- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-02-28 15:10:27+13:00
- Desc:
- Fix equation finding K Kappa and update parameters
- Permanent Source URI:
- http://models.cellml.org/workspace/82c/rawfile/ae54ed237584007ec1fb64b38d528cf2476c0869/BG_fit_parameters_CC/K_kappa.m
% 18 April: make it fit 6 state CC model
clear;
%% Set directories
main_dir = pwd;
data_dir = [main_dir '\data' filesep];
output_dir = [main_dir '\output' filesep];
storage_dir = [main_dir '\storage' filesep];
fixedz = false;
%% Define volumes (unit pL)
W_i = 38;
W_e = 5.182;
%% Load stoichiometric matrices
N_f = [1 0 0 0 0 0;
0 0 0 0 0 0;
0 1 0 0 0 0;
0 0 1 0 0 0;
0 0 0 1 1 0;
0 0 0 0 0 1;
0 0 0 0 0 0;
];
N_r = [0 0 0 0 0 0;
1 0 0 0 0 0;
0 0 0 0 0 0;
0 1 0 0 0 0;
0 0 1 0 0 0;
0 0 0 1 0 0;
0 0 0 0 1 1;
];
N_fT = transpose(N_f);
N_rT = transpose(N_r);
N = N_r - N_f;
% N_T = N_rT - N_fT;
num_cols = size(N,2); % number of reactions
I = eye(num_cols);
M = [I N_fT; I N_rT];
M_rref = rref(M);
%% Set up the vectors
% GHK permeability for K in Ks channel (see PSO_GHK_fitting_curve.m)
F = 96485;
load([storage_dir 'kr_G_GHK.mat']);
P_K = G_GHK/F * 1e12; % Unit pL/s
N_A = 6.022e23;
x_kr_channel = 5369/N_A*1e15; % channel density: unit fmol. Same as Pan K channel density
% load alpha_beta rates
if fixedz
load([storage_dir 'kr_alphabeta_fixedz.mat']);
else
load([storage_dir 'kr_alphabetaz_someIC.mat']);
% load([storage_dir 'kr_alphabetaz_zeroIC.mat']);
end
% unit s^-1
% [rc3 rc2 rc1 rc1IF rOIF]
% kf kr [=] 1/s
kf = [P_K/x_kr_channel % R_GHK
alpha];
kr = [P_K/x_kr_channel % R_GHK
beta];
k = [kf;kr];
W = [ones(size(N,2),1);W_i;W_e;ones(5,1)];
lambdaW = exp(pinv(M)*log(k));
lambda = lambdaW./W;
kappa = lambda(1:size(N,2)); % [=] mol/s if corresponding v [=] mol/s
K = lambda(size(N,2)+1:end); % [=] 1/mol if corresponding q [=] mol
if fixedz
save([output_dir 'K_kappa_Kr_fixedz.mat'],'kappa','K');
else
save([output_dir 'K_kappa_Kr_variablez.mat'],'kappa','K');
end
%% Checks
N_rref = rref(N);
R_mat = null(N,'r');
K_eq = kf./kr;
zero_est = R_mat'*K_eq;
k_est = exp(M*log(lambdaW));
diff = sum(abs((k-k_est)./k));
kdiff = [k,k_est];
if diff > 1
warning('lol DIFF is greater than 1, nublet.');
end
%% display text for cellml
rname = {'Kr','rC3', 'rC2', 'rC1', 'rC1IF', 'rOIF'};
Kname = {'Ki','Ke','C3','C2','C1','O','I'};
zname = {'C3', 'C2', 'C1', 'C1IF','OIF'};
for ik = 1:length(kappa)
fprintf('var kappa_%s: fmol_per_sec {init: %g, pub: out};\n', rname{ik}, kappa(ik));
end
for ik = 1:length(K)
fprintf('var K_%s: per_fmol {init: %g, pub: out};\n', Kname{ik}, K(ik));
end
for ik = 1:length(zf)
fprintf('var z_f%s: dimensionless {init: %g, pub: out};\n', zname{ik}, zf(ik));
end
for ik = 1:length(zr)
fprintf('var z_r%s: dimensionless {init: %g, pub: out};\n', zname{ik}, zr(ik));
end
if true
for ik = 1:length(zf)
fprintf('var z_f%s: dimensionless {pub: in};\n', zname{ik});
end
for ik = 1:length(zr)
fprintf('var z_r%s: dimensionless {pub: in};\n', zname{ik});
end
for ik = 1:length(zf)
fprintf('vars z_f%s and z_f%s;\n', zname{ik}, zname{ik});
end
for ik = 1:length(zr)
fprintf('vars z_r%s and z_r%s;\n', zname{ik}, zname{ik});
end
end