Location: BG_TCC @ 9050accc29fb / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-03-22 14:00:03+13:00
Desc:
Updating TCC channel density to literature value (Droogmans 1989)
Permanent Source URI:
https://models.physiomeproject.org/workspace/831/rawfile/9050accc29fbf95de010da3d2a5cfba7e9719a2e/parameter_finder/output/TEMP.cellml.txt
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def model individual_TCC 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 comp environment as
    var time: second {pub: out};
    // initial values
var q_Ca_i: fmol {init: 1e-888, pub: out};
var q_Ca_o: fmol {init: 1e-888, pub: out};
var q_S00: fmol {init: 1e-888, pub: out};
var q_S10: fmol {init: 1e-888, pub: out};
var q_S20: fmol {init: 1e-888, pub: out};
var q_S01: fmol {init: 1e-888, pub: out};
var q_S11: fmol {init: 1e-888, pub: out};
var q_S21: fmol {init: 1e-888, pub: out};
// From submodule
var v_TCC: fmol_per_sec {pub: in};
var v_b00: fmol_per_sec {pub: in};
var v_b01: fmol_per_sec {pub: in};
var v_b10: fmol_per_sec {pub: in};
var v_b11: fmol_per_sec {pub: in};
var v_g00: fmol_per_sec {pub: in};
var v_g10: fmol_per_sec {pub: in};
var v_g20: fmol_per_sec {pub: in};
ode(q_Ca_i, time) = vvv;
ode(q_Ca_o, time) = vvv;
ode(q_S00, time) = vvv;
ode(q_S10, time) = vvv;
ode(q_S20, time) = vvv;
ode(q_S01, time) = vvv;
ode(q_S11, time) = vvv;
ode(q_S21, time) = vvv;
enddef;

def comp TCC_parameters as
var kappa_TCC: fmol_per_sec {init: 3667.46, pub: out};
var kappa_b00: fmol_per_sec {init: 54.3421, pub: out};
var kappa_b01: fmol_per_sec {init: 2.00823, pub: out};
var kappa_b10: fmol_per_sec {init: 147.348, pub: out};
var kappa_b11: fmol_per_sec {init: 5.44529, pub: out};
var kappa_g00: fmol_per_sec {init: 0.363554, pub: out};
var kappa_g10: fmol_per_sec {init: 1.97154, pub: out};
var kappa_g20: fmol_per_sec {init: 2.6729, pub: out};
var K_Ca_i: per_fmol {init: 1.76045, pub: out};
var K_Ca_o: per_fmol {init: 11.6865, pub: out};
var K_S00: per_fmol {init: 4.87717, pub: out};
var K_S10: per_fmol {init: 0.899355, pub: out};
var K_S20: per_fmol {init: 0.663368, pub: out};
var K_S01: per_fmol {init: 131.975, pub: out};
var K_S11: per_fmol {init: 24.3362, pub: out};
var K_S21: per_fmol {init: 17.9505, pub: out};
enddef;
def comp TCC as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_TCC: fmol_per_sec {pub: in};
var kappa_b00: fmol_per_sec {pub: in};
var kappa_b01: fmol_per_sec {pub: in};
var kappa_b10: fmol_per_sec {pub: in};
var kappa_b11: fmol_per_sec {pub: in};
var kappa_g00: fmol_per_sec {pub: in};
var kappa_g10: fmol_per_sec {pub: in};
var kappa_g20: fmol_per_sec {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_Ca_o: per_fmol {pub: in};
var K_S00: per_fmol {pub: in};
var K_S10: per_fmol {pub: in};
var K_S20: per_fmol {pub: in};
var K_S01: per_fmol {pub: in};
var K_S11: per_fmol {pub: in};
var K_S21: per_fmol {pub: in};
// Input from global environment
var q_Ca_i: fmol {pub: in};
var q_Ca_o: fmol {pub: in};
var q_S00: fmol {pub: in};
var q_S10: fmol {pub: in};
var q_S20: fmol {pub: in};
var q_S01: fmol {pub: in};
var q_S11: fmol {pub: in};
var q_S21: fmol {pub: in};
// Constitutive parameters
var mu_Ca_i: J_per_mol;
var mu_Ca_o: J_per_mol;
var mu_S00: J_per_mol;
var mu_S10: J_per_mol;
var mu_S20: J_per_mol;
var mu_S01: J_per_mol;
var mu_S11: J_per_mol;
var mu_S21: J_per_mol;
var v_TCC: fmol_per_sec {pub: out};
var v_b00: fmol_per_sec {pub: out};
var v_b01: fmol_per_sec {pub: out};
var v_b10: fmol_per_sec {pub: out};
var v_b11: fmol_per_sec {pub: out};
var v_g00: fmol_per_sec {pub: out};
var v_g10: fmol_per_sec {pub: out};
var v_g20: fmol_per_sec {pub: out};
mu_Ca_i = R*T*ln(K_Ca_i*q_Ca_i);
mu_Ca_o = R*T*ln(K_Ca_o*q_Ca_o);
mu_S00 = R*T*ln(K_S00*q_S00);
mu_S10 = R*T*ln(K_S10*q_S10);
mu_S20 = R*T*ln(K_S20*q_S20);
mu_S01 = R*T*ln(K_S01*q_S01);
mu_S11 = R*T*ln(K_S11*q_S11);
mu_S21 = R*T*ln(K_S21*q_S21);
v_TCC = ppp;
v_b00 = ppp;
v_b01 = ppp;
v_b10 = ppp;
v_b11 = ppp;
v_g00 = ppp;
v_g10 = ppp;
v_g20 = ppp;
enddef;
def map between environment and TCC for
vars time and time;
vars q_Ca_i and q_Ca_i;
vars q_Ca_o and q_Ca_o;
vars q_S00 and q_S00;
vars q_S10 and q_S10;
vars q_S20 and q_S20;
vars q_S01 and q_S01;
vars q_S11 and q_S11;
vars q_S21 and q_S21;
vars v_TCC and v_TCC;
vars v_b00 and v_b00;
vars v_b01 and v_b01;
vars v_b10 and v_b10;
vars v_b11 and v_b11;
vars v_g00 and v_g00;
vars v_g10 and v_g10;
vars v_g20 and v_g20;
enddef;
def map between TCC and TCC_parameters for
vars kappa_TCC and kappa_TCC;
vars kappa_b00 and kappa_b00;
vars kappa_b01 and kappa_b01;
vars kappa_b10 and kappa_b10;
vars kappa_b11 and kappa_b11;
vars kappa_g00 and kappa_g00;
vars kappa_g10 and kappa_g10;
vars kappa_g20 and kappa_g20;
vars K_Ca_i and K_Ca_i;
vars K_Ca_o and K_Ca_o;
vars K_S00 and K_S00;
vars K_S10 and K_S10;
vars K_S20 and K_S20;
vars K_S01 and K_S01;
vars K_S11 and K_S11;
vars K_S21 and K_S21;
enddef;
def map between constants and TCC for
vars R and R;
 vars T and T;
enddef;
enddef;