The Full Beta-Carotene Model Exported from the MATLAB SimBiology Toolbox
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<annotation>
Created by The MathWorks, Inc. SimBiology tool, Version 3.4
</annotation>
<model id="mw5f251816_961b_4a15_9358_e2d679cb13ae" name="Beta-Carotene Pathway">
<listOfUnitDefinitions>
<unitDefinition id="MWDERIVEDUNIT_micrometer___3" name="micrometer^3">
<listOfUnits>
<unit kind="metre" exponent="3" multiplier="1" offset="0"/>
<unit kind="dimensionless" multiplier="1e-018" offset="0"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="MWDERIVEDUNIT_molecule__second" name="molecule/second">
<listOfUnits>
<unit kind="mole" multiplier="1" offset="0"/>
<unit kind="second" exponent="-1" multiplier="1" offset="0"/>
<unit kind="dimensionless" multiplier="1.66053872801495e-024" offset="0"/>
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<unitDefinition id="MWBUILTINPREFIX_milli_MWBUILTINUNIT_molarity" name="millimolarity">
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<unit kind="mole" multiplier="1" offset="0"/>
<unit kind="dimensionless" multiplier="1" offset="0"/>
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</unitDefinition>
<unitDefinition id="MWDERIVEDUNIT_1__second" name="1/second">
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<unit kind="second" exponent="-1" multiplier="1" offset="0"/>
<unit kind="dimensionless" multiplier="1" offset="0"/>
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<listOfCompartments>
<compartment id="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f" name="c" size="37"
units="MWDERIVEDUNIT_micrometer___3">
<annotation>Tyson CB, Lord PG, Wheals AE. Dependency of size of Saccharomyces cerevisiae
cells on growth rate. J Bacteriol. 1979 Apr138(1):92-8.</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species id="s_id0" name="farnesyl_PP" compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f"
initialConcentration="0" substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id1" name="GGPP_synth_endo"
compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f"
initialConcentration="1" substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id2" name="GGPP" compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f"
initialConcentration="0"
substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id3" name="GGPP_synth_exo"
compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f" initialConcentration="1"
substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id4" name="phytoene_synth_lycopene_cyc"
compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f" initialConcentration="1"
substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id5" name="phytoene"
compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f" initialConcentration="0"
substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id6" name="carotene_desat" compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f"
initialConcentration="1" substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id7" name="neurosporene" compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f"
initialConcentration="0" substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id8" name="lycopene" compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f"
initialConcentration="0" substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id9" name="hh_beta_carotene"
compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f" initialConcentration="0"
substanceUnits="mole" spatialSizeUnits="liter"/>
<species id="s_id10" name="beta_carotene" compartment="mw7040b0a4_f6d2_40f6_a3b4_d3ab5f710c4f"
initialConcentration="0" substanceUnits="mole" spatialSizeUnits="liter"/>
</listOfSpecies>
<listOfParameters>
<parameter id="mw3f0a1710_3497_424d_b3b8_2d41bf751c7f" name="influx" value="1000"
units="MWDERIVEDUNIT_molecule__second">
<notes>
The rate that the initial substrate, farnesyl diphosphate, enters the system from the
cell's metabolic process.
</notes>
</parameter>
</listOfParameters>
<listOfReactions>
<reaction id="r_id11" name="GGPP_synth_endo" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="s_id0"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s_id2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> mw003af2f8_aefd_4cca_87f1_9caac7e93ee2 </ci>
<ci> s_id1 </ci>
<ci> s_id0 </ci>
</apply>
<apply>
<plus/>
<ci> mwe59e57aa_b4b6_4a5a_8e10_eae9d0adcdc8 </ci>
<ci> s_id0 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="mwe59e57aa_b4b6_4a5a_8e10_eae9d0adcdc8" name="Km" value="0.0032"
units="MWBUILTINPREFIX_milli_MWBUILTINUNIT_molarity"/>
<parameter id="mw003af2f8_aefd_4cca_87f1_9caac7e93ee2" name="Kcat" value="0.025"
units="MWDERIVEDUNIT_1__second"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="r_id12" name="GGPP_synth_exo" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="s_id0"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s_id2"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> mw541d6b0c_24f7_4cfe_bb28_33fe2edb1773 </ci>
<ci> s_id3 </ci>
<ci> s_id0 </ci>
</apply>
<apply>
<plus/>
<ci> mwdb3455d4_49c2_469f_af55_87f988c0410f </ci>
<ci> s_id0 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="mwdb3455d4_49c2_469f_af55_87f988c0410f" name="Km" value="0.0032"
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<parameter id="mw541d6b0c_24f7_4cfe_bb28_33fe2edb1773" name="Kcat" value="0.125"
units="MWDERIVEDUNIT_1__second"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="r_id13" name="phytoene_synth" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="s_id2" stoichiometry="2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s_id5"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> mw1e366017_a545_441c_af60_721e86f054b8 </ci>
<ci> s_id4 </ci>
<ci> s_id2 </ci>
</apply>
<apply>
<plus/>
<ci> mw33a0beab_bb7e_4248_a96d_a48681d10258 </ci>
<ci> s_id2 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="mw33a0beab_bb7e_4248_a96d_a48681d10258" name="Km" value="0.003"
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<parameter id="mw1e366017_a545_441c_af60_721e86f054b8" name="Kcat" value="0.0526"
units="MWDERIVEDUNIT_1__second"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="r_id14" name="carotene_desat_1" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="s_id5"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s_id7"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> mw77731028_4b26_4d97_8342_5301dca3fcce </ci>
<ci> s_id6 </ci>
<ci> s_id5 </ci>
</apply>
<apply>
<plus/>
<ci> mw30d620f2_c8c4_4fd9_ba36_8e1463321d14 </ci>
<ci> s_id5 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="mw30d620f2_c8c4_4fd9_ba36_8e1463321d14" name="Km" value="0.0084"
units="MWBUILTINPREFIX_milli_MWBUILTINUNIT_molarity"/>
<parameter id="mw77731028_4b26_4d97_8342_5301dca3fcce" name="Kcat" value="11.9665"
units="MWDERIVEDUNIT_1__second"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="r_id15" name="carotene_desat_2" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="s_id7"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s_id8"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> mwb6aad4a4_b43d_4b80_b510_b6764f3a39fe </ci>
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<parameter id="mwcbc0263c_f9cc_48b9_b259_1e9163d1d7eb" name="Km" value="0.009"
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</reaction>
<reaction id="r_id16" name="neurosporene_cyc" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="s_id7"/>
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<listOfProducts>
<speciesReference species="s_id9"/>
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<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
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<ci> mw79b04e99_541a_4226_ace9_e51670a4b391 </ci>
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<ci> mw9807c1ba_754a_4354_b534_a3b08ae46ae5 </ci>
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</reaction>
<reaction id="r_id17" name="lycopene_cyc" reversible="false" fast="false">
<listOfReactants>
<speciesReference species="s_id8"/>
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<listOfProducts>
<speciesReference species="s_id10"/>
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<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> mw768530de_187e_4d3d_9f5f_7e44a709c8c8 </ci>
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<ci> mwe5f70a46_a0c6_4519_91ce_2f483e829edd </ci>
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<listOfParameters>
<parameter id="mwe5f70a46_a0c6_4519_91ce_2f483e829edd" name="Km" value="0.0018"
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<parameter id="mw768530de_187e_4d3d_9f5f_7e44a709c8c8" name="Kcat" value="0.00038623"
units="MWDERIVEDUNIT_1__second"/>
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</reaction>
<reaction id="mw1250a319_faa6_40be_934c_eaec51d62ada" name="initial_substrate_creation"
reversible="false" fast="false">
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