Location: BG_crossbridge_TRPN @ 0bfa438040c8 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-06-10 15:00:41+12:00
Desc:
Saving
Permanent Source URI:
https://models.cellml.org/workspace/7fb/rawfile/0bfa438040c840fcbdf4b32b8cec38a588e63828/parameter_finder/output/TEMP.cellml.txt
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def model individual_crossbridge_TRPN 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_TRPN: fmol {init: 1e-888, pub: out};
var q_Ca_i: fmol {init: 1e-888, pub: out};
var q_Ca_TRPN: fmol {init: 1e-888, pub: out};
var q_B_XB: fmol {init: 1e-888, pub: out};
var q_U_XB: fmol {init: 1e-888, pub: out};
var q_W_XB: fmol {init: 1e-888, pub: out};
var q_S_XB: fmol {init: 1e-888, pub: out};
// From submodule
var v_R_TRPNCa: fmol_per_sec {pub: in};
var v_R_BU: fmol_per_sec {pub: in};
var v_R_UW: fmol_per_sec {pub: in};
var v_R_WS: fmol_per_sec {pub: in};
var v_R_SU: fmol_per_sec {pub: in};
ode(q_TRPN, time) = vvv;
ode(q_Ca_i, time) = vvv;
ode(q_Ca_TRPN, time) = vvv;
ode(q_B_XB, time) = vvv;
ode(q_U_XB, time) = vvv;
ode(q_W_XB, time) = vvv;
ode(q_S_XB, time) = vvv;
enddef;

def comp crossbridge_TRPN_parameters as
var kappa_R_TRPNCa: fmol_per_sec {init: 22.8658, pub: out};
var kappa_R_BU: fmol_per_sec {init: 2.56831, pub: out};
var kappa_R_UW: fmol_per_sec {init: 0.338467, pub: out};
var kappa_R_WS: fmol_per_sec {init: 0.00796392, pub: out};
var kappa_R_SU: fmol_per_sec {init: 143351, pub: out};
var K_TRPN: per_fmol {init: 0.428971, pub: out};
var K_Ca_i: per_fmol {init: 6.33016, pub: out};
var K_Ca_TRPN: per_fmol {init: 0.127132, pub: out};
var K_B_XB: per_fmol {init: 5.95481, pub: out};
var K_U_XB: per_fmol {init: 2.23305, pub: out};
var K_W_XB: per_fmol {init: 14.6007, pub: out};
var K_S_XB: per_fmol {init: 3.65018e-06, pub: out};
enddef;
def comp crossbridge_TRPN as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R_TRPNCa: fmol_per_sec {pub: in};
var kappa_R_BU: fmol_per_sec {pub: in};
var kappa_R_UW: fmol_per_sec {pub: in};
var kappa_R_WS: fmol_per_sec {pub: in};
var kappa_R_SU: fmol_per_sec {pub: in};
var K_TRPN: per_fmol {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_Ca_TRPN: per_fmol {pub: in};
var K_B_XB: per_fmol {pub: in};
var K_U_XB: per_fmol {pub: in};
var K_W_XB: per_fmol {pub: in};
var K_S_XB: per_fmol {pub: in};
// Input from global environment
var q_TRPN: fmol {pub: in};
var q_Ca_i: fmol {pub: in};
var q_Ca_TRPN: fmol {pub: in};
var q_B_XB: fmol {pub: in};
var q_U_XB: fmol {pub: in};
var q_W_XB: fmol {pub: in};
var q_S_XB: fmol {pub: in};
// Constitutive parameters
var mu_TRPN: J_per_mol;
var mu_Ca_i: J_per_mol;
var mu_Ca_TRPN: J_per_mol;
var mu_B_XB: J_per_mol;
var mu_U_XB: J_per_mol;
var mu_W_XB: J_per_mol;
var mu_S_XB: J_per_mol;
var v_R_TRPNCa: fmol_per_sec {pub: out};
var v_R_BU: fmol_per_sec {pub: out};
var v_R_UW: fmol_per_sec {pub: out};
var v_R_WS: fmol_per_sec {pub: out};
var v_R_SU: fmol_per_sec {pub: out};
mu_TRPN = R*T*ln(K_TRPN*q_TRPN);
mu_Ca_i = R*T*ln(K_Ca_i*q_Ca_i);
mu_Ca_TRPN = R*T*ln(K_Ca_TRPN*q_Ca_TRPN);
mu_B_XB = R*T*ln(K_B_XB*q_B_XB);
mu_U_XB = R*T*ln(K_U_XB*q_U_XB);
mu_W_XB = R*T*ln(K_W_XB*q_W_XB);
mu_S_XB = R*T*ln(K_S_XB*q_S_XB);
v_R_TRPNCa = ppp;
v_R_BU = ppp;
v_R_UW = ppp;
v_R_WS = ppp;
v_R_SU = ppp;
enddef;
def map between environment and crossbridge_TRPN for
vars time and time;
vars q_TRPN and q_TRPN;
vars q_Ca_i and q_Ca_i;
vars q_Ca_TRPN and q_Ca_TRPN;
vars q_B_XB and q_B_XB;
vars q_U_XB and q_U_XB;
vars q_W_XB and q_W_XB;
vars q_S_XB and q_S_XB;
vars v_R_TRPNCa and v_R_TRPNCa;
vars v_R_BU and v_R_BU;
vars v_R_UW and v_R_UW;
vars v_R_WS and v_R_WS;
vars v_R_SU and v_R_SU;
enddef;
def map between crossbridge_TRPN and crossbridge_TRPN_parameters for
vars kappa_R_TRPNCa and kappa_R_TRPNCa;
vars kappa_R_BU and kappa_R_BU;
vars kappa_R_UW and kappa_R_UW;
vars kappa_R_WS and kappa_R_WS;
vars kappa_R_SU and kappa_R_SU;
vars K_TRPN and K_TRPN;
vars K_Ca_i and K_Ca_i;
vars K_Ca_TRPN and K_Ca_TRPN;
vars K_B_XB and K_B_XB;
vars K_U_XB and K_U_XB;
vars K_W_XB and K_W_XB;
vars K_S_XB and K_S_XB;
enddef;
def map between constants and crossbridge_TRPN for
vars R and R;
 vars T and T;
enddef;
enddef;