Continuum model of tubulin-driven neurite elongation (Graham et al 2006)

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Accession:59581
This model investigates the elongation over time of a single developing neurite (axon or dendrite). Our neurite growth model describes the elongation of a single,unbranched neurite in terms of the rate of extension of the microtubule cytoskeleton. The cytoskeleton is not explicitly modelled, but its construction is assumed to depend on the available free tubulin at the growing neurite tip.
References:
1 . Graham BP, Lauchlan K, McLean DR (2006) Dynamics of outgrowth in a continuum model of neurite elongation. J Comput Neurosci 20:43-60 [PubMed]
2 . Graham BP, van Ooyen A (2006) Mathematical modelling and numerical simulation of the morphological development of neurons. BMC Neurosci 7 Suppl 1:S9 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB;
Model Concept(s): Development;
Implementer(s): Graham, Bruce [B.Graham at cs.stir.ac.uk];
function varargout = CMNG_gui(varargin)
%CMNG_GUI M-file for CMNG_gui.fig
%      CMNG_GUI, by itself, creates a new CMNG_GUI or raises the existing
%      singleton*.
%
%      H = CMNG_GUI returns the handle to a new CMNG_GUI or the handle to
%      the existing singleton*.
%
%      CMNG_GUI('Property','Value',...) creates a new CMNG_GUI using the
%      given property value pairs. Unrecognized properties are passed via
%      varargin to CMNG_gui_OpeningFcn.  This calling syntax produces a
%      warning when there is an existing singleton*.
%
%      CMNG_GUI('CALLBACK') and CMNG_GUI('CALLBACK',hObject,...) call the
%      local function named CALLBACK in CMNG_GUI.M with the given input
%      arguments.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help CMNG_gui

% Last Modified by GUIDE v2.5 26-Oct-2005 17:33:08

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @CMNG_gui_OpeningFcn, ...
                   'gui_OutputFcn',  @CMNG_gui_OutputFcn, ...
                   'gui_LayoutFcn',  [], ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
   gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before CMNG_gui is made visible.
function CMNG_gui_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   unrecognized PropertyName/PropertyValue pairs from the
%            command line (see VARARGIN)

% Choose default command line output for CMNG_gui
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes CMNG_gui wait for user response (see UIRESUME)
% uiwait(handles.figure1);

% Set data to predefined values
initialize_gui(handles);


% --- Outputs from this function are returned to the command line.
function varargout = CMNG_gui_OutputFcn(hObject, eventdata, handles)
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;



function sim_time_Callback(hObject, eventdata, handles)
% hObject    handle to sim_time (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of sim_time as text
%        str2double(get(hObject,'String')) returns contents of sim_time as a double


% --- Executes during object creation, after setting all properties.
function sim_time_CreateFcn(hObject, eventdata, handles)
% hObject    handle to sim_time (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function dt_Callback(hObject, eventdata, handles)
% hObject    handle to dt (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of dt as text
%        str2double(get(hObject,'String')) returns contents of dt as a double


% --- Executes during object creation, after setting all properties.
function dt_CreateFcn(hObject, eventdata, handles)
% hObject    handle to dt (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes during object creation, after setting all properties.
function alpha_CreateFcn(hObject, eventdata, handles)
% hObject    handle to alpha (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called


% --- Executes on button press in run_button.
function run_button_Callback(hObject, eventdata, handles)
% hObject    handle to run_button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get parameter values
% simulation parameters
simp.tmax = str2double(get(handles.sim_time, 'String'));
simp.dt = str2double(get(handles.dt, 'String'));;
simp.N = str2double(get(handles.N, 'String'));
simp.kmax = str2double(get(handles.kmax, 'String'));
simp.mc = str2double(get(handles.mc, 'String'));
simp.ml = str2double(get(handles.ml, 'String'));
simp.datat = str2double(get(handles.datat, 'String'));
% model parameters
modp.D = str2double(get(handles.D, 'String'));
modp.a = str2double(get(handles.a, 'String'));
modp.g = str2double(get(handles.g, 'String'));
modp.rg = str2double(get(handles.rg, 'String'));
modp.sg = str2double(get(handles.sg, 'String'));
modp.e0 = str2double(get(handles.e0, 'String'));
GS = str2double(get(handles.GS, 'String'));
modp.l0 = str2double(get(handles.l0, 'String'));
modp.c0 = str2double(get(handles.c0, 'String'));
theta = str2double(get(handles.theta, 'String'));
modp.el = str2double(get(handles.el, 'String'));
modp.el = str2double(get(handles.el, 'String'));
alphath = modp.g*modp.sg/(modp.e0*modp.c0*modp.rg*modp.a);  % alpha_twid_h
modp.er = theta*modp.e0;        % soma tubulin autoregulation
modp.rdt = 0;                   % autoregulation time delay
modp.el = GS*modp.rg;           % growth cone flux-sink rate
modp.zl = GS*modp.sg;           % growth cone flux-source rate
set(handles.alpha, 'String', alphath);
set(handles.el, 'String', modp.el);
set(handles.zl, 'String', modp.el);

% Simulation with linear ICs
% calculated parameters
[calcp] = CMNG_calcparams(simp, modp);
% run model for jmax time steps
[C1, C01, CN1, l1] = CMNG_run(simp, modp, calcp, -1, modp);
[t, C1, C01, CN1, l1] = CMNG_dimen(simp, modp, C1, C01, CN1, l1);  % dimensionalise
Ca1 = [C01 C1 CN1];

% Plot results
plot(handles.axes1,t,l1,'k-');
hold on;
title(handles.axes1,'Length');
xlabel(handles.axes1,'Time');
ylabel(handles.axes1,'Length');

space=0:1/simp.N:1;
surf(handles.axes2,space,t,Ca1);
title(handles.axes2,'Concentration over Unit Space and Time');
xlabel(handles.axes2,'Space');
ylabel(handles.axes2,'Time');
zlabel(handles.axes2,'Concentration');
view(handles.axes2,90-37.5,30);


% --- Executes on button press in reset_button.
function reset_button_Callback(hObject, eventdata, handles)
% hObject    handle to reset_button (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Reset data to predefined values
initialize_gui(handles);


function N_Callback(hObject, eventdata, handles)
% hObject    handle to N (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of N as text
%        str2double(get(hObject,'String')) returns contents of N as a double


% --- Executes during object creation, after setting all properties.
function N_CreateFcn(hObject, eventdata, handles)
% hObject    handle to N (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function kmax_Callback(hObject, eventdata, handles)
% hObject    handle to kmax (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of kmax as text
%        str2double(get(hObject,'String')) returns contents of kmax as a double


% --- Executes during object creation, after setting all properties.
function kmax_CreateFcn(hObject, eventdata, handles)
% hObject    handle to kmax (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function mc_Callback(hObject, eventdata, handles)
% hObject    handle to mc (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of mc as text
%        str2double(get(hObject,'String')) returns contents of mc as a double


% --- Executes during object creation, after setting all properties.
function mc_CreateFcn(hObject, eventdata, handles)
% hObject    handle to mc (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function ml_Callback(hObject, eventdata, handles)
% hObject    handle to ml (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of ml as text
%        str2double(get(hObject,'String')) returns contents of ml as a double


% --- Executes during object creation, after setting all properties.
function ml_CreateFcn(hObject, eventdata, handles)
% hObject    handle to ml (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function datat_Callback(hObject, eventdata, handles)
% hObject    handle to datat (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of datat as text
%        str2double(get(hObject,'String')) returns contents of datat as a double


% --- Executes during object creation, after setting all properties.
function datat_CreateFcn(hObject, eventdata, handles)
% hObject    handle to datat (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function D_Callback(hObject, eventdata, handles)
% hObject    handle to D (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of D as text
%        str2double(get(hObject,'String')) returns contents of D as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function D_CreateFcn(hObject, eventdata, handles)
% hObject    handle to D (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function a_Callback(hObject, eventdata, handles)
% hObject    handle to a (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of a as text
%        str2double(get(hObject,'String')) returns contents of a as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function a_CreateFcn(hObject, eventdata, handles)
% hObject    handle to a (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function g_Callback(hObject, eventdata, handles)
% hObject    handle to g (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of g as text
%        str2double(get(hObject,'String')) returns contents of g as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function g_CreateFcn(hObject, eventdata, handles)
% hObject    handle to g (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function rg_Callback(hObject, eventdata, handles)
% hObject    handle to rg (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of rg as text
%        str2double(get(hObject,'String')) returns contents of rg as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function rg_CreateFcn(hObject, eventdata, handles)
% hObject    handle to rg (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function sg_Callback(hObject, eventdata, handles)
% hObject    handle to sg (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of sg as text
%        str2double(get(hObject,'String')) returns contents of sg as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function sg_CreateFcn(hObject, eventdata, handles)
% hObject    handle to sg (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function e0_Callback(hObject, eventdata, handles)
% hObject    handle to e0 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of e0 as text
%        str2double(get(hObject,'String')) returns contents of e0 as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function e0_CreateFcn(hObject, eventdata, handles)
% hObject    handle to e0 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function GS_Callback(hObject, eventdata, handles)
% hObject    handle to GS (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of GS as text
%        str2double(get(hObject,'String')) returns contents of GS as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function GS_CreateFcn(hObject, eventdata, handles)
% hObject    handle to GS (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function l0_Callback(hObject, eventdata, handles)
% hObject    handle to l0 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of l0 as text
%        str2double(get(hObject,'String')) returns contents of l0 as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function l0_CreateFcn(hObject, eventdata, handles)
% hObject    handle to l0 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function c0_Callback(hObject, eventdata, handles)
% hObject    handle to c0 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of c0 as text
%        str2double(get(hObject,'String')) returns contents of c0 as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function c0_CreateFcn(hObject, eventdata, handles)
% hObject    handle to c0 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes during object creation, after setting all properties.
function el_CreateFcn(hObject, eventdata, handles)
% hObject    handle to el (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called


% --- Executes during object creation, after setting all properties.
function zl_CreateFcn(hObject, eventdata, handles)
% hObject    handle to zl (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called



function theta_Callback(hObject, eventdata, handles)
% hObject    handle to theta (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of theta as text
%        str2double(get(hObject,'String')) returns contents of theta as a double

% Update calculated parameter values
update_params(handles);


% --- Executes during object creation, after setting all properties.
function theta_CreateFcn(hObject, eventdata, handles)
% hObject    handle to theta (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- AUTHOR-DEFINED UTILITY FUNCTIONS

% -- Sets up default parameter values
function initialize_gui(handles)

% simulation parameters
simp.dt = 0.01;                 % time step
simp.tmax = 100;                % simulation time
simp.datat = 100;               % data collection time step
simp.N = 100;                   % number of spatial points
simp.kmax = 10000;              % maximum corrector steps
simp.mc = 0.0001;               % tolerance on C;
simp.ml = 0.0001;               % tolerance on l;
set(handles.sim_time, 'String', simp.tmax);
set(handles.dt, 'String', simp.dt);
set(handles.datat, 'String', simp.datat);
set(handles.N, 'String', simp.N);
set(handles.kmax, 'String', simp.kmax);
set(handles.mc, 'String', simp.mc);
set(handles.ml, 'String', simp.ml);

% model parameters
modp.c0 = 10;                   % concentration scale
modp.l0 = 0.01;                 % initial (min) length;
modp.D = 30000;                 % diffusion constant
modp.a = 100;                   % active transport rate
modp.g = 0.002;                 % decay rate
modp.rg = 10;                   % growth rate constant
modp.sg = 100;                  % growth rate set point (threshold)
GS = 0.00001;
modp.e0 = 0.000002;             % soma flux-source rate (small growth)
alphath = modp.g*modp.sg/(modp.e0*modp.c0*modp.rg*modp.a);  % alpha_twid_h
theta = 0;                      % fractional autoregulation
modp.er = theta*modp.e0;        % soma tubulin autoregulation
modp.rdt = 0;                   % autoregulation time delay
modp.el = GS*modp.rg;           % growth cone flux-sink rate
modp.zl = GS*modp.sg;           % growth cone flux-source rate
set(handles.D, 'String', modp.D);
set(handles.a, 'String', modp.a);
set(handles.g, 'String', modp.g);
set(handles.rg, 'String', modp.rg);
set(handles.sg, 'String', modp.sg);
set(handles.GS, 'String', GS);
set(handles.alpha, 'String', alphath);
set(handles.e0, 'String', modp.e0);
set(handles.el, 'String', modp.el);
set(handles.zl, 'String', modp.el);
set(handles.l0, 'String', modp.l0);
set(handles.c0, 'String', modp.c0);



% -- Updates calculated parameter values
function update_params(handles)

% Get parameter values
% simulation parameters
simp.tmax = str2double(get(handles.sim_time, 'String'));
simp.dt = str2double(get(handles.dt, 'String'));;
simp.N = str2double(get(handles.N, 'String'));
simp.kmax = str2double(get(handles.kmax, 'String'));
simp.mc = str2double(get(handles.mc, 'String'));
simp.ml = str2double(get(handles.ml, 'String'));
simp.datat = str2double(get(handles.datat, 'String'));
% model parameters
modp.D = str2double(get(handles.D, 'String'));
modp.a = str2double(get(handles.a, 'String'));
modp.g = str2double(get(handles.g, 'String'));
modp.rg = str2double(get(handles.rg, 'String'));
modp.sg = str2double(get(handles.sg, 'String'));
modp.e0 = str2double(get(handles.e0, 'String'));
GS = str2double(get(handles.GS, 'String'));
modp.l0 = str2double(get(handles.l0, 'String'));
modp.c0 = str2double(get(handles.c0, 'String'));
theta = str2double(get(handles.theta, 'String'));
modp.el = str2double(get(handles.el, 'String'));
modp.el = str2double(get(handles.el, 'String'));
alphath = modp.g*modp.sg/(modp.e0*modp.c0*modp.rg*modp.a);  % alpha_twid_h
modp.er = theta*modp.e0;        % soma tubulin autoregulation
modp.rdt = 0;                   % autoregulation time delay
modp.el = GS*modp.rg;           % growth cone flux-sink rate
modp.zl = GS*modp.sg;           % growth cone flux-source rate
set(handles.alpha, 'String', alphath);
set(handles.el, 'String', modp.el);
set(handles.zl, 'String', modp.el);

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