- Author:
- Soroush Safaei <ssaf006@aucklanduni.ac.nz>
- Date:
- 2017-02-14 18:00:14+13:00
- Desc:
- I changed the parameters
- Permanent Source URI:
- https://models.cellml.org/workspace/297/rawfile/e6833ef12268a3202757b76191bfa57f7e55d867/BG/Acid_BG.cellml
<?xml version='1.0'?>
<model name="Acid_BG" 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.cellml">
<units name="mol_per_m3" units_ref="mol_per_m3"/>
<units name="mol_per_m3_s" units_ref="mol_per_m3_s"/>
<units name="per_m" units_ref="per_m"/>
<units name="per_s" units_ref="per_s"/>
<units name="m_per_s" units_ref="m_per_s"/>
<units name="m3_per_mol" units_ref="m3_per_mol"/>
<units name="J_per_mol_K" units_ref="J_per_mol_K"/>
<units name="J_per_C" units_ref="J_per_C"/>
<units name="C_per_mol" units_ref="C_per_mol"/>
</import>
<import xlink:href="Parameters.cellml">
<component component_ref="Parameters" name="Parameters"/>
</import>
<import xlink:href="Passive_Diffusion_module.cellml">
<component component_ref="module" name="CO2_Diffusion"/>
</import>
<import xlink:href="Passive_Diffusion_module.cellml">
<component component_ref="module" name="NH3_Diffusion"/>
</import>
<import xlink:href="Ion_Channel_module.cellml">
<component component_ref="module" name="NH4_Channel"/>
</import>
<import xlink:href="Ion_Channel_module.cellml">
<component component_ref="module" name="HCO3_Channel"/>
</import>
<import xlink:href="Ion_Channel_module.cellml">
<component component_ref="module" name="H_Channel"/>
</import>
<import xlink:href="Acid_Hydration_module.cellml">
<component component_ref="module" name="CO2_Hydration_int"/>
</import>
<import xlink:href="Acid_Hydration_module.cellml">
<component component_ref="module" name="NH4_Hydration_int"/>
</import>
<component name="AcidBase">
<variable initial_value="0.000000000006" name="u_E" public_interface="out" units="J_per_C"/>
<variable initial_value="0" name="q_CO2_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_CO2_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_HCO3_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_HCO3_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_NH4_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_NH4_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="0" name="q_NH3_i" public_interface="out" units="mol_per_m3"/>
<variable name="q_NH3_o" public_interface="out" units="mol_per_m3"/>
<variable initial_value="40e-6" name="q_H_i" public_interface="out" units="mol_per_m3"/>
<variable initial_value="20e-6" name="q_H_o" public_interface="out" units="mol_per_m3"/>
<variable name="v_Re_1" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_2" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_3" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_4" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_5" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_6" public_interface="in" units="mol_per_m3_s"/>
<variable name="v_Re_7" public_interface="in" units="mol_per_m3_s"/>
<variable name="pH_o" units="dimensionless"/>
<variable name="pH_i" units="dimensionless"/>
<variable name="t" public_interface="out" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_CO2_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_1</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>q_NH3_o</ci>
<piecewise>
<piece>
<cn cellml:units="dimensionless">0.00001</cn>
<apply>
<lt/>
<ci>t</ci>
<cn cellml:units="second">600</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">0.0</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_CO2_i</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_1</ci>
<ci>v_Re_2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_HCO3_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_3</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_HCO3_i</ci>
</apply>
<apply>
<plus/>
<ci>v_Re_3</ci>
<ci>v_Re_2</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH4_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_4</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH4_i</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_4</ci>
<ci>v_Re_5</ci>
</apply>
</apply>
<!-- ode(q_NH3_o, t) = -v_Re_6;-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH3_i</ci>
</apply>
<apply>
<plus/>
<ci>v_Re_6</ci>
<ci>v_Re_5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_H_o</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_7</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_H_i</ci>
</apply>
<apply>
<plus/>
<ci>v_Re_7</ci>
<ci>v_Re_2</ci>
<ci>v_Re_5</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_o</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="dimensionless" type="e-notation">1<sep/>-3</cn>
<ci>q_H_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_i</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="dimensionless" type="e-notation">1<sep/>-3</cn>
<ci>q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<connection>
<map_components component_1="CO2_Diffusion" component_2="AcidBase"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="q_o" variable_2="q_CO2_o"/>
<map_variables variable_1="q_i" variable_2="q_CO2_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_1"/>
</connection>
<connection>
<map_components component_1="CO2_Diffusion" component_2="Parameters"/>
<map_variables variable_1="K_Re" variable_2="K_Re_1"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="NH3_Diffusion" component_2="AcidBase"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="q_o" variable_2="q_NH3_o"/>
<map_variables variable_1="q_i" variable_2="q_NH3_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_6"/>
</connection>
<connection>
<map_components component_1="NH3_Diffusion" component_2="Parameters"/>
<map_variables variable_1="K_Re" variable_2="K_Re_6"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="NH4_Channel" component_2="AcidBase"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="u_E" variable_2="u_E"/>
<map_variables variable_1="q_o" variable_2="q_NH4_o"/>
<map_variables variable_1="q_i" variable_2="q_NH4_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_4"/>
</connection>
<connection>
<map_components component_1="NH4_Channel" component_2="Parameters"/>
<map_variables variable_1="K_Re" variable_2="K_Re_4"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="HCO3_Channel" component_2="AcidBase"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="u_E" variable_2="u_E"/>
<map_variables variable_1="q_o" variable_2="q_HCO3_o"/>
<map_variables variable_1="q_i" variable_2="q_HCO3_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_3"/>
</connection>
<connection>
<map_components component_1="HCO3_Channel" component_2="Parameters"/>
<map_variables variable_1="K_Re" variable_2="K_Re_3"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="H_Channel" component_2="AcidBase"/>
<map_variables variable_1="t" variable_2="t"/>
<map_variables variable_1="u_E" variable_2="u_E"/>
<map_variables variable_1="q_o" variable_2="q_H_o"/>
<map_variables variable_1="q_i" variable_2="q_H_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_7"/>
</connection>
<connection>
<map_components component_1="H_Channel" component_2="Parameters"/>
<map_variables variable_1="K_Re" variable_2="K_Re_7"/>
<map_variables variable_1="rho" variable_2="rho"/>
</connection>
<connection>
<map_components component_1="CO2_Hydration_int" component_2="AcidBase"/>
<map_variables variable_1="q_H" variable_2="q_H_i"/>
<map_variables variable_1="q_acid_weak" variable_2="q_CO2_i"/>
<map_variables variable_1="q_base_conj" variable_2="q_HCO3_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_2"/>
</connection>
<connection>
<map_components component_1="CO2_Hydration_int" component_2="Parameters"/>
<map_variables variable_1="K_Re" variable_2="K_Re_2"/>
<map_variables variable_1="K_H" variable_2="K_H_i"/>
<map_variables variable_1="K_acid_weak" variable_2="K_CO2_i"/>
<map_variables variable_1="K_base_conj" variable_2="K_HCO3_i"/>
</connection>
<connection>
<map_components component_1="NH4_Hydration_int" component_2="AcidBase"/>
<map_variables variable_1="q_H" variable_2="q_H_i"/>
<map_variables variable_1="q_acid_weak" variable_2="q_NH4_i"/>
<map_variables variable_1="q_base_conj" variable_2="q_NH3_i"/>
<map_variables variable_1="v_Re" variable_2="v_Re_5"/>
</connection>
<connection>
<map_components component_1="NH4_Hydration_int" component_2="Parameters"/>
<map_variables variable_1="K_Re" variable_2="K_Re_5"/>
<map_variables variable_1="K_H" variable_2="K_H_i"/>
<map_variables variable_1="K_acid_weak" variable_2="K_NH4_i"/>
<map_variables variable_1="K_base_conj" variable_2="K_NH3_i"/>
</connection>
</model>
