezier)); - n_sbml = n0 * (exp((-kbN) * time) + kappa * (1 - exp((-kbN) * time))); - p1_sbml = p11 + p12 * n_sbml / (K1 + n_sbml); - p2_sbml = Ca_Cyt.c / (K2 + Ca_Cyt.c); - der(p3_sbml) = (-k31 * Ca_Cyt.c * p3_sbml) + k31 * K3 * (1 - p3_sbml); - annotation( - __MathCore(RDF = " - - - - - - - - "), - experiment(StartTime = 0.0, StopTime = 120, NumberOfIntervals = -1, Algorithm = "dassl", Tolerance = 1e-06), - Documentation(info = " -

Ca Oscillations

-This example is a Modelica version of the model presented in A Minimal Generic Model of Bacteria-Induced Intracellular Ca2+ -Oscillations in Epithelial Cells by Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemoy. (Biophysical Journal Volume 88 April 2005 2976-2981) - -

Abstract

-The toxin &alpha-hemolysin expressed by uropathogenic Escherichia coli bacteria was recently shown as the first -pathophysiologically relevant protein to induce oscillations of the intracellular Ca2+ concentration in target cells. Here, we -propose a generic three-variable kinetic model describing the Ca2+ oscillations induced in single rat renal epithelial cells by this -toxin. Specifically, we take into account the interplay between 1), the cytosolic Ca2+ concentration; 2), IP3-sensitive Ca2+ -channels located in the membrane separating the cytosol and endoplasmic reticulum; and 3), toxin-related activation of -production of IP3 by phospholipase C. With these ingredients, the predicted response of cells exposed to the toxin is in good -agreement with the results of experiments. -

Simulations

-The simulation results are shown in the - Figure 1. This plot corresponds to Fig 1C of the paper (Oxhamre 2005). -
- - -\"Fig1: -", revisions = "")); - end Cytosol; - - model Endoplasmic_Reticulum - extends BioChem.Compartments.Compartment(V(start = 1)); - import BioChem.Math.*; - import BioChem.Constants.*; - - model CaER_ - extends BioChem.Substances.Substance; - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end CaER_; - - model Jch_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real Fch_0 = 8; - input Real p1_sbml; - input Real p2_sbml; - input Real p3_sbml; - equation - rr = Fch_0 * p1_sbml * p2_sbml * p3_sbml; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end Jch_; - - model Jleak_ - extends BioChem.Interfaces.Reactions.Uui; - parameter Real Fleak = 0.5; - equation - rr = Fleak; - annotation( - __MathCore(RDF = " - - - - - - - - - ")); - end Jleak_; - - inner Real Endoplasmic_Reticulum_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit."; - Endoplasmic_Reticulum.CaER_ CaER(c(start = 0)) annotation( - Placement(transformation(origin = {10.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -540))); - input Real p1_sbml; - input Real p2_sbml; - input Real p3_sbml; - BioChem.Interfaces.Nodes.SubstanceConnector Ca_Cyt_node annotation( - Placement(transformation(origin = {-90.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {-110.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - Endoplasmic_Reticulum.Jch_ Jch(p1_sbml = p1_sbml, p2_sbml = p2_sbml, p3_sbml = p3_sbml) annotation( - Placement(transformation(origin = {-80.0, -20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270))); - Endoplasmic_Reticulum.Jleak_ Jleak annotation( - Placement(transformation(origin = {-80.0, 43.7135}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90))); - BioChem.Interfaces.Nodes.SubstanceConnector CaER_node annotation( - Placement(transformation(origin = {90.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}))); - equation - connect(Jleak.p1, Ca_Cyt_node) annotation( - Line(origin = {-85.0, 22.1159}, points = {{5.0, 10.3476}, {5.0, 0.8841}, {-5.0, 0.8841}, {-5.0, -12.1159}}, smooth = Smooth.Bezier)); - connect(Jch.p1, Ca_Cyt_node) annotation( - Line(origin = {-85.0, -1.1875}, points = {{5.0, -7.5625}, {5.0, -1.8125}, {-5.0, -1.8125}, {-5.0, 11.1875}}, smooth = Smooth.Bezier)); - connect(CaER.n1, CaER_node) annotation( - Line(origin = {63.5, 5.0}, points = {{-53.5, 5.0}, {13.5, 5.0}, {13.5, -5.0}, {26.5, -5.0}}, smooth = Smooth.Bezier)); - connect(CaER.n1, Jleak.s1) annotation( - Line(origin = {-31.2, 38.6787}, points = {{41.2, -28.6787}, {28.2, -28.6787}, {28.2, 20.5363}, {-48.8, 20.5363}, {-48.8, 16.2848}}, smooth = Smooth.Bezier)); - connect(CaER.n1, Jch.s1) annotation( - Line(origin = {-31.2, -16.4506}, points = {{41.2, 26.4506}, {28.2, 26.4506}, {28.2, -19.0509}, {-48.8, -19.0509}, {-48.8, -14.7994}}, smooth = Smooth.Bezier)); - annotation( - __MathCore(RDF = " - - - - - - - - ")); - end Endoplasmic_Reticulum; - annotation( - __MathCore(RDF = " - - - - - - Dharuri - Harish - - Harish_Dharuri@kgi.edu - - Keck Graduate Institute - - - - - - 2005-08-25T11:00:43Z - - - 2008-08-21T11:54:50Z - - - - - - - - - - - - - - - - - - - - - - - - - ")); - annotation( - Documentation(info = " -

Ca Oscillations

-This example is a Modelica version of the model presented in A Minimal Generic Model of Bacteria-Induced Intracellular Ca2+ -Oscillations in Epithelial Cells by Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemoy. (Biophysical Journal Volume 88 April 2005 2976-2981).

- -See -Cytosol - for more documentation and simulation results. -", revisions = "")); - end CaOscillations; - - package GlucoseInsulinModel - extends BioChem.Icons.Example; - - model GlucoseInsulinModel - extends BioChem.Compartments.MainCompartment(V.start = 1.0); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.GastroIntestinalTract GastroIntestinalTract annotation( - Placement(transformation(origin = {-50, 80}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.TissueGlucose TissueGlucose annotation( - Placement(transformation(origin = {0, 60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.GlucoseRenalExcretion GlucoseRenalExcretion annotation( - Placement(transformation(origin = {125.793, -4.74893}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.PlasmaGlucose PlasmaGlucose annotation( - Placement(transformation(extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.PlasmaInsulin PlasmaInsulin annotation( - Placement(transformation(origin = {-80, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.UtilizationMuscleTissue UtilizationMuscleTissue annotation( - Placement(transformation(origin = {70, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ReversibleFlowReaction k_1_k_2(k_1 = 0.065, k_2 = 0.079) annotation( - Placement(transformation(origin = {0, 30}, extent = {{-6.52644, -6.52644}, {6.52644, 6.52644}}, rotation = -270))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.LiverInsulin LiverInsulin annotation( - Placement(transformation(origin = {-80, -73.9076}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.EndogenousGlucoseProduction EndogenousGlucoseProduction annotation( - Placement(transformation(origin = {-40, -45.0779}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ReversibleFlowReaction m_1_m_2(k_2 = 0.484, k_1 = 0.19) annotation( - Placement(transformation(origin = {-80, -36.3608}, extent = {{-6.36084, 6.36084}, {6.36084, -6.36084}}, rotation = 90))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.BetaCell BetaCell annotation( - Placement(transformation(origin = {23.4019, -74.2468}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.AdiposeTissue.AdiposeTissue adiposeTissue1 annotation( - Placement(transformation(origin = {70, 80}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(UtilizationMuscleTissue.I_connector, PlasmaInsulin.I_signal_connector) annotation( - Line(origin = {-35.44, 35.5}, points = {{94.44, 12.857}, {55.44, 12.86}, {48.33, 64.5}, {-52.076, 70.3333}, {-34.56, 6.90118}, {-26.6353, -15.5}, {-24.56, -41.27}, {-33.56, -41.27}, {-33.56, -41.182}}, color = {255, 0, 255}, pattern = LinePattern.Dash, arrow = {Arrow.Open, Arrow.None}, smooth = Smooth.Bezier)); - connect(adiposeTissue1.I_connector, PlasmaInsulin.I_signal_connector) annotation( - Line(origin = {-42.08, 44.79}, points = {{101.078, 43.5978}, {58.03, 43.6}, {12.08, 61.3825}, {-41.3655, 52.9023}, {-34.2421, 19.3206}, {-23.7266, -12.2259}, {-17.92, -36.99}, {-17.92, -47.1645}, {-19.65, -50.22}, {-26.92, -50.22}, {-26.9223, -50.4722}}, color = {255, 0, 255}, pattern = LinePattern.Dash, smooth = Smooth.Bezier)); - connect(TissueGlucose.U_idf_connector, adiposeTissue1.G_t_connector) annotation( - Line(origin = {38.75, 76.58}, points = {{-27.75, -10.58}, {-8.75, 3.42}, {16.25, 3.58}, {20.25, 3.58}}, color = {0, 0, 128}, thickness = 1, arrow = {Arrow.None, Arrow.Filled}, smooth = Smooth.Bezier)); - connect(BetaCell.G_connector, PlasmaGlucose.G_signal_connector) annotation( - Line(origin = {-0.71, -20.49}, points = {{24.11, -42.76}, {22.75, -9.7}, {-17.27, -9.7}, {-17.27, 20.49}, {-10.29, 20.68}}, color = {0, 0, 255}, pattern = LinePattern.Dash, arrow = {Arrow.Open, Arrow.None}, smooth = Smooth.Bezier)); - connect(BetaCell.G_p_connector, PlasmaGlucose.G_p_connector) annotation( - Line(origin = {3.93, -21.62}, points = {{26.99, -41.63}, {26.31, -4.5}, {-18.85, -4.5}, {-18.85, 14.62}, {-14.93, 14.62}}, color = {0, 0, 255}, pattern = LinePattern.Dash, arrow = {Arrow.Open, Arrow.None}, smooth = Smooth.Bezier)); - connect(GlucoseRenalExcretion.G_p_connector, PlasmaGlucose.G_p_connector) annotation( - Line(origin = {37.56, -14.05}, points = {{77.23, 0.94}, {56.28, -11.35}, {-17.56, -11.35}, {-52.49, -11.35}, {-52.49, 7.6}, {-48.56, 7.6}, {-48.56, 7.05}}, color = {0, 0, 255}, pattern = LinePattern.Dash, arrow = {Arrow.Open, Arrow.None}, smooth = Smooth.Bezier)); - connect(PlasmaGlucose.G_p_connector, EndogenousGlucoseProduction.G_p_connector) annotation( - Line(origin = {-30.33, -16.03}, points = {{19.33, 9.03}, {-9.67, 9.03}, {-9.67, -18.05}}, color = {0, 0, 255}, pattern = LinePattern.Dash, arrow = {Arrow.None, Arrow.Open}, smooth = Smooth.Bezier)); - connect(EndogenousGlucoseProduction.I_po_connector, BetaCell.I_po_connector) annotation( - Line(origin = {1.27, -51.13}, points = {{-30.27, 6.06}, {15.13, 6.06}, {15.13, -12.11}}, color = {255, 0, 255}, pattern = LinePattern.Dash, arrow = {Arrow.Open, Arrow.None}, smooth = Smooth.Bezier)); - connect(EndogenousGlucoseProduction.I_connector, PlasmaInsulin.I_signal_connector) annotation( - Line(origin = {-54.49, -15.15}, points = {{7.26, -18.93}, {7.26, 9.47}, {-14.51, 9.47}}, color = {255, 0, 255}, pattern = LinePattern.Dash, arrow = {Arrow.Open, Arrow.None}, smooth = Smooth.Bezier)); - connect(TissueGlucose.U_idm_connector, UtilizationMuscleTissue.G_t_connector) annotation( - Line(origin = {45, 46.91}, points = {{-34, 6.74021}, {-12.0967, -6.91}, {10, -6.74}, {14, -6.748}}, color = {0, 0, 128}, thickness = 1, arrow = {Arrow.None, Arrow.Filled}, smooth = Smooth.Bezier)); - connect(LiverInsulin.S_connector, BetaCell.S_connector) annotation( - Line(origin = {-9.95, -74.17}, points = {{-59.05, 0.07}, {18.35, 0.07}, {18.35, -0.07}, {22.35, -0.07}}, color = {128, 0, 128}, thickness = 1, arrow = {Arrow.Filled, Arrow.None}, smooth = Smooth.Bezier)); - connect(PlasmaGlucose.EGP_connector, EndogenousGlucoseProduction.EGP_connector) annotation( - Line(origin = {-19.75, -20.03}, points = {{19.58, 9.03}, {19.58, 0.03}, {-10.25, 0.03}, {-13.15, -4.55}, {-12.87, -14.05}}, color = {0, 0, 128}, thickness = 1, arrow = {Arrow.Filled, Arrow.None}, smooth = Smooth.Bezier)); - connect(PlasmaGlucose.E_connector, GlucoseRenalExcretion.productConnector1) annotation( - Line(origin = {86.84, -4.8}, points = {{-75.84, -0.05}, {23.95, -0.05}, {23.95, 0.05}, {27.95, 0.05}}, color = {0, 0, 128}, thickness = 1, arrow = {Arrow.None, Arrow.Filled}, smooth = Smooth.Bezier)); - connect(PlasmaGlucose.Ra_connector, GastroIntestinalTract.Ra_connector) annotation( - Line(origin = {-28.9, 31.7}, points = {{21.1, -20.7}, {21.1, -8.3}, {-21.1, -8.3}, {-21.1, 37.3}}, color = {0, 0, 128}, thickness = 1, arrow = {Arrow.Filled, Arrow.None}, smooth = Smooth.Bezier)); - connect(m_1_m_2.p1, PlasmaInsulin.I_connector) annotation( - Line(origin = {-80, -20.1024}, points = {{0, -9.10245}, {0, 9.10245}}, color = {128, 0, 128}, thickness = 1, smooth = Smooth.Bezier)); - connect(m_1_m_2.s1, LiverInsulin.I_connector) annotation( - Line(origin = {-80, -53.2122}, points = {{0, 9.6954}, {0, -9.6954}}, color = {128, 0, 128}, thickness = 1, smooth = Smooth.Bezier)); - connect(k_1_k_2.p1, TissueGlucose.G_connector) annotation( - Line(origin = {0, 43.17}, points = {{0, -5.83}, {0, 5.83}}, color = {0, 0, 128}, thickness = 1, smooth = Smooth.Bezier)); - connect(k_1_k_2.s1, PlasmaGlucose.G_connector) annotation( - Line(origin = {0, 16.83}, points = {{0, 5.83}, {0, -5.83}}, color = {0, 0, 128}, thickness = 1, smooth = Smooth.Bezier)); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Rectangle(origin = {-39.6875, -1.36711}, fillColor = {255, 0, 0}, pattern = LinePattern.None, fillPattern = FillPattern.Solid, extent = {{-55.2911, -15.5929}, {55.2911, 15.5929}}), Rectangle(origin = {-57.5522, -75}, fillColor = {128, 0, 0}, pattern = LinePattern.None, fillPattern = FillPattern.Solid, extent = {{-40.931, -15}, {40.931, 15}}), Rectangle(origin = {-40.7051, -45.0134}, fillColor = {128, 0, 0}, pattern = LinePattern.None, fillPattern = FillPattern.Solid, extent = {{-24.0839, -16.859}, {24.0839, 16.859}}), Rectangle(origin = {17.3745, 60}, fillColor = {255, 170, 127}, pattern = LinePattern.None, fillPattern = FillPattern.Solid, extent = {{-35, -18.3307}, {35, 18.3307}}), Rectangle(origin = {70, 58.6765}, fillColor = {255, 170, 127}, pattern = LinePattern.None, fillPattern = FillPattern.Solid, extent = {{-20, -38.6765}, {20, 38.6765}}), Line(origin = {100, -55.25}, points = {{-8.26, 0}, {8.26, 0}}, color = {0, 0, 128}, thickness = 1), Text(origin = {126.135, -55.59}, fillPattern = FillPattern.Solid, extent = {{-15.6548, -4.41}, {15.6548, 4.41}}, textString = "Glucose flow", fontName = "Arial"), Line(origin = {100, -66.03}, points = {{-8.26, 0}, {8.26, 0}}, color = {0, 0, 255}, pattern = LinePattern.Dash), Line(origin = {100, -85.28}, points = {{-8.26, 0}, {8.26, 0}}, color = {255, 0, 255}, pattern = LinePattern.Dash), Line(origin = {100, -75.36}, points = {{-8.26, 0}, {8.26, 0}}, color = {128, 0, 128}, thickness = 1), Text(origin = {128.34, -65.59}, fillPattern = FillPattern.Solid, extent = {{-17.8596, -4.41}, {17.8596, 4.41}}, textString = "Glucose signal", fontName = "Arial"), Text(origin = {124.953, -75.59}, fillPattern = FillPattern.Solid, extent = {{-13.3507, -4.41}, {13.3507, 4.41}}, textString = "Insulin flow", fontName = "Arial"), Text(origin = {126.987, -85.59}, fillPattern = FillPattern.Solid, extent = {{-15.3871, -4.41}, {15.3871, 4.41}}, textString = "Insulin signal", fontName = "Arial")}), - experiment(StartTime = 0.0, StopTime = 420, NumberOfIntervals = -1, Algorithm = "dassl", Tolerance = 1e-06), - Documentation(info = " -

A Whole Body Model of the Glucose Insulin System

- -This model is presented in Hierarchical modeling of diabetes by -Elin Nyman, ISRN:LiU-IKE-EX-09/14. Linköping University 2009.

- -This whole-body model of the glucose insulin system shows the flows and concentrations of insulin and glucose during and after a meal. Mechanistic details on a cellular level are included in the module describing the fat tissue. The model can be used to study diabetes and other related diseases. -

The Fat Tissue Module

-The module describing the fat cells includes the main parts of the insulin signaling network of fat cells. This process starts with insulin molecules that bind to the insulin receptor (IR) in the cell membrane. This activates (phosphorylates) IR. Active IR phosphorylates the insulin receptor substrate protein 1 (IRS1) inside the cell on selective tyrosine sites. These phosphorylations are used as docking sites by downstream effector molecules. The next important step in this path is the activation of protein kinase B (PKB). PKB regulates the translocation of vesicles including glucose transporter 4 (GLUT4) from the cytosol to the plasma membrane. The vesicles merge into the membrane where GLUT4 starts to transport glucose from the interstitial fluid to the inside of the cell. This signaling cascade is shown in Figure 1. GLUT1 or glucose transporter 1 is the other glucose transporter that exists in fat cells. GLUT1 continuously transports small amounts of glucose into the cells for the basal needs. - - - -\"Fig1:
-Figure 1: A simplified picture of the insulin signaling network and the glucose uptake in fat cells.
- - -

Simulations

-The simulation results of the whole body level are shown in the Figure 2, Figure 3 and Figure 4. The concentrations of insulin and glucose are shown in Figure 2 and the three flows: insulin from beta cells to liver, glucose from liver to plasma, and glucose from intestine to plasma, in Figure 3. - -Figure 4 shows a simulation of the glucose uptake by fat cells.
- - - - - - -\"Fig2: - -\"Fig3: - -\"Fig4: - - -", revisions = "")); - end GlucoseInsulinModel; - - package Utilities - extends BioChem.Icons.Library; - - package Parts - extends BioChem.Icons.Library; - - model GastroIntestinalTract - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Units.Concentration ra_signal; - BioChem.Units.Concentration q_sto; - BioChem.Units.Concentration d; - parameter Real f = 0.9; - parameter Real BW = 78; - BioChem.Substances.Substance Q_sto2(c.start = 0) annotation( - Placement(transformation(origin = {0, 50}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance Q_gut(c.start = 0) annotation( - Placement(transformation(origin = {0, -20}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction k_abs(k = 0.057) annotation( - Placement(transformation(origin = {38.33, -20}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.k_empt k_empt1 annotation( - Placement(transformation(origin = {0, 17.8419}, extent = {{-10, -10}, {10, 10}}, rotation = -90))); - BioChem.Substances.Substance Q_sto1(c.start = 0) annotation( - Placement(transformation(origin = {-60, 50}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.dirac dirac annotation( - Placement(transformation(origin = {-100, 50}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance Q_sto(c(start = 0) = q_sto) annotation( - Placement(transformation(origin = {100, 30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance D(c(start = 0) = d) annotation( - Placement(transformation(origin = {100, 5.76656}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector Ra_connector annotation( - Placement(transformation(origin = {0, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {0, -110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.BoundarySubstance GlucoseIntake(c.start = 78000) annotation( - Placement(transformation(origin = {-130, 50}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction k_gri(k = 0.0558) annotation( - Placement(transformation(origin = {-28.43, 50}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.BoundarySubstance End annotation( - Placement(transformation(origin = {80, -20}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance Ra_calc(c = ra_signal) annotation( - Placement(transformation(origin = {0, -50}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(Ra_calc.n1, Ra_connector) annotation( - Line(origin = {0, -65}, points = {{0, 15}, {0, -15}})); - connect(k_abs.p1, End.n1) annotation( - Line(origin = {64.79, -20}, points = {{-15.21, 0}, {15.21, 0}})); - connect(Q_sto1.n1, k_gri.s1) annotation( - Line(origin = {-49.84, 50}, points = {{-10.16, 0}, {10.16, 0}})); - connect(k_gri.p1, Q_sto2.n1) annotation( - Line(origin = {-8.59, 50}, points = {{-8.59, 0}, {8.59, 0}})); - connect(GlucoseIntake.n1, dirac.s1) annotation( - Line(origin = {-120.625, 50}, points = {{-9.375, 0}, {9.375, 0}})); - connect(D.n1, k_empt1.m2) annotation( - Line(origin = {34.2512, 9.30423}, points = {{65.7488, -3.53767}, {-20.2487, -3.53767}, {-20.2487, 3.53767}, {-25.2512, 3.53767}})); - connect(Q_sto.n1, k_empt1.m1) annotation( - Line(origin = {34.2512, 26.4209}, points = {{65.7488, 3.57905}, {-20.2487, 3.57905}, {-20.2487, -3.57905}, {-25.2512, -3.57905}})); - connect(dirac.p1, Q_sto1.n1) annotation( - Line(origin = {-74.375, 50}, points = {{-14.375, 0}, {14.375, 0}})); - connect(k_empt1.p1, Q_gut.n1) annotation( - Line(origin = {1.11022e-17, -6.70406}, points = {{1.11022e-17, 13.2959}, {-1.11022e-17, -13.2959}})); - connect(Q_sto2.n1, k_empt1.s1) annotation( - Line(origin = {-1.11022e-17, 39.5459}, points = {{1.11022e-17, 10.4541}, {-1.11022e-17, -10.4541}})); - connect(Q_gut.n1, k_abs.s1) annotation( - Line(origin = {13.54, -20}, points = {{-13.54, 0}, {13.54, 0}})); - ra_signal = f * k_abs.k * Q_gut.c / BW; - q_sto = Q_sto1.c + Q_sto2.c; - d = GlucoseIntake.c; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-7.23323, 45}, fillPattern = FillPattern.Solid, extent = {{-45, -45}, {45, 45}}, textString = "GI", fontName = "Arial"), Text(origin = {-2.44435, -51.2385}, fillPattern = FillPattern.Solid, extent = {{-93.0638, -41.2385}, {93.0638, 41.2385}}, textString = "tract", fontName = "Arial")})); - end GastroIntestinalTract; - - model BetaCell - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Units.Concentration i_po(start = 3.6); - BioChem.Units.Concentration g; - BioChem.Units.Concentration g_p; - BioChem.Units.Concentration y; - BioChem.Units.Concentration y_signal(start = 0); - BioChem.Units.Concentration s_signal; - parameter Real alpha = 0.05; - parameter Real beta = 0.11; - parameter Real S_b = 1.8; - parameter Real G_b = 95; - parameter Real K = 2.3; - parameter Real gamma = 0.5; - BioChem.Interfaces.Nodes.ModifierConnector G_connector annotation( - Placement(transformation(origin = {0, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {0, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector S_connector annotation( - Placement(transformation(origin = {-120, -8.88178e-16}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector I_po_connector annotation( - Placement(transformation(origin = {-90, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-70, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector G_p_connector annotation( - Placement(transformation(origin = {100, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {75.1683, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance S_calc(c = s_signal) annotation( - Placement(transformation(origin = {-90, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance signaltosubstance1 annotation( - Placement(transformation(origin = {2.22045e-16, 60}, extent = {{-10, -10}, {10, 10}}, rotation = -90))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance signaltosubstance2 annotation( - Placement(transformation(origin = {100, 60}, extent = {{-10, -10}, {10, 10}}, rotation = -90))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance signaltosubstance3 annotation( - Placement(transformation(origin = {60, -30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance I_po_signal(c = i_po) annotation( - Placement(transformation(origin = {-90, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance G(c = g) annotation( - Placement(transformation(origin = {0, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance G_p(c = g_p) annotation( - Placement(transformation(origin = {100, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance Y(c = y) annotation( - Placement(transformation(origin = {80, -30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance Y_signal(c = y_signal) annotation( - Placement(transformation(origin = {40, -30}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(Y_signal.n1, signaltosubstance3.s1) annotation( - Line(origin = {42.9167, -30}, points = {{-2.91667, 3.55271e-15}, {-2.91667, -3.55271e-15}, {5.83333, -3.55271e-15}})); - connect(signaltosubstance3.p1, Y.n1) annotation( - Line(origin = {74.1667, -30}, points = {{-2.91667, 0}, {-2.91667, 0}, {5.83333, 0}})); - connect(signaltosubstance2.p1, G_p.n1) annotation( - Line(origin = {100, 42.9167}, points = {{0, 5.83333}, {0, -2.91667}, {0, -2.91667}})); - connect(signaltosubstance1.p1, G.n1) annotation( - Line(origin = {1.62833e-16, 42.9167}, points = {{8.14164e-17, 5.83333}, {8.14164e-17, -2.91667}, {-1.62833e-16, -2.91667}})); - connect(I_po_connector, I_po_signal.n1) annotation( - Line(origin = {-90, 60}, points = {{0, 20}, {0, -20}})); - connect(G_p_connector, signaltosubstance2.s1) annotation( - Line(origin = {100, 75.625}, points = {{0, 4.375}, {0, -4.375}})); - connect(G_connector, signaltosubstance1.s1) annotation( - Line(origin = {9.99201e-17, 75.625}, points = {{-9.99201e-17, 4.375}, {9.99201e-17, -4.375}})); - connect(S_calc.n1, S_connector) annotation( - Line(origin = {-105, -4.44089e-16}, points = {{15, 4.44089e-16}, {-15, -4.44089e-16}})); - der(i_po) = if der(g_p) > 0 and g > G_b then (-gamma * i_po) + y + K * der(g) + S_b else (-gamma * i_po) + y + S_b; - der(y_signal) = if beta * (g - G_b) < (-S_b) then (-alpha * y_signal) - alpha * S_b else -alpha * (y_signal - beta * (g - G_b)); - s_signal = gamma * i_po; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-2.41533, 43.4019}, fillPattern = FillPattern.Solid, extent = {{-75.99, -51.46}, {75.99, 51.46}}, textString = "Beta", fontName = "Arial"), Text(origin = {1.61, -49.34}, fillPattern = FillPattern.Solid, extent = {{-73.89, -40.66}, {73.89, 40.66}}, textString = "cell", fontName = "Arial")})); - end BetaCell; - - model PlasmaInsulin - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Units.Concentration i_p_signal; - BioChem.Units.Concentration i_p; - BioChem.Units.Concentration i_signal; - parameter BioChem.Units.Volume V_I = 0.05; - BioChem.Substances.Substance I_p(c(start = 1.25) = i_p) annotation( - Placement(transformation(extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction m_4(k = 0.194) annotation( - Placement(transformation(origin = {-60, 0}, extent = {{10, -10}, {-10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector I_p_connector annotation( - Placement(transformation(origin = {120, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {110, 4.44089e-16}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ProductConnector I_connector annotation( - Placement(transformation(origin = {0, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {0, -110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector I_signal_connector annotation( - Placement(transformation(origin = {120, -30}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {110, -56.82}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance I_p_signal(c = i_p_signal) annotation( - Placement(transformation(origin = {60, 7.77156e-16}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance I_signal(c = i_signal) annotation( - Placement(transformation(origin = {60, -30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.BoundarySubstance Deg annotation( - Placement(transformation(origin = {-120, 0}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(Deg.n1, m_4.p1) annotation( - Line(origin = {-95.625, 1.11022e-17}, points = {{-24.375, -1.11022e-17}, {24.375, 1.11022e-17}})); - connect(I_signal.n1, I_signal_connector) annotation( - Line(origin = {90, -30}, points = {{-30, 0}, {30, 0}})); - connect(I_p_signal.n1, I_p_connector) annotation( - Line(origin = {90, 3.88578e-16}, points = {{-30, 3.88578e-16}, {30, -3.88578e-16}})); - connect(I_p.n1, I_connector) annotation( - Line(origin = {0, -40}, points = {{0, 40}, {0, -40}})); - connect(m_4.s1, I_p.n1) annotation( - Line(origin = {-24.375, -1.11022e-17}, points = {{-24.375, -1.11022e-17}, {24.375, 1.11022e-17}})); - i_p_signal = i_p; - i_signal = i_p / V_I; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-7.10543e-15, 46.05}, fillPattern = FillPattern.Solid, extent = {{-93.8311, -36.05}, {93.8311, 36.05}}, textString = "Plasma", fontName = "Arial"), Text(origin = {-3.55271e-15, -36.936}, fillPattern = FillPattern.Solid, extent = {{-86.0653, -45}, {86.0653, 45}}, textString = "insulin", fontName = "Arial")})); - end PlasmaInsulin; - - model PlasmaGlucose - extends BioChem.Compartments.Compartment(V.start = 1.0); - parameter Real V_G = 1.88; - BioChem.Units.Concentration g_p_signal; - BioChem.Units.Concentration g_p; - BioChem.Units.Concentration g_signal; - BioChem.Interfaces.Nodes.ProductConnector EGP_connector annotation( - Placement(transformation(origin = {4.44089e-16, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-1.73862, -110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector G_p_connector annotation( - Placement(transformation(origin = {-110, -70}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, -70}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector E_connector annotation( - Placement(transformation(origin = {120, -30}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {110, -48.4304}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ProductConnector Ra_connector annotation( - Placement(transformation(origin = {-80, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-77.9724, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector G_connector annotation( - Placement(transformation(origin = {0, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {0, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance G_p_signal(c = g_p_signal) annotation( - Placement(transformation(origin = {-110, -23.3921}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance G_signal(c = g_signal) annotation( - Placement(transformation(origin = {-120, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector G_signal_connector annotation( - Placement(transformation(origin = {-120, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 1.94}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance G_p(c.start = 178, c = g_p) annotation( - Placement(transformation(extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction Ra_reaction(k = 1) annotation( - Placement(transformation(origin = {-80, 50}, extent = {{-10, -10}, {10, 10}}, rotation = -90))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction EGP_reaction(k = 1) annotation( - Placement(transformation(origin = {0, -48}, extent = {{-10, 10}, {10, -10}}, rotation = 90))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.U_ii_reaction u_ii_reaction1 annotation( - Placement(transformation(origin = {90, 30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.BoundarySubstance U_ii annotation( - Placement(transformation(origin = {120, 30}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(U_ii.n1, u_ii_reaction1.p1) annotation( - Line(origin = {110.625, 30}, points = {{9.375, 0}, {-9.375, 0}})); - connect(G_p.n1, u_ii_reaction1.s1) annotation( - Line(origin = {56.9367, 15}, points = {{-56.9367, -15}, {17.5617, -15}, {17.5617, 15}, {21.8133, 15}})); - connect(EGP_reaction.s1, EGP_connector) annotation( - Line(origin = {2.10942e-16, -69.625}, points = {{-2.33147e-16, 10.375}, {2.33147e-16, -10.375}})); - connect(G_p.n1, EGP_reaction.p1) annotation( - Line(origin = {1.11022e-17, -18.375}, points = {{-1.11022e-17, 18.375}, {1.11022e-17, -18.375}})); - connect(Ra_connector, Ra_reaction.s1) annotation( - Line(origin = {-80, 70.625}, points = {{0, 9.375}, {0, -9.375}})); - connect(Ra_reaction.p1, G_p.n1) annotation( - Line(origin = {-53.3333, 12.9167}, points = {{-26.6667, 25.8333}, {-26.6667, -12.9167}, {53.3333, -12.9167}})); - connect(G_p.n1, E_connector) annotation( - Line(origin = {83.5, -15}, points = {{-83.5, 15}, {23.5, 15}, {23.5, -15}, {36.5, -15}})); - connect(G_p.n1, G_connector) annotation( - Line(origin = {0, 40}, points = {{0, -40}, {0, 40}})); - connect(G_p_signal.n1, G_p_connector) annotation( - Line(origin = {-110, -46.696}, points = {{0, 23.304}, {0, -23.304}})); - connect(G_signal.n1, G_signal_connector) annotation( - Line(origin = {-120, 20}, points = {{0, 20}, {0, -20}})); - g_p_signal = g_p; - g_signal = g_p_signal / V_G; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {9.76996e-15, 43.56}, fillPattern = FillPattern.Solid, extent = {{-83.88, -33.56}, {83.88, 33.56}}, textString = "Plasma", fontName = "Arial"), Text(origin = {2.66454e-15, -40}, fillPattern = FillPattern.Solid, extent = {{-86.96, -35.65}, {86.96, 35.65}}, textString = "glucose", fontName = "Arial")})); - end PlasmaGlucose; - - model LiverInsulin - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Units.Concentration s; - BioChem.Units.Concentration s_signal; - BioChem.Substances.Substance I_l(c.start = 5) annotation( - Placement(transformation(extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance S_signal(c = s_signal) annotation( - Placement(transformation(origin = {-70, 50}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.m_3 m_3 annotation( - Placement(transformation(origin = {-70, 0}, extent = {{10, -10}, {-10, 10}}))); - BioChem.Interfaces.Nodes.ProductConnector S_connector(c = s) annotation( - Placement(transformation(origin = {120, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {110, -1.93864}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector I_connector annotation( - Placement(transformation(origin = {7.10543e-15, 79.59}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {0, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction S_reaction(k = 1) annotation( - Placement(transformation(origin = {70, -7.21645e-16}, extent = {{10, -10}, {-10, 10}}))); - BioChem.Substances.BoundarySubstance Deg annotation( - Placement(transformation(origin = {-120, 0}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(m_3.p1, Deg.n1) annotation( - Line(origin = {-100.625, 1.11022e-17}, points = {{19.375, 1.11022e-17}, {-19.375, -1.11022e-17}})); - connect(S_reaction.s1, S_connector) annotation( - Line(origin = {100.625, -3.71925e-16}, points = {{-19.375, -3.71925e-16}, {19.375, 3.71925e-16}})); - connect(S_reaction.p1, I_l.n1) annotation( - Line(origin = {29.375, -3.4972e-16}, points = {{29.375, -3.4972e-16}, {-29.375, 3.4972e-16}})); - connect(I_connector, I_l.n1) annotation( - Line(origin = {3.55271e-15, 39.795}, points = {{3.55271e-15, 39.795}, {-3.55271e-15, -39.795}})); - connect(I_l.n1, m_3.s1) annotation( - Line(origin = {-29.375, -1.11022e-17}, points = {{29.375, 1.11022e-17}, {-29.375, -1.11022e-17}})); - connect(S_signal.n1, m_3.m1) annotation( - Line(origin = {-70, 29.5}, points = {{0, 20.5}, {0, -20.5}})); - s = s_signal; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {0.247749, 43.7203}, fillPattern = FillPattern.Solid, extent = {{-92.2066, -43.7203}, {92.2066, 43.7203}}, textString = "Liver", fontName = "Arial"), Text(origin = {-0.875609, -51.2968}, fillPattern = FillPattern.Solid, extent = {{-89.1244, -31.2968}, {89.1244, 31.2968}}, textString = "insulin", fontName = "Arial")})); - end LiverInsulin; - - model EndogenousGlucoseProduction - extends BioChem.Compartments.Compartment(V.start = 1.0); - parameter Real k_p1 = 2.7; - parameter Real k_p2 = 0.0021; - parameter Real k_p3 = 0.009; - parameter Real k_p4 = 0.0618; - BioChem.Units.Concentration egp_signal; - BioChem.Units.Concentration i_d; - BioChem.Units.Concentration g_p; - BioChem.Units.Concentration i_po; - BioChem.Interfaces.Nodes.ModifierConnector G_p_connector annotation( - Placement(transformation(origin = {0, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {2.22045e-16, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector EGP_connector annotation( - Placement(transformation(origin = {60, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {73.83, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector I_connector annotation( - Placement(transformation(origin = {-60, 80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-72.29, 110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector I_po_connector annotation( - Placement(transformation(origin = {120, -60}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {110, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction k_i1(k = 0.0079) annotation( - Placement(transformation(origin = {-90, 63.2158}, extent = {{10, -10}, {-10, 10}}, rotation = -270))); - BioChem.Substances.Substance I_1(c.start = 25) annotation( - Placement(transformation(origin = {-90, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction k_i2(k = 0.0079) annotation( - Placement(transformation(origin = {-90, 10}, extent = {{10, -10}, {-10, 10}}, rotation = -270))); - BioChem.Substances.Substance I_d(c.start = 25, c = i_d) annotation( - Placement(transformation(origin = {-90, -10}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction k_i3(k = 0.0079) annotation( - Placement(transformation(origin = {-90, -40}, extent = {{10, -10}, {-10, 10}}, rotation = -270))); - BioChem.Substances.BoundarySubstance End annotation( - Placement(transformation(origin = {-90, -60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance EGP_calc(c = egp_signal) annotation( - Placement(transformation(origin = {60, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance G_p(c = g_p) annotation( - Placement(transformation(origin = {8.88178e-16, 40}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance I_po(c = i_po) annotation( - Placement(transformation(origin = {80, -60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance signaltosubstance1 annotation( - Placement(transformation(origin = {100, -60}, extent = {{10, -10}, {-10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance signaltosubstance2 annotation( - Placement(transformation(origin = {0, 60}, extent = {{-10, -10}, {10, 10}}, rotation = -90))); - equation - connect(signaltosubstance2.p1, G_p.n1) annotation( - Line(origin = {3.10862e-16, 42.9167}, points = {{-2.88658e-16, 5.83333}, {-2.88658e-16, -2.91667}, {5.77316e-16, -2.91667}})); - connect(G_p_connector, signaltosubstance2.s1) annotation( - Line(origin = {-7.4015e-18, 74.1667}, points = {{7.4015e-18, 5.83333}, {7.4015e-18, -2.91667}, {-1.4803e-17, -2.91667}})); - connect(I_po_connector, signaltosubstance1.s1) annotation( - Line(origin = {115.625, -60}, points = {{4.375, 0}, {-4.375, 0}})); - connect(signaltosubstance1.p1, I_po.n1) annotation( - Line(origin = {84.375, -60}, points = {{4.375, 0}, {-4.375, 0}})); - connect(EGP_calc.n1, EGP_connector) annotation( - Line(origin = {60, 60}, points = {{0, -20}, {0, 20}})); - connect(End.n1, k_i3.p1) annotation( - Line(origin = {-90, -54.1667}, points = {{0, -5.83333}, {0, 2.91667}, {0, 2.91667}})); - connect(k_i3.s1, I_d.n1) annotation( - Line(origin = {-90, -19.375}, points = {{0, -9.375}, {0, 9.375}})); - connect(k_i2.p1, I_d.n1) annotation( - Line(origin = {-90, -7.08333}, points = {{0, 5.83333}, {0, -2.91667}, {0, -2.91667}})); - connect(I_1.n1, k_i2.s1) annotation( - Line(origin = {-90, 30.625}, points = {{0, 9.375}, {0, -9.375}})); - connect(k_i1.p1, I_1.n1) annotation( - Line(origin = {-90, 43.9886}, points = {{0, 7.97721}, {0, -3.9886}, {0, -3.9886}})); - connect(k_i1.s1, I_connector) annotation( - Line(origin = {-80, 78.1553}, points = {{-10, -3.68946}, {-10, 1.84473}, {20, 1.84473}})); - egp_signal = k_p1 - k_p2 * g_p - k_p3 * i_d - k_p4 * i_po; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-107.257, 0}, rotation = -270, fillPattern = FillPattern.Solid, extent = {{-25.4753, -2.74277}, {25.4753, 2.74277}}, textString = "delayed insulin signal", fontName = "Arial")}), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {4.68254, 4.83}, fillPattern = FillPattern.Solid, extent = {{-77.28, -45.17}, {77.28, 45.17}}, textString = "EGP", fontName = "Arial")})); - end EndogenousGlucoseProduction; - - model GlucoseRenalExcretion - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Interfaces.Nodes.ProductConnector productConnector1 annotation( - Placement(transformation(origin = {-120, -4.44089e-16}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 3.33067e-16}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.RenalReaction renalReaction1 annotation( - Placement(transformation(origin = {-90, 3.88578e-16}, extent = {{-10, 10}, {10, -10}}))); - BioChem.Interfaces.Nodes.ModifierConnector G_p_connector annotation( - Placement(transformation(origin = {-120, -70}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, -83.5976}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.BoundarySubstance E annotation( - Placement(transformation(extent = {{-10, -10}, {10, 10}}))); - equation - connect(renalReaction1.p1, E.n1) annotation( - Line(origin = {-39.375, 1.83187e-16}, points = {{-39.375, 1.83187e-16}, {39.375, -1.83187e-16}})); - connect(G_p_connector, G_p_connector) annotation( - Line(origin = {-120, -70}, points = {{0, 0}, {0, 0}})); - connect(G_p_connector, renalReaction1.m1) annotation( - Line(origin = {-75, -82.7488}, points = {{-45, 12.7488}, {-15, 12.7487}, {-15, 12.7488}, {-15, 73.7488}})); - connect(productConnector1, renalReaction1.s1) annotation( - Line(origin = {-110.625, -1.66533e-17}, points = {{-9.375, -4.27436e-16}, {9.375, 4.27436e-16}})); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-3.87096, 37.0935}, fillPattern = FillPattern.Solid, extent = {{-89.7, -30}, {89.7, 30}}, textString = "Renal", fontName = "Arial"), Text(origin = {-3.55271e-15, -46.0442}, fillPattern = FillPattern.Solid, extent = {{-95.9469, -26.0442}, {95.9469, 26.0442}}, textString = "excretion", fontName = "Arial")})); - end GlucoseRenalExcretion; - - model UtilizationMuscleTissue - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Interfaces.Nodes.ModifierConnector I_connector annotation( - Placement(transformation(origin = {-120, 50}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 83.5696}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ProductConnector G_t_connector annotation( - Placement(transformation(origin = {-120, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 1.62}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.BoundarySubstance U_idm annotation( - Placement(transformation(extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.UtilizationReaction UtilizationReaction(K_m0 = 225.59, V_m0 = 2.5, V_mX = 0.047, p_2U = 0.0331, part = 0.8) annotation( - Placement(transformation(origin = {-64.11, 0}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(UtilizationReaction.p1, U_idm.n1) annotation( - Line(origin = {-26.43, 1.11022e-17}, points = {{-26.43, 1.11022e-17}, {26.43, -1.11022e-17}})); - connect(UtilizationReaction.m1, I_connector) annotation( - Line(origin = {-82.74, 36.3333}, points = {{18.63, -27.3333}, {18.63, 13.6667}, {-37.26, 13.6667}})); - connect(G_t_connector, UtilizationReaction.s1) annotation( - Line(origin = {-97.68, -1.11022e-17}, points = {{-22.32, 1.11022e-17}, {22.32, -1.11022e-17}})); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-2.91, 52.76}, fillPattern = FillPattern.Solid, extent = {{-82.91, -30.17}, {82.91, 30.17}}, textString = "Muscle", fontName = "Arial"), Text(origin = {-7.10543e-15, -34.69}, fillPattern = FillPattern.Solid, extent = {{-77.92, -34.69}, {77.92, 34.69}}, textString = "tissue", fontName = "Arial")})); - end UtilizationMuscleTissue; - - model TissueGlucose - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Interfaces.Nodes.ProductConnector G_connector annotation( - Placement(transformation(origin = {0, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {0, -110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance G_t(c.start = 130) annotation( - Placement(transformation(extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector U_idf_connector annotation( - Placement(transformation(origin = {120, 40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {110, 60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.SubstrateConnector U_idm_connector annotation( - Placement(transformation(origin = {120, -40}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {110, -63.4979}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(G_t.n1, U_idm_connector) annotation( - Line(origin = {83.5, -20}, points = {{-83.5, 20}, {23.5, 20}, {23.5, -20}, {36.5, -20}})); - connect(G_t.n1, U_idf_connector) annotation( - Line(origin = {83.5, 20}, points = {{-83.5, -20}, {23.5, -20}, {23.5, 20}, {36.5, 20}})); - connect(G_t.n1, G_connector) annotation( - Line(origin = {0, -40}, points = {{0, 40}, {0, -40}})); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-0.55, -36.0512}, fillPattern = FillPattern.Solid, extent = {{-100.55, -33.9488}, {100.55, 33.9488}}, textString = "glucose", fontName = "Arial"), Text(origin = {3.56664, 43.6442}, fillPattern = FillPattern.Solid, extent = {{-86.4334, -33.6442}, {86.4334, 33.6442}}, textString = "Tissue", fontName = "Arial")})); - end TissueGlucose; - - package AdiposeTissue - extends BioChem.Icons.Library; - - model Adipocyte - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Substances.Substance IR(c.start = 2340000000000.0) annotation( - Placement(transformation(origin = {-110, 60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance IR_tot annotation( - Placement(transformation(origin = {110, 60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance IRS1(c.start = 16100000000.0) annotation( - Placement(transformation(origin = {-80, 30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance IRS1_P(c.start = 0) annotation( - Placement(transformation(origin = {-20, 30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ActivationReaction activationReaction2(k_1 = 0.038, k_2 = 580000000) annotation( - Placement(transformation(origin = {-50, 30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ActivationReaction activationReaction3(k_1 = 1.348, k_2 = 24800000) annotation( - Placement(transformation(origin = {-20, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance PKB(c.start = 16800000) annotation( - Placement(transformation(origin = {-50, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance PKB_P(c.start = 0) annotation( - Placement(transformation(origin = {10, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ActivationReaction activationReaction4(k_1 = 0.019, k_2 = 336000000) annotation( - Placement(transformation(origin = {10, -30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance IRS1_tot annotation( - Placement(transformation(origin = {110, 30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance PKB_tot annotation( - Placement(transformation(origin = {110, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.SignalSubstance GLUT4_tot annotation( - Placement(transformation(origin = {110, -30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.BoundarySubstance GlucoseUtilization annotation( - Placement(transformation(origin = {110, -80}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ModifierConnector modifierConnector1 annotation( - Placement(transformation(origin = {-80, 90}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 0}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ProductConnector productConnector1 annotation( - Placement(transformation(origin = {-7.77156e-16, -80}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-1.22125e-15, -110}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance GLUT4_MEMBRANE(c.start = 0) annotation( - Placement(transformation(origin = {40, -30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance GLUT4_CYTOSOL(c.start = 580000000) annotation( - Placement(transformation(origin = {-20, -30}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Substances.Substance IR_insulin(c.start = 0) annotation( - Placement(transformation(origin = {-50, 60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.MM_insulin MM_insulin1(k_1 = 2.464, k_2 = 54100000000.0, Km = 1499) annotation( - Placement(transformation(origin = {-80, 60}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.GlucoseUptakeReaction GlucoseUptake_GLUT4(k = 12.435, glut_1 = 0.071, Km1 = 0.012, Km4 = 3462, k_wholebody = 2.45) annotation( - Placement(transformation(origin = {40, -80}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(productConnector1, GlucoseUptake_GLUT4.s1) annotation( - Line(origin = {14.375, -80}, points = {{-14.375, 0}, {14.375, 0}})); - connect(GlucoseUptake_GLUT4.p1, GlucoseUtilization.n1) annotation( - Line(origin = {80.625, -80}, points = {{-29.375, 0}, {29.375, 0}})); - connect(GLUT4_MEMBRANE.n1, GlucoseUptake_GLUT4.m1) annotation( - Line(origin = {40, -50.5}, points = {{0, 20.5}, {0, -20.5}})); - connect(MM_insulin1.p1, IR_insulin.n1) annotation( - Line(origin = {-59.375, 60}, points = {{-9.375, 0}, {9.375, 0}})); - connect(modifierConnector1, MM_insulin1.m1) annotation( - Line(origin = {-80, 79.5}, points = {{0, 10.5}, {0, -10.5}})); - connect(IR.n1, MM_insulin1.s1) annotation( - Line(origin = {-100.625, 60}, points = {{-9.375, 0}, {9.375, 0}})); - connect(IR_insulin.n1, activationReaction2.m1) annotation( - Line(origin = {-50, 49.5}, points = {{0, 10.5}, {0, -10.5}})); - connect(GLUT4_CYTOSOL.n1, activationReaction4.s1) annotation( - Line(origin = {-10.625, -30}, points = {{-9.375, 0}, {9.375, 0}})); - connect(activationReaction4.p1, GLUT4_MEMBRANE.n1) annotation( - Line(origin = {30.625, -30}, points = {{-9.375, 0}, {9.375, 0}})); - IR_tot.c = IR.c + IR_insulin.c; - IRS1_tot.c = IRS1.c + IRS1_P.c; - PKB_tot.c = PKB.c + PKB_P.c; - GLUT4_tot.c = GLUT4_CYTOSOL.c + GLUT4_MEMBRANE.c; - connect(PKB_P.n1, activationReaction4.m1) annotation( - Line(origin = {10, -10.5}, points = {{0, 10.5}, {-1.77636e-15, -10.5}})); - connect(activationReaction3.p1, PKB_P.n1) annotation( - Line(origin = {0.625, 1.11022e-17}, points = {{-9.375, 1.11022e-17}, {9.375, -1.11022e-17}})); - connect(PKB.n1, activationReaction3.s1) annotation( - Line(origin = {-40.625, 1.11022e-17}, points = {{-9.375, -1.11022e-17}, {9.375, 1.11022e-17}})); - connect(IRS1_P.n1, activationReaction3.m1) annotation( - Line(origin = {-20, 19.5}, points = {{0, 10.5}, {0, -10.5}})); - connect(activationReaction2.p1, IRS1_P.n1) annotation( - Line(origin = {-29.375, 30}, points = {{-9.375, -3.55271e-15}, {9.375, 0}})); - connect(IRS1.n1, activationReaction2.s1) annotation( - Line(origin = {-70.625, 30}, points = {{-9.375, 0}, {9.375, 0}})); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Documentation(info = "", revisions = "")); - end Adipocyte; - - model AdiposeTissue - extends BioChem.Compartments.Compartment(V.start = 1.0); - BioChem.Interfaces.Nodes.ModifierConnector I_connector annotation( - Placement(transformation(origin = {-120, 50}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 83.8877}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Interfaces.Nodes.ProductConnector G_t_connector annotation( - Placement(transformation(origin = {-120, 0}, extent = {{-10, -10}, {10, 10}}), iconTransformation(origin = {-110, 1.61}, extent = {{-10, -10}, {10, 10}}))); - BioChem.Examples.GlucoseInsulinModel.Utilities.Parts.AdiposeTissue.Adipocyte adipocyte1 annotation( - Placement(transformation(origin = {0, 6.66134e-16}, extent = {{-10, -10}, {10, 10}}))); - equation - connect(adipocyte1.productConnector1, G_t_connector) annotation( - Line(origin = {-66.8, -8.2005}, points = {{66.8, -2.7995}, {66.8, -6.80075}, {-40.2, -6.80075}, {-40.2, 8.2005}, {-53.2, 8.2005}})); - connect(I_connector, adipocyte1.modifierConnector1) annotation( - Line(origin = {-40.2506, 25}, points = {{-79.7494, 25}, {25.2494, 25}, {25.2494, -25}, {29.2506, -25}})); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, -100}, {100, 100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {-3.97, 38.38}, fillPattern = FillPattern.Solid, extent = {{-96.03, -31.62}, {96.03, 31.62}}, textString = "Fat", fontName = "Arial"), Text(origin = {-2.5601, -40}, fillPattern = FillPattern.Solid, extent = {{-77.4399, -42.4487}, {77.4399, 42.4487}}, textString = "tissue", fontName = "Arial")})); - end AdiposeTissue; - end AdiposeTissue; - end Parts; - - package Reactions - extends BioChem.Icons.Library; - - model FlowReaction - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k; - equation - rr = s1.c * k; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end FlowReaction; - - model k_empt - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.TwoModifiers; - Real k; - Real aa; - Real cc; - parameter Real k_max = 0.0558; - parameter Real k_min = 0.008; - parameter Real b = 0.82; - parameter Real d = 0.01; - equation - rr = s1.c * k; - k = k_min + (k_max - k_min) / 2 * (Modelica.Math.tanh(aa * (m1.c - b * m2.c)) - Modelica.Math.tanh(cc * (m1.c - d * m2.c)) + 2); - aa = 5 / 2 / (1 - b) / m2.c; - cc = 5 / 2 / d / m2.c; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end k_empt; - - model dirac - extends BioChem.Interfaces.Reactions.Uui; - parameter Real k = 78000000; - equation - if time < 0.001 then - rr = k; - else - rr = 0; - end if; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end dirac; - - model m_3 - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - Real k; - parameter Real m_5 = 0.0304; - parameter Real m_1 = 0.19; - parameter Real m_6 = 0.6471; - equation - rr = s1.c * k; - k = ((-m_5 * m1.c) + m_6) * m_1 / (1 - ((-m_5 * m1.c) + m_6)); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end m_3; - - model ReversibleFlowReaction - extends BioChem.Interfaces.Reactions.Uur; - parameter Real k_1; - parameter Real k_2; - equation - rr = s1.c * k_1 - p1.c * k_2; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end ReversibleFlowReaction; - - model RenalReaction - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real k_e1 = 0.0005; - parameter Real k_e2 = 339; - equation - if m1.c > k_e2 then - rr = s1.c * (k_e1 * (m1.c - k_e2)); - else - rr = 0; - end if; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end RenalReaction; - - model UtilizationReaction - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - BioChem.Units.Concentration X; - Real V_max; - parameter Real part; - parameter Real V_m0; - parameter Real V_mX; - parameter Real K_m0; - parameter Real p_2U; - parameter Real I_b = 25; - equation - rr = V_max * s1.c / (K_m0 + s1.c); - V_max = part * (V_m0 + V_mX * X); - der(X) = (-p_2U * X) + p_2U * (m1.c - I_b); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end UtilizationReaction; - - model signaltosubstance - extends BioChem.Interfaces.Reactions.Uui; - equation - s1.c = p1.c; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end signaltosubstance; - - model U_ii_reaction - extends BioChem.Interfaces.Reactions.Uui; - equation - rr = 1; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end U_ii_reaction; - - model ActivationReaction - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real k_1; - parameter Real k_2; - equation - rr = k_1 * s1.c * m1.c - p1.c * k_2; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end ActivationReaction; - - model MM_insulin - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real k_1; - parameter Real k_2; - parameter Real Km; - equation - rr = k_1 * m1.c * s1.c / (Km + m1.c) - p1.c * k_2; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end MM_insulin; - - model GlucoseUptakeReaction - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real k_wholebody; - parameter Real k; - parameter Real Km4; - parameter Real Km1; - parameter Real glut_1; - equation - rr = k_wholebody * (k * m1.c * s1.c / (Km4 + s1.c) + glut_1 * s1.c / (Km1 + s1.c)); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10}))); - end GlucoseUptakeReaction; - end Reactions; - annotation( - Diagram(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utilities; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105}, {148.5, 105}}, preserveAspectRatio = true, grid = {10, 10})), - Documentation(info = " -

A Whole Body Model of the Glucose Insulin System

- -This model is presented in Hierarchical modeling of diabetes by -Elin Nyman, ISRN:LiU-IKE-EX-09/14. Linköping University 2009.

- - -See -GlucoseInsulinModel - for more documentation and simulation results. -", revisions = "")); - end GlucoseInsulinModel; annotation( Documentation(info = "

Examples

diff --git a/BioChem/Math/package.mo b/BioChem/Math/package.mo index b479718..7a21099 100644 --- a/BioChem/Math/package.mo +++ b/BioChem/Math/package.mo @@ -1,119 +1,9 @@ within BioChem; package Math - extends Icons.Library; - function log10 = Modelica.Math.log10 annotation( - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); + extends BioChem.Icons.Library; - function factorial "factorial function, product of all positive integers less than or equal to n" - input Integer n "input value"; - output Integer y "output value"; - protected - Integer i; - algorithm - y := n; - i := n; - while i > 1 loop - i := i - 1; - y := y * i; - end while; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "n!", fontName = "Arial")})); - end factorial; - - function sec "secant trigonometric function" - input Modelica.Units.SI.Angle alpha "input angle"; - output Real y "output value"; - algorithm - y := 1 / cos(alpha); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "sec( )", fontName = "Arial")})); - end sec; - - function cot "Cotangent trigonometric function" - input Modelica.Units.SI.Angle alpha "input angle"; - output Real y "output value"; - algorithm - y := 1 / tan(alpha); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "cot( )", fontName = "Arial")})); - end cot; - - function csc "cosecant trigonometric function" - input Modelica.Units.SI.Angle alpha "input angle"; - output Real y "output value"; - algorithm - y := 1 / sin(alpha); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "csc( )", fontName = "Arial")})); - end csc; - - function sech "hyperbolic secant trigonometric function" - input Modelica.Units.SI.Angle alpha "input angle"; - output Real y "output value"; - algorithm - y := 1 / cosh(alpha); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "sech( )", fontName = "Arial")})); - end sech; - - function csch "hyperbolic cosecant trigonometric function" - input Modelica.Units.SI.Angle alpha "input angle"; - output Real y "output value"; - algorithm - y := 1 / sinh(alpha); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "csch( )", fontName = "Arial")})); - end csch; - - function coth "hyperbolic cotangent trigonometric function" - input Modelica.Units.SI.Angle alpha "input angle"; - output Real y "output value"; - algorithm - y := 1 / tanh(alpha); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "coth( )", fontName = "Arial")})); - end coth; - - function root - input Real n "degree"; - input Real a "value"; - output Real y "output value"; - algorithm - y := a ^ (1 / n); - annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillPattern = FillPattern.Solid, extent = {{-100, -100}, {100, 100}}, textString = "root", fontName = "Arial")})); - end root; - - function piecewise "Piecewise function that corresponds to the SBML piecewice definition" - input Real[:] value "Input values in the form {value1,value2,...,valueN,valueN+1}."; - input Boolean[:] condition "Input conditions in the form {condition1,condition2,...,conditionN}. Not more than one condition is allowed to be true at any given time."; - output Real y "Output value selected from the list of inputs."; - protected - parameter Integer nin = size(condition, 1); - algorithm - y := value[nin + 1]; - for i in 1:nin loop - if condition[i] then - y := value[i]; - end if; - end for; - annotation( - Diagram(coordinateSystem(extent = {{-148.5, -105.0}, {148.5, 105.0}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100.0, -100.0}, {100.0, 100.0}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {0.0, -0.0}, fillPattern = FillPattern.Solid, extent = {{-100.0, -30.0}, {100.0, 30.0}}, textString = "piecewise()", fontName = "Arial")})); - end piecewise; annotation( - Diagram(coordinateSystem(extent = {{-148.5, 105}, {148.5, -105}}, preserveAspectRatio = true, grid = {10, 10})), - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(origin = {1.40855, -8.72502}, fillPattern = FillPattern.Solid, extent = {{-81.4085, -69.705}, {56.8628, 38.725}}, textString = "f(x)", fontName = "Arial")}), Documentation(info = "

Math

A number of mathematical functions are used in pathway models. Some of these can be found in diff --git a/BioChem/Reactions/Activation/package.mo b/BioChem/Reactions/Activation/package.mo index 18ae14f..84b242b 100644 --- a/BioChem/Reactions/Activation/package.mo +++ b/BioChem/Reactions/Activation/package.mo @@ -1,117 +1,6 @@ within BioChem.Reactions; package Activation "Activation kinetics reactions" - extends Icons.Library; - model Umar "Reversible mixed activation kinetics" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Activator; - parameter BioChem.Units.Concentration Kas=1 "Activation constant"; - parameter BioChem.Units.Concentration Kac=1 "Activation constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.Concentration KmP=1 "Backward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Backward maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + Kas/a1.c + (s1.c/KmS + p1.c/KmP)*(1 + Kac/a1.c)); - annotation(Documentation(info=" -

- Reversible mixed activation kinetics. -

- ")); - end Umar; - - model Umai "Irreversible mixed activation kinetics" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Activator; - parameter BioChem.Units.Concentration Kac=1 "Activation constant"; - parameter BioChem.Units.Concentration Kas=1 "Activation constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c*a1.c/(s1.c*(a1.c + Kac) + KmS*(a1.c + Kas)); - annotation(Documentation(info=" -

- Irreversible mixed activation kinetics. -

- ")); - end Umai; - - model Uctr "Reversible catalytic activation" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Activator; - parameter BioChem.Units.Concentration Ka=1 "Activation constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.Concentration KmP=1 "Backward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Backward maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + Ka/a1.c + (s1.c/KmS + p1.c/KmP)*(1 + Ka/a1.c)); - annotation(Documentation(info=" -

- Reversible catalytic activation. -

- ")); - end Uctr; - - model Ucti "Irreversible catalytic activation" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Activator; - parameter BioChem.Units.Concentration Ka=1 "Activation constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c*a1.c/((a1.c + Ka)*(s1.c + KmS)); - annotation(Documentation(info=" -

- Irreversible catalytic activation. -

- ")); - end Ucti; - - model Uar "Reversible specific activation kinetics" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Activator; - parameter BioChem.Units.Concentration Ka=1 "Activation constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.Concentration KmP=1 "Backward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Backward maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + s1.c/KmS + p1.c/KmP + Ka/a1.c); - annotation(Documentation(info=" -

- Reversible specific activation kinetics. -

- ")); - end Uar; - - model Uaii "Irreversible specific activation kinetics" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Activator; - parameter BioChem.Units.Concentration Ka=1 "Activation constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c*a1.c/(a1.c*(KmS + s1.c) + KmS*Ka); - annotation(Documentation(info=" -

- Irreversible specific activation kinetics. -

- ")); - end Uaii; - - model Uai "Irreversible substrate activation" - extends BioChem.Interfaces.Reactions.Uui; - parameter BioChem.Units.Concentration KSa=1 "Dissociation constant of substrate-activation site"; - parameter BioChem.Units.Concentration KSc=1 "Dissociation constant of substrate-active site"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/KSa*s1.c/KSa/(1 + s1.c/KSc + s1.c/KSa*s1.c/KSa + s1.c/KSa); - annotation(Documentation(info=" -

- Irreversible substrate activation. -

- ")); - end Uai; + extends BioChem.Icons.Library; annotation(Documentation(info="

Activation

diff --git a/BioChem/Reactions/BiSubstrate/package.mo b/BioChem/Reactions/BiSubstrate/package.mo index a1a93e1..698e8b2 100644 --- a/BioChem/Reactions/BiSubstrate/package.mo +++ b/BioChem/Reactions/BiSubstrate/package.mo @@ -1,113 +1,7 @@ within BioChem.Reactions; package BiSubstrate "Bi-substrate reactions" - extends Icons.Library; - model Ppbr "Ping pong bi-bi kinetics" - extends BioChem.Interfaces.Reactions.Basics.Reaction; - extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.TwoProducts; - parameter BioChem.Units.Concentration Keq=1 "Equilibrium constant"; - parameter BioChem.Units.Concentration KiS1=1 "Product inhibition constant of s1.c acting on the reverse reaction"; - parameter BioChem.Units.Concentration KiP2=1 "Product inhibition constant of p2.c acting on the forward reaction"; - parameter BioChem.Units.Concentration KmS1=1 "Concentration of s1.c such that v = vF/2 (Michaelis constant) at zero p1.c and zero p2.c"; - parameter BioChem.Units.Concentration KmS2=1 "Concentration of s2.c such that v = vF/2 (Michaelis constant) at saturating s1.c and zero p1.c"; - parameter BioChem.Units.Concentration KmP1=1 "Concentration of p1.c such that v = -vR/2 (Michaelis constant) at zero s1.c and zero s2.c"; - parameter BioChem.Units.Concentration KmP2=1 "Concentration of p2.c such that v = -vR/2 (Michaelis constant) at zero s1.c and saturating p1.c"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverse maximum velocity"; - protected - Real K1; - equation - s1.r=rr; - s2.r=rr; - p1.r=-rr; - p2.r=-rr; - K1=vF/(vR*Keq)*(KmP2*p1.c*(1 + s1.c/KiS1) + p2.c*(KmP1 + p1.c)); - rr=vF*(s1.c*s2.c - p1.c*p2.c/Keq)/(s1.c*s2.c + KmS2*s1.c + KmS1*s2.c*(1 + p2.c/KiP2) + K1); - annotation(Documentation(info=" -

- Ping pong bi-bi kinetics. -

- ")); - end Ppbr; - - model Ordubr "Ordered uni-bi kinetics" - extends BioChem.Interfaces.Reactions.Basics.Reaction; - extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; - extends BioChem.Interfaces.Reactions.Basics.TwoProducts; - parameter BioChem.Units.Concentration Keq=1 "Equilibrium constant"; - parameter BioChem.Units.Concentration KiP1=1 "Product inhibition constant of s1.c acting on the reverse reaction"; - parameter BioChem.Units.Concentration KmS1=1 "Concentration of s1.c such that v = vF/2 (Michaelis constant) at zero p1.c and zero p2.c"; - parameter BioChem.Units.Concentration KmP1=1 "Concentration of p1.c such that v = -vR/2 (Michaelis constant) at zero s1.c and zero s2.c"; - parameter BioChem.Units.Concentration KmP2=1 "Concentration of p2.c such that v = -vR/2 (Michaelis constant) at zero s1.c and saturating p1.c"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverse maximum velocity"; - equation - s1.r=rr; - p1.r=-rr; - p2.r=-rr; - rr=vF*(s1.c - p1.c*p2.c/Keq)/(KmS1 + s1.c*(1 + p1.c/KiP1) + vF/(vR*Keq)*(KmP2*p1.c + KmP1*p2.c + p1.c*p2.c)); - annotation(Documentation(info=" -

- Ordered uni-bi kinetics. -

- ")); - end Ordubr; - - model Ordbur "Ordered bi-uni kinetics" - extends BioChem.Interfaces.Reactions.Basics.Reaction; - extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.OneProduct; - parameter BioChem.Units.Concentration Keq=1 "Equilibrium constant"; - parameter BioChem.Units.Concentration KiS1=1 "Product inhibition constant of s1.c acting on the reverse reaction"; - parameter BioChem.Units.Concentration KmS1=1 "Concentration of s1.c such that v = vF/2 (Michaelis constant) at zero p1.c"; - parameter BioChem.Units.Concentration KmS2=1 "Concentration of B such that v = vF/2 (Michaelis constant) at saturating s1.c and zero p1.c"; - parameter BioChem.Units.Concentration KmP1=1 "Concentration of p1.c such that v = -vR/2 (Michaelis constant) at zero s1.c and zero s2.c"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverse maximum velocity"; - equation - s1.r=rr; - s2.r=rr; - p1.r=-rr; - rr=vF*(s1.c*s2.c - p1.c/Keq)/(s1.c*s2.c + KmS1*s2.c + KmS2*s1.c + vF/(vR*Keq)*(KmP1 + p1.c*(1 + s1.c/KiS1))); - annotation(Documentation(info=" -

- Ordered bi-uni kinetics. -

- ")); - end Ordbur; - - model Ordbbr "Ordered bi-bi kinetics" - extends BioChem.Interfaces.Reactions.Basics.Reaction; - extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.TwoProducts; - parameter BioChem.Units.Concentration Keq=1 "Equilibrium constant"; - parameter BioChem.Units.Concentration KiS1=1 "Product inhibition constant of s1.c acting on the reverse reaction"; - parameter BioChem.Units.Concentration KiS2=1 "Product inhibition constant of s2.c acting on the reverse reaction"; - parameter BioChem.Units.Concentration KiP1=1 "Product inhibition constant of p1.c acting on the forward reaction"; - parameter BioChem.Units.Concentration KmS1=1 "Concentration of s1.c such that v = vF/2 (Michaelis constant) at zero p1.c and zero p2.c"; - parameter BioChem.Units.Concentration KmS2=1 "Concentration of s2.c such that v = vF/2 (Michaelis constant) at saturating s1.c and zero p1.c"; - parameter BioChem.Units.Concentration KmP1=1 "Concentration of p1.c such that v = -vR/2 (Michaelis constant) at zero s1.c and zero s2.c"; - parameter BioChem.Units.Concentration KmP2=1 "Concentration of p2.c such that v = -vR/2 (Michaelis constant) at zero s1.c and saturating p1.c"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverse maximum velocity"; - protected - Real K1; - Real K2; - equation - s1.r=rr; - s2.r=rr; - p1.r=-rr; - p2.r=-rr; - K1=vF/(vR*Keq)*(KmP2*p1.c*(1 + s1.c/KiS1) + p2.c*K2); - K2=KmP1*(1 + KmS1*s2.c/(KiS1*KmS2) + p1.c*(1 + s2.c/KiS2)); - rr=vF*(s1.c*s2.c - p1.c*p2.c/Keq)/(s1.c*s2.c*(1 + p1.c/KiP1) + KmS2*(s1.c + KiS1) + KmS1*s2.c + K1); - annotation(Documentation(info=" -

- Ordered bi-bi kinetics. -

- ")); - end Ordbbr; - + extends BioChem.Icons.Library; + annotation(Documentation(info="

BiSubstrate

diff --git a/BioChem/Reactions/FastEquilibrium/package.mo b/BioChem/Reactions/FastEquilibrium/package.mo index c136e91..1ad6e32 100644 --- a/BioChem/Reactions/FastEquilibrium/package.mo +++ b/BioChem/Reactions/FastEquilibrium/package.mo @@ -1,257 +1,8 @@ within BioChem.Reactions; package FastEquilibrium "Base classes for reactions with fast (instant) equilibrium" - extends Icons.Library; - model Uuf "Uni-Uni fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; - extends BioChem.Interfaces.Reactions.Basics.OneProduct; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for the substrate"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for the product"; - equation - p1.c=s1.c*kP1/kS1; - s1.r + p1.r=0; - end Uuf; - - model Utf "Uni-Tri fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; - extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for the substrate"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - parameter BioChem.Units.EquilibriumCoefficient kP3=1 "Equilibrium coefficient for product 3"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - p3.c=s1.c*kP3/kS1; - s1.r + p1.r + p2.r + p3.r=0; - end Utf; - - model Ubf "Uni-Bi fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; - extends BioChem.Interfaces.Reactions.Basics.TwoProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for the substrate"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - s1.r + p1.r + p2.r=0; - end Ubf; - - model Ttf "Tri-Tri fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kS3=1 "Equilibrium coefficient for substrate 3"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - parameter BioChem.Units.EquilibriumCoefficient kP3=1 "Equilibrium coefficient for product 3"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - p3.c=s1.c*kP3/kS1; - s2.c=s1.c*kS2/kS1; - s3.c=s1.c*kS3/kS1; - s1.r + s2.r + s3.r + p1.r + p2.r + p3.r=0; - end Ttf; - - model Btf "Bi-Tri fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.ThreeProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - parameter BioChem.Units.EquilibriumCoefficient kP3=1 "Equilibrium coefficient for product 3"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - p3.c=s1.c*kP3/kS1; - s2.c=s1.c*kS2/kS1; - s1.r + s2.r + p1.r + p2.r + p3.r=0; - end Btf; - - model Bbf "Bi-Bi fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.TwoProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - s2.c=s1.c*kS2/kS1; - s1.r + s2.r + p1.r + p2.r=0; - end Bbf; - - model Qqf "Quad-Quad fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.FourSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.FourProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kS3=1 "Equilibrium coefficient for substrate 3"; - parameter BioChem.Units.EquilibriumCoefficient kS4=1 "Equilibrium coefficient for substrate 4"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - parameter BioChem.Units.EquilibriumCoefficient kP3=1 "Equilibrium coefficient for product 3"; - parameter BioChem.Units.EquilibriumCoefficient kP4=1 "Equilibrium coefficient for product 4"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - p3.c=s1.c*kP3/kS1; - p4.c=s1.c*kP4/kS1; - s2.c=s1.c*kS2/kS1; - s3.c=s1.c*kS3/kS1; - s4.c=s1.c*kS4/kS1; - s1.r + s2.r + s3.r + s4.r + p1.r + p2.r + p3.r + p4.r=0; - end Qqf; - - model Uqf - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; - extends BioChem.Interfaces.Reactions.Basics.FourProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for the substrate"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - parameter BioChem.Units.EquilibriumCoefficient kP3=1 "Equilibrium coefficient for product 3"; - parameter BioChem.Units.EquilibriumCoefficient kP4=1 "Equilibrium coefficient for product 4"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - p3.c=s1.c*kP3/kS1; - p4.c=s1.c*kP4/kS1; - s1.r + p1.r + p2.r + p3.r + p4.c=0; - end Uqf; - - model Bqf "Bi-Quad fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.FourProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - parameter BioChem.Units.EquilibriumCoefficient kP3=1 "Equilibrium coefficient for product 3"; - parameter BioChem.Units.EquilibriumCoefficient kP4=1 "Equilibrium coefficient for product 4"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - p3.c=s1.c*kP3/kS1; - p4.c=s1.c*kP4/kS1; - s2.c=s1.c*kS2/kS1; - s1.r + s2.r + p1.r + p2.r + p3.r + p4.r=0; - end Bqf; - - model Tqf "Tri-Quad fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.FourProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kS3=1 "Equilibrium coefficient for substrate 3"; - parameter BioChem.Units.EquilibriumCoefficient kP1=1 "Equilibrium coefficient for product 1"; - parameter BioChem.Units.EquilibriumCoefficient kP2=1 "Equilibrium coefficient for product 2"; - parameter BioChem.Units.EquilibriumCoefficient kP3=1 "Equilibrium coefficient for product 3"; - parameter BioChem.Units.EquilibriumCoefficient kP4=1 "Equilibrium coefficient for product 4"; - equation - p1.c=s1.c*kP1/kS1; - p2.c=s1.c*kP2/kS1; - p3.c=s1.c*kP3/kS1; - p4.c=s1.c*kP4/kS1; - s2.c=s1.c*kS2/kS1; - s3.c=s1.c*kS3/kS1; - s1.r + s2.r + s3.r + p1.r + p2.r + p3.r + p4.r=0; - end Tqf; - - model Mmf "Multi-Multi fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.MultipleSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; - parameter BioChem.Units.EquilibriumCoefficient kS[dimS]=fill(1, dimS) "Equilibrium coefficients for the substrates"; - parameter BioChem.Units.EquilibriumCoefficient kP[dimP]=fill(1, dimP) "Equilibrium coefficients for the products"; - equation - for i in 1:dimP loop - p[i].c=s[1].c*kP[i]/kS[1]; - end for; - for i in 2:dimS loop - s[i].c=s[1].c*kS[i]/kS[1]; - end for; - sum(s.r) + sum(p.r)=0; - end Mmf; - - model Umf "Uni-Multi fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.OneSubstrateReversible; - extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kP[dimP]=fill(1, dimP) "Equilibrium coefficients for the products"; - equation - for i in 1:dimP loop - p[i].c=s1.c*kP[i]/kS1; - end for; - s1.r + sum(p.r)=0; - end Umf; - - model Bmf "Bi-Multi fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.TwoSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kP[dimP]=fill(1, dimP) "Equilibrium coefficients for the products"; - equation - for i in 1:dimP loop - p[i].c=s1.c*kP[i]/kS1; - end for; - s2.c=s1.c*kS2/kS1; - s1.r + s2.r + sum(p.r)=0; - end Bmf; - - model Qmf "Quad-Multi fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.FourSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kS3=1 "Equilibrium coefficient for substrate 3"; - parameter BioChem.Units.EquilibriumCoefficient kS4=1 "Equilibrium coefficient for substrate 4"; - parameter BioChem.Units.EquilibriumCoefficient kP[dimP]=fill(1, dimP) "Equilibrium coefficients for the products"; - equation - for i in 1:dimP loop - p[i].c=s1.c*kP[i]/kS1; - end for; - s2.c=s1.c*kS2/kS1; - s3.c=s1.c*kS3/kS1; - s4.c=s1.c*kS4/kS1; - s1.r + s2.r + s3.r + s4.r + sum(p.r)=0; - end Qmf; - - model Tmf "Tri-Multi fast (instant) equilibrium reaction" - extends BioChem.Interfaces.Reactions.Basics.FastEquilibrium; - extends BioChem.Interfaces.Reactions.Basics.ThreeSubstratesReversible; - extends BioChem.Interfaces.Reactions.Basics.MultipleProducts; - parameter BioChem.Units.EquilibriumCoefficient kS1=1 "Equilibrium coefficient for substrate 1"; - parameter BioChem.Units.EquilibriumCoefficient kS2=1 "Equilibrium coefficient for substrate 2"; - parameter BioChem.Units.EquilibriumCoefficient kS3=1 "Equilibrium coefficient for substrate 3"; - parameter BioChem.Units.EquilibriumCoefficient kP[dimP]=fill(1, dimP) "Equilibrium coefficients for the products"; - equation - for i in 1:dimP loop - p[i].c=s1.c*kP[i]/kS1; - end for; - s2.c=s1.c*kS2/kS1; - s3.c=s1.c*kS3/kS1; - s1.r + s2.r + s3.r + sum(p.r)=0; - end Tmf; - + extends BioChem.Icons.Library; + annotation(Documentation(info="

FastEquilibrium

The reaction in the FastEquilibrium package is used to model reactions that are very fast, and could be seen as an instant balance. These models are approximated to very fast reactions, if translated to SBML. diff --git a/BioChem/Reactions/Hill/package.mo b/BioChem/Reactions/Hill/package.mo index 3c29864..5e55577 100644 --- a/BioChem/Reactions/Hill/package.mo +++ b/BioChem/Reactions/Hill/package.mo @@ -1,87 +1,7 @@ within BioChem.Reactions; package Hill "Hill reactions kinetics" extends BioChem.Icons.Library; - model Hillr "Reversible Hill kinetics" - extends BioChem.Interfaces.Reactions.Uur; - parameter Real h=1 "Hill Coefficient"; - parameter BioChem.Units.Concentration Keq=1 "Equilibrium constant"; - parameter BioChem.Units.Concentration sHalf=1 "Substrate concentration such that v = vF/2"; - parameter BioChem.Units.Concentration pHalf=1 "Product concentration such that v = -vF/2"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/sHalf*(1 - p1.c/(s1.c*Keq))*(s1.c/sHalf + p1.c/pHalf)^(h - 1)/(1 + (s1.c/sHalf + p1.c/pHalf)^h); - annotation(Documentation(info=" -

- Reversible Hill kinetics. -

- ")); - end Hillr; - - model Hillmr "Reversible Hill kinetics with one modifier" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real alfa=1 "Effect of s1 and p1 on binding of m"; - parameter Real h=1 "Hill Coefficient"; - parameter BioChem.Units.Concentration Keq=1 "Equilibrium constant"; - parameter BioChem.Units.Concentration m1Half=1 "Concentration of mA that half-saturates its binding site when s1.c = 0, p1.c = 0, m2.c = 0"; - parameter BioChem.Units.Concentration s1Half=1 "Substrate concentration such that v = vF/2"; - parameter BioChem.Units.Concentration p1Half=1 "Product concentration such that v = -vF/2"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - protected - Real K1; - Real K2; - equation - K1=(s1.c/s1Half + p1.c/p1Half)^h; - K2=(1 + (m1.c/m1Half)^h)/(1 + alfa*(m1.c/m1Half)^h); - rr=vF*s1.c/s1Half*(1 - p1.c/(s1.c*Keq))*(s1.c/s1Half + p1.c/p1Half)^(h - 1)/(K1 + K2); - annotation(Documentation(info=" -

- Reversible Hill kinetics with one modifier. -

- ")); - end Hillmr; - - model Hillmmr "Reversible Hill kinetics with two modifiers" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.TwoModifiers; - parameter Real alfa1=1 "Effect of s1 and p1 on binding of m"; - parameter Real alfa2=1 "Effect of s1 and p1 on binding of m"; - parameter Real alfa12=1 "Effect of s1 and p1 on binding of m"; - parameter BioChem.Units.Concentration Keq=1 "Equilibrium constant"; - parameter Real h=1 "Hill Coefficient"; - parameter BioChem.Units.Concentration m1Half=1 "Concentration of m1 that half-saturates its binding site when s1.c = 0, p1.c = 0, m2.c = 0"; - parameter BioChem.Units.Concentration m2Half=1 "Concentration of m1 that half-saturates its binding site when s1.c = 0, p1.c = 0, m1.c = 0"; - parameter BioChem.Units.Concentration s1Half=1 "Substrate concentration such that v = vF/2 when p1.c = 0 and the modifiers m1.c = 0, m2.c = 0"; - parameter BioChem.Units.Concentration p1Half=1 "Product concentration such that v = -vF/2 when p1.c = 0 and the modifiers m1.c = 0, m2.c = 0"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - protected - Real K1; - Real K2; - equation - K1=(s1.c/s1Half + p1.c/p1Half)^h; - K2=(1 + (m1.c/m1Half)^h + (m2.c/m2Half)^h)/(1 + alfa1*(m1.c/m1Half)^h + alfa2*(m2.c/m2Half)^h + alfa12*(m1.c/m1Half)^h*(m2.c/m2Half)^h); - rr=vF*s1.c/s1Half*(1 - p1.c/(s1.c*Keq))*(s1.c/s1Half + p1.c/p1Half)^(h - 1)/(K1 + K2); - annotation(Documentation(info=" -

- Reversible Hill kinetics with two modifiers. -

- ")); - end Hillmmr; - - model Hilli "Irreversible Hill kinetics" - extends BioChem.Interfaces.Reactions.Uui; - parameter Real h=1 "Hill Coefficient"; - parameter BioChem.Units.Concentration sHalf=1 "Substrate concentration such that v = vF/2"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c^h/(sHalf^h + s1.c^h); - annotation(Documentation(info=" -

- Irreversible Hill kinetics. -

- ")); - end Hilli; - + annotation(Documentation(info="

Hill

diff --git a/BioChem/Reactions/HyperbolicModifier/package.mo b/BioChem/Reactions/HyperbolicModifier/package.mo index fbe438d..6018872 100644 --- a/BioChem/Reactions/HyperbolicModifier/package.mo +++ b/BioChem/Reactions/HyperbolicModifier/package.mo @@ -1,42 +1,7 @@ within BioChem.Reactions; package HyperbolicModifier "Hyperbolic modifier kinetics reactions" - extends Icons.Library; - model Uhmr "Reversible general hyperbolic modifier kinetics" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real a=1 "Ratio of dissociaton constants, ES+M->ESM over E+M->EM"; - parameter Real b=1 "Ratio of rate constants, ESM->EM+P over ES->E+P"; - parameter Real Kd=1 "Dissociation constant of E+M->EM"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.Concentration KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverse maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)*(1 + b*m1.c/(a*Kd))/(1 + m1.c/Kd + (s1.c/KmS + p1.c/KmP)*(1 + m1.c/(a*Kd))); - annotation(Documentation(info=" -

- Reversible general hyperbolic modifier kinetics. -

- "), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Uhmr; - - model Uhmi "Irreversible general hyperbolic modifier kinetics" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Modifier; - parameter Real a=1 "Ratio of dissociaton constants, ES+M->ESM over E+M->EM"; - parameter Real b=1 "Ratio of rate constants, ESM->EM+P over ES->E+P"; - parameter Real Kd=1 "Dissociation constant of E+M->EM"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/KmS*(1 + b*m1.c/(a*Kd))/(1 + m1.c/Kd + s1.c/KmS*(1 + m1.c/(a*Kd))); - annotation(Documentation(info=" -

- Irreversible general hyperbolic modifier kinetics. -

- "), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Uhmi; - + extends BioChem.Icons.Library; + annotation(Documentation(info="

HyperbolicModifier

diff --git a/BioChem/Reactions/Inhibition/package.mo b/BioChem/Reactions/Inhibition/package.mo index 330c900..29402b5 100644 --- a/BioChem/Reactions/Inhibition/package.mo +++ b/BioChem/Reactions/Inhibition/package.mo @@ -1,184 +1,8 @@ within BioChem.Reactions; package Inhibition "Inhibition kinetics reactions" - extends Icons.Library; - model Uucr "Uncompetitive inhibition (reversible)" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter Real KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverese maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + (s1.c/KmS + p1.c/KmP)*(1 + i1.c/Ki)); - annotation(Documentation(info=" -

- Uncompetitive inhibition (reversible). -

- ")); - end Uucr; - - model Uuci "Irreversible uncompetitive inhibition" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/KmS/(1 + s1.c/KmS*(1 + i1.c/Ki)); - annotation(Documentation(info=" -

- Irreversible uncompetitive inhibition. -

- ")); - end Uuci; - - model Usir "Reversible substrate inhibition kinetics" - extends BioChem.Interfaces.Reactions.Uui; - parameter BioChem.Units.Concentration Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter Real KmP=1 "Reverese Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reversible maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + s1.c/KmS + p1.c/KmP + s1.c^2/Ki); - annotation(Documentation(info=" -

- Reversible substrate inhibition kinetics. -

- ")); - end Usir; - - model Usii "Irreversible substrate inhibition kinetics" - extends BioChem.Interfaces.Reactions.Uui; - parameter BioChem.Units.Concentration Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/KmS/(1 + s1.c/KmS + s1.c^2/Ki); - annotation(Documentation(info=" -

- Irreversible substrate inhibition kinetics. -

- ")); - end Usii; - - model Unir "Noncompetitive inhibition (reversible)" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter Real KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverese maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + i1.c/Ki + (s1.c/KmS + p1.c/KmP)*(1 + i1.c/Ki)); - annotation(Documentation(info=" -

- Noncompetitive inhibition (reversible). -

- ")); - end Unir; - - model Unii "Irreversible non-competitive inhibition kinetics" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/KmS/(1 + i1.c/Ki + s1.c/KmS*(1 + i1.c/Ki)); - annotation(Documentation(info=" -

- Irreversible non-competitive inhibition kinetics. -

- ")); - end Unii; - - model Umr "Reversible mixed inhibition kinetics" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Kis=1 "Specific (competitive) inhibition constant"; - parameter Real Kic=1 "Catalytic (non-competitive) inhibition constant"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter Real KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverese maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + i1.c/Kis + (s1.c/KmS + p1.c/KmP)*(1 + i1.c/Kic)); - annotation(Documentation(info=" -

- Reversible mixed inhibition kinetics. -

- ")); - end Umr; - - model Umi "Irreversible mixed inhibition kinetics" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Kic=1 "Catalytic inhibition constant"; - parameter Real Kis=1 "Specific inhibition constant"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/KmS/(1 + i1.c/Kis + s1.c/KmS*(1 + i1.c/Kic)); - annotation(Documentation(info=" -

- Irreversible mixed inhibition kinetics. -

- ")); - end Umi; - - model Ucir "Competitive inhibition (reversible)" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter Real KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverese maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + s1.c/KmS + p1.c/KmP + i1.c/Ki); - annotation(Documentation(info=" -

- Competitive inhibition (reversible). -

- ")); - end Ucir; - - model Ucii "Irreversible competitive inhibition kinetics" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Ki=1 "Inhibition constant for the substrate"; - parameter Real KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/KmS/(1 + s1.c/KmS + i1.c/Ki); - annotation(Documentation(info=" -

- Irreversible competitive inhibition kinetics. -

- ")); - end Ucii; - - model Ualii "Irreversible allosteric inhibition" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.Inhibitor; - parameter Real Kii=1 "Dissociation constant of the inhibitor from the inactive form of the enzyme"; - parameter Real Ks=1 "Dissociation constant of the substrate from the active form of the enzyme"; - parameter Real L=1 "Equibrilium constant between active and inactive enzyme"; - parameter Integer n=1 "Number of binding sites for substrate and inhibitor"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/Ks*(1 + s1.c/Ks)^(n - 1)/(L*(1 + i1.c/Kii)^n + (1 + s1.c/Ks)^n); - annotation(Documentation(info=" -

- Irreversible allosteric inhibition. -

- ")); - end Ualii; - + extends BioChem.Icons.Library; + annotation(Documentation(info="

Inhibition

diff --git a/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo b/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo index 93b905e..5baa585 100644 --- a/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/BiBi/package.mo @@ -3,37 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package BiBi "A+B -> C+D reactions" extends BioChem.Icons.Library; - model Bbifi "Bi-bi irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbi; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Bbifi; - - model Bbifafi "Bi-bi irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbi; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Bbifafi; - - model Bbifa "Bi-bi irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Bbi; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Bbifa; - - model Bbi "Bi-bi irrerversible reaction" - extends BioChem.Interfaces.Reactions.Bbi; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Bbi; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and two products.

diff --git a/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo b/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo index 60935da..9273c04 100644 --- a/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/BiTri/package.mo @@ -3,37 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package BiTri "A+B -> C+D+E reactions" extends BioChem.Icons.Library; - model Btifi "Bi-tri irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bti; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Btifi; - - model Btifafi "Bi-tri irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bti; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Btifafi; - - model Btifa "Bi-tri irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Bti; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Btifa; - - model Bti "Bi-tri irrerversible reaction" - extends BioChem.Interfaces.Reactions.Bti; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Bti; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and three products.

diff --git a/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo b/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo index 15e7d0a..3223ccb 100644 --- a/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/BiUni/package.mo @@ -3,37 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package BiUni "A+B -> C reactions" extends BioChem.Icons.Library; - model Buifi "Bi-uni irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bui; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Buifi; - - model Buifafi "Bi-uni irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bui; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Buifafi; - - model Buifa "Bi-uni irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Bui; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Buifa; - - model Bui "Bi-uni irrerversible reaction" - extends BioChem.Interfaces.Reactions.Bui; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V; - end Bui; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and one product.

diff --git a/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo b/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo index f68d40b..5e2bd40 100644 --- a/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/TriBi/package.mo @@ -3,37 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package TriBi "A+B+C -> D+E reactions" extends BioChem.Icons.Library; - model Tbifi "Tri-bi irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbi; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tbifi; - - model Tbifafi "Tri-bi irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbi; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tbifafi; - - model Tbifa "Tri-bi irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Tbi; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tbifa; - - model Tbi "Tri-bi irrerversible reaction" - extends BioChem.Interfaces.Reactions.Tbi; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tbi; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and two products

diff --git a/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo b/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo index 572e902..4ccb6fc 100644 --- a/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/TriTri/package.mo @@ -3,37 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package TriTri "A+B+C -> D+E+F reactions" extends Icons.Library; - model Ttifi "Tri-tri irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tti; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Ttifi; - - model Ttifafi "Tri-tri irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tti; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Ttifafi; - - model Ttifa "Tri-tri irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Tti; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Ttifa; - - model Tti "Tri-tri irrerversible reaction" - extends BioChem.Interfaces.Reactions.Tti; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tti; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and three products.

diff --git a/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo b/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo index f5b398b..17ad09a 100644 --- a/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/TriUni/package.mo @@ -3,37 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package TriUni "A+B+C -> D reactions" extends BioChem.Icons.Library; - model Tuifi "Tri-uni irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tui; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tuifi; - - model Tuifafi "Tri-uni irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tui; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tuifafi; - - model Tuifa "Tri-uni irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Tui; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tuifa; - - model Tui "Tri-uni irrerversible reaction" - extends BioChem.Interfaces.Reactions.Tui; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V; - end Tui; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and one product.

diff --git a/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo b/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo index 1339983..09e757b 100644 --- a/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/UniBi/package.mo @@ -3,53 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package UniBi "A -> B+C reactions" extends BioChem.Icons.Library; - model Ubifi "Uni-bi irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubi; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V; - end Ubifi; - - model Ubifafi "Uni-bi irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubi; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V; - end Ubifafi; - - model Ubifa "Uni-bi irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Ubi; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V; - annotation( - Documentation(info = " - -")); - end Ubifa; - - model Ubi "Uni-bi irrerversible reaction" - extends BioChem.Interfaces.Reactions.Ubi; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V; - annotation( - Documentation(info = " - -")); - end Ubi; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with one reactant and two products.

diff --git a/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo b/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo index b780b03..faa125e 100644 --- a/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/UniTri/package.mo @@ -3,37 +3,6 @@ within BioChem.Reactions.MassAction.Irreversible; package UniTri "A -> B+C+D reactions" extends BioChem.Icons.Library; - model Utifi "Uni-tri irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uti; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V; - end Utifi; - - model Utifafi "Uni-tri irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uti; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V; - end Utifafi; - - model Utifa "Uni-tri irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Uti; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V; - end Utifa; - - model Uti "Uni-tri irrerversible reaction" - extends BioChem.Interfaces.Reactions.Uti; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V; - end Uti; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with one reactant and three products.

diff --git a/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo b/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo index 7a62243..4b008bd 100644 --- a/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo +++ b/BioChem/Reactions/MassAction/Irreversible/UniUni/package.mo @@ -2,37 +2,6 @@ within BioChem.Reactions.MassAction.Irreversible; package UniUni "A -> B reactions" extends BioChem.Icons.Library; - model Uuifi "Uni-uni irrerversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - equation - rr=k1/iF1.c*s1.c^nS1*s1.V; - end Uuifi; - - model Uuifafi "Uni-uni irrerversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c/iF1.c*s1.c^nS1*s1.V; - end Uuifafi; - - model Uuifa "Uni-uni irrerversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Uui; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c*s1.c^nS1*s1.V; - end Uuifa; - - model Uui "Uni-uni irrerversible reaction" - extends BioChem.Interfaces.Reactions.Uui; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - equation - rr=k1*s1.c^nS1*s1.V; - end Uui; annotation(Documentation(info="

This package contains models for stoichiometric reactions with one reactant and one product.

diff --git a/BioChem/Reactions/MassAction/Reversible/BiBi/package.mo b/BioChem/Reactions/MassAction/Reversible/BiBi/package.mo index 592e864..2a568f2 100644 --- a/BioChem/Reactions/MassAction/Reversible/BiBi/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/BiBi/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package BiBi "A+B <-> C+D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Bbrfibi "Bi-bi reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfibi; - - model Bbrfibabi "Bi-bi reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfibabi; - - model Bbrfiba "Bi-bi reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfiba; - - model Bbrfi "Bi-bi reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfi; - - model Bbrfafibi "Bi-bi reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfafibi; - - model Bbrfafibabi "Bi-bi reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfafibabi; - - model Bbrfafiba "Bi-bi reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfafiba; - - model Bbrfafi "Bi-bi reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfafi; - - model Bbrfabi "Bi-bi reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfabi; - - model Bbrfababi "Bi-bi reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfababi; - - model Bbrfaba "Bi-bi reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfaba; - - model Bbrfa "Bi-bi reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrfa; - - model Bbrbi "Bi-bi reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrbi; - - model Bbrbabi "Bi-bi reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrbabi; - - model Bbrba "Bi-bi reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbrba; - - model Bbr "Bi-bi reversible reaction" - extends BioChem.Interfaces.Reactions.Bbr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bbr; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and two products.

diff --git a/BioChem/Reactions/MassAction/Reversible/BiTri/package.mo b/BioChem/Reactions/MassAction/Reversible/BiTri/package.mo index 27db76b..615616a 100644 --- a/BioChem/Reactions/MassAction/Reversible/BiTri/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/BiTri/package.mo @@ -1,182 +1,7 @@ within BioChem.Reactions.MassAction.Reversible; package BiTri "A+B <-> C+D+E reactions" - extends Icons.Library; - model Btrfibi "Bi-tri reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfibi; - - model Btrfibabi "Bi-tri reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfibabi; - - model Btrfiba "Bi-tri reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfiba; - - model Btrfi "Bi-tri reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfi; - - model Btrfafibi "Bi-tri reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfafibi; - - model Btrfafibabi "Bi-tri reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfafibabi; - - model Btrfafiba "Bi-tri reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfafiba; - - model Btrfafi "Bi-tri reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c/iF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfafi; - - model Btrfabi "Bi-tri reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfabi; - - model Btrfababi "Bi-tri reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfababi; - - model Btrfaba "Bi-tri reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfaba; - - model Btrfa "Bi-tri reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*aF1.c*s1.c^nS1*s2.c^nS2*s1.V - k2*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrfa; - - model Btrbi "Bi-tri reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*s1.c^nS1*s2.c^nS2*s1.V - k2/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrbi; - - model Btrbabi "Bi-tri reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c/iB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrbabi; - - model Btrba "Bi-tri reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Btr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*s1.c^nS1*s2.c^nS2*s1.V - k2*aB1.c*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btrba; - - model Btr "Bi-tri reversible reaction" - extends BioChem.Interfaces.Reactions.Btr; - parameter BioChem.Units.ReactionCoefficient k1=1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2=1 "Backwards reaction coefficient for the reaction"; - equation - rr=k1*s1.c^nS1*s2.c^nS2*s1.V - k2*p1.c^nP1*p2.c^nP2*p3.c^nP3*p1.V; - annotation(Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}))); - end Btr; + extends BioChem.Icons.Library; annotation(Documentation(info="

This package contains models for stoichiometric reactions with two reactants and three products.

diff --git a/BioChem/Reactions/MassAction/Reversible/BiUni/package.mo b/BioChem/Reactions/MassAction/Reversible/BiUni/package.mo index d604108..06659c7 100644 --- a/BioChem/Reactions/MassAction/Reversible/BiUni/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/BiUni/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package BiUni "A+B <-> C reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Burfibi "Bi-uni reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfibi; - - model Burfibabi "Bi-uni reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfibabi; - - model Burfiba "Bi-uni reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfiba; - - model Burfi "Bi-uni reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfi; - - model Burfafibi "Bi-uni reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfafibi; - - model Burfafibabi "Bi-uni reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfafibabi; - - model Burfafiba "Bi-uni reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfafiba; - - model Burfafi "Bi-uni reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfafi; - - model Burfabi "Bi-uni reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfabi; - - model Burfababi "Bi-uni reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfababi; - - model Burfaba "Bi-uni reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfaba; - - model Burfa "Bi-uni reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burfa; - - model Burbi "Bi-uni reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burbi; - - model Burbabi "Bi-uni reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burbabi; - - model Burba "Bi-uni reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Burba; - - model Bur "Bi-uni reversible reaction" - extends BioChem.Interfaces.Reactions.Bur; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Bur; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with two reactants and one product.

diff --git a/BioChem/Reactions/MassAction/Reversible/TriBi/package.mo b/BioChem/Reactions/MassAction/Reversible/TriBi/package.mo index 366d4c5..7ab8040 100644 --- a/BioChem/Reactions/MassAction/Reversible/TriBi/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/TriBi/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package TriBi "A+B+C <-> D+E reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Tbrfibi "Tri-bi reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfibi; - - model Tbrfibabi "Tri-bi reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfibabi; - - model Tbrfiba "Tri-bi reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfiba; - - model Tbrfi "Tri-bi reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfi; - - model Tbrfafibi "Tri-bi reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfafibi; - - model Tbrfafibabi "Tri-bi reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfafibabi; - - model Tbrfafiba "Tri-bi reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfafiba; - - model Tbrfafi "Tri-bi reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfafi; - - model Tbrfabi "Tri-bi reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfabi; - - model Tbrfababi "Tri-bi reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfababi; - - model Tbrfaba "Tri-bi reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfaba; - - model Tbrfa "Tri-bi reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrfa; - - model Tbrbi "Tri-bi reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrbi; - - model Tbrbabi "Tri-bi reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrbabi; - - model Tbrba "Tri-bi reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Tbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbrba; - - model Tbr "Tri-bi reversible reaction" - extends BioChem.Interfaces.Reactions.Tbr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tbr; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and two products

diff --git a/BioChem/Reactions/MassAction/Reversible/TriTri/package.mo b/BioChem/Reactions/MassAction/Reversible/TriTri/package.mo index 8b017cd..086f67d 100644 --- a/BioChem/Reactions/MassAction/Reversible/TriTri/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/TriTri/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package TriTri "A+B+C <-> D+E+F reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Ttrfibi "Tri-tri reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfibi; - - model Ttrfibabi "Tri-tri reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfibabi; - - model Ttrfiba "Tri-tri reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfiba; - - model Ttrfi "Tri-tri reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfi; - - model Ttrfafibi "Tri-tri reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfafibi; - - model Ttrfafibabi "Tri-tri reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfafibabi; - - model Ttrfafiba "Tri-tri reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfafiba; - - model Ttrfafi "Tri-tri reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfafi; - - model Ttrfabi "Tri-tri reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfabi; - - model Ttrfababi "Tri-tri reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfababi; - - model Ttrfaba "Tri-tri reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfaba; - - model Ttrfa "Tri-tri reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrfa; - - model Ttrbi "Tri-tri reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrbi; - - model Ttrbabi "Tri-tri reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrbabi; - - model Ttrba "Tri-tri reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Ttr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttrba; - - model Ttr "Tri-tri reversible reaction" - extends BioChem.Interfaces.Reactions.Ttr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ttr; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and three products.

diff --git a/BioChem/Reactions/MassAction/Reversible/TriUni/package.mo b/BioChem/Reactions/MassAction/Reversible/TriUni/package.mo index 6a546c1..fe72824 100644 --- a/BioChem/Reactions/MassAction/Reversible/TriUni/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/TriUni/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package TriUni "A+B+C <-> D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Turfibi "Tri-uni reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfibi; - - model Turfibabi "Tri-uni reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfibabi; - - model Turfiba "Tri-uni reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfiba; - - model Turfi "Tri-uni reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfi; - - model Turfafibi "Tri-uni reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfafibi; - - model Turfafibabi "Tri-uni reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfafibabi; - - model Turfafiba "Tri-uni reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfafiba; - - model Turfafi "Tri-uni reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfafi; - - model Turfabi "Tri-uni reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfabi; - - model Turfababi "Tri-uni reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfababi; - - model Turfaba "Tri-uni reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfaba; - - model Turfa "Tri-uni reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turfa; - - model Turbi "Tri-uni reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turbi; - - model Turbabi "Tri-uni reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turbabi; - - model Turba "Tri-uni reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Tur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Turba; - - model Tur "Tri-uni reversible reaction" - extends BioChem.Interfaces.Reactions.Tur; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s3.c ^ nS3 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Tur; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with three reactants and one product.

diff --git a/BioChem/Reactions/MassAction/Reversible/UniBi/package.mo b/BioChem/Reactions/MassAction/Reversible/UniBi/package.mo index 1b20aec..df37240 100644 --- a/BioChem/Reactions/MassAction/Reversible/UniBi/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/UniBi/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package UniBi "A <-> B+C reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Ubrfibi "Uni-bi reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfibi; - - model Ubrfibabi "Uni-bi reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfibabi; - - model Ubrfiba "Uni-bi reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfiba; - - model Ubrfi "Uni-bi reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfi; - - model Ubrfafibi "Uni-bi reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfafibi; - - model Ubrfafibabi "Uni-bi reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfafibabi; - - model Ubrfafiba "Uni-bi reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfafiba; - - model Ubrfafi "Uni-bi reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfafi; - - model Ubrfabi "Uni-bi reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfabi; - - model Ubrfababi "Uni-bi reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfababi; - - model Ubrfaba "Uni-bi reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfaba; - - model Ubrfa "Uni-bi reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrfa; - - model Ubrbi "Uni-bi reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrbi; - - model Ubrbabi "Uni-bi reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrbabi; - - model Ubrba "Uni-bi reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubrba; - - model Ubr "Uni-bi reversible reaction" - extends BioChem.Interfaces.Reactions.Ubr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Ubr; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with one reactant and two products.

diff --git a/BioChem/Reactions/MassAction/Reversible/UniTri/package.mo b/BioChem/Reactions/MassAction/Reversible/UniTri/package.mo index dfdfa5b..cef5ed1 100644 --- a/BioChem/Reactions/MassAction/Reversible/UniTri/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/UniTri/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package UniTri "A <-> B+C+D reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Utrfibi "Uni-tri reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfibi; - - model Utrfibabi "Uni-tri reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfibabi; - - model Utrfiba "Uni-tri reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfiba; - - model Utrfi "Uni-tri reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfi; - - model Utrfafibi "Uni-tri reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfafibi; - - model Utrfafibabi "Uni-tri reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfafibabi; - - model Utrfafiba "Uni-tri reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfafiba; - - model Utrfafi "Uni-tri reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfafi; - - model Utrfabi "Uni-tri reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfabi; - - model Utrfababi "Uni-tri reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfababi; - - model Utrfaba "Uni-tri reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfaba; - - model Utrfa "Uni-tri reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrfa; - - model Utrbi "Uni-tri reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrbi; - - model Utrbabi "Uni-tri reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrbabi; - - model Utrba "Uni-tri reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utrba; - - model Utr "Uni-tri reversible reaction" - extends BioChem.Interfaces.Reactions.Utr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Utr; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with one reactant and three products.

diff --git a/BioChem/Reactions/MassAction/Reversible/UniUni/package.mo b/BioChem/Reactions/MassAction/Reversible/UniUni/package.mo index 5e3ede8..b24a2e0 100644 --- a/BioChem/Reactions/MassAction/Reversible/UniUni/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/UniUni/package.mo @@ -1,231 +1,8 @@ within BioChem.Reactions.MassAction.Reversible; package UniUni "A <-> B reactions" - extends Icons.Library; + extends BioChem.Icons.Library; - model Uurfibi "Uni-uni reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfibi; - - model Uurfibabi "Uni-uni reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfibabi; - - model Uurfiba "Uni-uni reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfiba; - - model Uurfi "Uni-uni reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfi; - - model Uurfafibi "Uni-uni reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfafibi; - - model Uurfafibabi "Uni-uni reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfafibabi; - - model Uurfafiba "Uni-uni reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfafiba; - - model Uurfafi "Uni-uni reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfafi; - - model Uurfabi "Uni-uni reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfabi; - - model Uurfababi "Uni-uni reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfababi; - - model Uurfaba "Uni-uni reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfaba; - - model Uurfa "Uni-uni reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurfa; - - model Uurbi "Uni-uni reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurbi; - - model Uurbabi "Uni-uni reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurbabi; - - model Uurba "Uni-uni reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uurba; - - model Uur "Uni-uni reversible reaction" - extends BioChem.Interfaces.Reactions.Uur; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - annotation( - Documentation, - Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})), - Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); - end Uur; annotation( Documentation(info = "

This package contains models for stoichiometric reactions with one reactant and one product.

diff --git a/BioChem/Reactions/MassAction/Reversible/package.mo b/BioChem/Reactions/MassAction/Reversible/package.mo index d5feaf2..f8891fa 100644 --- a/BioChem/Reactions/MassAction/Reversible/package.mo +++ b/BioChem/Reactions/MassAction/Reversible/package.mo @@ -3,847 +3,6 @@ within BioChem.Reactions.MassAction; package Reversible "Reversible reactions" extends BioChem.Icons.Library; - package UniUni "A <-> B reactions" - extends BioChem.Icons.Library; - - model Uurfibi "Uni-uni reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Uurfibi; - - model Uurfibabi "Uni-uni reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Uurfibabi; - - model Uurfiba "Uni-uni reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Uurfiba; - - model Uurfi "Uni-uni reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Uurfi; - - model Uurfafibi "Uni-uni reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Uurfafibi; - - model Uurfafibabi "Uni-uni reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Uurfafibabi; - - model Uurfafiba "Uni-uni reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Uurfafiba; - - model Uurfafi "Uni-uni reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Uurfafi; - - model Uurfabi "Uni-uni reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Uurfabi; - - model Uurfababi "Uni-uni reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Uurfababi; - - model Uurfaba "Uni-uni reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Uurfaba; - - model Uurfa "Uni-uni reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Uurfa; - - model Uurbi "Uni-uni reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Uurbi; - - model Uurbabi "Uni-uni reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Uurbabi; - - model Uurba "Uni-uni reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Uur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Uurba; - - model Uur "Uni-uni reversible reaction" - extends BioChem.Interfaces.Reactions.Uur; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Uur; - annotation( - Documentation(info = " -

This package contains models for stoichiometric reactions with one reactant and one product.

- ")); - end UniUni; - - package UniTri "A <-> B+C+D reactions" - extends BioChem.Icons.Library; - - model Utrfibi "Uni-tri reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfibi; - - model Utrfibabi "Uni-tri reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfibabi; - - model Utrfiba "Uni-tri reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfiba; - - model Utrfi "Uni-tri reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfi; - - model Utrfafibi "Uni-tri reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfafibi; - - model Utrfafibabi "Uni-tri reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfafibabi; - - model Utrfafiba "Uni-tri reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfafiba; - - model Utrfafi "Uni-tri reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfafi; - - model Utrfabi "Uni-tri reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfabi; - - model Utrfababi "Uni-tri reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfababi; - - model Utrfaba "Uni-tri reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfaba; - - model Utrfa "Uni-tri reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrfa; - - model Utrbi "Uni-tri reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrbi; - - model Utrbabi "Uni-tri reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrbabi; - - model Utrba "Uni-tri reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Utr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utrba; - - model Utr "Uni-tri reversible reaction" - extends BioChem.Interfaces.Reactions.Utr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p3.c ^ nP3 * p1.V; - end Utr; - annotation( - Documentation(info = " -

This package contains models for stoichiometric reactions with one reactant and three products.

- ")); - end UniTri; - - package UniBi "A <-> B+C reactions" - extends Icons.Library; - - model Ubrfibi "Uni-bi reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfibi; - - model Ubrfibabi "Uni-bi reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfibabi; - - model Ubrfiba "Uni-bi reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfiba; - - model Ubrfi "Uni-bi reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfi; - - model Ubrfafibi "Uni-bi reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfafibi; - - model Ubrfafibabi "Uni-bi reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfafibabi; - - model Ubrfafiba "Uni-bi reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfafiba; - - model Ubrfafi "Uni-bi reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfafi; - - model Ubrfabi "Uni-bi reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfabi; - - model Ubrfababi "Uni-bi reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfababi; - - model Ubrfaba "Uni-bi reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfaba; - - model Ubrfa "Uni-bi reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrfa; - - model Ubrbi "Uni-bi reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrbi; - - model Ubrbabi "Uni-bi reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrbabi; - - model Ubrba "Uni-bi reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Ubr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubrba; - - model Ubr "Uni-bi reversible reaction" - extends BioChem.Interfaces.Reactions.Ubr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Ubr; - annotation( - Documentation(info = " -

This package contains models for stoichiometric reactions with one reactant and two products.

- ")); - end UniBi; - - package BiUni "A+B <-> C reactions" - extends Icons.Library; - - model Burfibi "Bi-uni reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Burfibi; - - model Burfibabi "Bi-uni reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Burfibabi; - - model Burfiba "Bi-uni reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Burfiba; - - model Burfi "Bi-uni reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Burfi; - - model Burfafibi "Bi-uni reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Burfafibi; - - model Burfafibabi "Bi-uni reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Burfafibabi; - - model Burfafiba "Bi-uni reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Burfafiba; - - model Burfafi "Bi-uni reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Burfafi; - - model Burfabi "Bi-uni reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Burfabi; - - model Burfababi "Bi-uni reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Burfababi; - - model Burfaba "Bi-uni reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Burfaba; - - model Burfa "Bi-uni reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Burfa; - - model Burbi "Bi-uni reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p1.V; - end Burbi; - - model Burbabi "Bi-uni reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p1.V; - end Burbabi; - - model Burba "Bi-uni reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Bur; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p1.V; - end Burba; - - model Bur "Bi-uni reversible reaction" - extends BioChem.Interfaces.Reactions.Bur; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p1.V; - end Bur; - annotation( - Documentation(info = " -

This package contains models for stoichiometric reactions with two reactants and one product.

- ")); - end BiUni; - - package BiBi "A+B <-> C+D reactions" - extends BioChem.Icons.Library; - - model Bbrfibi "Bi-bi reversible forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfibi; - - model Bbrfibabi "Bi-bi reversible forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfibabi; - - model Bbrfiba "Bi-bi reversible forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfiba; - - model Bbrfi "Bi-bi reversible forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfi; - - model Bbrfafibi "Bi-bi reversible forward activation, forward inhibition, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfafibi; - - model Bbrfafibabi "Bi-bi reversible forward activation, forward inhibition, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfafibabi; - - model Bbrfafiba "Bi-bi reversible forward activation, forward inhibition, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfafiba; - - model Bbrfafi "Bi-bi reversible forward activation, forward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c / iF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfafi; - - model Bbrfabi "Bi-bi reversible forward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfabi; - - model Bbrfababi "Bi-bi reversible forward activation, backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfababi; - - model Bbrfaba "Bi-bi reversible forward activation, backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfaba; - - model Bbrfa "Bi-bi reversible forward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorForward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * aF1.c * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrfa; - - model Bbrbi "Bi-bi reversible backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrbi; - - model Bbrbabi "Bi-bi reversible backward activation, backward inhibition reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - extends BioChem.Interfaces.Reactions.Modifiers.InhibitorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c / iB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrbabi; - - model Bbrba "Bi-bi reversible backward activation reaction" - extends BioChem.Interfaces.Reactions.Bbr; - extends BioChem.Interfaces.Reactions.Modifiers.ActivatorBackward; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * aB1.c * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbrba; - - model Bbr "Bi-bi reversible reaction" - extends BioChem.Interfaces.Reactions.Bbr; - parameter BioChem.Units.ReactionCoefficient k1 = 1 "Forwards reaction coefficient for the reaction"; - parameter BioChem.Units.ReactionCoefficient k2 = 1 "Backwards reaction coefficient for the reaction"; - equation - rr = k1 * s1.c ^ nS1 * s2.c ^ nS2 * s1.V - k2 * p1.c ^ nP1 * p2.c ^ nP2 * p1.V; - end Bbr; - annotation( - Documentation(info = " -

This package contains models for stoichiometric reactions with two reactants and two products.

- ")); - end BiBi; - - annotation( Documentation(info = "

This package contains models for reversible reactions with one to three reactants and products.

diff --git a/BioChem/Reactions/MichaelisMenten/package.mo b/BioChem/Reactions/MichaelisMenten/package.mo index d7358ad..e90cc6c 100644 --- a/BioChem/Reactions/MichaelisMenten/package.mo +++ b/BioChem/Reactions/MichaelisMenten/package.mo @@ -1,64 +1,6 @@ within BioChem.Reactions; package MichaelisMenten "Michaelis-Menten kinetics reactions" extends BioChem.Icons.Library; - model Uur "Uni-uni reversible simple Michaelis-Menten" - extends BioChem.Interfaces.Reactions.Uur; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.Concentration KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - parameter BioChem.Units.ReactionRate vR=1 "Reverse maximum velocity"; - equation - rr=(vF*s1.c/KmS - vR*p1.c/KmP)/(1 + s1.c/KmS + p1.c/KmP); - annotation(Documentation(info=" -

- Uni-uni reversible simple Michaelis-Menten. -

- ")); - end Uur; - - model Uui "Uni-uni irreversible simple Michaelis-Menten" - extends BioChem.Interfaces.Reactions.Uui; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*s1.c/(KmS + s1.c); - annotation(Documentation(info=" -

- Uni-uni irreversible simple Michaelis-Menten. -

- ")); - end Uui; - - model Uuhr "Uni-Uni reversible simple Michaelis-Menten with Haldane adjustment" - extends BioChem.Interfaces.Reactions.Uur; - parameter Real Keq=1 "Equilibrum constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.Concentration KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF/KmS*(s1.c - p1.c/Keq)/(1 + s1.c/KmS + p1.c/KmP); - annotation(Documentation(info=" -

- Uni-Uni reversible simple Michaelis-Menten with Haldane adjustment. -

- ")); - end Uuhr; - - model Isouur "Iso uni-uni" - extends BioChem.Interfaces.Reactions.Uur; - parameter Real Keq=1 "Equilibrum constant"; - parameter Real Kii=1 "Isoinhibition constant"; - parameter BioChem.Units.Concentration KmS=1 "Forward Michaelis-Menten constant"; - parameter BioChem.Units.Concentration KmP=1 "Reverse Michaelis-Menten constant"; - parameter BioChem.Units.ReactionRate vF=1 "Forward maximum velocity"; - equation - rr=vF*(s1.c - p1.c/Keq)/(s1.c*(1 + p1.c/Kii) + KmS*(1 + p1.c/KmP)); - annotation(Documentation(info=" -

- Iso uni-uni. -

- ")); - end Isouur; annotation(Documentation(info="

MichaelisMenten

diff --git a/BioChem/Substances/package.order b/BioChem/Substances/package.order index 22986dc..ec40563 100644 --- a/BioChem/Substances/package.order +++ b/BioChem/Substances/package.order @@ -1,4 +1,4 @@ Substance BoundarySubstance AmbientSubstance -SignalSubstance \ No newline at end of file +SignalSubstance diff --git a/BioChem/UsersGuide/ReleaseNotes.mo b/BioChem/UsersGuide/ReleaseNotes.mo index 0a4e037..b9b7e47 100644 --- a/BioChem/UsersGuide/ReleaseNotes.mo +++ b/BioChem/UsersGuide/ReleaseNotes.mo @@ -3,5 +3,5 @@ within BioChem.UsersGuide; class ReleaseNotes extends Modelica.Icons.ReleaseNotes; annotation( - Documentation(info = "

History

The first version of the library was created by Emma Larsdotter Nilsson at Linköping University. The current version of the library has been further developed by Erik Ulfhielm at Linköping University, and by MathCore Engineering AB.


Versions

")); + Documentation(info = "

History

The first version of the library was created by Emma Larsdotter Nilsson at Linköping University. The current version of the library has been further developed by Erik Ulfhielm at Linköping University, and by MathCore Engineering AB.


Versions

")); end ReleaseNotes; diff --git a/BioChem/package.mo b/BioChem/package.mo index 76bb073..40215cb 100644 --- a/BioChem/package.mo +++ b/BioChem/package.mo @@ -17,7 +17,7 @@ Users Guide discusses some aspects of the BioChem Library, including a "), uses(Modelica(version = "4.0.0")), - version = "1.1.1", + version = "1.1.2", Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Line(origin = {3.55271e-15, 3.76}, points = {{-50, -60}, {-50, -27.52}, {10, -27.52}}, smooth = Smooth.Bezier), Line(origin = {-1.135, 4.09474}, points = {{-48.865, 10}, {-48.865, -27.61}, {11.135, -27.61}}, arrow = {Arrow.None, Arrow.Open}, arrowSize = 30, smooth = Smooth.Bezier), Ellipse(origin = {30.4112, -23.4648}, lineColor = {0, 85, 0}, fillColor = {0, 170, 0}, fillPattern = FillPattern.Sphere, extent = {{-20.4112, -20}, {20.4112, 20}}), Ellipse(origin = {6.28735, -0.665395}, lineColor = {161, 107, 0}, fillColor = {250, 167, 0}, fillPattern = FillPattern.Sphere, extent = {{-76.2873, -79.3346}, {-35.4736, -39.3346}}), Ellipse(origin = {4.98569, -1.03187}, lineColor = {117, 0, 0}, fillColor = {170, 0, 0}, fillPattern = FillPattern.Sphere, extent = {{-75.8122, -6.13331}, {-34.9857, 33.8667}})}), Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}))); end BioChem; diff --git a/README.md b/README.md index 1491d19..f64e3a5 100644 --- a/README.md +++ b/README.md @@ -15,10 +15,12 @@ take place in-between these substances in a diverse number of biochemical pathwa ## Current release -Download [BioChem v1.1.1 for MSL v4.0.0 (2021-05-08)](../../archive/v1.1.1.zip) +Download [BioChem v1.1.2 for MSL v4.0.0 (2021-06-19)](../../archive/v1.1.2.zip) #### Release notes +* [Version v1.1.2 (2021-06-19)](../../archive/v1.1.2.zip) + * Bug removal: several duplication implementations within package.mo and seperate *.mo source files * [Version v1.1.1 (2021-05-08)](../../archive/v1.1.1.zip) * Removing a bug in the Icons package * Minor improvements