Location: BG_AE @ 8db4300e596b / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-26 11:44:51+12:00
Desc:
Adding readme on stoich of H, and updating n values
Permanent Source URI:
https://models.fieldml.org/workspace/882/rawfile/8db4300e596beb72efdffd9f564aa6875381ab9d/parameter_finder/output/TEMP.cellml.txt
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def model individual_AE 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 fF using unit fF;
        unit fC using unit fC;
        unit per_second using unit per_second;
        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 pL using unit pL;
   enddef;
def import using "units_and_constants/constants_BG.cellml" for
            comp constants using comp constants;
enddef;

    def comp environment as
    var time: second {pub: out};
    // initial values
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_H_i: fmol {init: 1e-888, pub: out};
var q_H_o: fmol {init: 1e-888, pub: out};
// From submodule
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};
ode(q_HCO3_i, time) = vvv;
ode(q_HCO3_o, time) = vvv;
ode(q_Cl_i, time) = vvv;
ode(q_Cl_o, time) = vvv;
ode(q_S1_AE, time) = vvv;
ode(q_S2_AE, time) = vvv;
ode(q_S3_AE, time) = vvv;
ode(q_S4_AE, time) = vvv;
ode(q_S5_AE, time) = vvv;
ode(q_S6_AE, time) = vvv;
ode(q_H_i, time) = vvv;
ode(q_H_o, time) = vvv;
enddef;

def comp AE_parameters as
var kappa_R61_AE: fmol_per_sec {init: 6.35519e-07, pub: out};
var kappa_R12_AE: fmol_per_sec {init: 2.03293, pub: out};
var kappa_R23_AE: fmol_per_sec {init: 267.589, pub: out};
var kappa_R34_AE: fmol_per_sec {init: 9.62669e-06, pub: out};
var kappa_R45_AE: fmol_per_sec {init: 263.129, pub: out};
var kappa_R56_AE: fmol_per_sec {init: 1.99905e+06, pub: out};
var K_HCO3_i: per_fmol {init: 5.51549e-06, pub: out};
var K_HCO3_o: per_fmol {init: 0.402195, pub: out};
var K_Cl_i: per_fmol {init: 0.0419022, pub: out};
var K_Cl_o: per_fmol {init: 0.00305555, pub: out};
var K_S1_AE: per_fmol {init: 2.00907, pub: out};
var K_S2_AE: per_fmol {init: 0.000868436, pub: out};
var K_S3_AE: per_fmol {init: 0.135307, pub: out};
var K_S4_AE: per_fmol {init: 0.1376, pub: out};
var K_S5_AE: per_fmol {init: 8.78222e-06, pub: out};
var K_S6_AE: per_fmol {init: 2.03802, pub: out};
var K_H_i: per_fmol {init: 0.00150496, pub: out};
var K_H_o: per_fmol {init: 0.432208, pub: out};
enddef;
def comp AE as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R61_AE: fmol_per_sec {pub: in};
var kappa_R12_AE: fmol_per_sec {pub: in};
var kappa_R23_AE: fmol_per_sec {pub: in};
var kappa_R34_AE: fmol_per_sec {pub: in};
var kappa_R45_AE: fmol_per_sec {pub: in};
var kappa_R56_AE: fmol_per_sec {pub: in};
var K_HCO3_i: per_fmol {pub: in};
var K_HCO3_o: per_fmol {pub: in};
var K_Cl_i: per_fmol {pub: in};
var K_Cl_o: per_fmol {pub: in};
var K_S1_AE: per_fmol {pub: in};
var K_S2_AE: per_fmol {pub: in};
var K_S3_AE: per_fmol {pub: in};
var K_S4_AE: per_fmol {pub: in};
var K_S5_AE: per_fmol {pub: in};
var K_S6_AE: per_fmol {pub: in};
var K_H_i: per_fmol {pub: in};
var K_H_o: per_fmol {pub: in};
// Input from global environment
var q_HCO3_i: fmol {pub: in};
var q_HCO3_o: fmol {pub: in};
var q_Cl_i: fmol {pub: in};
var q_Cl_o: fmol {pub: in};
var q_S1_AE: fmol {pub: in};
var q_S2_AE: fmol {pub: in};
var q_S3_AE: fmol {pub: in};
var q_S4_AE: fmol {pub: in};
var q_S5_AE: fmol {pub: in};
var q_S6_AE: fmol {pub: in};
var q_H_i: fmol {pub: in};
var q_H_o: fmol {pub: in};
// Constitutive parameters
var mu_HCO3_i: J_per_mol;
var mu_HCO3_o: J_per_mol;
var mu_Cl_i: J_per_mol;
var mu_Cl_o: J_per_mol;
var mu_S1_AE: J_per_mol;
var mu_S2_AE: J_per_mol;
var mu_S3_AE: J_per_mol;
var mu_S4_AE: J_per_mol;
var mu_S5_AE: J_per_mol;
var mu_S6_AE: J_per_mol;
var mu_H_i: J_per_mol;
var mu_H_o: J_per_mol;
var v_R61_AE: fmol_per_sec {pub: out};
var v_R12_AE: fmol_per_sec {pub: out};
var v_R23_AE: fmol_per_sec {pub: out};
var v_R34_AE: fmol_per_sec {pub: out};
var v_R45_AE: fmol_per_sec {pub: out};
var v_R56_AE: fmol_per_sec {pub: out};
mu_HCO3_i = R*T*ln(K_HCO3_i*q_HCO3_i);
mu_HCO3_o = R*T*ln(K_HCO3_o*q_HCO3_o);
mu_Cl_i = R*T*ln(K_Cl_i*q_Cl_i);
mu_Cl_o = R*T*ln(K_Cl_o*q_Cl_o);
mu_S1_AE = R*T*ln(K_S1_AE*q_S1_AE);
mu_S2_AE = R*T*ln(K_S2_AE*q_S2_AE);
mu_S3_AE = R*T*ln(K_S3_AE*q_S3_AE);
mu_S4_AE = R*T*ln(K_S4_AE*q_S4_AE);
mu_S5_AE = R*T*ln(K_S5_AE*q_S5_AE);
mu_S6_AE = R*T*ln(K_S6_AE*q_S6_AE);
mu_H_i = R*T*ln(K_H_i*q_H_i);
mu_H_o = R*T*ln(K_H_o*q_H_o);
v_R61_AE = kappa_R61_AE*(ppp);
v_R12_AE = kappa_R12_AE*(ppp);
v_R23_AE = kappa_R23_AE*(ppp);
v_R34_AE = kappa_R34_AE*(ppp);
v_R45_AE = kappa_R45_AE*(ppp);
v_R56_AE = kappa_R56_AE*(ppp);
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 q_H_i and q_H_i;
vars q_H_o and q_H_o;
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;
enddef;
def map between AE and AE_parameters 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;
vars K_H_i and K_H_i;
vars K_H_o and K_H_o;
enddef;
def map between constants and AE for
vars R and R;
 vars T and T;
enddef;
enddef;