Location: BG_NHE @ 006201ae4bd5 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-23 10:51:32+12:00
Desc:
Move ODE of channel states to channel component
Permanent Source URI:
https://staging.physiomeproject.org/workspace/880/rawfile/006201ae4bd5b8f10bb85c8d71c240f5c60a0052/parameter_finder/output/TEMP.cellml.txt
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def model individual_NHE 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_H_i: fmol {init: 1e-888, pub: out};
var q_H_o: 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_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};
// From submodule
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};
ode(q_H_i, time) = vvv;
ode(q_H_o, time) = vvv;
ode(q_Na_i, time) = vvv;
ode(q_Na_o, time) = vvv;
ode(q_S1_NHE, time) = vvv;
ode(q_S2_NHE, time) = vvv;
ode(q_S3_NHE, time) = vvv;
ode(q_S4_NHE, time) = vvv;
ode(q_S5_NHE, time) = vvv;
ode(q_S6_NHE, time) = vvv;
enddef;

def comp NHE_parameters as
var kappa_R61_NHE: fmol_per_sec {init: 3.97946, pub: out};
var kappa_R12_NHE: fmol_per_sec {init: 0.199355, pub: out};
var kappa_R23_NHE: fmol_per_sec {init: 46567.3, pub: out};
var kappa_R34_NHE: fmol_per_sec {init: 0.00101589, pub: out};
var kappa_R45_NHE: fmol_per_sec {init: 12689.2, pub: out};
var kappa_R56_NHE: fmol_per_sec {init: 54322.5, pub: out};
var K_H_i: per_fmol {init: 0.0427931, pub: out};
var K_H_o: per_fmol {init: 2034.44, pub: out};
var K_Na_i: per_fmol {init: 0.183198, pub: out};
var K_Na_o: per_fmol {init: 0.00870946, pub: out};
var K_S1_NHE: per_fmol {init: 0.0217565, pub: out};
var K_S2_NHE: per_fmol {init: 12.5212, pub: out};
var K_S3_NHE: per_fmol {init: 18.9878, pub: out};
var K_S4_NHE: per_fmol {init: 69.6824, pub: out};
var K_S5_NHE: per_fmol {init: 0.297906, pub: out};
var K_S6_NHE: per_fmol {init: 0.0800162, pub: out};
enddef;
def comp NHE as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R61_NHE: fmol_per_sec {pub: in};
var kappa_R12_NHE: fmol_per_sec {pub: in};
var kappa_R23_NHE: fmol_per_sec {pub: in};
var kappa_R34_NHE: fmol_per_sec {pub: in};
var kappa_R45_NHE: fmol_per_sec {pub: in};
var kappa_R56_NHE: fmol_per_sec {pub: in};
var K_H_i: per_fmol {pub: in};
var K_H_o: per_fmol {pub: in};
var K_Na_i: per_fmol {pub: in};
var K_Na_o: per_fmol {pub: in};
var K_S1_NHE: per_fmol {pub: in};
var K_S2_NHE: per_fmol {pub: in};
var K_S3_NHE: per_fmol {pub: in};
var K_S4_NHE: per_fmol {pub: in};
var K_S5_NHE: per_fmol {pub: in};
var K_S6_NHE: per_fmol {pub: in};
// Input from global environment
var q_H_i: fmol {pub: in};
var q_H_o: fmol {pub: in};
var q_Na_i: fmol {pub: in};
var q_Na_o: fmol {pub: in};
var q_S1_NHE: fmol {pub: in};
var q_S2_NHE: fmol {pub: in};
var q_S3_NHE: fmol {pub: in};
var q_S4_NHE: fmol {pub: in};
var q_S5_NHE: fmol {pub: in};
var q_S6_NHE: fmol {pub: in};
// Constitutive parameters
var mu_H_i: J_per_mol;
var mu_H_o: J_per_mol;
var mu_Na_i: J_per_mol;
var mu_Na_o: J_per_mol;
var mu_S1_NHE: J_per_mol;
var mu_S2_NHE: J_per_mol;
var mu_S3_NHE: J_per_mol;
var mu_S4_NHE: J_per_mol;
var mu_S5_NHE: J_per_mol;
var mu_S6_NHE: J_per_mol;
var v_R61_NHE: fmol_per_sec {pub: out};
var v_R12_NHE: fmol_per_sec {pub: out};
var v_R23_NHE: fmol_per_sec {pub: out};
var v_R34_NHE: fmol_per_sec {pub: out};
var v_R45_NHE: fmol_per_sec {pub: out};
var v_R56_NHE: fmol_per_sec {pub: out};
mu_H_i = R*T*ln(K_H_i*q_H_i);
mu_H_o = R*T*ln(K_H_o*q_H_o);
mu_Na_i = R*T*ln(K_Na_i*q_Na_i);
mu_Na_o = R*T*ln(K_Na_o*q_Na_o);
mu_S1_NHE = R*T*ln(K_S1_NHE*q_S1_NHE);
mu_S2_NHE = R*T*ln(K_S2_NHE*q_S2_NHE);
mu_S3_NHE = R*T*ln(K_S3_NHE*q_S3_NHE);
mu_S4_NHE = R*T*ln(K_S4_NHE*q_S4_NHE);
mu_S5_NHE = R*T*ln(K_S5_NHE*q_S5_NHE);
mu_S6_NHE = R*T*ln(K_S6_NHE*q_S6_NHE);
v_R61_NHE = kappa_R61_NHE*(ppp);
v_R12_NHE = kappa_R12_NHE*(ppp);
v_R23_NHE = kappa_R23_NHE*(ppp);
v_R34_NHE = kappa_R34_NHE*(ppp);
v_R45_NHE = kappa_R45_NHE*(ppp);
v_R56_NHE = kappa_R56_NHE*(ppp);
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;
enddef;
def map between NHE and NHE_parameters 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 constants and NHE for
vars R and R;
 vars T and T;
enddef;
enddef;