CellDesigner_Model.xml

<?xml version="1.0" encoding="UTF-8"?>
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<model metaid="untitled" id="untitled">
<annotation>
<celldesigner:extension>
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</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein id="pr1" name="aS" type="GENERIC"/>
<celldesigner:protein id="pr2" name="M" type="GENERIC"/>
<celldesigner:protein id="pr3" name="P" type="GENERIC"/>
<celldesigner:protein id="pr4" name="aS_in" type="GENERIC"/>
<celldesigner:protein id="pr5" name="M_in" type="GENERIC"/>
<celldesigner:protein id="pr6" name="P_in" type="GENERIC"/>
<celldesigner:protein id="pr8" name="aS_seq" type="GENERIC"/>
<celldesigner:protein id="pr9" name="aS_in_tot" type="GENERIC"/>
<celldesigner:protein id="pr10" name="M_tot" type="GENERIC"/>
<celldesigner:protein id="pr11" name="P_tot" type="GENERIC"/>
<celldesigner:protein id="pr12" name="M_seq" type="GENERIC"/>
<celldesigner:protein id="pr13" name="P_seq" type="GENERIC"/>
<celldesigner:protein id="pr16" name="totmassout" type="GENERIC"/>
<celldesigner:protein id="pr17" name="totmassin" type="GENERIC"/>
<celldesigner:protein id="pr20" name="all_tot_in" type="GENERIC"/>
<celldesigner:protein id="pr21" name="aS_tot" type="GENERIC"/>
<celldesigner:protein id="pr22" name="totaggrmassin" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00044" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00050" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00052" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00084" kind="metre"/>
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</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00085" kind="second"/>
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</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
<annotation>
<celldesigner:extension>
<celldesigner:name>c1</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
<compartment metaid="c2" id="c2" name="c2" size="1" units="volume" outside="default">
<annotation>
<celldesigner:extension>
<celldesigner:name>c2</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="s4" id="s4" name="aS" compartment="c1" initialAmount="5e-005" hasOnlySubstanceUnits="true" charge="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>concentration of synuclein monomers
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s5" id="s5" name="M" compartment="c1" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>Mass concentration of aggregate
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re4"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s6" id="s6" name="P" compartment="c1" initialAmount="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>Molar/molecular concentartion of aggregates (or mass/lenght)
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s1" id="s1" name="aS_in" compartment="c2" initialAmount="5e-005" hasOnlySubstanceUnits="true" charge="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>concentration of synuclein monomers
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s2" id="s2" name="M_in" compartment="c2" initialAmount="0" charge="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>Mass concentration of aggregate
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr5</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re10"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3" id="s3" name="P_in" compartment="c2" initialAmount="0" charge="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>Molar/molecular concentartion of aggregates (or mass/lenght)
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr6</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s7" id="s7" name="aS_seq" compartment="c2" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr8</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s8" id="s8" name="aS_in_tot" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr9</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s9" id="s9" name="M_tot" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr10</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s10" id="s10" name="P_tot" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr11</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s11" id="s11" name="M_seq" compartment="c2" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr12</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s12" id="s12" name="P_seq" compartment="c2" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr13</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s13" id="s13" name="totmassout" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr16</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s14" id="s14" name="totmassin" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr17</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s15" id="s15" name="all_tot_in" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr20</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s16" id="s16" name="aS_tot" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr21</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s17" id="s17" name="totaggrmassin" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr22</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter metaid="Kp_aS" id="Kp_aS" name="Kp_aS" value="10" units="substance"/>
<parameter metaid="Ks_aS" id="Ks_aS" name="Ks_aS" value="1" units="substance" constant="false"/>
<parameter metaid="kin" id="kin" name="kin" value="1" units="substance"/>
<parameter metaid="kout" id="kout" name="kout" value="1" units="substance" constant="false"/>
<parameter metaid="CDMT00087" id="kseq" name="kseq" value="0" units="substance"/>
<parameter metaid="kfree" id="kfree" name="kfree" value="1" units="substance"/>
<parameter metaid="S" id="S" name="S" value="100" units="substance" constant="false"/>
<parameter metaid="kn_mod" id="kn_mod" name="kn_mod" value="1" units="substance"/>
<parameter metaid="kplus_mod" id="kplus_mod" name="kplus_mod" value="1" units="substance"/>
<parameter metaid="koff_mod" id="koff_mod" name="koff_mod" value="1" units="substance"/>
<parameter metaid="k2_mod" id="k2_mod" name="k2_mod" value="1" units="substance"/>
<parameter metaid="kminus_mod" id="kminus_mod" name="kminus_mod" value="1" units="substance"/>
<parameter metaid="kminus_anit_mod" id="kminus_anti_mod" name="kminus_anti_mod" value="1" units="substance"/>
<parameter metaid="CDMT00092" id="kplus" name="kplus" value="500" units="substance"/>
<parameter metaid="CDMT00093" id="kn" name="kn" value="0.1" units="substance"/>
<parameter metaid="CDMT00094" id="koff" name="koff" value="0" units="substance"/>
<parameter metaid="CDMT00095" id="k2" name="k2" value="800" units="substance"/>
<parameter metaid="CDMT00096" id="kminus" name="kminus" value="0" units="substance"/>
<parameter metaid="kn_in" id="kn_in" name="kn_in" value="1" units="substance" constant="false"/>
<parameter metaid="kplus_in" id="kplus_in" name="kplus_in" value="1" units="substance" constant="false"/>
<parameter metaid="koff_in" id="koff_in" name="koff_in" value="1" units="substance" constant="false"/>
<parameter metaid="k2_in" id="k2_in" name="k2_in" value="1" units="substance" constant="false"/>
<parameter metaid="kminus_in" id="kminus_in" name="kminus_in" value="0" units="substance" constant="false"/>
<parameter metaid="Kp_aggr" id="Kp_aggr" name="Kp_aggr" value="1" units="substance"/>
<parameter metaid="kin_aggr" id="kin_aggr" name="kin_aggr" value="0" units="substance"/>
<parameter metaid="kout_aggr" id="kout_aggr" name="kout_aggr" value="1" units="substance" constant="false"/>
<parameter metaid="Ks_aggr" id="Ks_aggr" name="Ks_aggr" value="1" units="substance" constant="false"/>
<parameter metaid="kseq_aggr" id="kseq_aggr" name="kseq_aggr" value="0" units="substance"/>
<parameter metaid="kfree_aggr" id="kfree_aggr" name="kfree_aggr" value="1" units="substance"/>
<parameter metaid="n1" id="n1" name="n1" value="2" units="substance"/>
<parameter metaid="n2" id="n2" name="n2" value="2" units="substance"/>
<parameter metaid="nmin" id="nmin" name="nmin" value="2" units="substance"/>
<parameter metaid="phi" id="phi" name="phi" value="0.01" units="substance"/>
</listOfParameters>
<listOfRules>
<assignmentRule metaid="CDMT00086" variable="kout">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<divide/>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> Ks_aS </ci>
</apply>
<ci> Kp_aS </ci>
</apply>
<ci> kin </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00088" variable="Ks_aS">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> kseq </ci>
<ci> kfree </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00089" variable="s8">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> s1 </ci>
<ci> s7 </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00090" variable="s9">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<ci> S </ci>
<apply>
<plus/>
<ci> S </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<ci> s5 </ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<cn type="integer"> 1 </cn>
<apply>
<plus/>
<ci> S </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<plus/>
<ci> s2 </ci>
<ci> s11 </ci>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00091" variable="s10">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<ci> S </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> S </ci>
</apply>
</apply>
<ci> s6 </ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<cn type="integer"> 1 </cn>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> S </ci>
</apply>
</apply>
<apply>
<plus/>
<ci> s3 </ci>
<ci> s12 </ci>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00098" variable="kn_in">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kn </ci>
<ci> kn_mod </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00099" variable="kplus_in">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kplus </ci>
<ci> kplus_mod </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00100" variable="koff_in">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> koff </ci>
<ci> koff_mod </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00101" variable="k2_in">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k2 </ci>
<ci> k2_mod </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00102" variable="kminus_in">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kminus </ci>
<ci> kminus_mod </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00104" variable="kout_aggr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<divide/>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> Ks_aggr </ci>
</apply>
<ci> Kp_aggr </ci>
</apply>
<ci> kin_aggr </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00117" variable="Ks_aggr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> kseq_aggr </ci>
<ci> kfree_aggr </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00097" variable="s13">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> s4 </ci>
<ci> s5 </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00103" variable="s14">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<divide/>
<cn type="integer"> 1 </cn>
<ci> S </ci>
</apply>
<apply>
<plus/>
<ci> s1 </ci>
<ci> s7 </ci>
<ci> s2 </ci>
<ci> s11 </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00118" variable="s16">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<ci> S </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> S </ci>
</apply>
</apply>
<ci> s4 </ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<cn type="integer"> 1 </cn>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<ci> S </ci>
</apply>
</apply>
<apply>
<plus/>
<ci> s1 </ci>
<ci> s7 </ci>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00119" variable="s15">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> s1 </ci>
<ci> s7 </ci>
<ci> s2 </ci>
<ci> s11 </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00120" variable="s17">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<divide/>
<cn type="integer"> 1 </cn>
<ci> S </ci>
</apply>
<apply>
<plus/>
<ci> s2 </ci>
<ci> s11 </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule metaid="CDMT00121" variable="S">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<minus/>
<cn type="integer"> 1 </cn>
<ci> phi </ci>
</apply>
<ci> phi </ci>
</apply>
</math>
</assignmentRule>
</listOfRules>
<listOfReactions>
<reaction metaid="re1" id="re1" name="Primary nucleation out" reversible="false" fast="false">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>primary nucleation
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:name>Primary nucleation out</celldesigner:name>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s4" alias="sa1">
<celldesigner:linkAnchor position="ESE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s6" alias="sa3">
<celldesigner:linkAnchor position="WNW"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:listOfProductLinks>
<celldesigner:productLink product="s5" alias="sa2" targetLineIndex="-1,1">
<celldesigner:linkAnchor position="SSW"/>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
</celldesigner:productLink>
</celldesigner:listOfProductLinks>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00066" species="s4">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> n1 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00002" species="s6">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa3</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference metaid="CDMT00067" species="s5">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
<stoichiometryMath>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> n1 </ci>
</math>
</stoichiometryMath>
</speciesReference>
</listOfProducts>
<kineticLaw metaid="CDMT00004">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<power/>
<ci> s4 </ci>
<ci> n1 </ci>
</apply>
<ci> kn </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="re2" id="re2" name="Elongation out" reversible="false" fast="false">
<annotation>
<celldesigner:extension>
<celldesigner:name>Elongation out</celldesigner:name>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s4" alias="sa1">
<celldesigner:linkAnchor position="S"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s6" alias="sa3">
<celldesigner:linkAnchor position="SSE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:listOfReactantLinks>
<celldesigner:reactantLink reactant="s6" alias="sa3" targetLineIndex="-1,0">
<celldesigner:linkAnchor position="SW"/>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
</celldesigner:reactantLink>
</celldesigner:listOfReactantLinks>
<celldesigner:listOfProductLinks>
<celldesigner:productLink product="s5" alias="sa2" targetLineIndex="-1,1">
<celldesigner:linkAnchor position="SSE"/>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
<celldesigner:lineDirection index="2" value="unknown"/>
<celldesigner:lineDirection index="3" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>-0.027954136264574325,0.2554723775229828 0.5747180896427491,1.2561356960106167 1.108405192836154,0.9347105088600487</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
</celldesigner:productLink>
</celldesigner:listOfProductLinks>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="1">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
<celldesigner:lineDirection index="1" value="unknown"/>
<celldesigner:lineDirection index="2" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:editPoints>0.12455516014234869,0.39857651245551595 0.9786476868327398,0.13167259786476893</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
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</math>
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</math>
</stoichiometryMath>
</speciesReference>
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<kineticLaw metaid="CDMT00065">
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<apply>
<times/>
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<ci> kin_aggr </ci>
</apply>
</math>
</kineticLaw>
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<stoichiometryMath>
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</math>
</stoichiometryMath>
</speciesReference>
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<kineticLaw metaid="CDMT00078">
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<apply>
<times/>
<ci> s3 </ci>
<ci> kout_aggr </ci>
</apply>
</math>
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</annotation>
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<kineticLaw metaid="CDMT00030">
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<celldesigner:extension>
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</annotation>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> s1 </ci>
<ci> kseq </ci>
</apply>
</math>
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</reaction>
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</annotation>
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<speciesReference metaid="CDMT00035" species="s1">
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<celldesigner:alias>sa4</celldesigner:alias>
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</annotation>
</speciesReference>
</listOfProducts>
<kineticLaw metaid="CDMT00037">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> s7 </ci>
<ci> kfree </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="re27" id="re27" reversible="false" fast="false">
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<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
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<kineticLaw metaid="CDMT00113">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> s3 </ci>
<ci> kseq_aggr </ci>
</apply>
</math>
</kineticLaw>
</reaction>
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</speciesReference>
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<kineticLaw metaid="CDMT00114">
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<apply>
<times/>
<ci> s12 </ci>
<ci> kfree_aggr </ci>
</apply>
</math>
</kineticLaw>
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<reaction metaid="re29" id="re29" reversible="false" fast="false">
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<celldesigner:alias>sa11</celldesigner:alias>
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<kineticLaw metaid="CDMT00115">
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<apply>
<times/>
<ci> s2 </ci>
<ci> kseq_aggr </ci>
</apply>
</math>
</kineticLaw>
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<celldesigner:alias>sa6</celldesigner:alias>
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</speciesReference>
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<kineticLaw metaid="CDMT00116">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> s11 </ci>
<ci> kfree_aggr </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>