- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-05-09 16:04:32+12:00
- Desc:
- Init. Starting molar amounts of species are not correct
- Permanent Source URI:
- https://models.cellml.org/workspace/857/rawfile/ff6be264d70122a5a8a85719aa445ee42dac1811/parameter_finder/output/TEMP.cellml.txt
def model individual_sGC 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_B: fmol {init: 1e-888, pub: out};
var q_NO: fmol {init: 1e-888, pub: out};
var q_E6c: fmol {init: 1e-888, pub: out};
var q_E5c: fmol {init: 1e-888, pub: out};
var q_cGMP: fmol {init: 1e-888, pub: out};
var q_NO_product: fmol {init: 1e-888, pub: out};
// From submodule
var v_R_1_sGC: fmol_per_sec {pub: in};
var v_R_2_sGC: fmol_per_sec {pub: in};
var v_R_3_sGC: fmol_per_sec {pub: in};
var v_R_4_sGC: fmol_per_sec {pub: in};
var v_R_DNO_sGC: fmol_per_sec {pub: in};
ode(q_B, time) = vvv;
ode(q_NO, time) = vvv;
ode(q_E6c, time) = vvv;
ode(q_E5c, time) = vvv;
ode(q_cGMP, time) = vvv;
ode(q_NO_product, time) = vvv;
enddef;
def comp sGC_parameters as
var kappa_R_1_sGC: fmol_per_sec {init: 123.75, pub: out};
var kappa_R_2_sGC: fmol_per_sec {init: 0.12375, pub: out};
var kappa_R_3_sGC: fmol_per_sec {init: 0.12375, pub: out};
var kappa_R_4_sGC: fmol_per_sec {init: 0.00185625, pub: out};
var kappa_R_DNO_sGC: fmol_per_sec {init: 6.66667e-06, pub: out};
var K_B: per_fmol {init: 0.145208, pub: out};
var K_NO: per_fmol {init: 404.313, pub: out};
var K_E6c: per_fmol {init: 0.217811, pub: out};
var K_E5c: per_fmol {init: 0.00217811, pub: out};
var K_cGMP: per_fmol {init: 7.29923, pub: out};
var K_NO_product: per_fmol {init: 40.4313, pub: out};
enddef;
def comp sGC as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_R_1_sGC: fmol_per_sec {pub: in};
var kappa_R_2_sGC: fmol_per_sec {pub: in};
var kappa_R_3_sGC: fmol_per_sec {pub: in};
var kappa_R_4_sGC: fmol_per_sec {pub: in};
var kappa_R_DNO_sGC: fmol_per_sec {pub: in};
var K_B: per_fmol {pub: in};
var K_NO: per_fmol {pub: in};
var K_E6c: per_fmol {pub: in};
var K_E5c: per_fmol {pub: in};
var K_cGMP: per_fmol {pub: in};
var K_NO_product: per_fmol {pub: in};
// Input from global environment
var q_B: fmol {pub: in};
var q_NO: fmol {pub: in};
var q_E6c: fmol {pub: in};
var q_E5c: fmol {pub: in};
var q_cGMP: fmol {pub: in};
var q_NO_product: fmol {pub: in};
// Constitutive parameters
var mu_B: J_per_mol;
var mu_NO: J_per_mol;
var mu_E6c: J_per_mol;
var mu_E5c: J_per_mol;
var mu_cGMP: J_per_mol;
var mu_NO_product: J_per_mol;
var v_R_1_sGC: fmol_per_sec {pub: out};
var v_R_2_sGC: fmol_per_sec {pub: out};
var v_R_3_sGC: fmol_per_sec {pub: out};
var v_R_4_sGC: fmol_per_sec {pub: out};
var v_R_DNO_sGC: fmol_per_sec {pub: out};
mu_B = R*T*ln(K_B*q_B);
mu_NO = R*T*ln(K_NO*q_NO);
mu_E6c = R*T*ln(K_E6c*q_E6c);
mu_E5c = R*T*ln(K_E5c*q_E5c);
mu_cGMP = R*T*ln(K_cGMP*q_cGMP);
mu_NO_product = R*T*ln(K_NO_product*q_NO_product);
v_R_1_sGC = ppp;
v_R_2_sGC = ppp;
v_R_3_sGC = ppp;
v_R_4_sGC = ppp;
v_R_DNO_sGC = ppp;
enddef;
def map between environment and sGC for
vars time and time;
vars q_B and q_B;
vars q_NO and q_NO;
vars q_E6c and q_E6c;
vars q_E5c and q_E5c;
vars q_cGMP and q_cGMP;
vars q_NO_product and q_NO_product;
vars v_R_1_sGC and v_R_1_sGC;
vars v_R_2_sGC and v_R_2_sGC;
vars v_R_3_sGC and v_R_3_sGC;
vars v_R_4_sGC and v_R_4_sGC;
vars v_R_DNO_sGC and v_R_DNO_sGC;
enddef;
def map between sGC and sGC_parameters for
vars kappa_R_1_sGC and kappa_R_1_sGC;
vars kappa_R_2_sGC and kappa_R_2_sGC;
vars kappa_R_3_sGC and kappa_R_3_sGC;
vars kappa_R_4_sGC and kappa_R_4_sGC;
vars kappa_R_DNO_sGC and kappa_R_DNO_sGC;
vars K_B and K_B;
vars K_NO and K_NO;
vars K_E6c and K_E6c;
vars K_E5c and K_E5c;
vars K_cGMP and K_cGMP;
vars K_NO_product and K_NO_product;
enddef;
def map between constants and sGC for
vars R and R;
vars T and T;
enddef;
enddef;
