Location: FCU_cardiac_pH @ a7ca9c37511f / parameter_finder / output / TEMP.cellml.txt

Author:

Shelley Fong <sfon036@UoA.auckland.ac.nz>

Date:

2022-05-25 11:42:32+12:00

Desc:

Updating B1 with 2H in stoichiometry, and removing B2 buffer

Permanent Source URI:

https://staging.physiomeproject.org/workspace/885/rawfile/a7ca9c37511f8ffe16058a52cdb8c1a27230a16c/parameter_finder/output/TEMP.cellml.txt

def model FCU_cardiac_pH as
 def import using "units_and_constants/units_BG.cellml" for
            unit mM using unit mM;
unit fmol using unit fmol;
unit per_fmol using unit per_fmol;
            unit J_per_mol using unit J_per_mol;
unit fmol_per_sec using unit fmol_per_sec;
            unit C_per_mol using unit C_per_mol;
  unit J_per_C using unit J_per_C;
            unit microm3 using unit microm3;
  unit fF using unit fF;
            unit fC using unit fC;
  unit fA using unit fA;
            unit per_second using unit per_second;
  unit millivolt using unit millivolt;
            unit per_sec using unit per_sec;
  unit J_per_K_per_mol using unit J_per_K_per_mol;
            unit fmol_per_L using unit fmol_per_L;
  unit fmol_per_L_per_sec using unit fmol_per_L_per_sec;
            unit per_sec_per_fmol_per_L using unit per_sec_per_fmol_per_L;
  unit uM using unit uM;
            unit mM_per_sec using unit mM_per_sec;
  unit uM_per_sec using unit uM_per_sec;
            unit pL using unit pL;
  unit m_to_u using unit m_to_u;
 enddef;
def import using "units_and_constants/constants_BG.cellml" for
                comp constants using comp constants;
enddef;

def import using "AE/BG_AE.cellml" for
comp AE using comp AE;
enddef;
def import using "CHE/BG_CHE.cellml" for
comp CHE using comp CHE;
enddef;
def import using "CO2_hyd/BG_CO2_hyd.cellml" for
comp CO2_hyd using comp CO2_hyd;
enddef;
def import using "NBC/BG_NBC.cellml" for
comp NBC using comp NBC;
enddef;
def import using "NHE/BG_NHE.cellml" for
comp NHE using comp NHE;
enddef;
def import using "pH_B1/BG_pH_B1.cellml" for
comp pH_B1 using comp pH_B1;
enddef;
def import using "pH_B2/BG_pH_B2.cellml" for
comp pH_B2 using comp pH_B2;
enddef;

def comp BG_parameters as
var kappa_R61_AE: fmol_per_sec {init: 0.00234867, pub: out};
var kappa_R12_AE: fmol_per_sec {init: 7513.02, pub: out};
var kappa_R23_AE: fmol_per_sec {init: 516778, pub: out};
var kappa_R34_AE: fmol_per_sec {init: 0.0185914, pub: out};
var kappa_R45_AE: fmol_per_sec {init: 508165, pub: out};
var kappa_R56_AE: fmol_per_sec {init: 7.3878e+09, pub: out};
var kappa_R61_CHE: fmol_per_sec {init: 9.78487, pub: out};
var kappa_R12_CHE: fmol_per_sec {init: 0.0348831, pub: out};
var kappa_R23_CHE: fmol_per_sec {init: 39258, pub: out};
var kappa_R34_CHE: fmol_per_sec {init: 0.000148526, pub: out};
var kappa_R45_CHE: fmol_per_sec {init: 2.28502e+06, pub: out};
var kappa_R56_CHE: fmol_per_sec {init: 2.03037e+06, pub: out};
var kappa_Re_CO2hyd: fmol_per_sec {init: 0.0335708, pub: out};
var kappa_R61_NBC: fmol_per_sec {init: 0.940306, pub: out};
var kappa_R12_NBC: fmol_per_sec {init: 8.03772e+07, pub: out};
var kappa_R23_NBC: fmol_per_sec {init: 3.18851e+06, pub: out};
var kappa_R34_NBC: fmol_per_sec {init: 33.9127, pub: out};
var kappa_R45_NBC: fmol_per_sec {init: 0.0558481, pub: out};
var kappa_R56_NBC: fmol_per_sec {init: 12.1431, pub: out};
var kappa_R61_NHE: fmol_per_sec {init: 11.1987, pub: out};
var kappa_R12_NHE: fmol_per_sec {init: 0.56101, pub: out};
var kappa_R23_NHE: fmol_per_sec {init: 17590, pub: out};
var kappa_R34_NHE: fmol_per_sec {init: 0.000383734, pub: out};
var kappa_R45_NHE: fmol_per_sec {init: 4793.1, pub: out};
var kappa_R56_NHE: fmol_per_sec {init: 152870, pub: out};
var kappa_Re_B1: fmol_per_sec {init: 15.649, pub: out};
var kappa_Re_B2: fmol_per_sec {init: 4.79904, pub: out};
var K_HCO3_i: per_fmol {init: 0.0120343, pub: out};
var K_HCO3_o: per_fmol {init: 0.0102316, pub: out};
var K_Cl_i: per_fmol {init: 174.957, pub: out};
var K_Cl_o: per_fmol {init: 0.000148749, pub: out};
var K_S1_AE: per_fmol {init: 39823, pub: out};
var K_S2_AE: per_fmol {init: 6931, pub: out};
var K_S3_AE: per_fmol {init: 5132.36, pub: out};
var K_S4_AE: per_fmol {init: 5219.35, pub: out};
var K_S5_AE: per_fmol {init: 0.000817178, pub: out};
var K_S6_AE: per_fmol {init: 40396.9, pub: out};
var K_OH_i: per_fmol {init: 196.899, pub: out};
var K_OH_o: per_fmol {init: 167.405, pub: out};
var K_S1_CHE: per_fmol {init: 6.8867, pub: out};
var K_S2_CHE: per_fmol {init: 91237.1, pub: out};
var K_S3_CHE: per_fmol {init: 123586, pub: out};
var K_S4_CHE: per_fmol {init: 2123.29, pub: out};
var K_S5_CHE: per_fmol {init: 0.000181732, pub: out};
var K_S6_CHE: per_fmol {init: 0.118176, pub: out};
var K_CO2_i: per_fmol {init: 3.85394e+06, pub: out};
var K_H_i: per_fmol {init: 65.6391, pub: out};
var K_Na_i: per_fmol {init: 2093.48, pub: out};
var K_Na_o: per_fmol {init: 0.000412929, pub: out};
var K_S1_NBC: per_fmol {init: 16.0526, pub: out};
var K_S2_NBC: per_fmol {init: 16.3314, pub: out};
var K_S3_NBC: per_fmol {init: 0.000677973, pub: out};
var K_S4_NBC: per_fmol {init: 38707.3, pub: out};
var K_S5_NBC: per_fmol {init: 1.081e+08, pub: out};
var K_S6_NBC: per_fmol {init: 2.85793, pub: out};
var K_H_o: per_fmol {init: 12.947, pub: out};
var K_S1_NHE: per_fmol {init: 0.0791872, pub: out};
var K_S2_NHE: per_fmol {init: 73352.1, pub: out};
var K_S3_NHE: per_fmol {init: 514.873, pub: out};
var K_S4_NHE: per_fmol {init: 1889.51, pub: out};
var K_S5_NHE: per_fmol {init: 0.00724047, pub: out};
var K_S6_NHE: per_fmol {init: 0.291236, pub: out};
var K_B1: per_fmol {init: 70.7297, pub: out};
var K_HB1: per_fmol {init: 0.0160745, pub: out};
var K_B2: per_fmol {init: 230.64, pub: out};
var K_HB2: per_fmol {init: 0.00151172, pub: out};
enddef;
    def comp environment as
                var t: second {pub: out};
                var vol_myo: pL {init: 3.71, pub: out};
                var freq: dimensionless {init: 500};
var q_HCO3_i: fmol {init: 1e-888, pub: out};
var q_HCO3_o: fmol {init: 1e-888, pub: out};
var q_Cl_i: fmol {init: 1e-888, pub: out};
var q_Cl_o: fmol {init: 1e-888, pub: out};
var q_S1_AE: fmol {init: 1e-888, pub: out};
var q_S2_AE: fmol {init: 1e-888, pub: out};
var q_S3_AE: fmol {init: 1e-888, pub: out};
var q_S4_AE: fmol {init: 1e-888, pub: out};
var q_S5_AE: fmol {init: 1e-888, pub: out};
var q_S6_AE: fmol {init: 1e-888, pub: out};
var q_OH_i: fmol {init: 1e-888, pub: out};
var q_OH_o: fmol {init: 1e-888, pub: out};
var q_S1_CHE: fmol {init: 1e-888, pub: out};
var q_S2_CHE: fmol {init: 1e-888, pub: out};
var q_S3_CHE: fmol {init: 1e-888, pub: out};
var q_S4_CHE: fmol {init: 1e-888, pub: out};
var q_S5_CHE: fmol {init: 1e-888, pub: out};
var q_S6_CHE: fmol {init: 1e-888, pub: out};
var q_CO2_i: fmol {init: 1e-888, pub: out};
var q_H_i: fmol {init: 1e-888, pub: out};
var q_Na_i: fmol {init: 1e-888, pub: out};
var q_Na_o: fmol {init: 1e-888, pub: out};
var q_S1_NBC: fmol {init: 1e-888, pub: out};
var q_S2_NBC: fmol {init: 1e-888, pub: out};
var q_S3_NBC: fmol {init: 1e-888, pub: out};
var q_S4_NBC: fmol {init: 1e-888, pub: out};
var q_S5_NBC: fmol {init: 1e-888, pub: out};
var q_S6_NBC: fmol {init: 1e-888, pub: out};
var q_H_o: fmol {init: 1e-888, pub: out};
var q_S1_NHE: fmol {init: 1e-888, pub: out};
var q_S2_NHE: fmol {init: 1e-888, pub: out};
var q_S3_NHE: fmol {init: 1e-888, pub: out};
var q_S4_NHE: fmol {init: 1e-888, pub: out};
var q_S5_NHE: fmol {init: 1e-888, pub: out};
var q_S6_NHE: fmol {init: 1e-888, pub: out};
var q_B1: fmol {init: 1e-888, pub: out};
var q_HB1: fmol {init: 1e-888, pub: out};
var q_B2: fmol {init: 1e-888, pub: out};
var q_HB2: fmol {init: 1e-888, pub: out};

// AE imports
var v_R61_AE: fmol_per_sec {pub: in};
var v_R12_AE: fmol_per_sec {pub: in};
var v_R23_AE: fmol_per_sec {pub: in};
var v_R34_AE: fmol_per_sec {pub: in};
var v_R45_AE: fmol_per_sec {pub: in};
var v_R56_AE: fmol_per_sec {pub: in};


// CHE imports
var v_R61_CHE: fmol_per_sec {pub: in};
var v_R12_CHE: fmol_per_sec {pub: in};
var v_R23_CHE: fmol_per_sec {pub: in};
var v_R34_CHE: fmol_per_sec {pub: in};
var v_R45_CHE: fmol_per_sec {pub: in};
var v_R56_CHE: fmol_per_sec {pub: in};


// CO2_hyd imports
var v_Re_CO2hyd: fmol_per_sec {pub: in};


// NBC imports
var v_R61_NBC: fmol_per_sec {pub: in};
var v_R12_NBC: fmol_per_sec {pub: in};
var v_R23_NBC: fmol_per_sec {pub: in};
var v_R34_NBC: fmol_per_sec {pub: in};
var v_R45_NBC: fmol_per_sec {pub: in};
var v_R56_NBC: fmol_per_sec {pub: in};


// NHE imports
var v_R61_NHE: fmol_per_sec {pub: in};
var v_R12_NHE: fmol_per_sec {pub: in};
var v_R23_NHE: fmol_per_sec {pub: in};
var v_R34_NHE: fmol_per_sec {pub: in};
var v_R45_NHE: fmol_per_sec {pub: in};
var v_R56_NHE: fmol_per_sec {pub: in};


// pH_B1 imports
var v_Re_B1: fmol_per_sec {pub: in};


// pH_B2 imports
var v_Re_B2: fmol_per_sec {pub: in};


ode(q_HCO3_i, time) = + v_mAE  + v_mCO2_hyd  + v_mNBC ;
ode(q_HCO3_o, time) = + v_mAE  + v_mNBC ;
ode(q_Cl_i, time) = + v_mAE  + v_mCHE ;
ode(q_Cl_o, time) = + v_mAE  + v_mCHE ;
ode(q_S1_AE, time) = + v_mAE ;
ode(q_S2_AE, time) = + v_mAE ;
ode(q_S3_AE, time) = + v_mAE ;
ode(q_S4_AE, time) = + v_mAE ;
ode(q_S5_AE, time) = + v_mAE ;
ode(q_S6_AE, time) = + v_mAE ;
ode(q_OH_i, time) = + v_mCHE ;
ode(q_OH_o, time) = + v_mCHE ;
ode(q_S1_CHE, time) = + v_mCHE ;
ode(q_S2_CHE, time) = + v_mCHE ;
ode(q_S3_CHE, time) = + v_mCHE ;
ode(q_S4_CHE, time) = + v_mCHE ;
ode(q_S5_CHE, time) = + v_mCHE ;
ode(q_S6_CHE, time) = + v_mCHE ;
ode(q_CO2_i, time) = + v_mCO2_hyd ;
ode(q_H_i, time) = + v_mCO2_hyd  + v_mNHE  + v_mpH_B1  + v_mpH_B2 ;
ode(q_Na_i, time) = + v_mNBC  + v_mNHE ;
ode(q_Na_o, time) = + v_mNBC  + v_mNHE ;
ode(q_S1_NBC, time) = + v_mNBC ;
ode(q_S2_NBC, time) = + v_mNBC ;
ode(q_S3_NBC, time) = + v_mNBC ;
ode(q_S4_NBC, time) = + v_mNBC ;
ode(q_S5_NBC, time) = + v_mNBC ;
ode(q_S6_NBC, time) = + v_mNBC ;
ode(q_H_o, time) = + v_mNHE ;
ode(q_S1_NHE, time) = + v_mNHE ;
ode(q_S2_NHE, time) = + v_mNHE ;
ode(q_S3_NHE, time) = + v_mNHE ;
ode(q_S4_NHE, time) = + v_mNHE ;
ode(q_S5_NHE, time) = + v_mNHE ;
ode(q_S6_NHE, time) = + v_mNHE ;
ode(q_B1, time) = + v_mpH_B1 ;
ode(q_HB1, time) = + v_mpH_B1 ;
ode(q_B2, time) = + v_mpH_B2 ;
ode(q_HB2, time) = + v_mpH_B2 ;
enddef;

def map between environment and AE for
vars time and time;
vars q_HCO3_i and q_HCO3_i;
vars q_HCO3_o and q_HCO3_o;
vars q_Cl_i and q_Cl_i;
vars q_Cl_o and q_Cl_o;
vars q_S1_AE and q_S1_AE;
vars q_S2_AE and q_S2_AE;
vars q_S3_AE and q_S3_AE;
vars q_S4_AE and q_S4_AE;
vars q_S5_AE and q_S5_AE;
vars q_S6_AE and q_S6_AE;
vars v_R61_AE and v_R61_AE;
vars v_R12_AE and v_R12_AE;
vars v_R23_AE and v_R23_AE;
vars v_R34_AE and v_R34_AE;
vars v_R45_AE and v_R45_AE;
vars v_R56_AE and v_R56_AE;
vars q_mem and q_mem;
vars I_mem and q_mem_mAE;
enddef;

def map between environment and CHE for
vars time and time;
vars q_OH_i and q_OH_i;
vars q_OH_o and q_OH_o;
vars q_Cl_i and q_Cl_i;
vars q_Cl_o and q_Cl_o;
vars q_S1_CHE and q_S1_CHE;
vars q_S2_CHE and q_S2_CHE;
vars q_S3_CHE and q_S3_CHE;
vars q_S4_CHE and q_S4_CHE;
vars q_S5_CHE and q_S5_CHE;
vars q_S6_CHE and q_S6_CHE;
vars v_R61_CHE and v_R61_CHE;
vars v_R12_CHE and v_R12_CHE;
vars v_R23_CHE and v_R23_CHE;
vars v_R34_CHE and v_R34_CHE;
vars v_R45_CHE and v_R45_CHE;
vars v_R56_CHE and v_R56_CHE;
vars q_mem and q_mem;
vars I_mem and q_mem_mCHE;
enddef;

def map between environment and CO2_hyd for
vars time and time;
vars q_CO2_i and q_CO2_i;
vars q_HCO3_i and q_HCO3_i;
vars q_H_i and q_H_i;
vars v_Re_CO2hyd and v_Re_CO2hyd;
vars q_mem and q_mem;
vars I_mem and q_mem_mCO2_hyd;
enddef;

def map between environment and NBC for
vars time and time;
vars q_Na_i and q_Na_i;
vars q_Na_o and q_Na_o;
vars q_HCO3_i and q_HCO3_i;
vars q_HCO3_o and q_HCO3_o;
vars q_S1_NBC and q_S1_NBC;
vars q_S2_NBC and q_S2_NBC;
vars q_S3_NBC and q_S3_NBC;
vars q_S4_NBC and q_S4_NBC;
vars q_S5_NBC and q_S5_NBC;
vars q_S6_NBC and q_S6_NBC;
vars v_R61_NBC and v_R61_NBC;
vars v_R12_NBC and v_R12_NBC;
vars v_R23_NBC and v_R23_NBC;
vars v_R34_NBC and v_R34_NBC;
vars v_R45_NBC and v_R45_NBC;
vars v_R56_NBC and v_R56_NBC;
vars q_mem and q_mem;
vars I_mem and q_mem_mNBC;
enddef;

def map between environment and NHE for
vars time and time;
vars q_H_i and q_H_i;
vars q_H_o and q_H_o;
vars q_Na_i and q_Na_i;
vars q_Na_o and q_Na_o;
vars q_S1_NHE and q_S1_NHE;
vars q_S2_NHE and q_S2_NHE;
vars q_S3_NHE and q_S3_NHE;
vars q_S4_NHE and q_S4_NHE;
vars q_S5_NHE and q_S5_NHE;
vars q_S6_NHE and q_S6_NHE;
vars v_R61_NHE and v_R61_NHE;
vars v_R12_NHE and v_R12_NHE;
vars v_R23_NHE and v_R23_NHE;
vars v_R34_NHE and v_R34_NHE;
vars v_R45_NHE and v_R45_NHE;
vars v_R56_NHE and v_R56_NHE;
vars q_mem and q_mem;
vars I_mem and q_mem_mNHE;
enddef;

def map between environment and pH_B1 for
vars time and time;
vars q_H_i and q_H_i;
vars q_B1 and q_B1;
vars q_HB1 and q_HB1;
vars v_Re_B1 and v_Re_B1;
vars q_mem and q_mem;
vars I_mem and q_mem_mpH_B1;
enddef;

def map between environment and pH_B2 for
vars time and time;
vars q_H_i and q_H_i;
vars q_B2 and q_B2;
vars q_HB2 and q_HB2;
vars v_Re_B2 and v_Re_B2;
vars q_mem and q_mem;
vars I_mem and q_mem_mpH_B2;
enddef;

def map between BG_parameters and AE for
vars kappa_R61_AE and kappa_R61_AE;
vars kappa_R12_AE and kappa_R12_AE;
vars kappa_R23_AE and kappa_R23_AE;
vars kappa_R34_AE and kappa_R34_AE;
vars kappa_R45_AE and kappa_R45_AE;
vars kappa_R56_AE and kappa_R56_AE;
vars K_HCO3_i and K_HCO3_i;
vars K_HCO3_o and K_HCO3_o;
vars K_Cl_i and K_Cl_i;
vars K_Cl_o and K_Cl_o;
vars K_S1_AE and K_S1_AE;
vars K_S2_AE and K_S2_AE;
vars K_S3_AE and K_S3_AE;
vars K_S4_AE and K_S4_AE;
vars K_S5_AE and K_S5_AE;
vars K_S6_AE and K_S6_AE;
enddef;
def map between BG_parameters and CHE for
vars kappa_R61_CHE and kappa_R61_CHE;
vars kappa_R12_CHE and kappa_R12_CHE;
vars kappa_R23_CHE and kappa_R23_CHE;
vars kappa_R34_CHE and kappa_R34_CHE;
vars kappa_R45_CHE and kappa_R45_CHE;
vars kappa_R56_CHE and kappa_R56_CHE;
vars K_OH_i and K_OH_i;
vars K_OH_o and K_OH_o;
vars K_Cl_i and K_Cl_i;
vars K_Cl_o and K_Cl_o;
vars K_S1_CHE and K_S1_CHE;
vars K_S2_CHE and K_S2_CHE;
vars K_S3_CHE and K_S3_CHE;
vars K_S4_CHE and K_S4_CHE;
vars K_S5_CHE and K_S5_CHE;
vars K_S6_CHE and K_S6_CHE;
enddef;
def map between BG_parameters and CO2_hyd for
vars kappa_Re_CO2hyd and kappa_Re_CO2hyd;
vars K_CO2_i and K_CO2_i;
vars K_HCO3_i and K_HCO3_i;
vars K_H_i and K_H_i;
enddef;
def map between BG_parameters and NBC for
vars kappa_R61_NBC and kappa_R61_NBC;
vars kappa_R12_NBC and kappa_R12_NBC;
vars kappa_R23_NBC and kappa_R23_NBC;
vars kappa_R34_NBC and kappa_R34_NBC;
vars kappa_R45_NBC and kappa_R45_NBC;
vars kappa_R56_NBC and kappa_R56_NBC;
vars K_Na_i and K_Na_i;
vars K_Na_o and K_Na_o;
vars K_HCO3_i and K_HCO3_i;
vars K_HCO3_o and K_HCO3_o;
vars K_S1_NBC and K_S1_NBC;
vars K_S2_NBC and K_S2_NBC;
vars K_S3_NBC and K_S3_NBC;
vars K_S4_NBC and K_S4_NBC;
vars K_S5_NBC and K_S5_NBC;
vars K_S6_NBC and K_S6_NBC;
enddef;
def map between BG_parameters and NHE for
vars kappa_R61_NHE and kappa_R61_NHE;
vars kappa_R12_NHE and kappa_R12_NHE;
vars kappa_R23_NHE and kappa_R23_NHE;
vars kappa_R34_NHE and kappa_R34_NHE;
vars kappa_R45_NHE and kappa_R45_NHE;
vars kappa_R56_NHE and kappa_R56_NHE;
vars K_H_i and K_H_i;
vars K_H_o and K_H_o;
vars K_Na_i and K_Na_i;
vars K_Na_o and K_Na_o;
vars K_S1_NHE and K_S1_NHE;
vars K_S2_NHE and K_S2_NHE;
vars K_S3_NHE and K_S3_NHE;
vars K_S4_NHE and K_S4_NHE;
vars K_S5_NHE and K_S5_NHE;
vars K_S6_NHE and K_S6_NHE;
enddef;
def map between BG_parameters and pH_B1 for
vars kappa_Re_B1 and kappa_Re_B1;
vars K_H_i and K_H_i;
vars K_B1 and K_B1;
vars K_HB1 and K_HB1;
enddef;
def map between BG_parameters and pH_B2 for
vars kappa_Re_B2 and kappa_Re_B2;
vars K_H_i and K_H_i;
vars K_B2 and K_B2;
vars K_HB2 and K_HB2;
enddef;

def map between constants and AE for
	vars R and R;
	vars T and T;
enddef;
def map between constants and CHE for
	vars R and R;
	vars T and T;
enddef;
def map between constants and CO2_hyd for
	vars R and R;
	vars T and T;
enddef;
def map between constants and NBC for
	vars R and R;
	vars T and T;
enddef;
def map between constants and NHE for
	vars R and R;
	vars T and T;
enddef;
def map between constants and pH_B1 for
	vars R and R;
	vars T and T;
enddef;
def map between constants and pH_B2 for
	vars R and R;
	vars T and T;
enddef;

enddef;