- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-04-22 11:29:25+12:00
- Desc:
- Changing units to s for alpha and beta gate parameters
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/82d/rawfile/e8d0baabfe0103a19af7284c16d3df1ca4c592ee/parameter_finder/output/TEMP.cellml.txt
def model individual_Ks 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_K_i: fmol {init: 1e-888, pub: out};
var q_K_o: fmol {init: 1e-888, pub: out};
var q_S_Ks0: fmol {init: 1e-888, pub: out};
var q_S_Ks1: fmol {init: 1e-888, pub: out};
var q_S_Ks2: fmol {init: 1e-888, pub: out};
// From submodule
var v_Ks: fmol_per_sec {pub: in};
var v_xs1: fmol_per_sec {pub: in};
var v_xs2: fmol_per_sec {pub: in};
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
ode(q_S_Ks0, time) = vvv;
ode(q_S_Ks1, time) = vvv;
ode(q_S_Ks2, time) = vvv;
enddef;
def comp Ks_parameters as
var kappa_Ks: fmol_per_sec {init: 27.8683, pub: out};
var kappa_xs1: fmol_per_sec {init: 0.00829152, pub: out};
var kappa_xs2: fmol_per_sec {init: 0.0295644, pub: out};
var K_K_i: per_fmol {init: 1.42292, pub: out};
var K_K_o: per_fmol {init: 10.4348, pub: out};
var K_S_Ks0: per_fmol {init: 0.281155, pub: out};
var K_S_Ks1: per_fmol {init: 0.0394258, pub: out};
var K_S_Ks2: per_fmol {init: 0.0221145, pub: out};
enddef;
def comp Ks as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_Ks: fmol_per_sec {pub: in};
var kappa_xs1: fmol_per_sec {pub: in};
var kappa_xs2: fmol_per_sec {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
var K_S_Ks0: per_fmol {pub: in};
var K_S_Ks1: per_fmol {pub: in};
var K_S_Ks2: per_fmol {pub: in};
// Input from global environment
var q_K_i: fmol {pub: in};
var q_K_o: fmol {pub: in};
var q_S_Ks0: fmol {pub: in};
var q_S_Ks1: fmol {pub: in};
var q_S_Ks2: fmol {pub: in};
// Constitutive parameters
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var mu_S_Ks0: J_per_mol;
var mu_S_Ks1: J_per_mol;
var mu_S_Ks2: J_per_mol;
var v_Ks: fmol_per_sec {pub: out};
var v_xs1: fmol_per_sec {pub: out};
var v_xs2: fmol_per_sec {pub: out};
mu_K_i = R*T*ln(K_K_i*q_K_i);
mu_K_o = R*T*ln(K_K_o*q_K_o);
mu_S_Ks0 = R*T*ln(K_S_Ks0*q_S_Ks0);
mu_S_Ks1 = R*T*ln(K_S_Ks1*q_S_Ks1);
mu_S_Ks2 = R*T*ln(K_S_Ks2*q_S_Ks2);
v_Ks = ppp;
v_xs1 = ppp;
v_xs2 = ppp;
enddef;
def map between environment and Ks for
vars time and time;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars q_S_Ks0 and q_S_Ks0;
vars q_S_Ks1 and q_S_Ks1;
vars q_S_Ks2 and q_S_Ks2;
vars v_Ks and v_Ks;
vars v_xs1 and v_xs1;
vars v_xs2 and v_xs2;
enddef;
def map between Ks and Ks_parameters for
vars kappa_Ks and kappa_Ks;
vars kappa_xs1 and kappa_xs1;
vars kappa_xs2 and kappa_xs2;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
vars K_S_Ks0 and K_S_Ks0;
vars K_S_Ks1 and K_S_Ks1;
vars K_S_Ks2 and K_S_Ks2;
enddef;
def map between constants and Ks for
vars R and R;
vars T and T;
enddef;
enddef;
