- Author:
- WeiweiAi <wai484@aucklanduni.ac.nz>
- Date:
- 2024-02-09 13:41:13+13:00
- Desc:
- Add new model *fit_1.cellml;
Refit CO2_BG_V3;
Boron_acid_BG_V3_Hi using Boron version of ODE for q_H_i;
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/b61/rawfile/2325464752c3a2c9916a3a792f1e1ffc3ccf73b2/models/CellMLV2/Boron_base_BG_V3.cellml
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/2.0#" name="BG51">
<units name="dim">
<unit units="dimensionless"/>
</units>
<units name="per_s">
<unit exponent="-1" units="second"/>
</units>
<units name="mol_per_s">
<unit units="mole"/>
<unit exponent="-1" units="second"/>
</units>
<units name="per_mol">
<unit exponent="-1" units="mole"/>
</units>
<units name="per_mol2">
<unit exponent="-2" units="mole"/>
</units>
<units name="C_per_mol">
<unit units="coulomb"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="J_per_mol">
<unit units="joule"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="J_per_C">
<unit units="joule"/>
<unit exponent="-1" units="coulomb"/>
</units>
<component name="main">
<variable name="t" units="second"/>
<variable name="F" units="C_per_mol" initial_value="9.64853321e4"/>
<variable name="RT" units="J_per_mol" initial_value="2462.1911"/>
<variable name="u_e_m" units="J_per_C" initial_value="-0.057"/>
<variable name="epsilon" units="dim"/>
<variable name="q_H_i" units="mole" initial_value="4.786300923226380e-05"/>
<variable name="q_H_o" units="mole" initial_value="1.995262314968879e-05"/>
<variable name="q_NH3_i" units="mole" initial_value="0"/>
<variable name="q_NH3_o" units="mole" initial_value="0"/>
<variable name="q_NH4_i" units="mole" initial_value="0"/>
<variable name="q_NH4_o" units="mole"/>
<variable name="K_H_o" units="per_mol" initial_value="1"/>
<variable name="K_H_i" units="per_mol" initial_value="1"/>
<variable name="K_NH3_o" units="per_mol" initial_value="1e-8"/>
<variable name="K_NH3_i" units="per_mol" initial_value="1e-8"/>
<variable name="K_NH4_o" units="per_mol" initial_value="1e-5"/>
<variable name="K_NH4_i" units="per_mol" initial_value="1e-5"/>
<variable name="Q_H_o" units="dim"/>
<variable name="Q_H_i" units="dim"/>
<variable name="Q_NH3_o" units="dim"/>
<variable name="Q_NH3_i" units="dim"/>
<variable name="Q_NH4_o" units="dim"/>
<variable name="Q_NH4_i" units="dim"/>
<variable name="v_NH3_m" units="mol_per_s"/>
<variable name="v_NH3_max" units="mol_per_s" initial_value="1"/>
<variable name="gamma_NH3" units="dim" initial_value="1"/>
<variable name="v_H_m" units="mol_per_s"/>
<variable name="kappa_H_m" units="mol_per_s" initial_value="1e2"/>
<variable name="v_NH4_m" units="mol_per_s"/>
<variable name="kappa_NH4_m" units="mol_per_s" initial_value="1"/>
<variable name="v_NH4_o" units="mol_per_s"/>
<variable name="v_NH4_i" units="mol_per_s"/>
<variable name="kappa_NH4" units="mol_per_s" initial_value="1"/>
<variable name="pH_i" units="dim"/>
<variable name="pH_o" units="dim"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>epsilon</ci>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<times/>
<ci>F</ci>
<ci>u_e_m</ci>
</apply>
<ci>RT</ci>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
<apply>
<eq/>
<ci>q_NH4_o</ci>
<piecewise>
<piece>
<cn cellml:units="mole">0</cn>
<apply>
<lt/>
<ci>t</ci>
<cn cellml:units="second">100</cn>
</apply>
</piece>
<piece>
<cn cellml:units="mole">8.85958406334185</cn>
<apply>
<lt/>
<ci>t</ci>
<cn cellml:units="second">1500</cn>
</apply>
</piece>
<otherwise>
<cn cellml:units="mole">0</cn>
</otherwise>
</piecewise>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>Q_H_o</ci>
<apply>
<times/>
<ci>K_H_o</ci>
<ci>q_H_o</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Q_H_i</ci>
<apply>
<times/>
<ci>K_H_i</ci>
<ci>q_H_i</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Q_NH3_o</ci>
<apply>
<times/>
<ci>K_NH3_o</ci>
<ci>q_NH3_o</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Q_NH3_i</ci>
<apply>
<times/>
<ci>K_NH3_i</ci>
<ci>q_NH3_i</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Q_NH4_o</ci>
<apply>
<times/>
<ci>K_NH4_o</ci>
<ci>q_NH4_o</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>Q_NH4_i</ci>
<apply>
<times/>
<ci>K_NH4_i</ci>
<ci>q_NH4_i</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
<apply>
<eq/>
<ci>v_NH3_m</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>v_NH3_max</ci>
<apply>
<plus/>
<cn cellml:units="dim">1</cn>
<ci>gamma_NH3</ci>
</apply>
<apply>
<minus/>
<ci>Q_NH3_o</ci>
<ci>Q_NH3_i</ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<cn cellml:units="dim">2</cn>
<ci>gamma_NH3</ci>
</apply>
<ci>Q_NH3_o</ci>
<ci>Q_NH3_i</ci>
<apply>
<times/>
<cn cellml:units="dim">2</cn>
<ci>Q_NH3_o</ci>
<ci>Q_NH3_i</ci>
</apply>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v_H_m</ci>
<apply>
<times/>
<ci>kappa_H_m</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>Q_H_o</ci>
<ci>epsilon</ci>
</apply>
<ci>Q_H_i</ci>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v_NH4_m</ci>
<apply>
<times/>
<ci>kappa_NH4_m</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>Q_NH4_o</ci>
<ci>epsilon</ci>
</apply>
<ci>Q_NH4_i</ci>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v_NH4_o</ci>
<apply>
<times/>
<ci>kappa_NH4</ci>
<apply>
<minus/>
<ci>Q_NH4_o</ci>
<apply>
<times/>
<ci>Q_NH3_o</ci>
<ci>Q_H_o</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v_NH4_i</ci>
<apply>
<times/>
<ci>kappa_NH4</ci>
<apply>
<minus/>
<ci>Q_NH4_i</ci>
<apply>
<times/>
<ci>Q_NH3_i</ci>
<ci>Q_H_i</ci>
</apply>
</apply>
</apply>
</apply>
<!-- conservation equations-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_H_o</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_H_m</ci>
</apply>
<ci>v_NH4_o</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_H_i</ci>
</apply>
<apply>
<plus/>
<ci>v_H_m</ci>
<ci>v_NH4_i</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH3_o</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v_NH3_m</ci>
</apply>
<ci>v_NH4_o</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH3_i</ci>
</apply>
<apply>
<plus/>
<ci>v_NH3_m</ci>
<ci>v_NH4_i</ci>
</apply>
</apply>
<!-- ode(q_NH4_o, t) = -v_NH4_m-v_NH4_o;-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_NH4_i</ci>
</apply>
<apply>
<minus/>
<ci>v_NH4_m</ci>
<ci>v_NH4_i</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
<apply>
<eq/>
<ci>pH_i</ci>
<apply>
<minus/>
<apply>
<log/>
<apply>
<times/>
<cn type="e-notation" cellml:units="per_mol">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 type="e-notation" cellml:units="per_mol">1<sep/>-3</cn>
<ci>q_H_o</ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
</model>
