- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-11 16:50:16+12:00
- Desc:
- Updating version with Yang05 modifications
- Permanent Source URI:
- https://models.cellml.org/workspace/818/rawfile/ad3c1a3c060ce9500f56f3fae9cc78aa3db44a39/BG_HaiMurphy.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="individual_HaiMurphy" 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="units_and_constants/units_BG.cellml">
<units name="mM" units_ref="mM"/>
<units name="fmol" units_ref="fmol"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="microm3" units_ref="microm3"/>
<units name="fF" units_ref="fF"/>
<units name="fC" units_ref="fC"/>
<units name="fA" units_ref="fA"/>
<units name="per_second" units_ref="per_second"/>
<units name="millivolt" units_ref="millivolt"/>
<units name="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="fmol_per_L" units_ref="fmol_per_L"/>
<units name="fmol_per_L_per_sec" units_ref="fmol_per_L_per_sec"/>
<units name="per_sec_per_fmol_per_L" units_ref="per_sec_per_fmol_per_L"/>
<units name="uM" units_ref="uM"/>
<units name="mM_per_sec" units_ref="mM_per_sec"/>
<units name="uM_per_sec" units_ref="uM_per_sec"/>
<units name="pL" units_ref="pL"/>
<units name="m_to_u" units_ref="m_to_u"/>
</import>
<import xlink:href="units_and_constants/constants_BG.cellml">
<component component_ref="constants" name="constants"/>
</import>
<component name="environment">
<variable name="time" public_interface="out" units="second"/>
<!-- initial values-->
<variable initial_value="1" name="q_A" public_interface="out" units="fmol"/>
<variable initial_value="1" name="q_M" public_interface="out" units="fmol"/>
<variable initial_value="0" name="q_Mp" public_interface="out" units="fmol"/>
<variable initial_value="0" name="q_AM" public_interface="out" units="fmol"/>
<variable initial_value="0" name="q_AMp" public_interface="out" units="fmol"/>
<variable initial_value="570" name="q_Pi" public_interface="out" units="fmol"/>
<variable initial_value="1e-888" name="q_Ca_i" public_interface="out" units="fmol"/>
<variable initial_value="1e-888" name="q_cGMP" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="v_R_12" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_34" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_56" public_interface="in" units="fmol_per_sec"/>
<variable name="v_R_78" public_interface="in" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_A</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_34</ci>
</apply>
<ci>v_R_78</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_M</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_12</ci>
</apply>
<ci>v_R_78</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Mp</ci>
</apply>
<apply>
<minus/>
<ci>v_R_12</ci>
<ci>v_R_34</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_AM</ci>
</apply>
<apply>
<minus/>
<ci>v_R_56</ci>
<ci>v_R_78</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_AMp</ci>
</apply>
<apply>
<minus/>
<ci>v_R_34</ci>
<ci>v_R_56</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Pi</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_R_12</ci>
</apply>
<ci>v_R_56</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Ca_i</ci>
</apply>
<ci>vvv</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_cGMP</ci>
</apply>
<ci>vvv</ci>
</apply>
</math>
<!-- stress calculation: from original paper,
stress = AM + AMp -->
<variable name="stress" units="dimensionless"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>stress</ci>
<apply>
<divide/>
<apply>
<plus/>
<ci>q_AM</ci>
<ci>q_AMp</ci>
</apply>
<cn cellml:units="fmol">1</cn>
</apply>
</apply>
</math>
</component>
<component name="HaiMurphy_parameters">
<variable initial_value="0.117606" name="kappa_R_12" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="6.98167" name="kappa_R_34" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="2.11691" name="kappa_R_56" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0270688" name="kappa_R_78" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.532601" name="K_A" public_interface="out" units="per_fmol"/>
<variable initial_value="4.08193" name="K_M" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0351692" name="K_Mp" public_interface="out" units="per_fmol"/>
<variable initial_value="0.448094" name="K_AM" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0038607" name="K_AMp" public_interface="out" units="per_fmol"/>
<variable initial_value="250.692" name="K_Pi" public_interface="out" units="per_fmol"/>
<variable initial_value="0.145785" name="K_Ca_i" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0971738" name="K_cGMP" public_interface="out" units="per_fmol"/>
</component>
<component name="HaiMurphy">
<variable name="time" public_interface="in" units="second"/>
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- parameters-->
<variable name="kappa_R_12" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_34" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_56" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_R_78" public_interface="in" units="fmol_per_sec"/>
<variable name="K_A" public_interface="in" units="per_fmol"/>
<variable name="K_M" public_interface="in" units="per_fmol"/>
<variable name="K_Mp" public_interface="in" units="per_fmol"/>
<variable name="K_AM" public_interface="in" units="per_fmol"/>
<variable name="K_AMp" public_interface="in" units="per_fmol"/>
<variable name="K_Pi" public_interface="in" units="per_fmol"/>
<variable name="K_Ca_i" public_interface="in" units="per_fmol"/>
<variable name="K_cGMP" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_A" public_interface="in" units="fmol"/>
<variable name="q_M" public_interface="in" units="fmol"/>
<variable name="q_Mp" public_interface="in" units="fmol"/>
<variable name="q_AM" public_interface="in" units="fmol"/>
<variable name="q_AMp" public_interface="in" units="fmol"/>
<variable name="q_Pi" public_interface="in" units="fmol"/>
<variable name="q_Ca_i" public_interface="in" units="fmol"/>
<variable name="q_cGMP" public_interface="in" units="fmol"/>
<!-- Constitutive parameters-->
<variable name="mu_A" units="J_per_mol"/>
<variable name="mu_M" units="J_per_mol"/>
<variable name="mu_Mp" units="J_per_mol"/>
<variable name="mu_AM" units="J_per_mol"/>
<variable name="mu_AMp" units="J_per_mol"/>
<variable name="mu_Pi" units="J_per_mol"/>
<variable name="mu_Ca_i" units="J_per_mol"/>
<variable name="mu_cGMP" units="J_per_mol"/>
<variable name="v_R_12" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_34" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_56" public_interface="out" units="fmol_per_sec"/>
<variable name="v_R_78" public_interface="out" units="fmol_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_A</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_A</ci>
<ci>q_A</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_M</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_M</ci>
<ci>q_M</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Mp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Mp</ci>
<ci>q_Mp</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AM</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AM</ci>
<ci>q_AM</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AMp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AMp</ci>
<ci>q_AMp</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Pi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Pi</ci>
<ci>q_Pi</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Ca_i</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ca_i</ci>
<ci>q_Ca_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_cGMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_cGMP</ci>
<ci>q_cGMP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_12</ci>
<apply>
<times/>
<ci>kappa_R_12</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_M</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_Mp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_34</ci>
<apply>
<times/>
<ci>kappa_R_34</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_A</ci>
<ci>mu_Mp</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AMp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_56</ci>
<apply>
<times/>
<ci>kappa_R_56</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AMp</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AM</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_R_78</ci>
<apply>
<times/>
<ci>kappa_R_78</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AM</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_A</ci>
<ci>mu_M</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="HaiMurphy"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_A" variable_2="q_A"/>
<map_variables variable_1="q_M" variable_2="q_M"/>
<map_variables variable_1="q_Mp" variable_2="q_Mp"/>
<map_variables variable_1="q_AM" variable_2="q_AM"/>
<map_variables variable_1="q_AMp" variable_2="q_AMp"/>
<map_variables variable_1="q_Pi" variable_2="q_Pi"/>
<map_variables variable_1="q_Ca_i" variable_2="q_Ca_i"/>
<map_variables variable_1="q_cGMP" variable_2="q_cGMP"/>
<map_variables variable_1="v_R_12" variable_2="v_R_12"/>
<map_variables variable_1="v_R_34" variable_2="v_R_34"/>
<map_variables variable_1="v_R_56" variable_2="v_R_56"/>
<map_variables variable_1="v_R_78" variable_2="v_R_78"/>
</connection>
<connection>
<map_components component_1="HaiMurphy" component_2="HaiMurphy_parameters"/>
<map_variables variable_1="kappa_R_12" variable_2="kappa_R_12"/>
<map_variables variable_1="kappa_R_34" variable_2="kappa_R_34"/>
<map_variables variable_1="kappa_R_56" variable_2="kappa_R_56"/>
<map_variables variable_1="kappa_R_78" variable_2="kappa_R_78"/>
<map_variables variable_1="K_A" variable_2="K_A"/>
<map_variables variable_1="K_M" variable_2="K_M"/>
<map_variables variable_1="K_Mp" variable_2="K_Mp"/>
<map_variables variable_1="K_AM" variable_2="K_AM"/>
<map_variables variable_1="K_AMp" variable_2="K_AMp"/>
<map_variables variable_1="K_Pi" variable_2="K_Pi"/>
<map_variables variable_1="K_Ca_i" variable_2="K_Ca_i"/>
<map_variables variable_1="K_cGMP" variable_2="K_cGMP"/>
</connection>
<connection>
<map_components component_1="constants" component_2="HaiMurphy"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
