Location: BG_RTK @ 337f4e953679 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2023-09-26 13:49:51+13:00
Desc:
update picture bounds
Permanent Source URI:
https://models.physiomeproject.org/workspace/b2d/rawfile/337f4e95367975f05f77619783385b9e47c86d9c/parameter_finder/output/TEMP.cellml.txt
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def model individual_RTK 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_L: fmol {init: 1, pub: out};
var q_K1: fmol {init: 1e-3, pub: out};
var q_K2: fmol {init: 1e-3, pub: out};
var q_LK1: fmol {init: 1e-6, pub: out};
var q_K2P: fmol {init: 1e-9, pub: out};
var q_P: fmol {init: 1, pub: out};
var q_LK1K2: fmol {init: 1e-9, pub: out};
// From submodule
var v_Re1: fmol_per_sec {pub: in};
var v_Re2: fmol_per_sec {pub: in};
var v_Re3: fmol_per_sec {pub: in};
ode(q_L, time) = vvv;
ode(q_K1, time) = vvv;
ode(q_K2, time) = vvv;
ode(q_LK1, time) = vvv;
ode(q_K2P, time) = vvv;
ode(q_P, time) = vvv;
ode(q_LK1K2, time) = vvv;
enddef;

def comp RTK_parameters as
var kappa_Re1: fmol_per_sec {init: 0.000186898, pub: out};
var kappa_Re2: fmol_per_sec {init: 0.0125535, pub: out};
var kappa_Re3: fmol_per_sec {init: 132.879, pub: out};
var K_L: per_fmol {init: 197.162, pub: out};
var K_K1: per_fmol {init: 197.162, pub: out};
var K_K2: per_fmol {init: 4.01297e+09, pub: out};
var K_LK1: per_fmol {init: 0.00144219, pub: out};
var K_K2P: per_fmol {init: 3.79118e-07, pub: out};
var K_P: per_fmol {init: 2.54645e+07, pub: out};
var K_LK1K2: per_fmol {init: 2.14714e-05, pub: out};
enddef;
def comp RTK as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_Re1: fmol_per_sec {pub: in};
var kappa_Re2: fmol_per_sec {pub: in};
var kappa_Re3: fmol_per_sec {pub: in};
var K_L: per_fmol {pub: in};
var K_K1: per_fmol {pub: in};
var K_K2: per_fmol {pub: in};
var K_LK1: per_fmol {pub: in};
var K_K2P: per_fmol {pub: in};
var K_P: per_fmol {pub: in};
var K_LK1K2: per_fmol {pub: in};
// Input from global environment
var q_L: fmol {pub: in};
var q_K1: fmol {pub: in};
var q_K2: fmol {pub: in};
var q_LK1: fmol {pub: in};
var q_K2P: fmol {pub: in};
var q_P: fmol {pub: in};
var q_LK1K2: fmol {pub: in};
// Constitutive parameters
var mu_L: J_per_mol;
var mu_K1: J_per_mol;
var mu_K2: J_per_mol;
var mu_LK1: J_per_mol;
var mu_K2P: J_per_mol;
var mu_P: J_per_mol;
var mu_LK1K2: J_per_mol;
var v_Re1: fmol_per_sec {pub: out};
var v_Re2: fmol_per_sec {pub: out};
var v_Re3: fmol_per_sec {pub: out};
mu_L = R*T*ln(K_L*q_L);
mu_K1 = R*T*ln(K_K1*q_K1);
mu_K2 = R*T*ln(K_K2*q_K2);
mu_LK1 = R*T*ln(K_LK1*q_LK1);
mu_K2P = R*T*ln(K_K2P*q_K2P);
mu_P = R*T*ln(K_P*q_P);
mu_LK1K2 = R*T*ln(K_LK1K2*q_LK1K2);
v_Re1 = kappa_Re1*ppp;
v_Re2 = kappa_Re2*ppp;
v_Re3 = kappa_Re3*ppp;
enddef;
def map between environment and RTK for
vars time and time;
vars q_L and q_L;
vars q_K1 and q_K1;
vars q_K2 and q_K2;
vars q_LK1 and q_LK1;
vars q_K2P and q_K2P;
vars q_P and q_P;
vars q_LK1K2 and q_LK1K2;
vars v_Re1 and v_Re1;
vars v_Re2 and v_Re2;
vars v_Re3 and v_Re3;
enddef;
def map between RTK and RTK_parameters for
vars kappa_Re1 and kappa_Re1;
vars kappa_Re2 and kappa_Re2;
vars kappa_Re3 and kappa_Re3;
vars K_L and K_L;
vars K_K1 and K_K1;
vars K_K2 and K_K2;
vars K_LK1 and K_LK1;
vars K_K2P and K_K2P;
vars K_P and K_P;
vars K_LK1K2 and K_LK1K2;
enddef;
def map between constants and RTK for
vars R and R;
 vars T and T;
enddef;
enddef;