- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-09-17 11:23:45+12:00
- Desc:
- Updating matlab file
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/6e3/rawfile/e629303c64ead9493374345a194ef2097e1cf421/MATLAB/kinetic_parameters.m
% linalg for Ryanodine channel: gated by Ca, and allowing passage of Ca.
function [k, N_cT, K_C, W] = kinetic_parameters(M, include_type2_reactions, dims, Vol)
num_cols = dims.num_cols;
num_rows = dims.num_rows;
R = 8.3143;
T = 310;
F = 96485;
z = 2;
N_A = 6.022e23;
x_ryr = 1e15*50e3/N_A; % fmol Hinch: 50000 units
c_di = 1.7374E-04; % mM
c_sr = 5.5545E-01; % mM
% channel conductance (without gating)
k_ryr = 25; % 1/ms (Shannon/Stern value) WRONG UNITS FOR A CHANNEL
g_ryr = 103; % pS
E_Ca = (R*T/(z*F))*log(c_di/c_sr);
% finding permeability value by setting I_ohmic = I_ghk:
% P [=] pL/s (permeability)
V = -E_Ca;
P_ryr = 1e3*(V - E_Ca)*g_ryr*R*T*(1-exp(-z*F*V/(R*T)))/(((z*F)^2)*(c_sr-(c_di*exp(-z*F*V/(R*T)))));
k_ryr = P_ryr / x_ryr; % 1/mM.s both fwd and bwd
% gate transitions
ko = 35e3; % 1/(mM2.s)
ki = 500; % 1/(mM.s)
kim = 5; % 1/s
kom = 60; % 1/s
% rxnID: [RyR OC CCI CII IO]
% set up ensures detailed balance already
kf = [k_ryr, kom, ki, ko, kim];
kr = [k_ryr, ko, kim, kom, ki];
k = [kf, kr]';
N_cT = [];
K_C = [];
% volume vector
W = [ones(num_cols,1); Vol.V_SR; Vol.V_di; 1; 1; 1; 1];
end
