<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model id="ReceptorDynamics" areaUnits="microMetreSquared"
name="PlazaSur Receptor Dynamics" metaid="_ReceptorDynamics"
timeUnits="minute" lengthUnits="microMetre" substanceUnits="item"
volumeUnits="microMetreCubed">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<center>
<h2>PlazaSur Receptor Dynamics
</h2>
</center>
<p>SBML implementation of the dynamical equation used in PlazaSur.
<br/>
Notes on this implementation:
<ol>
<li>Assumes that the cell surface area is constant.
</li>
<li>The ligand concentration (l) is a constant parameter,
althought is spatially distributed in the simulations.
</li>
<li>The unbound receptor (u) reaches a steady-state value of 52.4.
</li>
</ol>
For further documentation see: http://www.duke.edu/~ccc14/msi-docs/index.html
<br/>
</p>
</body>
</notes>
<listOfUnitDefinitions>
<unitDefinition id="minute">
<listOfUnits>
<unit scale="0" exponent="1" multiplier="60" kind="second"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="microMetre">
<listOfUnits>
<unit scale="-6" exponent="1" multiplier="1" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="microMetreSquared">
<listOfUnits>
<unit scale="-6" exponent="2" multiplier="1" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="microMetreCubed">
<listOfUnits>
<unit scale="-6" exponent="3" multiplier="1" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="perMinute" name="per minute">
<listOfUnits>
<unit scale="0" exponent="-1" multiplier="60" kind="second"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="numPerMicroMetreCubed"
name="number per micrometre cubed">
<listOfUnits>
<unit scale="0" exponent="1" multiplier="1" kind="item"/>
<unit scale="-6" exponent="-3" multiplier="1" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="microMetreCubedPerNum"
name="micrometre cubed per number">
<listOfUnits>
<unit scale="0" exponent="-1" multiplier="1" kind="item"/>
<unit scale="-6" exponent="3" multiplier="1" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="numPerMicroMetreSquaredPerMinute"
name="number per micrometre squared per minute">
<listOfUnits>
<unit scale="0" exponent="1" multiplier="1" kind="item"/>
<unit scale="-6" exponent="-2" multiplier="1" kind="metre"/>
<unit scale="0" exponent="-1" multiplier="60" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="cellSurface" constant="true" spatialDimensions="2"
units="microMetreSquared" size="314">
<notes>
<p xmlns="http://www.w3.org/1999/xhtml">
The surface area of a 10 micrometer diameter sphere.
</p>
</notes>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species id="u" initialConcentration="100" constant="false"
hasOnlySubstanceUnits="false" name="unbound receptor"
boundaryCondition="false" compartment="cellSurface"/>
</listOfSpecies>
<listOfParameters>
<parameter id="a" constant="true" name="gene activity level"
value="1" units="dimensionless"/>
<parameter id="kappa" constant="true" name="affinity"
value="0.1" units="microMetreCubedPerNum"/>
<parameter id="p" constant="true" name="synthesis rate"
value="0.1" sboTerm="SBO:0000046"
units="numPerMicroMetreSquaredPerMinute"/>
<parameter id="tau" constant="true"
name="internalization rate" value="0.01"
units="perMinute"/>
<parameter id="delta" constant="true" name="degradation rate"
value="0.001" sboTerm="SBO:0000356" units="perMinute"/>
<parameter id="l" constant="true" name="ligand"
value="1" units="numPerMicroMetreCubed"/>
</listOfParameters>
<listOfReactions>
<reaction id="synthesis" name="synthesis" reversible="false"
fast="false" compartment="cellSurface">
<listOfProducts>
<speciesReference constant="false" species="u"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> cellSurface
</ci>
<apply>
<times/>
<ci> p
</ci>
<ci> a
</ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="binding" name="binding and internalization"
reversible="false" fast="false"
compartment="cellSurface">
<listOfReactants>
<speciesReference constant="false" species="u"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<apply>
<times/>
<apply>
<times/>
<apply>
<times/>
<ci> cellSurface
</ci>
<ci> u
</ci>
</apply>
<ci> tau
</ci>
</apply>
<ci> kappa
</ci>
</apply>
<ci> l
</ci>
</apply>
<apply>
<plus/>
<cn type="integer"> 1
</cn>
<apply>
<times/>
<ci> kappa
</ci>
<ci> l
</ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="degradation" name="degradation"
reversible="false" fast="false"
compartment="cellSurface">
<listOfReactants>
<speciesReference constant="false" species="u"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<times/>
<ci> delta
</ci>
<ci> u
</ci>
</apply>
<ci> cellSurface
</ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>