- Author:
- Soroush <ssaf006@aucklanduni.ac.nz>
- Date:
- 2020-05-10 21:27:00+12:00
- Desc:
- added new sedml
- Permanent Source URI:
- https://models.fieldml.org/workspace/297/rawfile/5c6d2c520a9faad399fd954401d658362d25ef03/BG/pH-BG.cellml
<?xml version='1.0'?>
<model name="Boron" 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="mM" units_ref="mol_per_m3"/>
<units name="mM_per_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="per_mM" 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>
<component name="main">
<variable name="t" units="second"/>
<variable initial_value="-0.057" name="mu_E" units="J_per_C"/>
<variable name="q_CO2_o" units="mM"/>
<variable initial_value="0.0" name="q_CO2_i" units="mM"/>
<variable initial_value="0.0" name="q_HCO3_i" units="mM"/>
<variable initial_value="0.0" name="q_HCO3_o" units="mM"/>
<variable initial_value="3.981071705534970e-05" name="q_H_i" units="mM"/>
<variable initial_value="1.995262314968879e-05" name="q_H_o" units="mM"/>
<variable initial_value="5.011872336272725e-05" name="q_H_Lim" units="mM"/>
<variable name="pH_i" units="dimensionless"/>
<variable name="pH_o" units="dimensionless"/>
<variable name="pH_Lim" units="dimensionless"/>
<variable name="v_Re_1" units="mM_per_s"/>
<variable name="v_Re_2" units="mM_per_s"/>
<variable name="v_Re_3" units="mM_per_s"/>
<variable name="v_Re_4" units="mM_per_s"/>
<variable name="v_Re_5" units="mM_per_s"/>
<variable initial_value="0.00001" name="K_CO2_o" public_interface="out" units="per_mM"/>
<variable initial_value="0.00001" name="K_CO2_i" public_interface="out" units="per_mM"/>
<variable initial_value="0.1" name="K_HCO3_o" public_interface="out" units="per_mM"/>
<variable initial_value="0.1" name="K_HCO3_i" public_interface="out" units="per_mM"/>
<variable initial_value="0.1" name="K_H_o" public_interface="out" units="per_mM"/>
<variable initial_value="0.1" name="K_H_i" public_interface="out" units="per_mM"/>
<variable initial_value="1e6" name="k_Re_1" public_interface="out" units="mM_per_s"/>
<variable initial_value="1e6" name="k_Re_2" public_interface="out" units="mM_per_s"/>
<variable initial_value="0.48" name="k_Re_3" public_interface="out" units="per_s"/>
<variable initial_value="300" name="k_Re_4" public_interface="out" units="per_s"/>
<variable initial_value="4e-5" name="k_Re_5" public_interface="out" units="mM_per_s"/>
<variable initial_value="296" name="T" units="kelvin"/>
<variable initial_value="8.314" name="R" units="J_per_mol_K"/>
<variable initial_value="96485" name="F" units="C_per_mol"/>
<variable initial_value="-1" name="z" units="dimensionless"/>
<variable initial_value="8000" name="rho" units="per_m"/>
<variable initial_value="26" name="beta" units="mM"/>
<variable initial_value="6e-5" name="P_CO2" units="m_per_s"/>
<variable initial_value="5e-9" name="P_HCO3" units="m_per_s"/>
<variable initial_value="1e-3" name="K_A" units="mM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>pH_Lim</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="per_mM" type="e-notation">1<sep/>-3</cn>
<ci>q_H_Lim</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_i</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="per_mM" type="e-notation">1<sep/>-3</cn>
<ci>q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>pH_o</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn cellml:units="per_mM" type="e-notation">1<sep/>-3</cn>
<ci>q_H_o</ci>
</apply>
</apply>
</apply>
</apply>
<!-- quantity equations-->
<apply>
<eq/>
<ci>q_CO2_o</ci>
<piecewise>
<piece>
<cn cellml:units="mM">0.0</cn>
<apply>
<lt/>
<ci>t</ci>
<cn cellml:units="second">100</cn>
</apply>
</piece>
<piece>
<cn cellml:units="mM">1.1877</cn>
<apply>
<lt/>
<ci>t</ci>
<cn cellml:units="second">2800</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="mM">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_3</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_1</ci>
<ci>v_Re_5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_HCO3_i</ci>
</apply>
<apply>
<plus/>
<ci>v_Re_2</ci>
<ci>v_Re_5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_H_i</ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="dimensionless">2.303</cn>
<ci>q_H_i</ci>
</apply>
<ci>beta</ci>
</apply>
<apply>
<minus/>
<ci>v_Re_2</ci>
<ci>v_Re_4</ci>
</apply>
</apply>
</apply>
<!-- flow equations-->
<apply>
<eq/>
<ci>v_Re_1</ci>
<apply>
<times/>
<ci>k_Re_1</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_CO2_o</ci>
<ci>q_CO2_o</ci>
</apply>
<apply>
<times/>
<ci>K_HCO3_o</ci>
<ci>q_HCO3_o</ci>
<ci>K_H_o</ci>
<ci>q_H_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_2</ci>
<apply>
<times/>
<ci>k_Re_2</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_CO2_i</ci>
<ci>q_CO2_i</ci>
</apply>
<apply>
<times/>
<ci>K_HCO3_i</ci>
<ci>q_HCO3_i</ci>
<ci>K_H_i</ci>
<ci>q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_3</ci>
<apply>
<times/>
<ci>k_Re_3</ci>
<apply>
<minus/>
<ci>q_CO2_o</ci>
<ci>q_CO2_i</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_Re_4</ci>
<piecewise>
<piece>
<apply>
<times/>
<ci>k_Re_4</ci>
<apply>
<minus/>
<ci>q_H_i</ci>
<ci>q_H_Lim</ci>
</apply>
</apply>
<apply>
<lt/>
<ci>pH_i</ci>
<ci>pH_Lim</ci>
</apply>
</piece>
<otherwise>
<cn cellml:units="mM_per_s">0.0</cn>
</otherwise>
</piecewise>
</apply>
<apply>
<eq/>
<ci>v_Re_5</ci>
<apply>
<times/>
<ci>k_Re_5</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_HCO3_o</ci>
<ci>q_HCO3_o</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<times/>
<ci>z</ci>
<ci>F</ci>
<ci>mu_E</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci>K_HCO3_i</ci>
<ci>q_HCO3_i</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
</model>
