- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-04-20 11:01:58+12:00
- Desc:
- storing gate particle number in comp environment
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/826/rawfile/43437bf2d1aa9e1e72cbb9984ecb6e4e2da1310f/parameter_finder/output/TEMP.cellml.txt
def model individual_fast_Na 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_Na_i: fmol {init: 1e-888, pub: out};
var q_Na_o: fmol {init: 1e-888, pub: out};
var q_000_Na: fmol {init: 1e-888, pub: out};
var q_100_Na: fmol {init: 1e-888, pub: out};
var q_200_Na: fmol {init: 1e-888, pub: out};
var q_300_Na: fmol {init: 1e-888, pub: out};
var q_010_Na: fmol {init: 1e-888, pub: out};
var q_110_Na: fmol {init: 1e-888, pub: out};
var q_210_Na: fmol {init: 1e-888, pub: out};
var q_310_Na: fmol {init: 1e-888, pub: out};
var q_001_Na: fmol {init: 1e-888, pub: out};
var q_101_Na: fmol {init: 1e-888, pub: out};
var q_201_Na: fmol {init: 1e-888, pub: out};
var q_301_Na: fmol {init: 1e-888, pub: out};
var q_011_Na: fmol {init: 1e-888, pub: out};
var q_111_Na: fmol {init: 1e-888, pub: out};
var q_211_Na: fmol {init: 1e-888, pub: out};
var q_311_Na: fmol {init: 1e-888, pub: out};
// From submodule
var v_Na: fmol_per_sec {pub: in};
var v_m000: fmol_per_sec {pub: in};
var v_m001: fmol_per_sec {pub: in};
var v_m010: fmol_per_sec {pub: in};
var v_m011: fmol_per_sec {pub: in};
var v_m100: fmol_per_sec {pub: in};
var v_m101: fmol_per_sec {pub: in};
var v_m110: fmol_per_sec {pub: in};
var v_m111: fmol_per_sec {pub: in};
var v_m200: fmol_per_sec {pub: in};
var v_m201: fmol_per_sec {pub: in};
var v_m210: fmol_per_sec {pub: in};
var v_m211: fmol_per_sec {pub: in};
var v_h000: fmol_per_sec {pub: in};
var v_h001: fmol_per_sec {pub: in};
var v_h100: fmol_per_sec {pub: in};
var v_h101: fmol_per_sec {pub: in};
var v_h200: fmol_per_sec {pub: in};
var v_h201: fmol_per_sec {pub: in};
var v_h300: fmol_per_sec {pub: in};
var v_h301: fmol_per_sec {pub: in};
var v_j000: fmol_per_sec {pub: in};
var v_j010: fmol_per_sec {pub: in};
var v_j100: fmol_per_sec {pub: in};
var v_j110: fmol_per_sec {pub: in};
var v_j200: fmol_per_sec {pub: in};
var v_j210: fmol_per_sec {pub: in};
var v_j300: fmol_per_sec {pub: in};
var v_j310: fmol_per_sec {pub: in};
ode(q_Na_i, time) = vvv;
ode(q_Na_o, time) = vvv;
ode(q_000_Na, time) = vvv;
ode(q_100_Na, time) = vvv;
ode(q_200_Na, time) = vvv;
ode(q_300_Na, time) = vvv;
ode(q_010_Na, time) = vvv;
ode(q_110_Na, time) = vvv;
ode(q_210_Na, time) = vvv;
ode(q_310_Na, time) = vvv;
ode(q_001_Na, time) = vvv;
ode(q_101_Na, time) = vvv;
ode(q_201_Na, time) = vvv;
ode(q_301_Na, time) = vvv;
ode(q_011_Na, time) = vvv;
ode(q_111_Na, time) = vvv;
ode(q_211_Na, time) = vvv;
ode(q_311_Na, time) = vvv;
enddef;
def comp fast_Na_parameters as
var kappa_Na: fmol_per_sec {init: 7.77684, pub: out};
var kappa_m000: fmol_per_sec {init: 5.28779e+06, pub: out};
var kappa_m001: fmol_per_sec {init: 1.63587, pub: out};
var kappa_m010: fmol_per_sec {init: 2.21713, pub: out};
var kappa_m011: fmol_per_sec {init: 6.85907e-07, pub: out};
var kappa_m100: fmol_per_sec {init: 1.65461e+09, pub: out};
var kappa_m101: fmol_per_sec {init: 511.883, pub: out};
var kappa_m110: fmol_per_sec {init: 693.768, pub: out};
var kappa_m111: fmol_per_sec {init: 0.000214629, pub: out};
var kappa_m200: fmol_per_sec {init: 1.29437e+11, pub: out};
var kappa_m201: fmol_per_sec {init: 40043.6, pub: out};
var kappa_m210: fmol_per_sec {init: 54272.1, pub: out};
var kappa_m211: fmol_per_sec {init: 0.01679, pub: out};
var kappa_h000: fmol_per_sec {init: 0.0472309, pub: out};
var kappa_h001: fmol_per_sec {init: 1.46117e-08, pub: out};
var kappa_h100: fmol_per_sec {init: 22.1687, pub: out};
var kappa_h101: fmol_per_sec {init: 6.85826e-06, pub: out};
var kappa_h200: fmol_per_sec {init: 3468.43, pub: out};
var kappa_h201: fmol_per_sec {init: 0.00107302, pub: out};
var kappa_h300: fmol_per_sec {init: 180885, pub: out};
var kappa_h301: fmol_per_sec {init: 0.05596, pub: out};
var kappa_j000: fmol_per_sec {init: 0.0184178, pub: out};
var kappa_j010: fmol_per_sec {init: 7.72244e-09, pub: out};
var kappa_j100: fmol_per_sec {init: 8.64473, pub: out};
var kappa_j110: fmol_per_sec {init: 3.62467e-06, pub: out};
var kappa_j200: fmol_per_sec {init: 1352.52, pub: out};
var kappa_j210: fmol_per_sec {init: 0.000567102, pub: out};
var kappa_j300: fmol_per_sec {init: 70536.7, pub: out};
var kappa_j310: fmol_per_sec {init: 0.0295755, pub: out};
var K_Na_i: per_fmol {init: 0.0810668, pub: out};
var K_Na_o: per_fmol {init: 0.538151, pub: out};
var K_000_Na: per_fmol {init: 0.00710114, pub: out};
var K_100_Na: per_fmol {init: 1.51291e-05, pub: out};
var K_200_Na: per_fmol {init: 9.6699e-08, pub: out};
var K_300_Na: per_fmol {init: 1.85417e-09, pub: out};
var K_010_Na: per_fmol {init: 16936, pub: out};
var K_110_Na: per_fmol {init: 36.0825, pub: out};
var K_210_Na: per_fmol {init: 0.230624, pub: out};
var K_310_Na: per_fmol {init: 0.00442215, pub: out};
var K_001_Na: per_fmol {init: 22953.8, pub: out};
var K_101_Na: per_fmol {init: 48.9036, pub: out};
var K_201_Na: per_fmol {init: 0.312571, pub: out};
var K_301_Na: per_fmol {init: 0.00599345, pub: out};
var K_011_Na: per_fmol {init: 5.47441e+10, pub: out};
var K_111_Na: per_fmol {init: 1.16634e+08, pub: out};
var K_211_Na: per_fmol {init: 745472, pub: out};
var K_311_Na: per_fmol {init: 14294.2, pub: out};
enddef;
def comp fast_Na as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_Na: fmol_per_sec {pub: in};
var kappa_m000: fmol_per_sec {pub: in};
var kappa_m001: fmol_per_sec {pub: in};
var kappa_m010: fmol_per_sec {pub: in};
var kappa_m011: fmol_per_sec {pub: in};
var kappa_m100: fmol_per_sec {pub: in};
var kappa_m101: fmol_per_sec {pub: in};
var kappa_m110: fmol_per_sec {pub: in};
var kappa_m111: fmol_per_sec {pub: in};
var kappa_m200: fmol_per_sec {pub: in};
var kappa_m201: fmol_per_sec {pub: in};
var kappa_m210: fmol_per_sec {pub: in};
var kappa_m211: fmol_per_sec {pub: in};
var kappa_h000: fmol_per_sec {pub: in};
var kappa_h001: fmol_per_sec {pub: in};
var kappa_h100: fmol_per_sec {pub: in};
var kappa_h101: fmol_per_sec {pub: in};
var kappa_h200: fmol_per_sec {pub: in};
var kappa_h201: fmol_per_sec {pub: in};
var kappa_h300: fmol_per_sec {pub: in};
var kappa_h301: fmol_per_sec {pub: in};
var kappa_j000: fmol_per_sec {pub: in};
var kappa_j010: fmol_per_sec {pub: in};
var kappa_j100: fmol_per_sec {pub: in};
var kappa_j110: fmol_per_sec {pub: in};
var kappa_j200: fmol_per_sec {pub: in};
var kappa_j210: fmol_per_sec {pub: in};
var kappa_j300: fmol_per_sec {pub: in};
var kappa_j310: fmol_per_sec {pub: in};
var K_Na_i: per_fmol {pub: in};
var K_Na_o: per_fmol {pub: in};
var K_000_Na: per_fmol {pub: in};
var K_100_Na: per_fmol {pub: in};
var K_200_Na: per_fmol {pub: in};
var K_300_Na: per_fmol {pub: in};
var K_010_Na: per_fmol {pub: in};
var K_110_Na: per_fmol {pub: in};
var K_210_Na: per_fmol {pub: in};
var K_310_Na: per_fmol {pub: in};
var K_001_Na: per_fmol {pub: in};
var K_101_Na: per_fmol {pub: in};
var K_201_Na: per_fmol {pub: in};
var K_301_Na: per_fmol {pub: in};
var K_011_Na: per_fmol {pub: in};
var K_111_Na: per_fmol {pub: in};
var K_211_Na: per_fmol {pub: in};
var K_311_Na: per_fmol {pub: in};
// Input from global environment
var q_Na_i: fmol {pub: in};
var q_Na_o: fmol {pub: in};
var q_000_Na: fmol {pub: in};
var q_100_Na: fmol {pub: in};
var q_200_Na: fmol {pub: in};
var q_300_Na: fmol {pub: in};
var q_010_Na: fmol {pub: in};
var q_110_Na: fmol {pub: in};
var q_210_Na: fmol {pub: in};
var q_310_Na: fmol {pub: in};
var q_001_Na: fmol {pub: in};
var q_101_Na: fmol {pub: in};
var q_201_Na: fmol {pub: in};
var q_301_Na: fmol {pub: in};
var q_011_Na: fmol {pub: in};
var q_111_Na: fmol {pub: in};
var q_211_Na: fmol {pub: in};
var q_311_Na: fmol {pub: in};
// Constitutive parameters
var mu_Na_i: J_per_mol;
var mu_Na_o: J_per_mol;
var mu_000_Na: J_per_mol;
var mu_100_Na: J_per_mol;
var mu_200_Na: J_per_mol;
var mu_300_Na: J_per_mol;
var mu_010_Na: J_per_mol;
var mu_110_Na: J_per_mol;
var mu_210_Na: J_per_mol;
var mu_310_Na: J_per_mol;
var mu_001_Na: J_per_mol;
var mu_101_Na: J_per_mol;
var mu_201_Na: J_per_mol;
var mu_301_Na: J_per_mol;
var mu_011_Na: J_per_mol;
var mu_111_Na: J_per_mol;
var mu_211_Na: J_per_mol;
var mu_311_Na: J_per_mol;
var v_Na: fmol_per_sec {pub: out};
var v_m000: fmol_per_sec {pub: out};
var v_m001: fmol_per_sec {pub: out};
var v_m010: fmol_per_sec {pub: out};
var v_m011: fmol_per_sec {pub: out};
var v_m100: fmol_per_sec {pub: out};
var v_m101: fmol_per_sec {pub: out};
var v_m110: fmol_per_sec {pub: out};
var v_m111: fmol_per_sec {pub: out};
var v_m200: fmol_per_sec {pub: out};
var v_m201: fmol_per_sec {pub: out};
var v_m210: fmol_per_sec {pub: out};
var v_m211: fmol_per_sec {pub: out};
var v_h000: fmol_per_sec {pub: out};
var v_h001: fmol_per_sec {pub: out};
var v_h100: fmol_per_sec {pub: out};
var v_h101: fmol_per_sec {pub: out};
var v_h200: fmol_per_sec {pub: out};
var v_h201: fmol_per_sec {pub: out};
var v_h300: fmol_per_sec {pub: out};
var v_h301: fmol_per_sec {pub: out};
var v_j000: fmol_per_sec {pub: out};
var v_j010: fmol_per_sec {pub: out};
var v_j100: fmol_per_sec {pub: out};
var v_j110: fmol_per_sec {pub: out};
var v_j200: fmol_per_sec {pub: out};
var v_j210: fmol_per_sec {pub: out};
var v_j300: fmol_per_sec {pub: out};
var v_j310: fmol_per_sec {pub: out};
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_000_Na = R*T*ln(K_000_Na*q_000_Na);
mu_100_Na = R*T*ln(K_100_Na*q_100_Na);
mu_200_Na = R*T*ln(K_200_Na*q_200_Na);
mu_300_Na = R*T*ln(K_300_Na*q_300_Na);
mu_010_Na = R*T*ln(K_010_Na*q_010_Na);
mu_110_Na = R*T*ln(K_110_Na*q_110_Na);
mu_210_Na = R*T*ln(K_210_Na*q_210_Na);
mu_310_Na = R*T*ln(K_310_Na*q_310_Na);
mu_001_Na = R*T*ln(K_001_Na*q_001_Na);
mu_101_Na = R*T*ln(K_101_Na*q_101_Na);
mu_201_Na = R*T*ln(K_201_Na*q_201_Na);
mu_301_Na = R*T*ln(K_301_Na*q_301_Na);
mu_011_Na = R*T*ln(K_011_Na*q_011_Na);
mu_111_Na = R*T*ln(K_111_Na*q_111_Na);
mu_211_Na = R*T*ln(K_211_Na*q_211_Na);
mu_311_Na = R*T*ln(K_311_Na*q_311_Na);
v_Na = ppp;
v_m000 = ppp;
v_m001 = ppp;
v_m010 = ppp;
v_m011 = ppp;
v_m100 = ppp;
v_m101 = ppp;
v_m110 = ppp;
v_m111 = ppp;
v_m200 = ppp;
v_m201 = ppp;
v_m210 = ppp;
v_m211 = ppp;
v_h000 = ppp;
v_h001 = ppp;
v_h100 = ppp;
v_h101 = ppp;
v_h200 = ppp;
v_h201 = ppp;
v_h300 = ppp;
v_h301 = ppp;
v_j000 = ppp;
v_j010 = ppp;
v_j100 = ppp;
v_j110 = ppp;
v_j200 = ppp;
v_j210 = ppp;
v_j300 = ppp;
v_j310 = ppp;
enddef;
def map between environment and fast_Na for
vars time and time;
vars q_Na_i and q_Na_i;
vars q_Na_o and q_Na_o;
vars q_000_Na and q_000_Na;
vars q_100_Na and q_100_Na;
vars q_200_Na and q_200_Na;
vars q_300_Na and q_300_Na;
vars q_010_Na and q_010_Na;
vars q_110_Na and q_110_Na;
vars q_210_Na and q_210_Na;
vars q_310_Na and q_310_Na;
vars q_001_Na and q_001_Na;
vars q_101_Na and q_101_Na;
vars q_201_Na and q_201_Na;
vars q_301_Na and q_301_Na;
vars q_011_Na and q_011_Na;
vars q_111_Na and q_111_Na;
vars q_211_Na and q_211_Na;
vars q_311_Na and q_311_Na;
vars v_Na and v_Na;
vars v_m000 and v_m000;
vars v_m001 and v_m001;
vars v_m010 and v_m010;
vars v_m011 and v_m011;
vars v_m100 and v_m100;
vars v_m101 and v_m101;
vars v_m110 and v_m110;
vars v_m111 and v_m111;
vars v_m200 and v_m200;
vars v_m201 and v_m201;
vars v_m210 and v_m210;
vars v_m211 and v_m211;
vars v_h000 and v_h000;
vars v_h001 and v_h001;
vars v_h100 and v_h100;
vars v_h101 and v_h101;
vars v_h200 and v_h200;
vars v_h201 and v_h201;
vars v_h300 and v_h300;
vars v_h301 and v_h301;
vars v_j000 and v_j000;
vars v_j010 and v_j010;
vars v_j100 and v_j100;
vars v_j110 and v_j110;
vars v_j200 and v_j200;
vars v_j210 and v_j210;
vars v_j300 and v_j300;
vars v_j310 and v_j310;
enddef;
def map between fast_Na and fast_Na_parameters for
vars kappa_Na and kappa_Na;
vars kappa_m000 and kappa_m000;
vars kappa_m001 and kappa_m001;
vars kappa_m010 and kappa_m010;
vars kappa_m011 and kappa_m011;
vars kappa_m100 and kappa_m100;
vars kappa_m101 and kappa_m101;
vars kappa_m110 and kappa_m110;
vars kappa_m111 and kappa_m111;
vars kappa_m200 and kappa_m200;
vars kappa_m201 and kappa_m201;
vars kappa_m210 and kappa_m210;
vars kappa_m211 and kappa_m211;
vars kappa_h000 and kappa_h000;
vars kappa_h001 and kappa_h001;
vars kappa_h100 and kappa_h100;
vars kappa_h101 and kappa_h101;
vars kappa_h200 and kappa_h200;
vars kappa_h201 and kappa_h201;
vars kappa_h300 and kappa_h300;
vars kappa_h301 and kappa_h301;
vars kappa_j000 and kappa_j000;
vars kappa_j010 and kappa_j010;
vars kappa_j100 and kappa_j100;
vars kappa_j110 and kappa_j110;
vars kappa_j200 and kappa_j200;
vars kappa_j210 and kappa_j210;
vars kappa_j300 and kappa_j300;
vars kappa_j310 and kappa_j310;
vars K_Na_i and K_Na_i;
vars K_Na_o and K_Na_o;
vars K_000_Na and K_000_Na;
vars K_100_Na and K_100_Na;
vars K_200_Na and K_200_Na;
vars K_300_Na and K_300_Na;
vars K_010_Na and K_010_Na;
vars K_110_Na and K_110_Na;
vars K_210_Na and K_210_Na;
vars K_310_Na and K_310_Na;
vars K_001_Na and K_001_Na;
vars K_101_Na and K_101_Na;
vars K_201_Na and K_201_Na;
vars K_301_Na and K_301_Na;
vars K_011_Na and K_011_Na;
vars K_111_Na and K_111_Na;
vars K_211_Na and K_211_Na;
vars K_311_Na and K_311_Na;
enddef;
def map between constants and fast_Na for
vars R and R;
vars T and T;
enddef;
enddef;
