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new Chemical.Example.AlbuminTitration = Figge-Fencl model of albumin …
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…equilibrium with hydrogen ions [H+]
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@MarekMatejak
MarekMatejak committed May 25, 2014
1 parent 59b8f0f commit 0faff22
Showing 1 changed file with 126 additions and 5 deletions.
131 changes: 126 additions & 5 deletions Physiolibrary/Chemical.mo
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Expand Up @@ -807,7 +807,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
annotation (Placement(transformation(extent={{-32,-76},{-52,-56}})));
Components.Speciation
T0_in_T(NumberOfSubunitTypes=4)
annotation (Placement(transformation(extent={{68,-76},{48,-56}})));
annotation (Placement(transformation(extent={{68,-74},{48,-54}})));
Physiolibrary.Chemical.Components.Substance OxyRHm[4](
each Simulation=SimulationType.SteadyState,
each isDependent=true,
Expand Down Expand Up @@ -887,7 +887,7 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
smooth=Smooth.None));
connect(quaternaryForm.products[1], T0_in_T.species)
annotation (Line(
points={{16,-74},{48,-74}},
points={{16,-74},{32,-74},{32,-72},{48,-72}},
color={107,45,134},
thickness=1,
smooth=Smooth.None));
Expand Down Expand Up @@ -997,21 +997,21 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
smooth=Smooth.None));
connect(T0_in_T.subunitSpecies, DeoxyTHm.q_out)
annotation (Line(
points={{58,-56},{84,-56},{84,-26},{80,-26}},
points={{58,-54},{84,-54},{84,-26},{80,-26}},
color={107,45,134},
thickness=1,
smooth=Smooth.None));
connect(add1.y, T0_in_T.totalSubunitAmount)
annotation (Line(
points={{44,-58.4},{44,-66},{50,-66}},
points={{44,-58.4},{44,-64},{50,-64}},
color={0,0,127},
smooth=Smooth.Bezier));
connect(R0_in_R.totalSubsystemAmount, totalHb.fragment[1]) annotation (Line(
points={{-42,-74},{-42,-87},{70,-87}},
color={0,0,127},
smooth=Smooth.Bezier));
connect(T0_in_T.totalSubsystemAmount, totalHb.fragment[2]) annotation (Line(
points={{58,-74},{58,-74},{58,-85},{70,-85}},
points={{58,-72},{58,-72},{58,-85},{70,-85}},
color={0,0,127},
smooth=Smooth.Bezier));
connect(OxyRHm.solute, sum1.u[1:4]) annotation (Line(
Expand Down Expand Up @@ -1062,6 +1062,126 @@ package Chemical "Domain with Molar Concentration and Molar Flow"
end Allosteric_Hemoglobin2_MWC;

end Hemoglobin;

model AlbuminTitration "Figge-Fencl model (22. Dec. 2007)"
extends Modelica.Icons.Example;

parameter Integer n=218 "Number of weak acid group in albumin molecule";
parameter Real pKAs[n]=cat(1,{8.5},fill(4.0,98),fill(11.7,18),fill(12.5,24),fill(5.8,2),fill(6.0,2),{7.6,7.8,7.8,8,8},fill(10.3,50),{7.19,7.29,7.17,7.56,7.08,7.38,6.82,6.43,4.92,5.83,6.24,6.8,5.89,5.2,6.8,5.5,8,3.1})
"acid dissociation constants";

Physiolibrary.Chemical.Components.Substance A[n](
each Simulation=Physiolibrary.Types.SimulationType.SteadyState,
each solute_start=0.0005) "deprotonated acid groups"
annotation (Placement(transformation(extent={{4,-16},{24,4}})));
Physiolibrary.Chemical.Components.ChemicalReaction react[n](
each nP=2,
K=fill(10.0, n) .^ (-pKAs .+ 3))
annotation (Placement(transformation(extent={{-44,-2},{-24,18}})));
Physiolibrary.Chemical.Sources.UnlimitedSolutionStorage H(
q_out(conc(nominal=10^(-7.4 + 3))),
Conc=10^(-7.4 + 3),
Simulation=Physiolibrary.Types.SimulationType.SteadyState,
isIsolatedInSteadyState=false,
useConcentrationInput=true) "hydrogen ions activity" annotation (Placement(
transformation(
extent={{-10,-10},{10,10}},
rotation=180,
origin={14,22})));
Physiolibrary.Chemical.Components.Substance HA[n](
each Simulation=Physiolibrary.Types.SimulationType.SteadyState,
each isDependent=true,
each solute_start=0.0005) "protonated acid groups"
annotation (Placement(transformation(extent={{-76,-2},{-56,18}})));
Physiolibrary.SteadyStates.Components.MolarConservationLaw
molarConservationLaw[n](
each n=2,
each Simulation=Physiolibrary.Types.SimulationType.SteadyState,
each Total=0.001)
annotation (Placement(transformation(extent={{36,-28},{56,-8}})));
Modelica.Blocks.Math.Sum HAsum(nin=n) "total amount of protonated groups"
annotation (Placement(transformation(extent={{-54,-80},{-34,-60}})));
Physiolibrary.Blocks.Math.Exponentiation pow
annotation (Placement(transformation(extent={{26,82},{34,90}})));
Modelica.Blocks.Math.Gain gain(k=-1)
annotation (Placement(transformation(extent={{-44,74},{-24,94}})));
Physiolibrary.Blocks.Math.Add add(k=3)
annotation (Placement(transformation(extent={{-10,74},{10,94}})));
Modelica.Blocks.Sources.Clock pH(offset=5) "source of pH"
annotation (Placement(transformation(extent={{-84,74},{-64,94}})));
Modelica.Blocks.Math.Division division "protonated groups per molecule"
annotation (Placement(transformation(extent={{-20,-88},{0,-68}})));
Physiolibrary.Blocks.Math.Add charge(k=-118) "charge of albumin molecule"
annotation (Placement(transformation(extent={{10,-88},{30,-68}})));
equation
connect(react.products[1], A.q_out) annotation (Line(
points={{-24,7.5},{-12,7.5},{-12,-6},{14,-6}},
color={107,45,134},
thickness=1,
smooth=Smooth.None));
for i in 1:n loop
connect(react[i].products[2], H.q_out) annotation (Line(
points={{-24,8.5},{-14,8.5},{-14,22},{4,22}},
color={107,45,134},
thickness=1,
smooth=Smooth.None));
end for;
connect(HA.q_out, react.substrates[1]) annotation (Line(
points={{-66,8},{-44,8}},
color={107,45,134},
thickness=1,
smooth=Smooth.None));
connect(A.solute, molarConservationLaw.fragment[1]) annotation (Line(
points={{14,-16},{14,-22},{36,-22},{36,-23}},
color={0,0,127},
smooth=Smooth.None));
connect(HA.solute, molarConservationLaw.fragment[2]) annotation (Line(
points={{-66,-2},{-66,-24},{36,-24},{36,-21}},
color={0,0,127},
smooth=Smooth.None));
connect(HA.solute, HAsum.u) annotation (Line(
points={{-66,-2},{-66,-70},{-56,-70}},
color={0,0,127},
smooth=Smooth.None));
connect(pow.y, H.concentration) annotation (Line(
points={{34.4,86},{44,86},{44,22},{24,22}},
color={0,0,127},
smooth=Smooth.None));
connect(gain.y, add.u) annotation (Line(
points={{-23,84},{-12,84}},
color={0,0,127},
smooth=Smooth.None));
connect(add.y, pow.exponent) annotation (Line(
points={{11,84},{26,84},{26,83.6}},
color={0,0,127},
smooth=Smooth.None));
connect(pH.y, gain.u) annotation (Line(
points={{-63,84},{-46,84}},
color={0,0,127},
smooth=Smooth.None));
connect(HAsum.y, division.u1) annotation (Line(
points={{-33,-70},{-28,-70},{-28,-72},{-22,-72}},
color={0,0,127},
smooth=Smooth.None));
connect(molarConservationLaw[1].totalAmountOfSubstance, division.u2)
annotation (Line(
points={{56,-22},{78,-22},{78,-94},{-24,-94},{-24,-84},{-22,-84}},
color={0,0,127},
smooth=Smooth.None));
connect(division.y, charge.u) annotation (Line(
points={{1,-78},{8,-78}},
color={0,0,127},
smooth=Smooth.None));
annotation ( Diagram(coordinateSystem(
preserveAspectRatio=false, extent={{-100,-100},{100,100}},
experiment(StopTime=4)), graphics), Documentation(revisions="<html>
<p><i>2014</i></p>
<p>Marek Matejak, Charles University, Prague, Czech Republic </p>
</html>", info="<html>
<p>Data and model is described in</p>
<p><font style=\"color: #222222; \">Jame Figge: Role of non-volatile weak acids (albumin, phosphate and citrate). In: Stewart&apos;s Textbook of Acid-Base, 2nd Edition, John A. Kellum, Paul WG Elbers editors, &nbsp;AcidBase org, 2009, pp. 216-232.</font></p>
</html>"));
end AlbuminTitration;
end Examples;

package Components
Expand Down Expand Up @@ -1647,6 +1767,7 @@ It works in two modes:
annotation (Placement(
transformation(extent={{-10,90},{10,110}})));

protected
parameter Real numberOfSubunit[NumberOfSubunitTypes] = ones(NumberOfSubunitTypes)
"Number of identical subunits instances in macromolecule. First should be non-zero.";

Expand Down

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