- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-10-04 15:43:15+13:00
- Desc:
- adding mu_Pi to reaction velocities
- Permanent Source URI:
- https://models.cellml.org/workspace/6f9/rawfile/80f3a851cec1c487b4d2e024b519e218b31b42fc/BG_GiProtein.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_GiProtein" 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"/>
<!--Initial conditions-->
<variable initial_value="0.000219725" name="q_R_M2_init" units="fmol"/>
<variable initial_value="0.145305" name="q_Gi_init" units="fmol"/>
<variable initial_value="1e-6" name="q_R_M2Gi_init" units="fmol"/>
<variable initial_value="1.697e-06" name="q_LR_M2_init" units="fmol"/>
<variable initial_value="1e-6" name="q_LR_M2Gi_init" units="fmol"/>
<variable initial_value="0.0009519" name="q_aGi_GTP_init" units="fmol"/>
<variable initial_value="0.00097622" name="q_beta_gamma_Gi_init" units="fmol"/>
<variable initial_value="2.44948e-05" name="q_aGi_GDP_init" units="fmol"/>
<variable initial_value="570" name="q_Pi_init" units="fmol"/>
<!-- Global value-->
<variable name="q_R_M2" public_interface="out" units="fmol"/>
<variable name="q_Gi" public_interface="out" units="fmol"/>
<variable name="q_R_M2Gi" public_interface="out" units="fmol"/>
<variable name="q_LR_M2" public_interface="out" units="fmol"/>
<variable name="q_LR_M2Gi" public_interface="out" units="fmol"/>
<variable name="q_aGi_GTP" public_interface="out" units="fmol"/>
<variable name="q_beta_gamma_Gi" public_interface="out" units="fmol"/>
<variable name="q_aGi_GDP" public_interface="out" units="fmol"/>
<variable name="q_Pi" public_interface="out" units="fmol"/>
<!-- From submodule-->
<variable name="q_R_M2_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_Gi_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_R_M2Gi_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_LR_M2_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_LR_M2Gi_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_aGi_GTP_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_beta_gamma_Gi_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_aGi_GDP_mGiProtein" public_interface="in" units="fmol"/>
<variable name="q_Pi_mGiProtein" public_interface="in" units="fmol"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>q_R_M2</ci>
<apply>
<plus/>
<ci>q_R_M2_mGiProtein</ci>
<ci>q_R_M2_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Gi</ci>
<apply>
<plus/>
<ci>q_Gi_mGiProtein</ci>
<ci>q_Gi_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_R_M2Gi</ci>
<apply>
<plus/>
<ci>q_R_M2Gi_mGiProtein</ci>
<ci>q_R_M2Gi_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_M2</ci>
<apply>
<plus/>
<ci>q_LR_M2_mGiProtein</ci>
<ci>q_LR_M2_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_LR_M2Gi</ci>
<apply>
<plus/>
<ci>q_LR_M2Gi_mGiProtein</ci>
<ci>q_LR_M2Gi_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_aGi_GTP</ci>
<apply>
<plus/>
<ci>q_aGi_GTP_mGiProtein</ci>
<ci>q_aGi_GTP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_beta_gamma_Gi</ci>
<apply>
<plus/>
<ci>q_beta_gamma_Gi_mGiProtein</ci>
<ci>q_beta_gamma_Gi_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_aGi_GDP</ci>
<apply>
<plus/>
<ci>q_aGi_GDP_mGiProtein</ci>
<ci>q_aGi_GDP_init</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Pi</ci>
<apply>
<plus/>
<ci>q_Pi_mGiProtein</ci>
<ci>q_Pi_init</ci>
</apply>
</apply>
</math>
</component>
<component name="GiProtein_parameters">
<variable initial_value="0.16294" name="kappa_act1_Gi" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.0230431" name="kappa_act2_Gi" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="1.31745" name="kappa_hyd_Gi" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="190969" name="kappa_reassoc_Gi" public_interface="out" units="fmol_per_sec"/>
<variable initial_value="0.00473662" name="K_R_M2" public_interface="out" units="per_fmol"/>
<variable initial_value="368.378" name="K_Gi" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0290698" name="K_R_M2Gi" public_interface="out" units="per_fmol"/>
<variable initial_value="0.000669859" name="K_LR_M2" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0290698" name="K_LR_M2Gi" public_interface="out" units="per_fmol"/>
<variable initial_value="0.0176522" name="K_aGi_GTP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00180315" name="K_beta_gamma_Gi" public_interface="out" units="per_fmol"/>
<variable initial_value="0.00296944" name="K_aGi_GDP" public_interface="out" units="per_fmol"/>
<variable initial_value="0.000216011" name="K_Pi" public_interface="out" units="per_fmol"/>
</component>
<component name="GiProtein">
<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"/>
<!-- BG parameters-->
<variable name="kappa_act1_Gi" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_act2_Gi" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_hyd_Gi" public_interface="in" units="fmol_per_sec"/>
<variable name="kappa_reassoc_Gi" public_interface="in" units="fmol_per_sec"/>
<variable name="K_R_M2" public_interface="in" units="per_fmol"/>
<variable name="K_Gi" public_interface="in" units="per_fmol"/>
<variable name="K_R_M2Gi" public_interface="in" units="per_fmol"/>
<variable name="K_LR_M2" public_interface="in" units="per_fmol"/>
<variable name="K_LR_M2Gi" public_interface="in" units="per_fmol"/>
<variable name="K_aGi_GTP" public_interface="in" units="per_fmol"/>
<variable name="K_beta_gamma_Gi" public_interface="in" units="per_fmol"/>
<variable name="K_aGi_GDP" public_interface="in" units="per_fmol"/>
<variable name="K_Pi" public_interface="in" units="per_fmol"/>
<!-- Input from global environment-->
<variable name="q_R_M2_global" public_interface="in" units="fmol"/>
<variable name="q_Gi_global" public_interface="in" units="fmol"/>
<variable name="q_R_M2Gi_global" public_interface="in" units="fmol"/>
<variable name="q_LR_M2_global" public_interface="in" units="fmol"/>
<variable name="q_LR_M2Gi_global" public_interface="in" units="fmol"/>
<variable name="q_aGi_GTP_global" public_interface="in" units="fmol"/>
<variable name="q_beta_gamma_Gi_global" public_interface="in" units="fmol"/>
<variable name="q_aGi_GDP_global" public_interface="in" units="fmol"/>
<variable name="q_Pi_global" public_interface="in" units="fmol"/>
<!-- Output to global environment-->
<variable initial_value="1e-16" name="q_R_M2" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_Gi" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_R_M2Gi" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_M2" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_LR_M2Gi" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_aGi_GTP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_beta_gamma_Gi" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_aGi_GDP" public_interface="out" units="fmol"/>
<variable initial_value="1e-16" name="q_Pi" public_interface="out" units="fmol"/>
<!-- Bond variables-->
<variable name="vact1_Gi" units="fmol_per_sec"/>
<variable name="vact2_Gi" units="fmol_per_sec"/>
<variable name="vhyd_Gi" units="fmol_per_sec"/>
<variable name="vreassoc_Gi" units="fmol_per_sec"/>
<variable name="mu_R_M2" units="J_per_mol"/>
<variable name="mu_Gi" units="J_per_mol"/>
<variable name="mu_R_M2Gi" units="J_per_mol"/>
<variable name="mu_LR_M2" units="J_per_mol"/>
<variable name="mu_LR_M2Gi" units="J_per_mol"/>
<variable name="mu_aGi_GTP" units="J_per_mol"/>
<variable name="mu_beta_gamma_Gi" units="J_per_mol"/>
<variable name="mu_aGi_GDP" units="J_per_mol"/>
<variable name="mu_Pi" units="J_per_mol"/>
<!-- Constitutive equations-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>mu_R_M2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_M2</ci>
<ci>q_R_M2_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Gi</ci>
<ci>q_Gi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_R_M2Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_R_M2Gi</ci>
<ci>q_R_M2Gi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_M2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_M2</ci>
<ci>q_LR_M2_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_LR_M2Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_LR_M2Gi</ci>
<ci>q_LR_M2Gi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_aGi_GTP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_aGi_GTP</ci>
<ci>q_aGi_GTP_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_beta_gamma_Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_beta_gamma_Gi</ci>
<ci>q_beta_gamma_Gi_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_aGi_GDP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_aGi_GDP</ci>
<ci>q_aGi_GDP_global</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_global</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vact1_Gi</ci>
<apply>
<times/>
<ci>kappa_act1_Gi</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_R_M2</ci>
<ci>mu_Gi</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_aGi_GTP</ci>
<ci>mu_beta_gamma_Gi</ci>
<ci>mu_R_M2</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vact2_Gi</ci>
<apply>
<times/>
<ci>kappa_act2_Gi</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_LR_M2</ci>
<ci>mu_Gi</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_aGi_GTP</ci>
<ci>mu_beta_gamma_Gi</ci>
<ci>mu_LR_M2</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vhyd_Gi</ci>
<apply>
<times/>
<ci>kappa_hyd_Gi</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_aGi_GTP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_aGi_GDP</ci>
<ci>mu_Pi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>vreassoc_Gi</ci>
<apply>
<times/>
<ci>kappa_reassoc_Gi</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_aGi_GDP</ci>
<ci>mu_beta_gamma_Gi</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_Gi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_M2</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_R_M2Gi</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_Gi</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>vact1_Gi</ci>
</apply>
<ci>vact2_Gi</ci>
</apply>
<ci>vreassoc_Gi</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_M2</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_LR_M2Gi</ci>
</apply>
<cn cellml:units="fmol_per_sec">0</cn>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_aGi_GTP</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>vact1_Gi</ci>
<ci>vact2_Gi</ci>
</apply>
<ci>vhyd_Gi</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_beta_gamma_Gi</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>vact1_Gi</ci>
<ci>vact2_Gi</ci>
</apply>
<ci>vreassoc_Gi</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci>q_aGi_GDP</ci>
</apply>
<apply>
<minus/>
<ci>vhyd_Gi</ci>
<ci>vreassoc_Gi</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="environment" component_2="GiProtein"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="q_R_M2_mGiProtein" variable_2="q_R_M2"/>
<map_variables variable_1="q_R_M2" variable_2="q_R_M2_global"/>
<map_variables variable_1="q_Gi_mGiProtein" variable_2="q_Gi"/>
<map_variables variable_1="q_Gi" variable_2="q_Gi_global"/>
<map_variables variable_1="q_R_M2Gi_mGiProtein" variable_2="q_R_M2Gi"/>
<map_variables variable_1="q_R_M2Gi" variable_2="q_R_M2Gi_global"/>
<map_variables variable_1="q_LR_M2_mGiProtein" variable_2="q_LR_M2"/>
<map_variables variable_1="q_LR_M2" variable_2="q_LR_M2_global"/>
<map_variables variable_1="q_LR_M2Gi_mGiProtein" variable_2="q_LR_M2Gi"/>
<map_variables variable_1="q_LR_M2Gi" variable_2="q_LR_M2Gi_global"/>
<map_variables variable_1="q_aGi_GTP_mGiProtein" variable_2="q_aGi_GTP"/>
<map_variables variable_1="q_aGi_GTP" variable_2="q_aGi_GTP_global"/>
<map_variables variable_1="q_beta_gamma_Gi_mGiProtein" variable_2="q_beta_gamma_Gi"/>
<map_variables variable_1="q_beta_gamma_Gi" variable_2="q_beta_gamma_Gi_global"/>
<map_variables variable_1="q_aGi_GDP_mGiProtein" variable_2="q_aGi_GDP"/>
<map_variables variable_1="q_aGi_GDP" variable_2="q_aGi_GDP_global"/>
<map_variables variable_1="q_Pi_mGiProtein" variable_2="q_Pi"/>
<map_variables variable_1="q_Pi" variable_2="q_Pi_global"/>
</connection>
<connection>
<map_components component_1="GiProtein_parameters" component_2="GiProtein"/>
<map_variables variable_1="kappa_act1_Gi" variable_2="kappa_act1_Gi"/>
<map_variables variable_1="kappa_act2_Gi" variable_2="kappa_act2_Gi"/>
<map_variables variable_1="kappa_hyd_Gi" variable_2="kappa_hyd_Gi"/>
<map_variables variable_1="kappa_reassoc_Gi" variable_2="kappa_reassoc_Gi"/>
<map_variables variable_1="K_R_M2" variable_2="K_R_M2"/>
<map_variables variable_1="K_Gi" variable_2="K_Gi"/>
<map_variables variable_1="K_R_M2Gi" variable_2="K_R_M2Gi"/>
<map_variables variable_1="K_LR_M2" variable_2="K_LR_M2"/>
<map_variables variable_1="K_LR_M2Gi" variable_2="K_LR_M2Gi"/>
<map_variables variable_1="K_aGi_GTP" variable_2="K_aGi_GTP"/>
<map_variables variable_1="K_beta_gamma_Gi" variable_2="K_beta_gamma_Gi"/>
<map_variables variable_1="K_aGi_GDP" variable_2="K_aGi_GDP"/>
<map_variables variable_1="K_Pi" variable_2="K_Pi"/>
</connection>
<connection>
<map_components component_1="constants" component_2="GiProtein"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
</connection>
</model>
