- Author:
- aram148 <a.rampadarath@auckland.ac.nz>
- Date:
- 2021-12-17 11:46:34+13:00
- Desc:
- Added the Matlab 7 airway code
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6b0/rawfile/9ac5ec0fe3f8ae60e6020b99146573defeb5a5e9/VSM_ftu/VSM - Exported.cellml
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<times/>
<apply>
<plus/>
<apply>
<times/>
<ci>k_m4</ci>
<ci>K2</ci>
<ci>K1</ci>
</apply>
<apply>
<times/>
<ci>k_m2</ci>
<ci>K4</ci>
<ci>p</ci>
</apply>
</apply>
<ci>c</ci>
</apply>
<apply>
<times/>
<ci>K4</ci>
<ci>K2</ci>
<apply>
<plus/>
<ci>K1</ci>
<ci>p</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>phi2</ci>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<times/>
<ci>k_m2</ci>
<ci>p</ci>
</apply>
<apply>
<times/>
<ci>k_m4</ci>
<ci>K3</ci>
</apply>
</apply>
<apply>
<plus/>
<ci>K3</ci>
<ci>p</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>y</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>phi1</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>y</ci>
</apply>
</apply>
<apply>
<times/>
<ci>phi2</ci>
<ci>y</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>c</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>J_release</ci>
<ci>J_serca</ci>
</apply>
<apply>
<times/>
<ci>delta</ci>
<apply>
<minus/>
<ci>J_in</ci>
<ci>J_pm</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>cs</ci>
</apply>
<apply>
<times/>
<ci>gamma</ci>
<apply>
<minus/>
<ci>J_serca</ci>
<ci>J_release</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>p</ci>
<apply>
<times/>
<apply>
<divide/>
<cn cellml:units="dimensionless">0.35</cn>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<exp/>
<apply>
<times/>
<apply>
<minus/>
<cn cellml:units="dimensionless">0.0699</cn>
</apply>
<apply>
<minus/>
<ci>time</ci>
<cn cellml:units="second">50</cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<gt/>
<ci>time</ci>
<cn cellml:units="second">50</cn>
</apply>
</apply>
</apply>
</math>
</component>
<component name="ca_parameters">
<variable initial_value="2000" name="k_1" public_interface="out" units="per_mM_per_sec"/>
<variable initial_value="1.0" name="k_2" public_interface="out" units="per_mM_per_sec"/>
<variable initial_value="2000" name="k_3" public_interface="out" units="per_mM_per_sec"/>
<variable initial_value="1.0" name="k_4" public_interface="out" units="per_mM_per_sec"/>
<variable initial_value="100" name="k_5" public_interface="out" units="per_mM_per_sec"/>
<variable initial_value="260" name="k_m1" public_interface="out" units="per_sec"/>
<variable initial_value="1.05" name="k_m2" public_interface="out" units="per_sec"/>
<variable initial_value="1886" name="k_m3" public_interface="out" units="per_sec"/>
<variable initial_value="0.145" name="k_m4" public_interface="out" units="per_sec"/>
<variable initial_value="8.2" name="k_m5" public_interface="out" units="per_sec"/>
<variable initial_value="0.0072" name="k_ryr0" public_interface="out" units="per_sec"/>
<variable initial_value="0.334" name="k_ryr1" public_interface="out" units="per_sec"/>
<variable initial_value="0.5" name="k_ryr2" public_interface="out" units="mM"/>
<variable initial_value="38" name="k_ryr3" public_interface="out" units="mM"/>
<variable initial_value="5.55" name="k_ipr" public_interface="out" units="per_sec"/>
<variable initial_value="5.0" name="k_RyR" public_interface="out" units="per_sec"/>
<variable initial_value="-50" name="Vm" public_interface="out" units="mV"/>
<variable initial_value="12" name="km" public_interface="out" units="mV"/>
<variable initial_value="9" name="gca" public_interface="out" units="nS_per_mM"/>
<variable initial_value="96485" name="F" public_interface="out" units="C_per_mol"/>
<variable initial_value="8345" name="R" public_interface="out" units="mJ_per_K_per_mol"/>
<variable initial_value="310" name="T" public_interface="out" units="kelvin"/>
<variable initial_value="0.05" name="alpha0" public_interface="out" units="mM_per_sec"/>
<variable initial_value="0.25" name="alpha1" public_interface="out" units="dimensionless"/>
<variable initial_value="1" name="alpha2" public_interface="out" units="per_sec"/>
<variable initial_value="0.1" name="Jer" public_interface="out" units="per_sec"/>
<variable initial_value="4.5" name="Ve" public_interface="out" units="mM_per_sec"/>
<variable initial_value="0.1" name="Ke" public_interface="out" units="mM"/>
<variable initial_value="4.5" name="Vp" public_interface="out" units="mM_per_sec"/>
<variable initial_value="0.4" name="Kp" public_interface="out" units="mM"/>
<variable initial_value="5.5" name="gamma" public_interface="out" units="dimensionless"/>
<variable initial_value="0.05" name="delta" public_interface="out" units="dimensionless"/>
</component>
<component name="calcium">
<variable name="time" public_interface="in" units="second"/>
<variable name="k1" public_interface="out" units="per_sec"/>
<variable name="k2h" public_interface="out" units="per_sec"/>
<variable initial_value="0.5962" name="k1a" units="per_sec"/>
<variable name="c" public_interface="in" units="mM"/>
<variable initial_value="1.35" name="k1b" units="mM"/>
<variable initial_value="156.9" name="tau" units="second"/>
<variable initial_value="0" name="P" units="dimensionless"/>
<variable name="kon" units="dimensionless"/>
<variable name="koff" units="dimensionless"/>
<variable initial_value="242.14" name="k2b" units="per_sec"/>
<variable initial_value="0.000125" name="kon1" units="dimensionless"/>
<variable initial_value="0.8988" name="kon2" units="mM"/>
<variable initial_value="0.4629" name="koff1" units="dimensionless"/>
<variable initial_value="20.035" name="koff2" units="dimensionless"/>
<variable name="p" public_interface="in" units="mM"/>
<math cellml:xmlns="http://www.w3.org/1998/Math/MathML" xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
<apply>
<eq/>
<ci>kon</ci>
<apply>
<plus/>
<ci>kon1</ci>
<apply>
<divide/>
<apply>
<power/>
<ci>c</ci>
<cn cellml:units="dimensionless">2</cn>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>kon2</ci>
<cn cellml:units="dimensionless">2</cn>
</apply>
<apply>
<power/>
<ci>c</ci>
<cn cellml:units="dimensionless">2</cn>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>koff</ci>
<apply>
<plus/>
<ci>koff1</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>koff2</ci>
<ci>p</ci>
</apply>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<ci>p</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>P</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<apply>
<divide/>
<cn cellml:units="dimensionless">1</cn>
<ci>tau</ci>
</apply>
<ci>kon</ci>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>P</ci>
</apply>
</apply>
<apply>
<times/>
<ci>koff</ci>
<ci>P</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k2h</ci>
<apply>
<times/>
<ci>k2b</ci>
<apply>
<power/>
<ci>P</ci>
<cn cellml:units="dimensionless">2</cn>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k1</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k1a</ci>
<apply>
<power/>
<ci>c</ci>
<cn cellml:units="dimensionless">4</cn>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>k1b</ci>
<cn cellml:units="dimensionless">4</cn>
</apply>
<apply>
<power/>
<ci>c</ci>
<cn cellml:units="dimensionless">4</cn>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="sGC">
<variable initial_value="1" name="Eb" public_interface="out" units="dimensionless"/>
<variable initial_value="0" name="E6c" public_interface="out" units="dimensionless"/>
<variable name="E5c" public_interface="out" units="dimensionless"/>
<variable initial_value="220" name="NO" public_interface="out" units="nM"/>
<variable initial_value="2.0" name="k_one" units="per_nM_per_sec"/>
<variable initial_value="100" name="km1" units="per_sec"/>
<variable initial_value="0.1" name="k_two" units="per_sec"/>
<variable initial_value="0.003" name="k_three" units="per_nM_per_sec"/>
<variable name="k_four" units="per_sec"/>
<variable initial_value="0" name="cGMP" public_interface="out" units="uM"/>
<variable name="vd" public_interface="out" units="dimensionless"/>
<variable name="vp" public_interface="out" units="dimensionless"/>
<variable initial_value="0.8520" name="Vm_sgc" units="dimensionless"/>
<variable name="Vm_pde" units="dimensionless"/>
<variable initial_value="2.0" name="Km_pde" units="uM"/>
<variable initial_value="0.0195" name="K_pde" units="per_sec"/>
<variable initial_value="0.01" name="k_dno" units="per_sec"/>
<variable initial_value="220" name="J_no" units="nM"/>
<variable initial_value="2" name="m" units="dimensionless"/>
<variable initial_value="0.011" name="K_four" units="dimensionless"/>
<variable name="time" public_interface="in" units="second"/>
<variable initial_value="0.0086" name="k_mclpb" units="per_sec"/>
<variable initial_value="0.0327" name="k_mlcpc" units="per_sec"/>
<variable initial_value="5.5" name="K_mlcpm" units="uM"/>
<variable initial_value="2" name="n_mlcoh" units="dimensionless"/>
<variable name="k2y" public_interface="out" units="per_sec"/>
<math cellml:xmlns="http://www.w3.org/1998/Math/MathML" xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Eb</ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<apply>
<minus/>
<ci>k_one</ci>
</apply>
<ci>Eb</ci>
<ci>NO</ci>
</apply>
<apply>
<times/>
<ci>km1</ci>
<ci>E6c</ci>
</apply>
<apply>
<times/>
<ci>k_four</ci>
<ci>E5c</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>E6c</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k_one</ci>
<ci>Eb</ci>
<ci>NO</ci>
</apply>
<apply>
<times/>
<ci>km1</ci>
<ci>E6c</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_two</ci>
<ci>E6c</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_three</ci>
<ci>E6c</ci>
<ci>NO</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>E5c</ci>
<apply>
<minus/>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>Eb</ci>
</apply>
<ci>E6c</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>cGMP</ci>
</apply>
<apply>
<minus/>
<ci>vd</ci>
<ci>vp</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>NO</ci>
</apply>
<apply>
<minus/>
<ci>J_no</ci>
<apply>
<times/>
<ci>k_dno</ci>
<ci>NO</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vd</ci>
<apply>
<times/>
<ci>Vm_sgc</ci>
<ci>E5c</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>vp</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>cGMP</ci>
<ci>Vm_pde</ci>
</apply>
<apply>
<plus/>
<ci>Km_pde</ci>
<ci>cGMP</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Vm_pde</ci>
<apply>
<times/>
<ci>K_pde</ci>
<ci>cGMP</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>k_four</ci>
<apply>
<times/>
<ci>K_four</ci>
<apply>
<power/>
<ci>cGMP</ci>
<ci>m</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k2y</ci>
<apply>
<plus/>
<ci>k_mclpb</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k_mlcpc</ci>
<apply>
<power/>
<ci>cGMP</ci>
<ci>n_mlcoh</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci>cGMP</ci>
<ci>n_mlcoh</ci>
</apply>
<apply>
<power/>
<ci>K_mlcpm</ci>
<ci>n_mlcoh</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="sGC" component_2="NO_sGC"/>
<map_variables variable_1="Eb" variable_2="Eb"/>
<map_variables variable_1="E5c" variable_2="E5c"/>
<map_variables variable_1="E6c" variable_2="E6c"/>
<map_variables variable_1="NO" variable_2="NO"/>
<map_variables variable_1="cGMP" variable_2="cGMP"/>
<map_variables variable_1="vd" variable_2="vd"/>
<map_variables variable_1="vp" variable_2="vp"/>
</connection>
<connection>
<map_components component_1="calcium" component_2="asm_ca"/>
<map_variables variable_1="c" variable_2="c"/>
<map_variables variable_1="p" variable_2="p"/>
</connection>
<connection>
<map_components component_1="asm_ca" component_2="Ca_ag"/>
<map_variables variable_1="c" variable_2="c"/>
<map_variables variable_1="p" variable_2="p"/>
</connection>
<connection>
<map_components component_1="calcium" component_2="model_parameters1"/>
<map_variables variable_1="k1" variable_2="k1"/>
</connection>
<connection>
<map_components component_1="kay2" component_2="model_parameters1"/>
<map_variables variable_1="k2" variable_2="k2"/>
</connection>
<connection>
<map_components component_1="sGC" component_2="kay2"/>
<map_variables variable_1="k2y" variable_2="k2y"/>
</connection>
<connection>
<map_components component_1="calcium" component_2="kay2"/>
<map_variables variable_1="k2h" variable_2="k2h"/>
</connection>
<connection>
<map_components component_1="M" component_2="Environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Mp" component_2="Environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="AMp" component_2="Environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="AM" component_2="Environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Environment" component_2="calcium"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Environment" component_2="asm_ca"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Environment" component_2="sGC"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="M" component_2="model_parameters1"/>
<map_variables variable_1="k7" variable_2="k7"/>
</connection>
<connection>
<map_components component_1="M" component_2="calcium"/>
<map_variables variable_1="k1" variable_2="k1"/>
</connection>
<connection>
<map_components component_1="M" component_2="kay2"/>
<map_variables variable_1="k2" variable_2="k2"/>
</connection>
<connection>
<map_components component_1="Mp" component_2="model_parameters1"/>
<map_variables variable_1="k4" variable_2="k4"/>
<map_variables variable_1="k3" variable_2="k3"/>
</connection>
<connection>
<map_components component_1="Mp" component_2="calcium"/>
<map_variables variable_1="k1" variable_2="k1"/>
</connection>
<connection>
<map_components component_1="Mp" component_2="kay2"/>
<map_variables variable_1="k2" variable_2="k2"/>
</connection>
<connection>
<map_components component_1="AMp" component_2="model_parameters1"/>
<map_variables variable_1="k5" variable_2="k5"/>
<map_variables variable_1="k6" variable_2="k6"/>
<map_variables variable_1="k4" variable_2="k4"/>
<map_variables variable_1="k3" variable_2="k3"/>
</connection>
<connection>
<map_components component_1="AM" component_2="model_parameters1"/>
<map_variables variable_1="k5" variable_2="k5"/>
<map_variables variable_1="k6" variable_2="k6"/>
<map_variables variable_1="k7" variable_2="k7"/>
</connection>
<connection>
<map_components component_1="AM" component_2="M"/>
<map_variables variable_1="AM" variable_2="AM"/>
</connection>
<connection>
<map_components component_1="AM" component_2="AMp"/>
<map_variables variable_1="AMp" variable_2="AMp"/>
<map_variables variable_1="AM" variable_2="AM"/>
</connection>
<connection>
<map_components component_1="M" component_2="Mp"/>
<map_variables variable_1="M" variable_2="M"/>
<map_variables variable_1="Mp" variable_2="Mp"/>
</connection>
<connection>
<map_components component_1="Mp" component_2="AMp"/>
<map_variables variable_1="Mp" variable_2="Mp"/>
<map_variables variable_1="AMp" variable_2="AMp"/>
</connection>
<connection>
<map_components component_1="phosphorylation" component_2="AMp"/>
<map_variables variable_1="AMp" variable_2="AMp"/>
</connection>
<connection>
<map_components component_1="phosphorylation" component_2="Mp"/>
<map_variables variable_1="Mp" variable_2="Mp"/>
</connection>
<connection>
<map_components component_1="stress" component_2="AMp"/>
<map_variables variable_1="AMp" variable_2="AMp"/>
</connection>
<connection>
<map_components component_1="stress" component_2="AM"/>
<map_variables variable_1="AM" variable_2="AM"/>
</connection>
<connection>
<map_components component_1="ca_parameters" component_2="asm_ca"/>
<map_variables variable_1="k_1" variable_2="k_1"/>
<map_variables variable_1="k_2" variable_2="k_2"/>
<map_variables variable_1="k_3" variable_2="k_3"/>
<map_variables variable_1="k_4" variable_2="k_4"/>
<map_variables variable_1="k_5" variable_2="k_5"/>
<map_variables variable_1="k_m1" variable_2="k_m1"/>
<map_variables variable_1="k_m2" variable_2="k_m2"/>
<map_variables variable_1="k_m3" variable_2="k_m3"/>
<map_variables variable_1="k_m4" variable_2="k_m4"/>
<map_variables variable_1="k_m5" variable_2="k_m5"/>
<map_variables variable_1="gamma" variable_2="gamma"/>
<map_variables variable_1="delta" variable_2="delta"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="alpha0" variable_2="alpha0"/>
<map_variables variable_1="alpha1" variable_2="alpha1"/>
<map_variables variable_1="alpha2" variable_2="alpha2"/>
<map_variables variable_1="k_ipr" variable_2="k_ipr"/>
<map_variables variable_1="k_RyR" variable_2="k_RyR"/>
<map_variables variable_1="Jer" variable_2="Jer"/>
<map_variables variable_1="k_ryr0" variable_2="k_ryr0"/>
<map_variables variable_1="k_ryr1" variable_2="k_ryr1"/>
<map_variables variable_1="k_ryr2" variable_2="k_ryr2"/>
<map_variables variable_1="k_ryr3" variable_2="k_ryr3"/>
<map_variables variable_1="Ve" variable_2="Ve"/>
<map_variables variable_1="Ke" variable_2="Ke"/>
<map_variables variable_1="Vp" variable_2="Vp"/>
<map_variables variable_1="Kp" variable_2="Kp"/>
<map_variables variable_1="gca" variable_2="gca"/>
<map_variables variable_1="Vm" variable_2="Vm"/>
<map_variables variable_1="km" variable_2="km"/>
</connection>
</model>
