- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-12-11 10:51:51+13:00
- Desc:
- Fixing v_L in stoichiometric matrix
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/7dd/rawfile/11c646d284e483214a27bedbed0e87e45de20c6a/parameter_finder/output/TEMP.cellml.txt
def model individual_GPCR_M2_reduced 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_RM2_inactive: fmol {init: 1e-888, pub: out};
var q_L_RM2_inactive: fmol {init: 1e-888, pub: out};
var q_LM2: fmol {init: 1e-888, pub: out};
var q_RM2: fmol {init: 1e-888, pub: out};
var q_Gi: fmol {init: 1e-888, pub: out};
var q_RM2_Gi: fmol {init: 1e-888, pub: out};
var q_L_RM2: fmol {init: 1e-888, pub: out};
var q_L_RM2_Gi: fmol {init: 1e-888, pub: out};
var q_Gia_GTP: fmol {init: 1e-888, pub: out};
var q_Gibetagamma: fmol {init: 1e-888, pub: out};
var q_Gia_GDP: fmol {init: 1e-888, pub: out};
var q_GTP: fmol {init: 1e-888, pub: out};
var q_GDP: fmol {init: 1e-888, pub: out};
var q_Pi: fmol {init: 1e-888, pub: out};
var q_RM2_tag: fmol {init: 1e-888, pub: out};
var q_L_RM2_tag: fmol {init: 1e-888, pub: out};
var q_RM2_GRKArr: fmol {init: 1e-888, pub: out};
var q_L_RM2_GRKArr: fmol {init: 1e-888, pub: out};
var q_GRKArr: fmol {init: 1e-888, pub: out};
// From submodule
var v_Rswitch_M2: fmol_per_sec {pub: in};
var v_LRswitch_M2: fmol_per_sec {pub: in};
var v_C_M2: fmol_per_sec {pub: in};
var v_R_M2: fmol_per_sec {pub: in};
var v_L_M2: fmol_per_sec {pub: in};
var v_Act1_Gi: fmol_per_sec {pub: in};
var v_Act2_Gi: fmol_per_sec {pub: in};
var v_Hyd_Gi: fmol_per_sec {pub: in};
var v_Reassoc_Gi: fmol_per_sec {pub: in};
var v_InternR_M2: fmol_per_sec {pub: in};
var v_InternLR_M2: fmol_per_sec {pub: in};
ode(q_RM2_inactive, time) = vvv;
ode(q_L_RM2_inactive, time) = vvv;
ode(q_LM2, time) = vvv;
ode(q_RM2, time) = vvv;
ode(q_Gi, time) = vvv;
ode(q_RM2_Gi, time) = vvv;
ode(q_L_RM2, time) = vvv;
ode(q_L_RM2_Gi, time) = vvv;
ode(q_Gia_GTP, time) = vvv;
ode(q_Gibetagamma, time) = vvv;
ode(q_Gia_GDP, time) = vvv;
ode(q_GTP, time) = vvv;
ode(q_GDP, time) = vvv;
ode(q_Pi, time) = vvv;
ode(q_RM2_tag, time) = vvv;
ode(q_L_RM2_tag, time) = vvv;
ode(q_RM2_GRKArr, time) = vvv;
ode(q_L_RM2_GRKArr, time) = vvv;
ode(q_GRKArr, time) = vvv;
enddef;
def comp GPCR_M2_reduced_parameters as
var kappa_Rswitch_M2: fmol_per_sec {init: 3.25763, pub: out};
var kappa_LRswitch_M2: fmol_per_sec {init: 0.00165864, pub: out};
var kappa_C_M2: fmol_per_sec {init: 14461.5, pub: out};
var kappa_R_M2: fmol_per_sec {init: 736.312, pub: out};
var kappa_L_M2: fmol_per_sec {init: 5769.58, pub: out};
var kappa_Act1_Gi: fmol_per_sec {init: 0.0114404, pub: out};
var kappa_Act2_Gi: fmol_per_sec {init: 0.381268, pub: out};
var kappa_Hyd_Gi: fmol_per_sec {init: 0.585749, pub: out};
var kappa_Reassoc_Gi: fmol_per_sec {init: 0.0140382, pub: out};
var kappa_InternR_M2: fmol_per_sec {init: 0.0665538, pub: out};
var kappa_InternLR_M2: fmol_per_sec {init: 2.218, pub: out};
var K_RM2_inactive: per_fmol {init: 0.892359, pub: out};
var K_L_RM2_inactive: per_fmol {init: 1752.63, pub: out};
var K_LM2: per_fmol {init: 0.0519039, pub: out};
var K_RM2: per_fmol {init: 0.00892359, pub: out};
var K_Gi: per_fmol {init: 0.0207076, pub: out};
var K_RM2_Gi: per_fmol {init: 0.1907, pub: out};
var K_L_RM2: per_fmol {init: 0.175263, pub: out};
var K_L_RM2_Gi: per_fmol {init: 0.286109, pub: out};
var K_Gia_GTP: per_fmol {init: 0.0397027, pub: out};
var K_Gibetagamma: per_fmol {init: 0.412109, pub: out};
var K_Gia_GDP: per_fmol {init: 0.176744, pub: out};
var K_GTP: per_fmol {init: 0.019367, pub: out};
var K_GDP: per_fmol {init: 0.000190324, pub: out};
var K_Pi: per_fmol {init: 8.16257e-05, pub: out};
var K_RM2_tag: per_fmol {init: 0.200446, pub: out};
var K_L_RM2_tag: per_fmol {init: 0.00601463, pub: out};
var K_RM2_GRKArr: per_fmol {init: 0.00436786, pub: out};
var K_L_RM2_GRKArr: per_fmol {init: 0.000131063, pub: out};
var K_GRKArr: per_fmol {init: 6.3345, pub: out};
enddef;
def comp GPCR_M2_reduced as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_Rswitch_M2: fmol_per_sec {pub: in};
var kappa_LRswitch_M2: fmol_per_sec {pub: in};
var kappa_C_M2: fmol_per_sec {pub: in};
var kappa_R_M2: fmol_per_sec {pub: in};
var kappa_L_M2: fmol_per_sec {pub: in};
var kappa_Act1_Gi: fmol_per_sec {pub: in};
var kappa_Act2_Gi: fmol_per_sec {pub: in};
var kappa_Hyd_Gi: fmol_per_sec {pub: in};
var kappa_Reassoc_Gi: fmol_per_sec {pub: in};
var kappa_InternR_M2: fmol_per_sec {pub: in};
var kappa_InternLR_M2: fmol_per_sec {pub: in};
var K_RM2_inactive: per_fmol {pub: in};
var K_L_RM2_inactive: per_fmol {pub: in};
var K_LM2: per_fmol {pub: in};
var K_RM2: per_fmol {pub: in};
var K_Gi: per_fmol {pub: in};
var K_RM2_Gi: per_fmol {pub: in};
var K_L_RM2: per_fmol {pub: in};
var K_L_RM2_Gi: per_fmol {pub: in};
var K_Gia_GTP: per_fmol {pub: in};
var K_Gibetagamma: per_fmol {pub: in};
var K_Gia_GDP: per_fmol {pub: in};
var K_GTP: per_fmol {pub: in};
var K_GDP: per_fmol {pub: in};
var K_Pi: per_fmol {pub: in};
var K_RM2_tag: per_fmol {pub: in};
var K_L_RM2_tag: per_fmol {pub: in};
var K_RM2_GRKArr: per_fmol {pub: in};
var K_L_RM2_GRKArr: per_fmol {pub: in};
var K_GRKArr: per_fmol {pub: in};
// Input from global environment
var q_RM2_inactive: fmol {pub: in};
var q_L_RM2_inactive: fmol {pub: in};
var q_LM2: fmol {pub: in};
var q_RM2: fmol {pub: in};
var q_Gi: fmol {pub: in};
var q_RM2_Gi: fmol {pub: in};
var q_L_RM2: fmol {pub: in};
var q_L_RM2_Gi: fmol {pub: in};
var q_Gia_GTP: fmol {pub: in};
var q_Gibetagamma: fmol {pub: in};
var q_Gia_GDP: fmol {pub: in};
var q_GTP: fmol {pub: in};
var q_GDP: fmol {pub: in};
var q_Pi: fmol {pub: in};
var q_RM2_tag: fmol {pub: in};
var q_L_RM2_tag: fmol {pub: in};
var q_RM2_GRKArr: fmol {pub: in};
var q_L_RM2_GRKArr: fmol {pub: in};
var q_GRKArr: fmol {pub: in};
// Constitutive parameters
var mu_RM2_inactive: J_per_mol;
var mu_L_RM2_inactive: J_per_mol;
var mu_LM2: J_per_mol;
var mu_RM2: J_per_mol;
var mu_Gi: J_per_mol;
var mu_RM2_Gi: J_per_mol;
var mu_L_RM2: J_per_mol;
var mu_L_RM2_Gi: J_per_mol;
var mu_Gia_GTP: J_per_mol;
var mu_Gibetagamma: J_per_mol;
var mu_Gia_GDP: J_per_mol;
var mu_GTP: J_per_mol;
var mu_GDP: J_per_mol;
var mu_Pi: J_per_mol;
var mu_RM2_tag: J_per_mol;
var mu_L_RM2_tag: J_per_mol;
var mu_RM2_GRKArr: J_per_mol;
var mu_L_RM2_GRKArr: J_per_mol;
var mu_GRKArr: J_per_mol;
var v_Rswitch_M2: fmol_per_sec {pub: out};
var v_LRswitch_M2: fmol_per_sec {pub: out};
var v_C_M2: fmol_per_sec {pub: out};
var v_R_M2: fmol_per_sec {pub: out};
var v_L_M2: fmol_per_sec {pub: out};
var v_Act1_Gi: fmol_per_sec {pub: out};
var v_Act2_Gi: fmol_per_sec {pub: out};
var v_Hyd_Gi: fmol_per_sec {pub: out};
var v_Reassoc_Gi: fmol_per_sec {pub: out};
var v_InternR_M2: fmol_per_sec {pub: out};
var v_InternLR_M2: fmol_per_sec {pub: out};
mu_RM2_inactive = R*T*ln(K_RM2_inactive*q_RM2_inactive);
mu_L_RM2_inactive = R*T*ln(K_L_RM2_inactive*q_L_RM2_inactive);
mu_LM2 = R*T*ln(K_LM2*q_LM2);
mu_RM2 = R*T*ln(K_RM2*q_RM2);
mu_Gi = R*T*ln(K_Gi*q_Gi);
mu_RM2_Gi = R*T*ln(K_RM2_Gi*q_RM2_Gi);
mu_L_RM2 = R*T*ln(K_L_RM2*q_L_RM2);
mu_L_RM2_Gi = R*T*ln(K_L_RM2_Gi*q_L_RM2_Gi);
mu_Gia_GTP = R*T*ln(K_Gia_GTP*q_Gia_GTP);
mu_Gibetagamma = R*T*ln(K_Gibetagamma*q_Gibetagamma);
mu_Gia_GDP = R*T*ln(K_Gia_GDP*q_Gia_GDP);
mu_GTP = R*T*ln(K_GTP*q_GTP);
mu_GDP = R*T*ln(K_GDP*q_GDP);
mu_Pi = R*T*ln(K_Pi*q_Pi);
mu_RM2_tag = R*T*ln(K_RM2_tag*q_RM2_tag);
mu_L_RM2_tag = R*T*ln(K_L_RM2_tag*q_L_RM2_tag);
mu_RM2_GRKArr = R*T*ln(K_RM2_GRKArr*q_RM2_GRKArr);
mu_L_RM2_GRKArr = R*T*ln(K_L_RM2_GRKArr*q_L_RM2_GRKArr);
mu_GRKArr = R*T*ln(K_GRKArr*q_GRKArr);
v_Rswitch_M2 = ppp;
v_LRswitch_M2 = ppp;
v_C_M2 = ppp;
v_R_M2 = ppp;
v_L_M2 = ppp;
v_Act1_Gi = ppp;
v_Act2_Gi = ppp;
v_Hyd_Gi = ppp;
v_Reassoc_Gi = ppp;
v_InternR_M2 = ppp;
v_InternLR_M2 = ppp;
enddef;
def map between environment and GPCR_M2_reduced for
vars time and time;
vars q_RM2_inactive and q_RM2_inactive;
vars q_L_RM2_inactive and q_L_RM2_inactive;
vars q_LM2 and q_LM2;
vars q_RM2 and q_RM2;
vars q_Gi and q_Gi;
vars q_RM2_Gi and q_RM2_Gi;
vars q_L_RM2 and q_L_RM2;
vars q_L_RM2_Gi and q_L_RM2_Gi;
vars q_Gia_GTP and q_Gia_GTP;
vars q_Gibetagamma and q_Gibetagamma;
vars q_Gia_GDP and q_Gia_GDP;
vars q_GTP and q_GTP;
vars q_GDP and q_GDP;
vars q_Pi and q_Pi;
vars q_RM2_tag and q_RM2_tag;
vars q_L_RM2_tag and q_L_RM2_tag;
vars q_RM2_GRKArr and q_RM2_GRKArr;
vars q_L_RM2_GRKArr and q_L_RM2_GRKArr;
vars q_GRKArr and q_GRKArr;
vars v_Rswitch_M2 and v_Rswitch_M2;
vars v_LRswitch_M2 and v_LRswitch_M2;
vars v_C_M2 and v_C_M2;
vars v_R_M2 and v_R_M2;
vars v_L_M2 and v_L_M2;
vars v_Act1_Gi and v_Act1_Gi;
vars v_Act2_Gi and v_Act2_Gi;
vars v_Hyd_Gi and v_Hyd_Gi;
vars v_Reassoc_Gi and v_Reassoc_Gi;
vars v_InternR_M2 and v_InternR_M2;
vars v_InternLR_M2 and v_InternLR_M2;
enddef;
def map between GPCR_M2_reduced and GPCR_M2_reduced_parameters for
vars kappa_Rswitch_M2 and kappa_Rswitch_M2;
vars kappa_LRswitch_M2 and kappa_LRswitch_M2;
vars kappa_C_M2 and kappa_C_M2;
vars kappa_R_M2 and kappa_R_M2;
vars kappa_L_M2 and kappa_L_M2;
vars kappa_Act1_Gi and kappa_Act1_Gi;
vars kappa_Act2_Gi and kappa_Act2_Gi;
vars kappa_Hyd_Gi and kappa_Hyd_Gi;
vars kappa_Reassoc_Gi and kappa_Reassoc_Gi;
vars kappa_InternR_M2 and kappa_InternR_M2;
vars kappa_InternLR_M2 and kappa_InternLR_M2;
vars K_RM2_inactive and K_RM2_inactive;
vars K_L_RM2_inactive and K_L_RM2_inactive;
vars K_LM2 and K_LM2;
vars K_RM2 and K_RM2;
vars K_Gi and K_Gi;
vars K_RM2_Gi and K_RM2_Gi;
vars K_L_RM2 and K_L_RM2;
vars K_L_RM2_Gi and K_L_RM2_Gi;
vars K_Gia_GTP and K_Gia_GTP;
vars K_Gibetagamma and K_Gibetagamma;
vars K_Gia_GDP and K_Gia_GDP;
vars K_GTP and K_GTP;
vars K_GDP and K_GDP;
vars K_Pi and K_Pi;
vars K_RM2_tag and K_RM2_tag;
vars K_L_RM2_tag and K_L_RM2_tag;
vars K_RM2_GRKArr and K_RM2_GRKArr;
vars K_L_RM2_GRKArr and K_L_RM2_GRKArr;
vars K_GRKArr and K_GRKArr;
enddef;
def map between constants and GPCR_M2_reduced for
vars R and R;
vars T and T;
enddef;
enddef;
