- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2025-03-04 11:42:07+13:00
- Desc:
- Adding CellML
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/ca5/rawfile/3f7111fec2c03cdf160291973b2c01fe78f9d260/BG_H_pump.cellml
<?xml version='1.0' encoding='UTF-8'?>
<model name="BG_Hpump" 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/units.cellml">
<units name="fmol" units_ref="fmol"/>
<units name="J_per_K_mol" units_ref="J_per_K_mol"/>
<units name="fmol_per_s" units_ref="fmol_per_s"/>
<units name="J_per_mol" units_ref="J_per_mol"/>
<units name="per_fmol" units_ref="per_fmol"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
</import>
<import xlink:href="params_BG.cellml">
<component component_ref="params_BG" name="params_BG"/>
</import>
<component name="BG_Hpump">
<!-- q1 -- E_o_Pi
q2 -- E_o
q3 -- E_i_ATP
q4 -- E_i_Pi_H-->
<variable name="t" units="second"/>
<variable name="R" public_interface="in" units="J_per_K_mol"/>
<variable name="T" public_interface="in" units="kelvin"/>
<variable name="F" public_interface="in" units="C_per_mol"/>
<variable name="K_Hi" public_interface="in" units="per_fmol"/>
<variable name="q_init_Hi" public_interface="in" units="fmol"/>
<variable name="K_Ho" public_interface="in" units="per_fmol"/>
<variable name="q_init_Ho" public_interface="in" units="fmol"/>
<variable name="K_Pi" public_interface="in" units="per_fmol"/>
<variable name="q_init_Pi" public_interface="in" units="fmol"/>
<variable name="K_ATPi" public_interface="in" units="per_fmol"/>
<variable name="q_init_ATPi" public_interface="in" units="fmol"/>
<variable name="K_ADPi" public_interface="in" units="per_fmol"/>
<variable name="q_init_ADPi" public_interface="in" units="fmol"/>
<variable name="K_1" public_interface="in" units="per_fmol"/>
<variable name="q_init_1" public_interface="in" units="fmol"/>
<variable name="K_2" public_interface="in" units="per_fmol"/>
<variable name="q_init_2" public_interface="in" units="fmol"/>
<variable name="K_3" public_interface="in" units="per_fmol"/>
<variable name="q_init_3" public_interface="in" units="fmol"/>
<variable name="K_4" public_interface="in" units="per_fmol"/>
<variable name="q_init_4" public_interface="in" units="fmol"/>
<variable name="kappa_r1" public_interface="in" units="fmol_per_s"/>
<variable name="kappa_r2" public_interface="in" units="fmol_per_s"/>
<variable name="kappa_r3" public_interface="in" units="fmol_per_s"/>
<variable name="kappa_r4" public_interface="in" units="fmol_per_s"/>
<variable name="mu_Hi" units="J_per_mol"/>
<variable name="mu_Ho" units="J_per_mol"/>
<variable name="mu_Pi" units="J_per_mol"/>
<variable name="mu_ATPi" units="J_per_mol"/>
<variable name="mu_ADPi" units="J_per_mol"/>
<variable name="mu_1" units="J_per_mol"/>
<variable name="v_1" units="fmol_per_s"/>
<variable name="mu_2" units="J_per_mol"/>
<variable name="v_2" units="fmol_per_s"/>
<variable name="mu_3" units="J_per_mol"/>
<variable name="v_3" units="fmol_per_s"/>
<variable name="mu_4" units="J_per_mol"/>
<variable name="v_4" units="fmol_per_s"/>
<variable name="A_f_r1" units="J_per_mol"/>
<variable name="v_r1" units="fmol_per_s"/>
<variable name="A_r_r1" units="J_per_mol"/>
<variable name="A_f_r2" units="J_per_mol"/>
<variable name="v_r2" units="fmol_per_s"/>
<variable name="A_r_r2" units="J_per_mol"/>
<variable name="A_f_r3" units="J_per_mol"/>
<variable name="v_r3" units="fmol_per_s"/>
<variable name="A_r_r3" units="J_per_mol"/>
<variable name="A_f_r4" units="J_per_mol"/>
<variable name="v_r4" units="fmol_per_s"/>
<variable name="A_r_r4" units="J_per_mol"/>
<variable name="q_Hi" units="fmol"/>
<variable name="q_Ho" units="fmol"/>
<variable name="q_Pi" units="fmol"/>
<variable name="q_ATPi" units="fmol"/>
<variable name="q_ADPi" units="fmol"/>
<variable initial_value="q_init_1" name="q_1" units="fmol"/>
<variable initial_value="q_init_2" name="q_2" units="fmol"/>
<variable initial_value="q_init_3" name="q_3" units="fmol"/>
<variable initial_value="q_init_4" name="q_4" units="fmol"/>
<variable name="z_zr1" public_interface="in" units="dimensionless"/>
<variable name="z_zr2" public_interface="in" units="dimensionless"/>
<variable name="mu_zr1" units="J_per_mol"/>
<variable name="mu_zr2" units="J_per_mol"/>
<variable name="V_Vm" units="volt"/>
<variable name="V0_Vm" public_interface="in" units="volt"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>V0_Vm</ci>
<ci>V_Vm</ci>
</apply>
<apply>
<eq/>
<ci>mu_Hi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Hi</ci>
<ci>q_Hi</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Hi</ci>
<ci>q_init_Hi</ci>
</apply>
<apply>
<eq/>
<ci>mu_Ho</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_Ho</ci>
<ci>q_Ho</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>q_Ho</ci>
<ci>q_init_Ho</ci>
</apply>
<apply>
<eq/>
<ci>q_Pi</ci>
<ci>q_init_Pi</ci>
</apply>
<apply>
<eq/>
<ci>q_ATPi</ci>
<ci>q_init_ATPi</ci>
</apply>
<apply>
<eq/>
<ci>q_ADPi</ci>
<ci>q_init_ADPi</ci>
</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_ATPi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ATPi</ci>
<ci>q_ATPi</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_ADPi</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ADPi</ci>
<ci>q_ADPi</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_1</ci>
<ci>q_1</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_1</ci>
</apply>
<ci>v_1</ci>
</apply>
<apply>
<eq/>
<ci>mu_2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_2</ci>
<ci>q_2</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_2</ci>
</apply>
<ci>v_2</ci>
</apply>
<apply>
<eq/>
<ci>mu_3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_3</ci>
<ci>q_3</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_3</ci>
</apply>
<ci>v_3</ci>
</apply>
<apply>
<eq/>
<ci>mu_4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_4</ci>
<ci>q_4</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_4</ci>
</apply>
<ci>v_4</ci>
</apply>
<apply>
<eq/>
<ci>v_r1</ci>
<apply>
<times/>
<ci>kappa_r1</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_f_r1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_r_r1</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_r2</ci>
<apply>
<times/>
<ci>kappa_r2</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_f_r2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_r_r2</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_r3</ci>
<apply>
<times/>
<ci>kappa_r3</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_f_r3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_r_r3</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_r4</ci>
<apply>
<times/>
<ci>kappa_r4</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_f_r4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>A_r_r4</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_1</ci>
<apply>
<minus/>
<ci>v_r4</ci>
<ci>v_r1</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_2</ci>
<apply>
<minus/>
<ci>v_r1</ci>
<ci>v_r2</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_3</ci>
<apply>
<minus/>
<ci>v_r2</ci>
<ci>v_r3</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>v_4</ci>
<apply>
<minus/>
<ci>v_r3</ci>
<ci>v_r4</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_zr1</ci>
<apply>
<times/>
<ci>z_zr1</ci>
<ci>F</ci>
<ci>V_Vm</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_zr2</ci>
<apply>
<times/>
<ci>z_zr2</ci>
<ci>F</ci>
<ci>V_Vm</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>A_f_r1</ci>
<ci>mu_1</ci>
</apply>
<apply>
<eq/>
<ci>A_r_r1</ci>
<apply>
<plus/>
<ci>mu_2</ci>
<ci>mu_Pi</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>A_f_r2</ci>
<apply>
<plus/>
<ci>mu_2</ci>
<ci>mu_ATPi</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>A_r_r2</ci>
<ci>mu_3</ci>
</apply>
<apply>
<eq/>
<ci>A_f_r3</ci>
<apply>
<plus/>
<ci>mu_3</ci>
<ci>mu_Hi</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>A_r_r3</ci>
<apply>
<plus/>
<ci>mu_4</ci>
<ci>mu_ADPi</ci>
<ci>mu_zr1</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>A_f_r4</ci>
<ci>mu_4</ci>
</apply>
<apply>
<eq/>
<ci>A_r_r4</ci>
<apply>
<plus/>
<ci>mu_1</ci>
<ci>mu_Ho</ci>
<ci>mu_zr2</ci>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="params_BG" component_2="BG_Hpump"/>
<map_variables variable_1="R" variable_2="R"/>
<map_variables variable_1="T" variable_2="T"/>
<map_variables variable_1="F" variable_2="F"/>
<map_variables variable_1="K_Hi" variable_2="K_Hi"/>
<map_variables variable_1="q_init_Hi" variable_2="q_init_Hi"/>
<map_variables variable_1="K_Ho" variable_2="K_Ho"/>
<map_variables variable_1="q_init_Ho" variable_2="q_init_Ho"/>
<map_variables variable_1="K_Pi" variable_2="K_Pi"/>
<map_variables variable_1="q_init_Pi" variable_2="q_init_Pi"/>
<map_variables variable_1="K_ATPi" variable_2="K_ATPi"/>
<map_variables variable_1="q_init_ATPi" variable_2="q_init_ATPi"/>
<map_variables variable_1="K_ADPi" variable_2="K_ADPi"/>
<map_variables variable_1="q_init_ADPi" variable_2="q_init_ADPi"/>
<map_variables variable_1="K_1" variable_2="K_1"/>
<map_variables variable_1="q_init_1" variable_2="q_init_1"/>
<map_variables variable_1="K_2" variable_2="K_2"/>
<map_variables variable_1="q_init_2" variable_2="q_init_2"/>
<map_variables variable_1="K_3" variable_2="K_3"/>
<map_variables variable_1="q_init_3" variable_2="q_init_3"/>
<map_variables variable_1="K_4" variable_2="K_4"/>
<map_variables variable_1="q_init_4" variable_2="q_init_4"/>
<map_variables variable_1="kappa_r1" variable_2="kappa_r1"/>
<map_variables variable_1="kappa_r2" variable_2="kappa_r2"/>
<map_variables variable_1="kappa_r3" variable_2="kappa_r3"/>
<map_variables variable_1="kappa_r4" variable_2="kappa_r4"/>
<map_variables variable_1="z_zr1" variable_2="z_zr1"/>
<map_variables variable_1="z_zr2" variable_2="z_zr2"/>
<map_variables variable_1="V_E" variable_2="V0_Vm"/>
</connection>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#model">
<bqs:reference xmlns:bqs="http://www.cellml.org/bqs/1.0#" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<dc:subject xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<bqs:subject_type xmlns:bqs="http://www.cellml.org/bqs/1.0#">keyword</bqs:subject_type>
<rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Bag xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:li xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">protein-modules</rdf:li>
</rdf:Bag>
</rdf:value>
</dc:subject>
</bqs:reference>
</rdf:Description>
</rdf:RDF>
</model>
