- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-05-31 18:20:34+12:00
- Desc:
- increased guess of forward kinetic rate constant in all reactions
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/674/rawfile/b22d4b553a41f8ed56c3e4a790af928d6bbe8213/aplusbequalsc.cellml
<?xml version='1.0' encoding='UTF-8'?>
<!-- BG model of cAMP, based on saucerman2003, v1
20may21 initialising file
24may21: basal reaction with AC.
given Km and kcat for kinetic versions of enzyme reaction, recreate BG parameters by setting k1+ = 1, k2+ = 0, K_E = 1 to be able to solve for K_S, K_C, kappa1 and kappa2
See Pan thesis section 4.2 -->
<model name="BG_cAMP" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
<units name="per_sec">
<unit exponent="-1" units="second"/>
</units>
<units name="J_per_K_per_mol">
<unit units="joule"/>
<unit exponent="-1" units="kelvin"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="C_per_mol">
<unit units="coulomb"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="fmol">
<unit prefix="femto" units="mole"/>
</units>
<units name="fmol_per_L">
<unit prefix="femto" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="fmol_per_L_per_sec">
<unit units="fmol_per_L"/>
<unit exponent="-1" units="second"/>
</units>
<units name="per_sec_per_fmol_per_L">
<unit exponent="-1" units="second"/>
<unit exponent="-1" units="fmol_per_L"/>
</units>
<units name="per_sec_per_mM">
<unit exponent="-1" units="second"/>
<unit exponent="-1" units="mM"/>
</units>
<units name="fmol_per_sec">
<unit units="fmol"/>
<unit exponent="-1" units="second"/>
</units>
<units name="J_per_mol">
<unit units="joule"/>
<unit exponent="-1" units="mole"/>
</units>
<units name="mM">
<unit prefix="milli" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="mM_per_s">
<unit units="mM"/>
<unit exponent="-1" units="second"/>
</units>
<units name="per_mol">
<unit exponent="-1" units="mole"/>
</units>
<units name="mol_per_sec">
<unit units="mole"/>
<unit exponent="-1" units="second"/>
</units>
<component name="environment">
<variable initial_value="0" name="t" units="second"/>
<!-- Physical parameters-->
<variable initial_value="8.31" name="R" units="J_per_K_per_mol"/>
<variable initial_value="310" name="T" units="kelvin"/>
<variable initial_value="96485" name="F" units="C_per_mol"/>
<!-- kinetic parameters - for comparing. (basal reaction)-->
<variable initial_value="1" name="kp" units="per_sec_per_mM"/>
<variable initial_value="0.83" name="km" units="per_sec"/>
<variable initial_value="1" name="qa" units="mM"/>
<variable initial_value="2" name="qb" units="mM"/>
<variable initial_value="0" name="qc" units="mM"/>
<!-- kinetic states-->
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>qa</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>km</ci>
<ci>qc</ci>
</apply>
<apply>
<times/>
<ci>kp</ci>
<ci>qa</ci>
<ci>qb</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>qb</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>km</ci>
<ci>qc</ci>
</apply>
<apply>
<times/>
<ci>kp</ci>
<ci>qa</ci>
<ci>qb</ci>
</apply>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>qc</ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci>kp</ci>
<ci>qa</ci>
<ci>qb</ci>
</apply>
<apply>
<times/>
<ci>km</ci>
<ci>qc</ci>
</apply>
</apply>
</apply>
</math>
<!-- BG parameters and states and conditions-->
<variable initial_value="0.9398" name="kappa" units="mM_per_s"/>
<variable initial_value="1" name="K_A" units="per_mol"/>
<variable initial_value="1" name="K_B" units="per_mol"/>
<variable initial_value="0.9398" name="K_C" units="per_mol"/>
<variable initial_value="1" name="vol" units="litre"/>
<variable initial_value="1" name="q_A" units="mole"/>
<variable initial_value="2" name="q_B" units="mole"/>
<variable initial_value="0" name="q_C" units="mole"/>
<variable name="v" units="mol_per_sec"/>
<variable name="c_A" units="mM"/>
<variable name="c_B" units="mM"/>
<variable name="c_C" units="mM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v</ci>
<apply>
<times/>
<ci>kappa</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>K_A</ci>
<ci>q_A</ci>
<ci>K_B</ci>
<ci>q_B</ci>
</apply>
<apply>
<times/>
<ci>K_C</ci>
<ci>q_C</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>c_A</ci>
<apply>
<divide/>
<ci>q_A</ci>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_B</ci>
<apply>
<divide/>
<ci>q_B</ci>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_C</ci>
<apply>
<divide/>
<ci>q_C</ci>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_A</ci>
</apply>
<apply>
<minus/>
<ci>v</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_B</ci>
</apply>
<apply>
<minus/>
<ci>v</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_C</ci>
</apply>
<ci>v</ci>
</apply>
</math>
</component>
</model>
