- Author:
- JuliaMusgrave <jmus753@aucklanduni.ac.nz>
- Date:
- 2025-09-19 08:17:14+12:00
- Desc:
- Updated main scripts to provide more input to make it clear to the user which simulation is running
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d52/rawfile/4bac6e1b6e7452bea431403085b0ca3d0c516b3b/CellML/musgrave_2025_nondiabetic_isoton.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="musgrave_2025_nondiabetic_isoton" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:xlink="http://www.w3.org/1999/xlink">
<import xlink:href="nondiabetic_calcium.cellml">
<component component_ref="Ca_data" name="Ca_transient"/>
</import>
<units name="kilopascal">
<unit prefix="kilo" units="pascal"/>
</units>
<units name="gigapascal_per_metre">
<unit prefix="giga" units="pascal"/>
<unit exponent="-1" units="metre"/>
</units>
<units name="gigapascal_second_per_metre">
<unit prefix="giga" units="pascal"/>
<unit units="second"/>
<unit exponent="-1" units="metre"/>
</units>
<units name="micrometre">
<unit prefix="micro" units="metre"/>
</units>
<units name="micrometre_per_second">
<unit prefix="micro" units="metre"/>
<unit exponent="-1" units="second"/>
</units>
<units name="per_micrometre">
<unit exponent="-1" prefix="micro" units="metre"/>
</units>
<units name="per_second">
<unit exponent="-1" units="second"/>
</units>
<units name="micromolar">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="molar">
<unit units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="kilojoule_per_mole">
<unit prefix="kilo" units="joule"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="kilojoule_per_mole_per_kelvin">
<unit prefix="kilo" units="joule"/>
<unit exponent="-1" units="mole"/>
<unit exponent="-1" units="kelvin"/>
</units>
<units name="kilopascal_second">
<unit prefix="kilo" units="pascal"/>
<unit units="second"/>
</units>
<units name="gigapascal_second_per_metre">
<unit prefix="giga" units="pascal"/>
<unit units="second"/>
<unit exponent="-1" units="metre"/>
</units>
<units name="gigapascal_second2_per_metre">
<unit prefix="giga" units="pascal"/>
<unit exponent="2" units="second"/>
<unit exponent="-1" units="metre"/>
</units>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
</component>
<component name="force_generation">
<variable name="Fa" public_interface="out" units="kilopascal"/>
<variable initial_value="0" name="Fp1" public_interface="out" units="kilopascal"/>
<variable name="Fp2" public_interface="out" units="kilopascal"/>
<variable name="Ft" public_interface="out" units="kilopascal"/>
<variable name="K" units="gigapascal_per_metre"/>
<variable initial_value="27800" name="K_myo" units="gigapascal_per_metre"/>
<variable initial_value="0.361" name="rho_myo" units="dimensionless"/>
<variable initial_value="13.3" name="Kp1" units="gigapascal_per_metre"/>
<variable initial_value="0.07" name="mu" units="gigapascal_second_per_metre"/>
<variable initial_value="0.515" name="Kp2" units="gigapascal_per_metre"/>
<variable initial_value="7.2" name="phi_p" units="dimensionless"/>
<variable initial_value="1.87" name="Lr" public_interface="out" units="micrometre"/>
<variable name="B" public_interface="in" units="dimensionless"/>
<variable name="xB" public_interface="in" units="micrometre"/>
<variable name="C" public_interface="in" units="dimensionless"/>
<variable name="xC" public_interface="in" units="micrometre"/>
<variable name="dL" public_interface="in" units="micrometre_per_second"/>
<variable name="L" public_interface="in" units="micrometre"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>K</ci>
<apply>
<times/>
<ci>K_myo</ci>
<ci>rho_myo</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Fa</ci>
<apply>
<times/>
<ci>K</ci>
<apply>
<plus/>
<apply>
<times/>
<ci>B</ci>
<ci>xB</ci>
</apply>
<apply>
<times/>
<ci>C</ci>
<ci>xC</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>Fp1</ci>
</apply>
<apply>
<times/>
<ci>Kp1</ci>
<apply>
<minus/>
<ci>dL</ci>
<apply>
<divide/>
<ci>Fp1</ci>
<ci>mu</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Fp2</ci>
<apply>
<times/>
<ci>Kp2</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<times/>
<ci>phi_p</ci>
<apply>
<minus/>
<ci>L</ci>
<ci>Lr</ci>
</apply>
</apply>
</apply>
<cn cellml:units="dimensionless">1</cn>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>Ft</ci>
<apply>
<plus/>
<ci>Fa</ci>
<ci>Fp1</ci>
<ci>Fp2</ci>
</apply>
</apply>
</math>
</component>
<component name="crossbridge_cycling_rates">
<variable name="k1" public_interface="out" units="per_second"/>
<variable name="k_1" public_interface="out" units="per_second"/>
<variable initial_value="88.8" name="k2" public_interface="out" units="per_second"/>
<variable name="k_2" public_interface="out" units="per_second"/>
<variable name="k3" public_interface="out" units="per_second"/>
<variable name="k_3" public_interface="out" units="per_second"/>
<variable initial_value="89" name="k1_i" units="per_second"/>
<variable initial_value="6.68" name="k_1_i" units="per_second"/>
<variable initial_value="113" name="k_2_i" units="per_second"/>
<variable initial_value="96.6" name="k3_i" units="per_second"/>
<variable initial_value="257" name="phi_s1" units="per_micrometre"/>
<variable initial_value="44.9" name="phi_s3" units="per_micrometre"/>
<variable initial_value="0.281e-3" name="k_dATP" units="molar"/>
<variable initial_value="-30" name="G_ATP0" units="kilojoule_per_mole"/>
<variable initial_value="8.314e-3" name="R" units="kilojoule_per_mole_per_kelvin"/>
<variable initial_value="310" name="T" units="kelvin"/>
<variable name="G_ATP" units="kilojoule_per_mole"/>
<variable name="Pi" public_interface="in" units="molar"/>
<variable name="ATP" public_interface="in" units="molar"/>
<variable initial_value="36e-6" name="ADP" units="molar"/>
<variable name="xB" public_interface="in" units="micrometre"/>
<variable name="xC" public_interface="in" units="micrometre"/>
<variable name="xC0" public_interface="in" units="micrometre"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>k1</ci>
<apply>
<times/>
<ci>k1_i</ci>
<apply>
<exp/>
<apply>
<times/>
<apply>
<minus/>
<ci>phi_s1</ci>
</apply>
<ci>xB</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k_1</ci>
<apply>
<times/>
<ci>k_1_i</ci>
<ci>Pi</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>k_2</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k_2_i</ci>
<ci>k_dATP</ci>
</apply>
<apply>
<plus/>
<ci>k_dATP</ci>
<ci>ATP</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k3</ci>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci>k3_i</ci>
<ci>ATP</ci>
</apply>
<apply>
<plus/>
<ci>k_dATP</ci>
<ci>ATP</ci>
</apply>
</apply>
<apply>
<exp/>
<apply>
<times/>
<ci>phi_s3</ci>
<apply>
<minus/>
<ci>xC</ci>
<ci>xC0</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>G_ATP</ci>
<apply>
<plus/>
<ci>G_ATP0</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<divide/>
<apply>
<times/>
<ci>ADP</ci>
<ci>Pi</ci>
</apply>
<ci>ATP</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>k_3</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>k1</ci>
<ci>k2</ci>
<ci>k3</ci>
</apply>
<apply>
<times/>
<ci>k_1</ci>
<ci>k_2</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<minus/>
<ci>G_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="thin_filament_regulation">
<variable initial_value="0.2" name="CaTn" units="dimensionless"/>
<variable initial_value="100" name="k_tn" units="per_second"/>
<variable initial_value="0.33" name="Ca50" units="micromolar"/>
<variable initial_value="2" name="n_tn" units="dimensionless"/>
<variable initial_value="1000" name="k0" units="per_second"/>
<variable initial_value="327" name="k_0" units="per_second"/>
<variable initial_value="5" name="n_Tm" units="dimensionless"/>
<variable initial_value="0.77" name="N" public_interface="out" units="dimensionless"/>
<variable name="A" public_interface="in" units="dimensionless"/>
<variable name="time" public_interface="in" units="second"/>
<variable name="Ca" public_interface="in" units="micromolar"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>CaTn</ci>
</apply>
<apply>
<times/>
<ci>k_tn</ci>
<apply>
<minus/>
<apply>
<times/>
<apply>
<power/>
<apply>
<divide/>
<ci>Ca</ci>
<ci>Ca50</ci>
</apply>
<ci>n_tn</ci>
</apply>
<apply>
<minus/>
<cn cellml:units="dimensionless">1</cn>
<ci>CaTn</ci>
</apply>
</apply>
<ci>CaTn</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>N</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>k_0</ci>
<ci>A</ci>
<apply>
<power/>
<ci>CaTn</ci>
<apply>
<divide/>
<apply>
<minus/>
<ci>n_Tm</ci>
</apply>
<cn cellml:units="dimensionless">2</cn>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>k0</ci>
<ci>N</ci>
<apply>
<power/>
<ci>CaTn</ci>
<apply>
<divide/>
<ci>n_Tm</ci>
<cn cellml:units="dimensionless">2</cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="crossbridge_strain_and_states">
<variable initial_value="1e-3" name="B" public_interface="out" units="dimensionless"/>
<variable initial_value="0" name="xB" public_interface="out" units="micrometre"/>
<variable initial_value="1e-3" name="C" public_interface="out" units="dimensionless"/>
<variable initial_value="0.01" name="xC" public_interface="out" units="micrometre"/>
<variable name="Z" units="dimensionless"/>
<variable name="A" public_interface="out" units="dimensionless"/>
<variable name="N" public_interface="in" units="dimensionless"/>
<variable name="k1" public_interface="in" units="per_second"/>
<variable name="k_1" public_interface="in" units="per_second"/>
<variable name="k2" public_interface="in" units="per_second"/>
<variable name="k_2" public_interface="in" units="per_second"/>
<variable name="k3" public_interface="in" units="per_second"/>
<variable name="k_3" public_interface="in" units="per_second"/>
<variable name="xC0" public_interface="in" units="micrometre"/>
<variable name="dL" public_interface="in" units="micrometre_per_second"/>
<variable name="L" public_interface="in" units="micrometre"/>
<variable initial_value="2.3" name="L_max" units="micrometre"/>
<variable initial_value="5" name="phi_l" units="dimensionless"/>
<variable initial_value="0.029" name="phi_v" units="dimensionless"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Z</ci>
<piecewise>
<piece>
<apply>
<plus/>
<cn cellml:units="dimensionless">1</cn>
<apply>
<times/>
<ci>phi_l</ci>
<apply>
<minus/>
<apply>
<divide/>
<ci>L</ci>
<ci>L_max</ci>
</apply>
<cn cellml:units="dimensionless">1</cn>
</apply>
</apply>
</apply>
<apply>
<lt/>
<ci>L</ci>
<ci>L_max</ci>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">1</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>A</ci>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>Z</ci>
<ci>N</ci>
</apply>
<ci>B</ci>
</apply>
<ci>C</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>B</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k1</ci>
<ci>A</ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci>k_1</ci>
<ci>k2</ci>
</apply>
<ci>B</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_2</ci>
<ci>C</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>C</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<times/>
<ci>k2</ci>
<ci>B</ci>
</apply>
<apply>
<times/>
<apply>
<plus/>
<ci>k_2</ci>
<ci>k3</ci>
</apply>
<ci>C</ci>
</apply>
</apply>
<apply>
<times/>
<ci>k_3</ci>
<ci>A</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>xB</ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>A</ci>
<ci>k1</ci>
</apply>
<apply>
<times/>
<ci>C</ci>
<ci>k_2</ci>
</apply>
</apply>
</apply>
<ci>B</ci>
</apply>
<ci>xB</ci>
</apply>
<apply>
<times/>
<ci>phi_v</ci>
<ci>dL</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>xC</ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci>B</ci>
<ci>k2</ci>
</apply>
<apply>
<times/>
<ci>A</ci>
<ci>k_3</ci>
</apply>
</apply>
</apply>
<ci>C</ci>
</apply>
<apply>
<minus/>
<ci>xC</ci>
<ci>xC0</ci>
</apply>
</apply>
<apply>
<times/>
<ci>phi_v</ci>
<ci>dL</ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="length_control">
<variable initial_value="0" name="IntF" units="kilopascal_second"/>
<variable initial_value="5e-5" name="nu" units="gigapascal_second_per_metre"/>
<variable initial_value="1e-5" name="m" units="gigapascal_second2_per_metre"/>
<variable initial_value="2.2" name="L0" units="micrometre"/>
<variable name="dL" public_interface="out" units="micrometre_per_second"/>
<variable initial_value="2.2" name="L" public_interface="out" units="micrometre"/>
<variable initial_value="12" name="F_after" units="kilopascal"/>
<variable name="time" public_interface="in" units="second"/>
<variable name="dIntF" units="kilopascal"/>
<variable name="Ft" public_interface="in" units="kilopascal"/>
<variable name="Lr" public_interface="in" units="micrometre"/>
<variable name="t_twitch" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>dIntF</ci>
<apply>
<minus/>
<ci>F_after</ci>
<ci>Ft</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>IntF</ci>
</apply>
<ci>dIntF</ci>
</apply>
<apply>
<eq/>
<ci>dL</ci>
<apply>
<min/>
<apply>
<divide/>
<apply>
<plus/>
<ci>IntF</ci>
<apply>
<times/>
<ci>nu</ci>
<apply>
<minus/>
<ci>Lr</ci>
<ci>L</ci>
</apply>
</apply>
</apply>
<ci>m</ci>
</apply>
<cn cellml:units="micrometre_per_second">0</cn>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>L</ci>
</apply>
<ci>dL</ci>
</apply>
</math>
</component>
<component name="model_parameters">
<variable initial_value="0.01" name="xC0" public_interface="out" units="micrometre"/>
<variable initial_value="1e-3" name="Pi" public_interface="out" units="molar"/>
<variable initial_value="5e-3" name="ATP" public_interface="out" units="molar"/>
</component>
<connection>
<map_components component_1="thin_filament_regulation" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="crossbridge_strain_and_states" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="force_generation" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Ca_transient" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="length_control" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="force_generation" component_2="crossbridge_strain_and_states"/>
<map_variables variable_1="B" variable_2="B"/>
<map_variables variable_1="C" variable_2="C"/>
<map_variables variable_1="xB" variable_2="xB"/>
<map_variables variable_1="xC" variable_2="xC"/>
</connection>
<connection>
<map_components component_1="force_generation" component_2="length_control"/>
<map_variables variable_1="dL" variable_2="dL"/>
<map_variables variable_1="L" variable_2="L"/>
<map_variables variable_1="Ft" variable_2="Ft"/>
<map_variables variable_1="Lr" variable_2="Lr"/>
</connection>
<connection>
<map_components component_1="crossbridge_cycling_rates" component_2="crossbridge_strain_and_states"/>
<map_variables variable_1="xB" variable_2="xB"/>
<map_variables variable_1="xC" variable_2="xC"/>
<map_variables variable_1="k1" variable_2="k1"/>
<map_variables variable_1="k_1" variable_2="k_1"/>
<map_variables variable_1="k2" variable_2="k2"/>
<map_variables variable_1="k_2" variable_2="k_2"/>
<map_variables variable_1="k3" variable_2="k3"/>
<map_variables variable_1="k_3" variable_2="k_3"/>
</connection>
<connection>
<map_components component_1="crossbridge_cycling_rates" component_2="model_parameters"/>
<map_variables variable_1="Pi" variable_2="Pi"/>
<map_variables variable_1="ATP" variable_2="ATP"/>
<map_variables variable_1="xC0" variable_2="xC0"/>
</connection>
<connection>
<map_components component_1="thin_filament_regulation" component_2="crossbridge_strain_and_states"/>
<map_variables variable_1="A" variable_2="A"/>
<map_variables variable_1="N" variable_2="N"/>
</connection>
<connection>
<map_components component_1="thin_filament_regulation" component_2="Ca_transient"/>
<map_variables variable_1="Ca" variable_2="Ca"/>
</connection>
<connection>
<map_components component_1="crossbridge_strain_and_states" component_2="model_parameters"/>
<map_variables variable_1="xC0" variable_2="xC0"/>
</connection>
<connection>
<map_components component_1="crossbridge_strain_and_states" component_2="length_control"/>
<map_variables variable_1="dL" variable_2="dL"/>
<map_variables variable_1="L" variable_2="L"/>
</connection>
<connection>
<map_components component_1="Ca_transient" component_2="length_control"/>
<map_variables variable_1="t_twitch" variable_2="t_twitch"/>
</connection>
</model>
