Location: BG_cAMP @ cd875ffb40aa / BG_cAMP.cellml
- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-07-07 17:08:09+12:00
- Desc:
- Renaming variables
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/674/rawfile/cd875ffb40aaefb17d7d2609b05efcc9a98ac286/BG_cAMP.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/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#">
<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_fmol">
<unit exponent="-1" units="fmol"/>
</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="uM">
<unit prefix="micro" units="mole"/>
<unit exponent="-1" units="litre"/>
</units>
<units name="mM_per_sec">
<unit units="mM"/>
<unit exponent="-1.0" units="second"/>
</units>
<units name="uM_per_sec">
<unit units="uM"/>
<unit exponent="-1.0" units="second"/>
</units>
<units name="pL">
<unit prefix="pico" units="litre"/>
</units>
<units name="m_to_u">
<unit prefix="micro" units="second"/>
<unit prefix="milli" 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="1.03e0" name="Km_basal_mM" units="mM"/>
<variable initial_value="1.03e12" name="Km_basal" units="fmol_per_L"/>
<variable initial_value="1e-12" name="k1p_basal" units="per_sec_per_fmol_per_L"/>
<variable initial_value="0.83" name="k1m_basal" units="per_sec"/>
<variable initial_value="0.2" name="k2p_basal" units="per_sec"/>
<variable initial_value="2.41e-13" name="k2m_basal" units="per_sec_per_fmol_per_L"/>
<variable initial_value="49.7e-6" name="AC_tot" units="mM"/>
<variable initial_value="0.00263157894736842" name="ATP_kinetic" units="mM"/>
<!-- kinetic states-->
<variable initial_value="0.002631579" name="cAMP_kinetic" units="mM"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>cAMP_kinetic</ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci>k2p_basal</ci>
<ci>AC_tot</ci>
<ci>ATP_kinetic</ci>
</apply>
<apply>
<plus/>
<ci>Km_basal_mM</ci>
<ci>ATP_kinetic</ci>
</apply>
</apply>
</apply>
</math>
<!-- Bond graph parameters, found using pinv of kinetic parameters-->
<!-- with fastKineticConstant = 1e6 (Pan cardiac: NaK). with hacked FSK = 0-->
<!-- var kappa_1a: fmol_per_sec {init: 5.41578e+11};
var kappa_1b: fmol_per_sec {init: 1.13076e-07};
var kappa_2a: fmol_per_sec {init: 2.48718e+06};
var kappa_2b: fmol_per_sec {init: 6.71144e-10};
var kappa_4a: fmol_per_sec {init: 2.78218e+10};
var kappa_4b: fmol_per_sec {init: 0.000107007};
var kappa_5: fmol_per_sec {init: 1.18022e+06};
var kappa_6: fmol_per_sec {init: 2.10739e+07};
var K_ATP: per_fmol {init: 0.847302};
var K_cAMP: per_fmol {init: 0.847302};
var K_AC: per_fmol {init: 2.02667e-06};
var K_AC_ATP: per_fmol {init: 1.76872e+06};
var K_GsT_AC: per_fmol {init: 0.047452};
var K_GsT_AC_ATP: per_fmol {init: 1.26649e+10};
var K_PDE: per_fmol {init: 4.24206e-05};
var K_PDE_cAMP: per_fmol {init: 46726};
var K_5AMP: per_fmol {init: 0.847302};
var K_IBMX: per_fmol {init: 6.65794e-07};
var K_PDEinh: per_fmol {init: 0.847302};
var K_GsT: per_fmol {init: 5.85344e-05};
var kappa_3a: fmol_per_sec {init: 0};
var kappa_3b: fmol_per_sec {init: 0};
var kappa_7: fmol_per_sec {init: 0};
var K_FSK: per_fmol {init: 1e3};
var K_FSK_AC: per_fmol {init: 1e3};
var K_FSK_AC_ATP: per_fmol {init: 1e3};-->
<!-- 29jun21 with fastKineticConstant = 1e6 and with FSK-->
<variable initial_value="3.44253e+14" name="kappa_1a" units="fmol_per_sec"/>
<variable initial_value="7.18767e-05" name="kappa_1b" units="fmol_per_sec"/>
<variable initial_value="1.96372e+08" name="kappa_2a" units="fmol_per_sec"/>
<variable initial_value="5.29893e-08" name="kappa_2b" units="fmol_per_sec"/>
<variable initial_value="5.66431e+11" name="kappa_3a" units="fmol_per_sec"/>
<variable initial_value="6.5864e-23" name="kappa_3b" units="fmol_per_sec"/>
<variable initial_value="1.2493e+11" name="kappa_4a" units="fmol_per_sec"/>
<variable initial_value="0.000480501" name="kappa_4b" units="fmol_per_sec"/>
<variable initial_value="5.65404" name="kappa_5" units="fmol_per_sec"/>
<variable initial_value="85233.3" name="kappa_6" units="fmol_per_sec"/>
<variable initial_value="2.45853e+07" name="kappa_7" units="fmol_per_sec"/>
<variable initial_value="4.3404e-05" name="K_ATP" units="per_fmol"/>
<variable initial_value="4.3404e-05" name="K_cAMP" units="per_fmol"/>
<variable initial_value="6.22408e-05" name="K_AC" units="per_fmol"/>
<variable initial_value="2782.54" name="K_AC_ATP" units="per_fmol"/>
<variable initial_value="11.7325" name="K_GsT_AC" units="per_fmol"/>
<variable initial_value="1.6041e+08" name="K_GsT_AC_ATP" units="per_fmol"/>
<variable initial_value="0.0406746" name="K_FSK_AC" units="per_fmol"/>
<variable initial_value="1.51828e+06" name="K_FSK_AC_ATP" units="per_fmol"/>
<variable initial_value="0.184418" name="K_PDE" units="per_fmol"/>
<variable initial_value="10405.8" name="K_PDE_cAMP" units="per_fmol"/>
<variable initial_value="4.3404e-05" name="K_5AMP" units="per_fmol"/>
<variable initial_value="3.19681e-05" name="K_IBMX" units="per_fmol"/>
<variable initial_value="176865" name="K_PDEinh" units="per_fmol"/>
<variable initial_value="0.000471254" name="K_GsT" units="per_fmol"/>
<variable initial_value="1.48524e-08" name="K_FSK" units="per_fmol"/>
<!-- States (and initial conditions)-->
<!-- 28Jun21: this set works -->
<!-- var q_ATP: fmol {init: 1.90E-02};
var q_AC: fmol {init: 1.89E-3};
var q_cAMP: fmol {init: 3.21E-02};
var q_cAMP_noPDE: fmol {init: 3.21E-02};
var q_AC_ATP: fmol {init: 1e-3};
var q_FSK: fmol {init: 1e-9};
var q_FSK_AC: fmol {init: 1e-13};
var q_FSK_AC_ATP: fmol {init: 1e-13};
var q_GsT: fmol {init: 9.52E-04};
var q_GsT_AC: fmol {init: 1e-3};
var q_GsT_AC_ATP: fmol {init: 1e-13};
var q_PDE: fmol {init: 1.48E-03};
var q_PDEinh: fmol {init: 1e-13};
var q_PDE_cAMP: fmol {init: 1e-16};
var q_IBMX: fmol {init: 3.80E-06};
var q_5AMP: fmol {init: 1e-3};-->
<!-- 29jun21 original concs, but complexes = 1e-13 . -->
<variable initial_value="1.90E-02" name="q_ATP" units="fmol"/>
<variable initial_value="1.89E-3" name="q_AC" units="fmol"/>
<variable initial_value="3.21E-02" name="q_cAMP" units="fmol"/>
<variable initial_value="3.21E-02" name="q_cAMP_noPDE" units="fmol"/>
<variable initial_value="1e-13" name="q_AC_ATP" units="fmol"/>
<variable initial_value="1e-9" name="q_FSK" units="fmol"/>
<variable initial_value="1e-13" name="q_FSK_AC" units="fmol"/>
<variable initial_value="1e-13" name="q_FSK_AC_ATP" units="fmol"/>
<variable initial_value="9.52E-04" name="q_GsT" units="fmol"/>
<variable initial_value="1e-13" name="q_GsT_AC" units="fmol"/>
<variable initial_value="1e-13" name="q_GsT_AC_ATP" units="fmol"/>
<variable initial_value="1.48E-03" name="q_PDE" units="fmol"/>
<variable initial_value="1e-13" name="q_PDEinh" units="fmol"/>
<variable initial_value="1e-18" name="q_PDE_cAMP" units="fmol"/>
<variable initial_value="3.80E-06" name="q_IBMX" units="fmol"/>
<variable initial_value="1e-13" name="q_5AMP" units="fmol"/>
<!-- Bond variables-->
<variable name="v1a" units="fmol_per_sec"/>
<variable name="v1b" units="fmol_per_sec"/>
<variable name="v2a" units="fmol_per_sec"/>
<variable name="v2b" units="fmol_per_sec"/>
<variable name="v3a" units="fmol_per_sec"/>
<variable name="v3b" units="fmol_per_sec"/>
<variable name="v4a" units="fmol_per_sec"/>
<variable name="v4b" units="fmol_per_sec"/>
<variable name="v5" units="fmol_per_sec"/>
<variable name="v6" units="fmol_per_sec"/>
<variable name="v7" units="fmol_per_sec"/>
<variable name="mu_ATP" units="J_per_mol"/>
<variable name="mu_AC" units="J_per_mol"/>
<variable name="mu_cAMP" units="J_per_mol"/>
<variable name="mu_AC_ATP" units="J_per_mol"/>
<variable name="mu_FSK" units="J_per_mol"/>
<variable name="mu_FSK_AC" units="J_per_mol"/>
<variable name="mu_FSK_AC_ATP" units="J_per_mol"/>
<variable name="mu_GsT" units="J_per_mol"/>
<variable name="mu_GsT_AC" units="J_per_mol"/>
<variable name="mu_GsT_AC_ATP" units="J_per_mol"/>
<variable name="mu_PDE" units="J_per_mol"/>
<variable name="mu_PDEinh" units="J_per_mol"/>
<variable name="mu_PDE_cAMP" units="J_per_mol"/>
<variable name="mu_IBMX" units="J_per_mol"/>
<variable name="mu_5AMP" units="J_per_mol"/>
<!-- Concentrations - for plotting-->
<variable name="c_ATP" units="uM"/>
<variable name="c_cAMP" units="uM"/>
<variable name="c_cAMP_noPDE" units="uM"/>
<variable name="c_FSK" units="uM"/>
<variable name="c_GsT" units="uM"/>
<variable name="c_PDE" units="uM"/>
<variable name="c_IBMX" units="uM"/>
<variable name="c_5AMP" units="uM"/>
<variable name="c_AC" units="uM"/>
<variable name="c_AC_ATP" units="uM"/>
<variable name="c_GsT_AC_ATP" units="uM"/>
<variable name="c_GsT_AC" units="uM"/>
<variable initial_value="38.0" name="vol" units="pL"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>c_ATP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_ATP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_cAMP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_cAMP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_cAMP_noPDE</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_cAMP_noPDE</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_FSK</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_FSK</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_IBMX</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_IBMX</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_GsT</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_GsT</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_PDE</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_PDE</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_5AMP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_5AMP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_AC</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_AC</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_AC_ATP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_AC_ATP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_GsT_AC_ATP</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_GsT_AC_ATP</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>c_GsT_AC</ci>
<apply>
<divide/>
<apply>
<times/>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
<ci>q_GsT_AC</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
<!-- Constitutive equations-->
<apply>
<eq/>
<ci>mu_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_ATP</ci>
<ci>q_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AC</ci>
<ci>q_AC</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_cAMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_cAMP</ci>
<ci>q_cAMP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_AC_ATP</ci>
<ci>q_AC_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_FSK_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_FSK_AC</ci>
<ci>q_FSK_AC</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_FSK</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_FSK</ci>
<ci>q_FSK</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_FSK_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_FSK_AC_ATP</ci>
<ci>q_FSK_AC_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GsT_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GsT_AC_ATP</ci>
<ci>q_GsT_AC_ATP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GsT_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GsT_AC</ci>
<ci>q_GsT_AC</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_GsT</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_GsT</ci>
<ci>q_GsT</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PDE_cAMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PDE_cAMP</ci>
<ci>q_PDE_cAMP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PDE</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PDE</ci>
<ci>q_PDE</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_IBMX</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_IBMX</ci>
<ci>q_IBMX</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_PDEinh</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_PDEinh</ci>
<ci>q_PDEinh</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>mu_5AMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
<apply>
<ln/>
<apply>
<times/>
<ci>K_5AMP</ci>
<ci>q_5AMP</ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v1a</ci>
<apply>
<times/>
<ci>kappa_1a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AC</ci>
<ci>mu_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v1b</ci>
<apply>
<times/>
<ci>kappa_1b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AC</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v2a</ci>
<apply>
<times/>
<ci>kappa_2a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_GsT_AC</ci>
<ci>mu_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GsT_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v2b</ci>
<apply>
<times/>
<ci>kappa_2b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GsT_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_GsT_AC</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v3a</ci>
<apply>
<times/>
<ci>kappa_3a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_FSK_AC</ci>
<ci>mu_ATP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_FSK_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v3b</ci>
<apply>
<times/>
<ci>kappa_3b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_FSK_AC_ATP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_FSK_AC</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v4a</ci>
<apply>
<times/>
<ci>kappa_4a</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_PDE</ci>
<ci>mu_cAMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PDE_cAMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v4b</ci>
<apply>
<times/>
<ci>kappa_4b</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PDE_cAMP</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_PDE</ci>
<ci>mu_5AMP</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v5</ci>
<apply>
<times/>
<ci>kappa_5</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_PDE</ci>
<ci>mu_IBMX</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_PDEinh</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v6</ci>
<apply>
<times/>
<ci>kappa_6</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_AC</ci>
<ci>mu_GsT</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_GsT_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<eq/>
<ci>v7</ci>
<apply>
<times/>
<ci>kappa_7</ci>
<apply>
<minus/>
<apply>
<exp/>
<apply>
<divide/>
<apply>
<plus/>
<ci>mu_FSK</ci>
<ci>mu_AC</ci>
</apply>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
<apply>
<exp/>
<apply>
<divide/>
<ci>mu_FSK_AC</ci>
<apply>
<times/>
<ci>R</ci>
<ci>T</ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
<!-- velocity in uM_per_sec-->
<variable name="v1b_kinetic" units="uM_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>v1b_kinetic</ci>
<apply>
<divide/>
<apply>
<times/>
<ci>v1b</ci>
<cn cellml:units="m_to_u" type="e-notation">1<sep/>3</cn>
</apply>
<ci>vol</ci>
</apply>
</apply>
<!-- saucerman: not all reactions are accounted for.-->
<!-- ode(q_ATP, t) = 0{fmol_per_sec};
ode(q_AC, t) = -v6;
ode(q_cAMP, t) = v1b+v2b+v3b-v4a;
ode(q_cAMP_noPDE, t) = v1b+v3b+v2b;
ode(q_FSK, t) = -v7;
ode(q_FSK_AC, t) = v7;
ode(q_GsT, t) = -v6;
ode(q_GsT_AC, t) = v6;
ode(q_PDE_cAMP, t) = 0{fmol_per_sec};
ode(q_PDE, t) = -v5;
ode(q_IBMX, t) = -v5;
ode(q_PDEinh, t) = v5;
ode(q_5AMP, t) = v4b;
ode(q_AC_ATP, t) = 0{fmol_per_sec};
ode(q_FSK_AC_ATP, t) = 0{fmol_per_sec};
ode(q_GsT_AC_ATP, t) = 0{fmol_per_sec};-->
<!-- correct BG model-->
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_ATP</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>v1a</ci>
</apply>
<ci>v3a</ci>
</apply>
<ci>v2a</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_AC</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<ci>v1b</ci>
<ci>v1a</ci>
</apply>
<ci>v6</ci>
</apply>
<ci>v7</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_AC_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v1a</ci>
<ci>v1b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_cAMP</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>v1b</ci>
<ci>v3b</ci>
<ci>v2b</ci>
</apply>
<ci>v4a</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_FSK</ci>
</apply>
<apply>
<minus/>
<ci>v7</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_FSK_AC</ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<ci>v7</ci>
<ci>v3b</ci>
</apply>
<ci>v3a</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_FSK_AC_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v3a</ci>
<ci>v3b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_GsT</ci>
</apply>
<apply>
<minus/>
<ci>v6</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_GsT_AC</ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci>v6</ci>
<ci>v2a</ci>
</apply>
<ci>v2b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_GsT_AC_ATP</ci>
</apply>
<apply>
<minus/>
<ci>v2a</ci>
<ci>v2b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_PDE_cAMP</ci>
</apply>
<apply>
<minus/>
<ci>v4a</ci>
<ci>v4b</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_PDE</ci>
</apply>
<apply>
<minus/>
<apply>
<minus/>
<ci>v4b</ci>
<ci>v4a</ci>
</apply>
<ci>v5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_IBMX</ci>
</apply>
<apply>
<minus/>
<ci>v5</ci>
</apply>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_PDEinh</ci>
</apply>
<ci>v5</ci>
</apply>
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>t</ci>
</bvar>
<ci>q_5AMP</ci>
</apply>
<ci>v4b</ci>
</apply>
</math>
<!-- calculate velocity wrt changing concentration rate-->
<variable name="PDE_ACT_4a" units="mM_per_sec"/>
<variable name="PDE_ACT_4ab" units="mM_per_sec"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>PDE_ACT_4a</ci>
<apply>
<divide/>
<ci>v4a</ci>
<ci>vol</ci>
</apply>
</apply>
<apply>
<eq/>
<ci>PDE_ACT_4ab</ci>
<apply>
<divide/>
<apply>
<minus/>
<ci>v4a</ci>
<ci>v4b</ci>
</apply>
<ci>vol</ci>
</apply>
</apply>
</math>
</component>
</model>