Location: BG_to_channel @ df158b8da6f9 / Kernik_matlab_parameter_fitting / r_gate_fitting.m

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-07-06 16:26:48+12:00
Desc:
Updating to LRd 34.4 pL cell parameters
Permanent Source URI:
https://models.physiomeproject.org/workspace/82e/rawfile/df158b8da6f9e06d71a561bb13fe0733e7556f9d/Kernik_matlab_parameter_fitting/r_gate_fitting.m
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% based on Na_h gate by Pan.

clear;
% clc;
% close all;

%% Options
run_optimisation = true;

%% Set directories
current_dir = pwd;
main_dir = current_dir; %
data_dir = [main_dir '\data' filesep];
output_dir = [main_dir '\output' filesep];
storage_dir = [main_dir '\storage' filesep];

%% Steady-state gating parameters and time constants
V = transpose(-120:1:50);
alpha_r = 0.05536*exp(V/11.684);
beta_r = 0.22084*exp(V/-202.599);
        
tau_r = 1./(alpha_r + beta_r) + 0.696758421171499998;
g_ss_r = alpha_r./(alpha_r + beta_r);

%% Fit bond graph parameters to model
% params: [kf, zf, kr, zr];
error_func_alpha = @(params) square_error(alpha_r - calc_alpha(params,V/1000));
error_func_beta = @(params) square_error(beta_r - calc_beta(params,V/1000));
error_func_gss = @(params) square_error(g_ss_r - p2gss(params,V));
error_func_tau = @(params) square_error(tau_r- p2tau(params,V));

error_func = @(params) error_func_alpha(params) + error_func_beta(params) + error_func_gss(params) + error_func_tau(params);
% error_func = @(params) error_func_gss(params) + error_func_tau(params);


A = [];
b = [];
Aeq = [];
beq = [];
lb = [0; -10; 0; -10];
ub = [Inf; 10; Inf; 10];

options_unc = optimoptions('fminunc','MaxFunEvals',10000);
options_ps = optimoptions('particleswarm','UseParallel',false,'HybridFcn',@fmincon,...
    'SwarmSize',1500,'FunctionTolerance',1e-14);

if run_optimisation
    [params_vec,fval,exitflag,output] = particleswarm(error_func,4,lb,ub,options_ps);
    save([storage_dir 'to_r_parameters.mat'],'params_vec');
else
    load([storage_dir 'to_r_parameters.mat']);
end
% [params_vec,fval,exitflag,output,grad,hessian] = fminunc(error_func,params_vec,options_unc);

%% Plot
% find things again over a wider V range
if true
    V2 = transpose(-120:1:50);
else
    V2 = V;
end

alpha_r = 0.05536*exp(V/11.684);
beta_r = 0.22084*exp(V/-202.599);       
tau_r = 1./(alpha_r + beta_r);
g_ss_r = alpha_r./(alpha_r + beta_r);

g_ss_fit = p2gss(params_vec,V2);
h1 = figure;
plot(V2,g_ss_r,'kx');
hold on;
plot(V2,g_ss_fit,'k');
legend('kinetic','Fitted');
xlabel('Voltage (mV)');
ylabel('h_{ss}');
set(gca,'FontSize',28);
xlim([-120 60]);
set(gca,'XTick',-120:30:60);
set(gca,'YTick',0:0.2:1);
xticklabels({-120,'',-60,'',0,'',60});
yticklabels({0,'','','','',1});
set(gca,'LineWidth',3);
grid on;

tau_fit = p2tau(params_vec,V2);
h2 = figure;
plot(V2,tau_r,'kx');
hold on;
plot(V2,tau_fit,'k');
legend('kinetic','Fitted');
xlabel('Voltage (mV)');
ylabel('\tau_r (ms)');
set(gca,'FontSize',28);
xlim([-120 60]);
set(gca,'XTick',-120:30:60);
% set(gca,'YTick',0:0.2:1);
xticklabels({-120,'',-60,'',0,'',60});
% yticklabels({0,'','','','',1});
set(gca,'LineWidth',3);
set(gca,'xgrid','on');

% print_figure(h1,output_dir,'g_ss_r');
% print_figure(h2,output_dir,'tau_r');

alpha_fit = calc_alpha(params_vec,V2/1000);
beta_fit = calc_beta(params_vec,V2/1000);
figure,
subplot(1,2,1)
plot(V2,alpha_r,'x',V2,alpha_fit);
legend('original','fit');
subplot(1,2,2)
plot(V2,beta_r,'x',V2,beta_fit);
legend('original','fit');