Location: BG_Na_background @ ee4f9b7507ac / matlab_parameter_fitting / PSO_GHK_fitting_curve.m

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-07-06 16:25:53+12:00
Desc:
Updating to LRd 34.4 pL cell parameters
Permanent Source URI:
https://models.physiomeproject.org/workspace/82b/rawfile/ee4f9b7507acea6a3a4a0a95a7780ce304e8f26e/matlab_parameter_fitting/PSO_GHK_fitting_curve.m
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clear;
% clc;
% close all;

%% Options
run_optimisation = true;

%% Set up directories
current_dir = pwd;
Idx_backslash = find(current_dir == filesep);
main_dir = current_dir; %(1:Idx_backslash(end));
output_dir = [main_dir '\output' filesep];
storage_dir = current_dir; %[main_dir '\storage' filesep];

%% Define constants - coonsistent with VOLTS.
R = 8.314;
T = 310;
F = 96485;

%% Plot I-V curves
% UNITS:
%     I = G_GHK * [K] [=] mA
%     G_GHK = I/[K] [=] Amp.litre/mol
%     G_PMR [=] mS [=] mA/V
    
V = (-120:1:60)/1000;

cNao = 132;   % mM
cNai = 9;
z = 1;
Cm = 153400e-9; % Unit microF
% Cm = 60000e-9; % Unit microF

G_pmr = 0.00029*Cm; % g_Cab: milliS_per_microF {init: 0.003016}; 

E_Na = R*T/(z*F)*log(cNao/cNai);

I_lin = G_pmr*(V-E_Na); % Unit mA    don't consider gating variable: just finding conductance.

Vstart = 1;
Vend = length(V);
error_func = @(G_GHK) square_error(I_lin(Vstart:Vend) - calc_IGHK(G_GHK,V(Vstart:Vend),cNai,cNao));

A = [];
b = [];
Aeq = [];
beq = [];
lb = [-Inf];
ub = [Inf];

options_ps = optimoptions('particleswarm','UseParallel',false,'HybridFcn',@fminunc,'SwarmSize',1000, ...
    'FunctionTolerance', 1e-9);

if run_optimisation
    [G_GHK,fval,exitflag,output] = particleswarm(error_func,1,lb,ub,options_ps);
    save([storage_dir '\nab_G_GHK.mat'],'G_GHK');
else
    load([storage_dir '\nab_G_GHK.mat']);
end

G_GHK2 = 0.00001;

I_GHK = calc_IGHK(G_GHK,V,cNai,cNao);
I_GHK2 = calc_IGHK(G_GHK2,V,cNai,cNao);

h = figure;
% subplot(1,2,1)
plot(1000*V,1e6*I_lin,'k--',1000*V,1e6*I_GHK);
legend('LRd','BG','Location','southeast');
ylabel('Current (nA)');
xlabel('Voltage (mV)');
set(gca,'FontSize',16);
grid on

% subplot(1,2,2)
% plot(1000*V,1e6*I_lin,'k--',1000*V, 1e6*I_GHK2);
% legend('LRd','BG_test','Location','southeast');
% ylabel('Current (nA)');
% xlabel('Voltage (mV)');
% set(gca,'FontSize',16);

% print_figure(h,output_dir,'tcc_IV_curve');