- Author:
- AnandR <a.rampadarath@auckland.ac.nz>
- Date:
- 2019-04-05 14:25:01+13:00
- Desc:
- Added some semgen annotated models (AnandR)
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/584/rawfile/ade7933153a72bb89e0b02d75db92d6e4be285f5/semgen_annotated_models/Terkildsen_NaK_kinetic_Fig3b.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="Terkildsen_NaK_kinetic_Fig3b" cmeta:id="metaid0">
<units name="mM">
<unit prefix="milli" units="mole" />
</units>
<units name="per_second_per_mM">
<unit exponent="-1.0" units="second" />
<unit exponent="-1.0" units="mM" />
</units>
<units name="C_per_mol">
<unit exponent="-1.0" units="mole" />
<unit units="coulomb" />
</units>
<units name="mV">
<unit prefix="milli" units="volt" />
</units>
<units name="per_second">
<unit exponent="-1.0" units="second" />
</units>
<units name="mJ_per_K_per_mol">
<unit prefix="milli" units="joule" />
<unit exponent="-1.0" units="kelvin" />
<unit exponent="-1.0" units="mole" />
</units>
<units name="mV_per_sec">
<unit units="mV" />
<unit exponent="-1.0" units="second" />
</units>
<units name="per_second3">
<unit exponent="-3.0" units="second" />
</units>
<units name="per_second_per_mM2">
<unit exponent="-2.0" units="mM" />
<unit exponent="-1.0" units="second" />
</units>
<component name="environment">
<variable cmeta:id="environment.t" initial_value="0" name="t" units="second" />
<variable cmeta:id="environment.R" initial_value="8314" name="R" units="mJ_per_K_per_mol" />
<variable cmeta:id="environment.T" initial_value="310" name="T" units="kelvin" />
<variable cmeta:id="environment.F" initial_value="96485" name="F" units="C_per_mol" />
<variable cmeta:id="environment.K0d_nak_nai" initial_value="579.7295" name="K0d_nak_nai" units="mM" />
<variable cmeta:id="environment.K0d_nak_nae" initial_value="0.0349" name="K0d_nak_nae" units="mM" />
<variable cmeta:id="environment.Kd_nak_nai2" initial_value="5.6399" name="Kd_nak_nai2" units="mM" />
<variable cmeta:id="environment.Kd_nak_nae2" initial_value="1.0617e4" name="Kd_nak_nae2" units="mM" />
<variable cmeta:id="environment.Kd_nak_ke" initial_value="1.0817" name="Kd_nak_ke" units="mM" />
<variable cmeta:id="environment.Kd_nak_ki" initial_value="1.6795e4" name="Kd_nak_ki" units="mM" />
<variable cmeta:id="environment.Kd_nak_MgATP" initial_value="140.3709" name="Kd_nak_MgATP" units="mM" />
<variable cmeta:id="environment.rate_f_nak_1" initial_value="1.4232e3" name="rate_f_nak_1" units="per_second" />
<variable cmeta:id="environment.rate_f_nak_2" initial_value="1.1565e4" name="rate_f_nak_2" units="per_second" />
<variable cmeta:id="environment.rate_f_nak_3" initial_value="194.4506" name="rate_f_nak_3" units="per_second" />
<variable cmeta:id="environment.rate_f_nak_4" initial_value="3.0630e4" name="rate_f_nak_4" units="per_second" />
<variable cmeta:id="environment.rate_r_nak_1" initial_value="225.9048" name="rate_r_nak_1" units="per_second_per_mM" />
<variable cmeta:id="environment.rate_r_nak_2" initial_value="3.6355e4" name="rate_r_nak_2" units="per_second" />
<variable cmeta:id="environment.rate_r_nak_3" initial_value="2.8104e5" name="rate_r_nak_3" units="per_second_per_mM2" />
<variable cmeta:id="environment.rate_r_nak_4" initial_value="1.5740e6" name="rate_r_nak_4" units="per_second" />
<variable cmeta:id="environment.factor_nak_del" initial_value="-0.0550" name="factor_nak_del" units="dimensionless" />
<variable cmeta:id="environment.pKd_nak_hpi" initial_value="6.7700" name="pKd_nak_hpi" units="dimensionless" />
<variable cmeta:id="environment.Kd_nak_kpi" initial_value="292" name="Kd_nak_kpi" units="mM" />
<variable cmeta:id="environment.Kd_nak_napi" initial_value="224" name="Kd_nak_napi" units="mM" />
<variable cmeta:id="environment.Vm" initial_value="0" name="Vm" units="mV" />
<variable cmeta:id="environment.Ki" initial_value="140" name="Ki" units="mM" />
<variable cmeta:id="environment.Ke" initial_value="0" name="Ke" units="mM" />
<variable cmeta:id="environment.Nai" initial_value="50" name="Nai" units="mM" />
<variable cmeta:id="environment.Nae" initial_value="150" name="Nae" units="mM" />
<variable cmeta:id="environment.MgATP" initial_value="10" name="MgATP" units="mM" />
<variable cmeta:id="environment.MgADP" initial_value="0.02" name="MgADP" units="mM" />
<variable cmeta:id="environment.Pi_total" initial_value="0.5" name="Pi_total" units="mM" />
<variable cmeta:id="environment.H" initial_value="3.9812e-5" name="H" units="mM" />
<variable cmeta:id="environment.Pi" name="Pi" units="mM" />
<variable cmeta:id="environment.Kd_nak_nae1" name="Kd_nak_nae1" units="mM" />
<variable cmeta:id="environment.Kd_nak_nai1" name="Kd_nak_nai1" units="mM" />
<variable cmeta:id="environment.Nae_bound1" name="Nae_bound1" units="dimensionless" />
<variable cmeta:id="environment.Nai_bound1" name="Nai_bound1" units="dimensionless" />
<variable cmeta:id="environment.Nae_bound2" name="Nae_bound2" units="dimensionless" />
<variable cmeta:id="environment.Nai_bound2" name="Nai_bound2" units="dimensionless" />
<variable cmeta:id="environment.Ke_bound" name="Ke_bound" units="dimensionless" />
<variable cmeta:id="environment.Ki_bound" name="Ki_bound" units="dimensionless" />
<variable cmeta:id="environment.MgATP_bound" name="MgATP_bound" units="dimensionless" />
<variable cmeta:id="environment.alpha_f_nak_1" name="alpha_f_nak_1" units="per_second" />
<variable cmeta:id="environment.alpha_f_nak_2" name="alpha_f_nak_2" units="per_second" />
<variable cmeta:id="environment.alpha_f_nak_3" name="alpha_f_nak_3" units="per_second" />
<variable cmeta:id="environment.alpha_f_nak_4" name="alpha_f_nak_4" units="per_second" />
<variable cmeta:id="environment.alpha_r_nak_1" name="alpha_r_nak_1" units="per_second" />
<variable cmeta:id="environment.alpha_r_nak_2" name="alpha_r_nak_2" units="per_second" />
<variable cmeta:id="environment.alpha_r_nak_3" name="alpha_r_nak_3" units="per_second" />
<variable cmeta:id="environment.alpha_r_nak_4" name="alpha_r_nak_4" units="per_second" />
<variable cmeta:id="environment.sig_nak" name="sig_nak" units="per_second3" />
<variable cmeta:id="environment.v_cyc_nak" name="v_cyc_nak" units="per_second" />
<variable cmeta:id="environment.v_cyc_nak_normalised" name="v_cyc_nak_normalised" units="dimensionless" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>Pi</ci>
<apply>
<divide />
<ci>Pi_total</ci>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1</cn>
<apply>
<divide />
<ci>Ki</ci>
<ci>Kd_nak_kpi</ci>
</apply>
<apply>
<divide />
<ci>H</ci>
<apply>
<power />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">10</cn>
<apply>
<minus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">3.0</cn>
<ci>pKd_nak_hpi</ci>
</apply>
</apply>
</apply>
<apply>
<divide />
<ci>Nai</ci>
<ci>Kd_nak_napi</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<apply>
<diff />
<bvar>
<ci>t</ci>
</bvar>
<ci>Ke</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="mM_per_sec">1</cn>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>Kd_nak_nae1</ci>
<apply>
<times />
<ci>K0d_nak_nae</ci>
<apply>
<exp />
<apply>
<divide />
<apply>
<times />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>factor_nak_del</ci>
</apply>
<ci>F</ci>
<ci>Vm</ci>
</apply>
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>Kd_nak_nai1</ci>
<apply>
<times />
<ci>K0d_nak_nai</ci>
<apply>
<exp />
<apply>
<divide />
<apply>
<times />
<ci>factor_nak_del</ci>
<ci>F</ci>
<ci>Vm</ci>
</apply>
<apply>
<times />
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>Nae_bound1</ci>
<apply>
<divide />
<ci>Nae</ci>
<ci>Kd_nak_nae1</ci>
</apply>
</apply>
<apply>
<eq />
<ci>Nai_bound1</ci>
<apply>
<divide />
<ci>Nai</ci>
<ci>Kd_nak_nai1</ci>
</apply>
</apply>
<apply>
<eq />
<ci>Nae_bound2</ci>
<apply>
<divide />
<ci>Nae</ci>
<ci>Kd_nak_nae2</ci>
</apply>
</apply>
<apply>
<eq />
<ci>Nai_bound2</ci>
<apply>
<divide />
<ci>Nai</ci>
<ci>Kd_nak_nai2</ci>
</apply>
</apply>
<apply>
<eq />
<ci>Ke_bound</ci>
<apply>
<divide />
<ci>Ke</ci>
<ci>Kd_nak_ke</ci>
</apply>
</apply>
<apply>
<eq />
<ci>Ki_bound</ci>
<apply>
<divide />
<ci>Ki</ci>
<ci>Kd_nak_ki</ci>
</apply>
</apply>
<apply>
<eq />
<ci>MgATP_bound</ci>
<apply>
<divide />
<ci>MgATP</ci>
<ci>Kd_nak_MgATP</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq />
<ci>alpha_f_nak_1</ci>
<apply>
<divide />
<apply>
<times />
<ci>rate_f_nak_1</ci>
<ci>Nai_bound1</ci>
<apply>
<power />
<ci>Nai_bound2</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>Nai_bound1</ci>
<apply>
<power />
<ci>Nai_bound2</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1</cn>
<ci>Nai_bound2</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>Ki_bound</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>alpha_f_nak_2</ci>
<ci>rate_f_nak_2</ci>
</apply>
<apply>
<eq />
<ci>alpha_f_nak_3</ci>
<apply>
<divide />
<apply>
<times />
<ci>rate_f_nak_3</ci>
<apply>
<power />
<ci>Ke_bound</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>Nae_bound1</ci>
<apply>
<power />
<ci>Nae_bound2</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>Nae_bound2</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>Ke_bound</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>alpha_f_nak_4</ci>
<apply>
<divide />
<apply>
<times />
<ci>rate_f_nak_4</ci>
<ci>MgATP_bound</ci>
</apply>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>MgATP_bound</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>alpha_r_nak_1</ci>
<apply>
<times />
<ci>rate_r_nak_1</ci>
<ci>MgADP</ci>
</apply>
</apply>
<apply>
<eq />
<ci>alpha_r_nak_2</ci>
<apply>
<divide />
<apply>
<times />
<ci>rate_r_nak_2</ci>
<ci>Nae_bound1</ci>
<apply>
<power />
<ci>Nae_bound2</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>Nae_bound1</ci>
<apply>
<power />
<ci>Nae_bound2</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>Nae_bound2</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>Ke_bound</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>alpha_r_nak_3</ci>
<apply>
<divide />
<apply>
<times />
<ci>rate_r_nak_3</ci>
<ci>Pi</ci>
<ci>H</ci>
</apply>
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>MgATP_bound</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>alpha_r_nak_4</ci>
<apply>
<divide />
<apply>
<times />
<ci>rate_r_nak_4</ci>
<apply>
<power />
<ci>Ki_bound</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<minus />
<apply>
<plus />
<apply>
<times />
<ci>Nai_bound1</ci>
<apply>
<power />
<ci>Nai_bound2</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1.0</cn>
<ci>Nai_bound2</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
<apply>
<power />
<apply>
<plus />
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1</cn>
<ci>Ki_bound</ci>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">2</cn>
</apply>
</apply>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="dimensionless">1</cn>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>sig_nak</ci>
<apply>
<plus />
<apply>
<times />
<ci>alpha_r_nak_1</ci>
<ci>alpha_r_nak_2</ci>
<ci>alpha_r_nak_3</ci>
</apply>
<apply>
<times />
<ci>alpha_r_nak_1</ci>
<ci>alpha_r_nak_2</ci>
<ci>alpha_f_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_r_nak_1</ci>
<ci>alpha_f_nak_3</ci>
<ci>alpha_f_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_2</ci>
<ci>alpha_f_nak_3</ci>
<ci>alpha_f_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_r_nak_2</ci>
<ci>alpha_r_nak_3</ci>
<ci>alpha_r_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_1</ci>
<ci>alpha_r_nak_2</ci>
<ci>alpha_r_nak_3</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_1</ci>
<ci>alpha_r_nak_2</ci>
<ci>alpha_f_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_1</ci>
<ci>alpha_f_nak_3</ci>
<ci>alpha_f_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_r_nak_1</ci>
<ci>alpha_r_nak_3</ci>
<ci>alpha_r_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_2</ci>
<ci>alpha_r_nak_3</ci>
<ci>alpha_r_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_1</ci>
<ci>alpha_f_nak_2</ci>
<ci>alpha_r_nak_3</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_1</ci>
<ci>alpha_f_nak_2</ci>
<ci>alpha_f_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_r_nak_1</ci>
<ci>alpha_r_nak_2</ci>
<ci>alpha_r_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_r_nak_1</ci>
<ci>alpha_f_nak_3</ci>
<ci>alpha_r_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_2</ci>
<ci>alpha_f_nak_3</ci>
<ci>alpha_r_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_f_nak_1</ci>
<ci>alpha_f_nak_2</ci>
<ci>alpha_f_nak_3</ci>
</apply>
</apply>
</apply>
<apply>
<eq />
<ci>v_cyc_nak</ci>
<apply>
<divide />
<apply>
<minus />
<apply>
<times />
<ci>alpha_f_nak_1</ci>
<ci>alpha_f_nak_2</ci>
<ci>alpha_f_nak_3</ci>
<ci>alpha_f_nak_4</ci>
</apply>
<apply>
<times />
<ci>alpha_r_nak_1</ci>
<ci>alpha_r_nak_2</ci>
<ci>alpha_r_nak_3</ci>
<ci>alpha_r_nak_4</ci>
</apply>
</apply>
<ci>sig_nak</ci>
</apply>
</apply>
<!--Normalising to cycle velocity at Ke = 5.4 mM-->
<apply>
<eq />
<ci>v_cyc_nak_normalised</ci>
<apply>
<divide />
<ci>v_cyc_nak</ci>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.1#" cellml:units="per_second">51.1069</cn>
</apply>
</apply>
</math>
</component>
<rdf:RDF xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:ro="http://www.obofoundry.org/ro/ro.owl#" xmlns:opb="http://bhi.washington.edu/OPB#">
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