- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-12-16 11:41:05+13:00
- Desc:
- Updating vols with LRd values and updating parameters
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/827/rawfile/9d2b43525cbcce7efb8e5753c84b213017aa635b/parameter_finder/output/TEMP.cellml.txt
def model individual_NaK 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_1_NaK: fmol {init: 1e-888, pub: out};
var q_2_NaK: fmol {init: 1e-888, pub: out};
var q_3_NaK: fmol {init: 1e-888, pub: out};
var q_4_NaK: fmol {init: 1e-888, pub: out};
var q_5_NaK: fmol {init: 1e-888, pub: out};
var q_6_NaK: fmol {init: 1e-888, pub: out};
var q_7_NaK: fmol {init: 1e-888, pub: out};
var q_8_NaK: fmol {init: 1e-888, pub: out};
var q_9_NaK: fmol {init: 1e-888, pub: out};
var q_10_NaK: fmol {init: 1e-888, pub: out};
var q_11_NaK: fmol {init: 1e-888, pub: out};
var q_12_NaK: fmol {init: 1e-888, pub: out};
var q_13_NaK: fmol {init: 1e-888, pub: out};
var q_14_NaK: fmol {init: 1e-888, pub: out};
var q_15_NaK: fmol {init: 1e-888, pub: out};
var q_K_i: fmol {init: 1e-888, pub: out};
var q_K_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_MgATP: fmol {init: 1e-888, pub: out};
var q_MgADP: fmol {init: 1e-888, pub: out};
var q_Pi: fmol {init: 1e-888, pub: out};
var q_H_i: fmol {init: 1e-888, pub: out};
// From submodule
var v_1_NaK: fmol_per_sec {pub: in};
var v_2_NaK: fmol_per_sec {pub: in};
var v_3_NaK: fmol_per_sec {pub: in};
var v_4_NaK: fmol_per_sec {pub: in};
var v_5_NaK: fmol_per_sec {pub: in};
var v_6_NaK: fmol_per_sec {pub: in};
var v_7_NaK: fmol_per_sec {pub: in};
var v_8_NaK: fmol_per_sec {pub: in};
var v_9_NaK: fmol_per_sec {pub: in};
var v_10_NaK: fmol_per_sec {pub: in};
var v_11_NaK: fmol_per_sec {pub: in};
var v_12_NaK: fmol_per_sec {pub: in};
var v_13_NaK: fmol_per_sec {pub: in};
var v_14_NaK: fmol_per_sec {pub: in};
var v_15_NaK: fmol_per_sec {pub: in};
ode(q_1_NaK, time) = vvv;
ode(q_2_NaK, time) = vvv;
ode(q_3_NaK, time) = vvv;
ode(q_4_NaK, time) = vvv;
ode(q_5_NaK, time) = vvv;
ode(q_6_NaK, time) = vvv;
ode(q_7_NaK, time) = vvv;
ode(q_8_NaK, time) = vvv;
ode(q_9_NaK, time) = vvv;
ode(q_10_NaK, time) = vvv;
ode(q_11_NaK, time) = vvv;
ode(q_12_NaK, time) = vvv;
ode(q_13_NaK, time) = vvv;
ode(q_14_NaK, time) = vvv;
ode(q_15_NaK, time) = vvv;
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
ode(q_Na_i, time) = vvv;
ode(q_Na_o, time) = vvv;
ode(q_MgATP, time) = vvv;
ode(q_MgADP, time) = vvv;
ode(q_Pi, time) = vvv;
ode(q_H_i, time) = vvv;
enddef;
def comp NaK_parameters as
var kappa_1_NaK: fmol_per_sec {init: 28701.2, pub: out};
var kappa_2_NaK: fmol_per_sec {init: 1.02749e+06, pub: out};
var kappa_3_NaK: fmol_per_sec {init: 36989.9, pub: out};
var kappa_4_NaK: fmol_per_sec {init: 110769, pub: out};
var kappa_5_NaK: fmol_per_sec {init: 143.043, pub: out};
var kappa_6_NaK: fmol_per_sec {init: 0.203578, pub: out};
var kappa_7_NaK: fmol_per_sec {init: 73.4728, pub: out};
var kappa_8_NaK: fmol_per_sec {init: 70.4896, pub: out};
var kappa_9_NaK: fmol_per_sec {init: 19895.6, pub: out};
var kappa_10_NaK: fmol_per_sec {init: 1.40388e+06, pub: out};
var kappa_11_NaK: fmol_per_sec {init: 7905.94, pub: out};
var kappa_12_NaK: fmol_per_sec {init: 6193.15, pub: out};
var kappa_13_NaK: fmol_per_sec {init: 0.55667, pub: out};
var kappa_14_NaK: fmol_per_sec {init: 6163.37, pub: out};
var kappa_15_NaK: fmol_per_sec {init: 1.34489, pub: out};
var K_1_NaK: per_fmol {init: 1.17033e+06, pub: out};
var K_2_NaK: per_fmol {init: 8172.83, pub: out};
var K_3_NaK: per_fmol {init: 228.295, pub: out};
var K_4_NaK: per_fmol {init: 76.2363, pub: out};
var K_5_NaK: per_fmol {init: 101.833, pub: out};
var K_6_NaK: per_fmol {init: 6990.92, pub: out};
var K_7_NaK: per_fmol {init: 157.403, pub: out};
var K_8_NaK: per_fmol {init: 494.813, pub: out};
var K_9_NaK: per_fmol {init: 1.06726e+06, pub: out};
var K_10_NaK: per_fmol {init: 3781.29, pub: out};
var K_11_NaK: per_fmol {init: 53.588, pub: out};
var K_12_NaK: per_fmol {init: 68.4084, pub: out};
var K_13_NaK: per_fmol {init: 349.31, pub: out};
var K_14_NaK: per_fmol {init: 105.854, pub: out};
var K_15_NaK: per_fmol {init: 22775, pub: out};
var K_K_i: per_fmol {init: 0.000123928, pub: out};
var K_K_o: per_fmol {init: 0.455493, pub: out};
var K_Na_i: per_fmol {init: 0.00344241, pub: out};
var K_Na_o: per_fmol {init: 0.00256511, pub: out};
var K_MgATP: per_fmol {init: 0.0445571, pub: out};
var K_MgADP: per_fmol {init: 0.204939, pub: out};
var K_Pi: per_fmol {init: 2.00757, pub: out};
var K_H_i: per_fmol {init: 2.00757, pub: out};
enddef;
def comp NaK as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_1_NaK: fmol_per_sec {pub: in};
var kappa_2_NaK: fmol_per_sec {pub: in};
var kappa_3_NaK: fmol_per_sec {pub: in};
var kappa_4_NaK: fmol_per_sec {pub: in};
var kappa_5_NaK: fmol_per_sec {pub: in};
var kappa_6_NaK: fmol_per_sec {pub: in};
var kappa_7_NaK: fmol_per_sec {pub: in};
var kappa_8_NaK: fmol_per_sec {pub: in};
var kappa_9_NaK: fmol_per_sec {pub: in};
var kappa_10_NaK: fmol_per_sec {pub: in};
var kappa_11_NaK: fmol_per_sec {pub: in};
var kappa_12_NaK: fmol_per_sec {pub: in};
var kappa_13_NaK: fmol_per_sec {pub: in};
var kappa_14_NaK: fmol_per_sec {pub: in};
var kappa_15_NaK: fmol_per_sec {pub: in};
var K_1_NaK: per_fmol {pub: in};
var K_2_NaK: per_fmol {pub: in};
var K_3_NaK: per_fmol {pub: in};
var K_4_NaK: per_fmol {pub: in};
var K_5_NaK: per_fmol {pub: in};
var K_6_NaK: per_fmol {pub: in};
var K_7_NaK: per_fmol {pub: in};
var K_8_NaK: per_fmol {pub: in};
var K_9_NaK: per_fmol {pub: in};
var K_10_NaK: per_fmol {pub: in};
var K_11_NaK: per_fmol {pub: in};
var K_12_NaK: per_fmol {pub: in};
var K_13_NaK: per_fmol {pub: in};
var K_14_NaK: per_fmol {pub: in};
var K_15_NaK: per_fmol {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
var K_Na_i: per_fmol {pub: in};
var K_Na_o: per_fmol {pub: in};
var K_MgATP: per_fmol {pub: in};
var K_MgADP: per_fmol {pub: in};
var K_Pi: per_fmol {pub: in};
var K_H_i: per_fmol {pub: in};
// Input from global environment
var q_1_NaK: fmol {pub: in};
var q_2_NaK: fmol {pub: in};
var q_3_NaK: fmol {pub: in};
var q_4_NaK: fmol {pub: in};
var q_5_NaK: fmol {pub: in};
var q_6_NaK: fmol {pub: in};
var q_7_NaK: fmol {pub: in};
var q_8_NaK: fmol {pub: in};
var q_9_NaK: fmol {pub: in};
var q_10_NaK: fmol {pub: in};
var q_11_NaK: fmol {pub: in};
var q_12_NaK: fmol {pub: in};
var q_13_NaK: fmol {pub: in};
var q_14_NaK: fmol {pub: in};
var q_15_NaK: fmol {pub: in};
var q_K_i: fmol {pub: in};
var q_K_o: fmol {pub: in};
var q_Na_i: fmol {pub: in};
var q_Na_o: fmol {pub: in};
var q_MgATP: fmol {pub: in};
var q_MgADP: fmol {pub: in};
var q_Pi: fmol {pub: in};
var q_H_i: fmol {pub: in};
// Constitutive parameters
var mu_1_NaK: J_per_mol;
var mu_2_NaK: J_per_mol;
var mu_3_NaK: J_per_mol;
var mu_4_NaK: J_per_mol;
var mu_5_NaK: J_per_mol;
var mu_6_NaK: J_per_mol;
var mu_7_NaK: J_per_mol;
var mu_8_NaK: J_per_mol;
var mu_9_NaK: J_per_mol;
var mu_10_NaK: J_per_mol;
var mu_11_NaK: J_per_mol;
var mu_12_NaK: J_per_mol;
var mu_13_NaK: J_per_mol;
var mu_14_NaK: J_per_mol;
var mu_15_NaK: J_per_mol;
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var mu_Na_i: J_per_mol;
var mu_Na_o: J_per_mol;
var mu_MgATP: J_per_mol;
var mu_MgADP: J_per_mol;
var mu_Pi: J_per_mol;
var mu_H_i: J_per_mol;
var v_1_NaK: fmol_per_sec {pub: out};
var v_2_NaK: fmol_per_sec {pub: out};
var v_3_NaK: fmol_per_sec {pub: out};
var v_4_NaK: fmol_per_sec {pub: out};
var v_5_NaK: fmol_per_sec {pub: out};
var v_6_NaK: fmol_per_sec {pub: out};
var v_7_NaK: fmol_per_sec {pub: out};
var v_8_NaK: fmol_per_sec {pub: out};
var v_9_NaK: fmol_per_sec {pub: out};
var v_10_NaK: fmol_per_sec {pub: out};
var v_11_NaK: fmol_per_sec {pub: out};
var v_12_NaK: fmol_per_sec {pub: out};
var v_13_NaK: fmol_per_sec {pub: out};
var v_14_NaK: fmol_per_sec {pub: out};
var v_15_NaK: fmol_per_sec {pub: out};
mu_1_NaK = R*T*ln(K_1_NaK*q_1_NaK);
mu_2_NaK = R*T*ln(K_2_NaK*q_2_NaK);
mu_3_NaK = R*T*ln(K_3_NaK*q_3_NaK);
mu_4_NaK = R*T*ln(K_4_NaK*q_4_NaK);
mu_5_NaK = R*T*ln(K_5_NaK*q_5_NaK);
mu_6_NaK = R*T*ln(K_6_NaK*q_6_NaK);
mu_7_NaK = R*T*ln(K_7_NaK*q_7_NaK);
mu_8_NaK = R*T*ln(K_8_NaK*q_8_NaK);
mu_9_NaK = R*T*ln(K_9_NaK*q_9_NaK);
mu_10_NaK = R*T*ln(K_10_NaK*q_10_NaK);
mu_11_NaK = R*T*ln(K_11_NaK*q_11_NaK);
mu_12_NaK = R*T*ln(K_12_NaK*q_12_NaK);
mu_13_NaK = R*T*ln(K_13_NaK*q_13_NaK);
mu_14_NaK = R*T*ln(K_14_NaK*q_14_NaK);
mu_15_NaK = R*T*ln(K_15_NaK*q_15_NaK);
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_Na_i = R*T*ln(K_Na_i*q_Na_i);
mu_Na_o = R*T*ln(K_Na_o*q_Na_o);
mu_MgATP = R*T*ln(K_MgATP*q_MgATP);
mu_MgADP = R*T*ln(K_MgADP*q_MgADP);
mu_Pi = R*T*ln(K_Pi*q_Pi);
mu_H_i = R*T*ln(K_H_i*q_H_i);
v_1_NaK = ppp;
v_2_NaK = ppp;
v_3_NaK = ppp;
v_4_NaK = ppp;
v_5_NaK = ppp;
v_6_NaK = ppp;
v_7_NaK = ppp;
v_8_NaK = ppp;
v_9_NaK = ppp;
v_10_NaK = ppp;
v_11_NaK = ppp;
v_12_NaK = ppp;
v_13_NaK = ppp;
v_14_NaK = ppp;
v_15_NaK = ppp;
enddef;
def map between environment and NaK for
vars time and time;
vars q_1_NaK and q_1_NaK;
vars q_2_NaK and q_2_NaK;
vars q_3_NaK and q_3_NaK;
vars q_4_NaK and q_4_NaK;
vars q_5_NaK and q_5_NaK;
vars q_6_NaK and q_6_NaK;
vars q_7_NaK and q_7_NaK;
vars q_8_NaK and q_8_NaK;
vars q_9_NaK and q_9_NaK;
vars q_10_NaK and q_10_NaK;
vars q_11_NaK and q_11_NaK;
vars q_12_NaK and q_12_NaK;
vars q_13_NaK and q_13_NaK;
vars q_14_NaK and q_14_NaK;
vars q_15_NaK and q_15_NaK;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars q_Na_i and q_Na_i;
vars q_Na_o and q_Na_o;
vars q_MgATP and q_MgATP;
vars q_MgADP and q_MgADP;
vars q_Pi and q_Pi;
vars q_H_i and q_H_i;
vars v_1_NaK and v_1_NaK;
vars v_2_NaK and v_2_NaK;
vars v_3_NaK and v_3_NaK;
vars v_4_NaK and v_4_NaK;
vars v_5_NaK and v_5_NaK;
vars v_6_NaK and v_6_NaK;
vars v_7_NaK and v_7_NaK;
vars v_8_NaK and v_8_NaK;
vars v_9_NaK and v_9_NaK;
vars v_10_NaK and v_10_NaK;
vars v_11_NaK and v_11_NaK;
vars v_12_NaK and v_12_NaK;
vars v_13_NaK and v_13_NaK;
vars v_14_NaK and v_14_NaK;
vars v_15_NaK and v_15_NaK;
enddef;
def map between NaK and NaK_parameters for
vars kappa_1_NaK and kappa_1_NaK;
vars kappa_2_NaK and kappa_2_NaK;
vars kappa_3_NaK and kappa_3_NaK;
vars kappa_4_NaK and kappa_4_NaK;
vars kappa_5_NaK and kappa_5_NaK;
vars kappa_6_NaK and kappa_6_NaK;
vars kappa_7_NaK and kappa_7_NaK;
vars kappa_8_NaK and kappa_8_NaK;
vars kappa_9_NaK and kappa_9_NaK;
vars kappa_10_NaK and kappa_10_NaK;
vars kappa_11_NaK and kappa_11_NaK;
vars kappa_12_NaK and kappa_12_NaK;
vars kappa_13_NaK and kappa_13_NaK;
vars kappa_14_NaK and kappa_14_NaK;
vars kappa_15_NaK and kappa_15_NaK;
vars K_1_NaK and K_1_NaK;
vars K_2_NaK and K_2_NaK;
vars K_3_NaK and K_3_NaK;
vars K_4_NaK and K_4_NaK;
vars K_5_NaK and K_5_NaK;
vars K_6_NaK and K_6_NaK;
vars K_7_NaK and K_7_NaK;
vars K_8_NaK and K_8_NaK;
vars K_9_NaK and K_9_NaK;
vars K_10_NaK and K_10_NaK;
vars K_11_NaK and K_11_NaK;
vars K_12_NaK and K_12_NaK;
vars K_13_NaK and K_13_NaK;
vars K_14_NaK and K_14_NaK;
vars K_15_NaK and K_15_NaK;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
vars K_Na_i and K_Na_i;
vars K_Na_o and K_Na_o;
vars K_MgATP and K_MgATP;
vars K_MgADP and K_MgADP;
vars K_Pi and K_Pi;
vars K_H_i and K_H_i;
enddef;
def map between constants and NaK for
vars R and R;
vars T and T;
enddef;
enddef;
