- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-09-17 09:56:09+12:00
- Desc:
- Updating matlab file
- Permanent Source URI:
- https://models.cellml.org/workspace/6f7/rawfile/65af8998c27a5adff6f3a1cc61ba8769b8b2b0d7/BG_LRGbinding_B1AR.cellml
<?xml version='1.0' encoding='UTF-8'?>
<!-- BG model of ligand binding receptor, based on substep within beta1 adrenergic receptor activation (saucerman2003)
Species: L(igand), R(eceptor), LR, RG, LRG
1sep21 initialising file
6sept21 with parameters from saucerman2003 for beta1adrenergic receptor or iancu2007 for muscarinic receptor-->
<model name="BG_LRGbinding_B1AR" 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="per_sec" units_ref="per_sec"/>
<units name="J_per_K_per_mol" units_ref="J_per_K_per_mol"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
<units name="fmol" units_ref="fmol"/>
<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="per_fmol" units_ref="per_fmol"/>
<units name="fmol_per_sec" units_ref="fmol_per_sec"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="mM" units_ref="mM"/>
<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"/>
<variable initial_value="0" name="q_L_B1_init" units="fmol"/>
<variable initial_value="0.0000508778" name="q_R_B1_init" units="fmol"/>
<variable initial_value="0.0290876489" name="q_Gs_init" units="fmol"/>
<variable initial_value="0" name="q_LR_B1_init" units="fmol"/>
<variable initial_value="0.0000508778" name="q_R_B1Gs_init" units="fmol"/>
<variable initial_value="0.0000508778" name="q_LR_B1Gs_init" units="fmol"/>
<!-- Global value-->
<variable name="q_L_B1" public_interface="out" units="fmol"/>
<variable name="q_R_B1" public_interface="out" units="fmol"/>
<variable name="q_Gs" public_interface="out" units="fmol"/>
<variable name="q_LR_B1" public_interface="out" units="fmol"/>
<variable name="q_R_B1Gs" public_interface="out" units="fmol"/>
<variable name="q_LR_B1Gs" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="q_L_B1_mLRGbinding_B1AR" public_interface="in" units="fmol"/>
<variable name="q_R_B1_mLRGbinding_B1AR" public_interface="in" units="fmol"/>
<variable name="q_Gs_mLRGbinding_B1AR" public_interface="in" units="fmol"/>
<variable name="q_LR_B1_mLRGbinding_B1AR" public_interface="in" units="fmol"/>
<variable name="q_R_B1Gs_mLRGbinding_B1AR" public_interface="in" units="fmol"/>
<variable name="q_LR_B1Gs_mLRGbinding_B1AR" public_interface="in" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_L_B1</ci>
<apply>
<plus/>
<ci>q_L_B1_mLRGbinding_B1AR</ci>
<ci>q_L_B1_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_R_B1</ci>
<apply>
<plus/>
<ci>q_R_B1_mLRGbinding_B1AR</ci>
<ci>q_R_B1_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Gs</ci>
<apply>
<plus/>
<ci>q_Gs_mLRGbinding_B1AR</ci>
<ci>q_Gs_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_B1</ci>
<apply>
<plus/>
<ci>q_LR_B1_mLRGbinding_B1AR</ci>
<ci>q_LR_B1_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_R_B1Gs</ci>
<apply>
<plus/>
<ci>q_R_B1Gs_mLRGbinding_B1AR</ci>
<ci>q_R_B1Gs_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_B1Gs</ci>
<apply>
<plus/>
<ci>q_LR_B1Gs_mLRGbinding_B1AR</ci>
<ci>q_LR_B1Gs_init</ci>
</apply>
</apply>
</math>
</component>
<component name="LRGbinding_parameters">
<variable initial_value="12348" name="kappa_sig1_B1" units="fmol_per_sec"/>
<variable initial_value="115.247" name="kappa_sig2_B1" units="fmol_per_sec"/>
<variable initial_value="25.0713" name="kappa_sig3_B1" units="fmol_per_sec"/>
<variable initial_value="20531.2" name="kappa_sig4_B1" units="fmol_per_sec"/>
<variable initial_value="0.0943832" name="K_L_B1" units="per_fmol"/>
<variable initial_value="0.436088" name="K_R_B1" units="per_fmol"/>
<variable initial_value="0.156932" name="K_Gs" units="per_fmol"/>
<variable initial_value="214.78" name="K_LR_B1" units="per_fmol"/>
<variable initial_value="77.6889" name="K_R_B1Gs" units="per_fmol"/>
<variable initial_value="71.888" name="K_LR_B1Gs" units="per_fmol"/>
</component>
<component name="LRGbinding_B1AR">
<variable name="time" public_interface="in" units="second"/>
<!-- Physical parameters-->
<variable name="R" public_interface="in" units="J_per_K_per_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<!-- Bond graph parameters, found using pinv of kinetic parameters-->
<variable name="kappa_sig1_B1" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_sig2_B1" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_sig3_B1" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_sig4_B1" public_interface="in" units="fmol_per_sec"/>
<variable name="K_L_B1" public_interface="in" units="per_fmol"/>
<variable name="K_R_B1" public_interface="in" units="per_fmol"/>
<variable name="K_Gs" public_interface="in" units="per_fmol"/>
<variable name="K_LR_B1" public_interface="in" units="per_fmol"/>
<variable name="K_R_B1Gs" public_interface="in" units="per_fmol"/>
<variable name="K_LR_B1Gs" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_L_B1_global" public_interface="in" units="fmol"/>
<variable name="q_R_B1_global" public_interface="in" units="fmol"/>
<variable name="q_Gs_global" public_interface="in" units="fmol"/>
<variable name="q_LR_B1_global" public_interface="in" units="fmol"/>
<variable name="q_R_B1Gs_global" public_interface="in" units="fmol"/>
<variable name="q_LR_B1Gs_global" public_interface="in" units="fmol"/>
<!-- Output to global environment-->
<variable initial_value="1e-16" name="q_L_B1" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_R_B1" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_Gs" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_B1" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_R_B1Gs" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_B1Gs" public_interface="out" units="fmol"/>
<!-- Bond variables-->
<variable name="mu_L_B1" units="J_per_mol"/>
<variable name="mu_R_B1" units="J_per_mol"/>
<variable name="mu_Gs" units="J_per_mol"/>
<variable name="mu_LR_B1" units="J_per_mol"/>
<variable name="mu_R_B1Gs" units="J_per_mol"/>
<variable name="mu_LR_B1Gs" units="J_per_mol"/>
<variable name="vsig1_B1" units="fmol_per_sec"/>
<variable name="vsig2_B1" units="fmol_per_sec"/>
<variable name="vsig3_B1" units="fmol_per_sec"/>
<variable name="vsig4_B1" units="fmol_per_sec"/>
<!-- -->
<variable initial_value="34.4" name="vol" units="pL"/>
<!-- Constitutive equations-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_L_B1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_L_B1</ci>
<ci>q_L_B1_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_B1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_B1</ci>
<ci>q_R_B1_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Gs</ci>
<ci>q_Gs_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_B1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_B1</ci>
<ci>q_LR_B1_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_B1Gs</ci>
<ci>q_R_B1Gs_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_B1Gs</ci>
<ci>q_LR_B1Gs_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vsig1_B1</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kappa_sig1_B1</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_B1</ci>
<ci>mu_Gs</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_R_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vsig2_B1</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kappa_sig2_B1</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_B1Gs</ci>
<ci>mu_L_B1</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vsig3_B1</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kappa_sig3_B1</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_LR_B1</ci>
<ci>mu_Gs</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR_B1Gs</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vsig4_B1</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kappa_sig4_B1</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_B1</ci>
<ci>mu_L_B1</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_LR_B1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_L_B1</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>vsig2_B1</ci>
</apply>
<ci>vsig4_B1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_B1</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>vsig1_B1</ci>
</apply>
<ci>vsig4_B1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Gs</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>vsig1_B1</ci>
</apply>
<ci>vsig3_B1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_B1</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>vsig3_B1</ci>
</apply>
<ci>vsig4_B1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_B1Gs</ci>
</apply>
<apply>
<minus/>
<ci>vsig1_B1</ci>
<ci>vsig2_B1</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_B1Gs</ci>
</apply>
<apply>
<plus/>
<ci>vsig2_B1</ci>
<ci>vsig3_B1</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="LRGbinding_B1AR"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_L_B1_mLRGbinding_B1AR" variable_2="q_L_B1"/>
<map_variables variable_1="q_L_B1" variable_2="q_L_B1_global"/>
<map_variables variable_1="q_R_B1_mLRGbinding_B1AR" variable_2="q_R_B1"/>
<map_variables variable_1="q_R_B1" variable_2="q_R_B1_global"/>
<map_variables variable_1="q_Gs_mLRGbinding_B1AR" variable_2="q_Gs"/>
<map_variables variable_1="q_Gs" variable_2="q_Gs_global"/>
<map_variables variable_1="q_LR_B1_mLRGbinding_B1AR" variable_2="q_LR_B1"/>
<map_variables variable_1="q_LR_B1" variable_2="q_LR_B1_global"/>
<map_variables variable_1="q_R_B1Gs_mLRGbinding_B1AR" variable_2="q_R_B1Gs"/>
<map_variables variable_1="q_R_B1Gs" variable_2="q_R_B1Gs_global"/>
<map_variables variable_1="q_LR_B1Gs_mLRGbinding_B1AR" variable_2="q_LR_B1Gs"/>
<map_variables variable_1="q_LR_B1Gs" variable_2="q_LR_B1Gs_global"/>
</connection>
<connection>
<map_components component_1="LRGbinding_parameters" component_2="LRGbinding_B1AR"/>
<map_variables variable_1="kappa_sig1_B1" variable_2="kappa_sig1_B1"/>
<map_variables variable_1="kappa_sig2_B1" variable_2="kappa_sig2_B1"/>
<map_variables variable_1="kappa_sig3_B1" variable_2="kappa_sig3_B1"/>
<map_variables variable_1="kappa_sig4_B1" variable_2="kappa_sig4_B1"/>
<map_variables variable_1="K_L_B1" variable_2="K_L_B1"/>
<map_variables variable_1="K_R_B1" variable_2="K_R_B1"/>
<map_variables variable_1="K_Gs" variable_2="K_Gs"/>
<map_variables variable_1="K_LR_B1" variable_2="K_LR_B1"/>
<map_variables variable_1="K_R_B1Gs" variable_2="K_R_B1Gs"/>
<map_variables variable_1="K_LR_B1Gs" variable_2="K_LR_B1Gs"/>
</connection>
<connection>
<map_components component_1="constants" component_2="LRGbinding_B1AR"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
