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Qual Paper SI Material | |||
{{Box|font=150%|width=50%|float=left|text=14px|boarder=solid #aaa 1px|Qual Project Source Code|[[File:Github2.png|left|100px]] All source code used in my qualifying exam project can be found [https://github.com/subroutines/djhbrm here in my github repo for the project]. An online version of my qual with enhanced features like citation data popup graphics and animations can be found on [[:Category:Synaptic Plasticity|this page]]}} | |||
{{Clear}} | |||
==SI Fig. 1 - Actin Filament Surface Hull== | |||
<html><iframe width="560" height="315" src="//www.youtube.com/embed/JH-hGjzhEFQ" frameborder="0" allowfullscreen></iframe></html> | |||
==SI Fig. 2 - Brownian Motion Matlab Code== | |||
{{ExpandBox|width=80%|float=left|opener=View|Brownian Motion Matlab Code| | |||
<syntaxhighlight lang="matlab" line start="1" highlight="1" enclose="div"> | |||
function [boom] = BradsBrownianMotionScript() | |||
format compact; | |||
format short; | |||
close all; | |||
% Note: This matlab script requires 'msdanalyzer' toolbox | |||
%-------------############################------------------% | |||
% STARTING PARAMETERS | |||
%-------------############################------------------% | |||
D = .3; % Diffusion Rate | |||
Ds = .1; % Diffusion Scalar (Ds = Dn) | |||
Dn = D/(D/Ds); % new D after scaling L | |||
d = 2; % dimensions | |||
dT = 1; % time step | |||
k = sqrt(d*D); % stdev of D's step size distribution | |||
MSD = 2*d*D; % mean squared displacement | |||
L = sqrt(2*d*D); % average diagonal (2D) step size | |||
Lx = L/sqrt(2); % average linear (1D) step size | |||
Ls = 1/sqrt(D/Ds); % scales Lx values for Dn | |||
MSDtest = [1 0 0]; % test: D, Dn, or L | |||
Scale = 1/10; % scale of model | |||
Ndots = 100; | |||
Nsteps = Ndots; | |||
xyl = ones(2,Ndots); | |||
xyds = ones(2,Ndots); | |||
lims = ((D+1)^2)*10; | |||
%===========================================================% | |||
% LIVE PARTICLE DIFFUSION | |||
%-----------------------------------------------------------% | |||
for t = 1:Nsteps | |||
xyds = STEPxyds(Ndots, k); | |||
[xyl] = AMPARSTEP(Ndots, xyds, xyl); | |||
MAINPLOT(xyl, lims); | |||
end | |||
%===========================================================% | |||
%===========================================================% | |||
% MSD RANDOM STEPS ANALYSIS | |||
%-----------------------------------------------------------% | |||
tracks = cell(Ndots, 1); | |||
stepN = 1; | |||
for t = 1:Nsteps | |||
xyds = STEPxyds(Ndots, k); | |||
[xyl] = AMPARSTEP(Ndots, xyds, xyl); | |||
[tracks] = MSDfun(stepN, Nsteps, tracks, xyds); | |||
stepN = stepN+1; | |||
end | |||
MSDfunction(tracks,Ndots,Nsteps,D,Dn,L,dT,k,Scale,MSDtest); | |||
%===========================================================% | |||
% MSD UNIFORM STEPS ANALYSIS | |||
%-----------------------------------------------------------% | |||
stepN = 1; | |||
for t = 1:Nsteps | |||
xyds = stepsize(Ndots, Lx); | |||
[xyl xyds] = MSDAMPARSTEP(Ndots, xyds, xyl, Ls); | |||
[tracks] = MSDfun(stepN, Nsteps, tracks, xyds); | |||
stepN = stepN+1; | |||
end | |||
MSDfunction(tracks,Ndots,Nsteps,D,Dn,L,dT,k,Scale,MSDtest); | |||
boom = 'done'; | |||
%-------------############################------------------% | |||
end % ## END MAIN FUNCTION ## | |||
%-------------############################------------------% | |||
%% | |||
%% | |||
%-------------############################------------------% | |||
% ## SUBFUNCTIONS ## | |||
%-------------############################------------------% | |||
%-------------------------------------------% | |||
% STEP SIZE GENERATOR | |||
%-------------------------------------------% | |||
function xyds = STEPxyds(Ndots, k) | |||
xyds = (k * randn(2,Ndots)); | |||
end | |||
%-------------------------------------------% | |||
% MOVE PARTICLES MAIN FUNCTION | |||
%-------------------------------------------% | |||
function [xyl] = AMPARSTEP(Ndots, xyds, xyl) | |||
for j = 1:Ndots | |||
xyl(:,j) = xyl(:,j)+xyds(:,j); | |||
end | |||
end | |||
%-------------------------------------------% | |||
% LIVE DIFFUSION PLOT | |||
%-------------------------------------------% | |||
function [] = MAINPLOT(xyl, lims) | |||
%-------------------------------------------% | |||
xlim = [-lims lims]; | |||
ylim = [-lims lims]; | |||
zlim = [-5 5]; | |||
%=================================% | |||
% MAIN 2D PLOT | |||
%---------------------------------% | |||
figure(1) | |||
subplot(2,1,1), | |||
AMPARPlot = gscatter(xyl(1,:),xyl(2,:)); | |||
axis([xlim, ylim]); | |||
set(AMPARPlot,'marker','.','markersize',[6],'color',[1 0 0]) | |||
%=================================% | |||
% 3D PLOT | |||
%---------------------------------% | |||
figure(1); | |||
subplot(2,1,2), | |||
gscatter(xyl(1,:),xyl(2,:)); view(20, 30); | |||
axis normal; | |||
grid off | |||
axis([xlim, ylim, zlim]); | |||
set(gca, 'Box', 'on'); | |||
end | |||
%-------------------------------------------% | |||
% MANUAL STEP SIZE FUNCTION | |||
%-------------------------------------------% | |||
function xyds = stepsize(Ndots, Lx) | |||
%-------------------------------------------% | |||
Lx(1:2,1:Ndots) = Lx; | |||
xyd = randi([0 1],Ndots,2)'; | |||
xyd(xyd == 0) = -1; | |||
xyds = (Lx.*xyd); | |||
end | |||
%-------------------------------------------% | |||
% MSD SCALED STEPS FUNCTION | |||
%-------------------------------------------% | |||
function [xyl xyds] = MSDAMPARSTEP(Ndots, xyds, xyl, Ls) | |||
for j = 1:Ndots | |||
xyds(:,j) = xyds(:,j)*Ls; | |||
xyl(:,j) = xyl(:,j)+xyds(:,j); | |||
end | |||
end | |||
%-------------------------------------------% | |||
% MSD TRACKS GENERATOR | |||
%-------------------------------------------% | |||
function [tracks] = MSDfun(stepN, Nsteps, tracks, xyds) | |||
time = (0:Nsteps-1)'; | |||
xymsd = xyds'; | |||
xymsd = cumsum(xymsd,1); | |||
tracks{stepN} = [time xymsd]; | |||
end | |||
%-------------------------------------------% | |||
% MSD TRACKS ANALYSIS | |||
%-------------------------------------------% | |||
function [] = MSDfunction(tracks,Ndots,Nsteps,D,Dn,L,dT,k,Scale,MSDtest) | |||
SPACE_UNITS = 'µm'; | |||
TIME_UNITS = 's'; | |||
N_PARTICLES = Ndots; | |||
N_TIME_STEPS = Nsteps; | |||
N_DIM = 2; | |||
oD = D; % raw µm^2/s | |||
D = D*Scale; % to-scale µm^2/s | |||
oDn = Dn; % raw µm^2/s | |||
Dn = Dn*Scale; % to-scale µm^2/s | |||
oL = L; % raw µm | |||
L = L*Scale; % to-scale µm | |||
dTbase = dT; % raw time-step | |||
dT = dT*Scale; % to-scale time-step | |||
k = k; % stdv of step distribution | |||
ma = msdanalyzer(2, SPACE_UNITS, TIME_UNITS); | |||
ma = ma.addAll(tracks); | |||
disp(ma) | |||
figure | |||
ma.plotTracks; | |||
ma.labelPlotTracks; | |||
ma = ma.computeMSD; | |||
ma.msd; | |||
t = (0 : N_TIME_STEPS)' * dT; | |||
[T1, T2] = meshgrid(t, t); | |||
all_delays = unique( abs(T1 - T2) ); | |||
figure | |||
ma.plotMSD; | |||
cla | |||
ma.plotMeanMSD(gca, true) | |||
mmsd = ma.getMeanMSD; | |||
t = mmsd(:,1); | |||
x = mmsd(:,2); | |||
dx = mmsd(:,3) ./ sqrt(mmsd(:,4)); | |||
errorbar(t, x, dx, 'k') | |||
[fo, gof] = ma.fitMeanMSD; | |||
plot(fo) | |||
ma.labelPlotMSD; | |||
legend off | |||
ma = ma.fitMSD; | |||
good_enough_fit = ma.lfit.r2fit > 0.8; | |||
Dmean = mean( ma.lfit.a(good_enough_fit) ) / 2 / ma.n_dim; | |||
Dstd = std( ma.lfit.a(good_enough_fit) ) / 2 / ma.n_dim; | |||
Dheader1 = ['Raw Unscaled Values']; | |||
Dhead1 = [' D Dn L']; | |||
Ddat1 = [oD oDn oL]; | |||
disp(' ') | |||
disp(Dheader1) | |||
disp(Dhead1) | |||
disp(Ddat1) | |||
yourtesthead = ['YOU ARE TESTING DIFFUSION FOR:']; | |||
if MSDtest(1) | |||
yourtest = [' D: original diffusion rate']; | |||
elseif MSDtest(2) | |||
yourtest = [' Dn: new diffusion rate']; | |||
elseif MSDtest(3) | |||
yourtest = [' L: step length']; | |||
else | |||
yourtest = [' generic diffusion rate']; | |||
end | |||
disp(yourtesthead) | |||
disp(yourtest) | |||
disp(' ') | |||
fprintf('Estimation of raw D coefficient from MSD:\n') | |||
fprintf('D = %.3g ± %.3g (mean ± std, N = %d)\n', ... | |||
Dmean, Dstd, sum(good_enough_fit)); | |||
% Retrieve instantaneous velocities, per track | |||
trackV = ma.getVelocities; | |||
% Pool track data together | |||
TV = vertcat( trackV{:} ); | |||
% Velocities are returned in a N x (nDim+1) array: [ T Vx Vy ...]. So the | |||
% velocity vector in 2D is: | |||
V = TV(:, 2:3); | |||
% Compute diffusion coefficient | |||
varV = var(V); | |||
mVarV = mean(varV); % Take the mean of the two estimates | |||
Dest = mVarV / 2 * dT; | |||
Dheader2 = ['Scaling to model...']; | |||
Dhead2 = [' D Dn L']; | |||
Ddat2 = [D Dn L]; | |||
disp(' ') | |||
disp(Dheader2) | |||
disp(Dhead2) | |||
disp(Ddat2) | |||
fprintf('Estimation from velocities histogram:\n') | |||
fprintf('Tested D = %.3g %s, compare to scaled Des value of %.3g %s\n', ... | |||
Dest, [SPACE_UNITS '²/' TIME_UNITS], D, [SPACE_UNITS '²/' TIME_UNITS]); | |||
% printf('D.psd target value was %.3g %s\n', ... | |||
% Dest, msdDpsd, [SPACE_UNITS '²/' TIME_UNITS]); | |||
end | |||
</syntaxhighlight> | |||
}} | |||
<br /><br /> | |||
{{Clear}} | |||
==SI Fig. 3 - Title== | |||
Text Text Text | |||
==SI Fig. 4 - Title== | |||
Text Text Text | |||
==SI Fig. 5 - Title== | |||
Text Text Text | |||
[[Category:Synaptic Plasticity]] |
Latest revision as of 12:08, 5 January 2015
Qual Paper SI Material
Qual Project Source Code
SI Fig. 1 - Actin Filament Surface Hull
<html><iframe width="560" height="315" src="//www.youtube.com/embed/JH-hGjzhEFQ" frameborder="0" allowfullscreen></iframe></html>
SI Fig. 2 - Brownian Motion Matlab Code
Brownian Motion Matlab Code
function [boom] = BradsBrownianMotionScript()
format compact;
format short;
close all;
% Note: This matlab script requires 'msdanalyzer' toolbox
%-------------############################------------------%
% STARTING PARAMETERS
%-------------############################------------------%
D = .3; % Diffusion Rate
Ds = .1; % Diffusion Scalar (Ds = Dn)
Dn = D/(D/Ds); % new D after scaling L
d = 2; % dimensions
dT = 1; % time step
k = sqrt(d*D); % stdev of D's step size distribution
MSD = 2*d*D; % mean squared displacement
L = sqrt(2*d*D); % average diagonal (2D) step size
Lx = L/sqrt(2); % average linear (1D) step size
Ls = 1/sqrt(D/Ds); % scales Lx values for Dn
MSDtest = [1 0 0]; % test: D, Dn, or L
Scale = 1/10; % scale of model
Ndots = 100;
Nsteps = Ndots;
xyl = ones(2,Ndots);
xyds = ones(2,Ndots);
lims = ((D+1)^2)*10;
%===========================================================%
% LIVE PARTICLE DIFFUSION
%-----------------------------------------------------------%
for t = 1:Nsteps
xyds = STEPxyds(Ndots, k);
[xyl] = AMPARSTEP(Ndots, xyds, xyl);
MAINPLOT(xyl, lims);
end
%===========================================================%
%===========================================================%
% MSD RANDOM STEPS ANALYSIS
%-----------------------------------------------------------%
tracks = cell(Ndots, 1);
stepN = 1;
for t = 1:Nsteps
xyds = STEPxyds(Ndots, k);
[xyl] = AMPARSTEP(Ndots, xyds, xyl);
[tracks] = MSDfun(stepN, Nsteps, tracks, xyds);
stepN = stepN+1;
end
MSDfunction(tracks,Ndots,Nsteps,D,Dn,L,dT,k,Scale,MSDtest);
%===========================================================%
% MSD UNIFORM STEPS ANALYSIS
%-----------------------------------------------------------%
stepN = 1;
for t = 1:Nsteps
xyds = stepsize(Ndots, Lx);
[xyl xyds] = MSDAMPARSTEP(Ndots, xyds, xyl, Ls);
[tracks] = MSDfun(stepN, Nsteps, tracks, xyds);
stepN = stepN+1;
end
MSDfunction(tracks,Ndots,Nsteps,D,Dn,L,dT,k,Scale,MSDtest);
boom = 'done';
%-------------############################------------------%
end % ## END MAIN FUNCTION ##
%-------------############################------------------%
%%
%%
%-------------############################------------------%
% ## SUBFUNCTIONS ##
%-------------############################------------------%
%-------------------------------------------%
% STEP SIZE GENERATOR
%-------------------------------------------%
function xyds = STEPxyds(Ndots, k)
xyds = (k * randn(2,Ndots));
end
%-------------------------------------------%
% MOVE PARTICLES MAIN FUNCTION
%-------------------------------------------%
function [xyl] = AMPARSTEP(Ndots, xyds, xyl)
for j = 1:Ndots
xyl(:,j) = xyl(:,j)+xyds(:,j);
end
end
%-------------------------------------------%
% LIVE DIFFUSION PLOT
%-------------------------------------------%
function [] = MAINPLOT(xyl, lims)
%-------------------------------------------%
xlim = [-lims lims];
ylim = [-lims lims];
zlim = [-5 5];
%=================================%
% MAIN 2D PLOT
%---------------------------------%
figure(1)
subplot(2,1,1),
AMPARPlot = gscatter(xyl(1,:),xyl(2,:));
axis([xlim, ylim]);
set(AMPARPlot,'marker','.','markersize',[6],'color',[1 0 0])
%=================================%
% 3D PLOT
%---------------------------------%
figure(1);
subplot(2,1,2),
gscatter(xyl(1,:),xyl(2,:)); view(20, 30);
axis normal;
grid off
axis([xlim, ylim, zlim]);
set(gca, 'Box', 'on');
end
%-------------------------------------------%
% MANUAL STEP SIZE FUNCTION
%-------------------------------------------%
function xyds = stepsize(Ndots, Lx)
%-------------------------------------------%
Lx(1:2,1:Ndots) = Lx;
xyd = randi([0 1],Ndots,2)';
xyd(xyd == 0) = -1;
xyds = (Lx.*xyd);
end
%-------------------------------------------%
% MSD SCALED STEPS FUNCTION
%-------------------------------------------%
function [xyl xyds] = MSDAMPARSTEP(Ndots, xyds, xyl, Ls)
for j = 1:Ndots
xyds(:,j) = xyds(:,j)*Ls;
xyl(:,j) = xyl(:,j)+xyds(:,j);
end
end
%-------------------------------------------%
% MSD TRACKS GENERATOR
%-------------------------------------------%
function [tracks] = MSDfun(stepN, Nsteps, tracks, xyds)
time = (0:Nsteps-1)';
xymsd = xyds';
xymsd = cumsum(xymsd,1);
tracks{stepN} = [time xymsd];
end
%-------------------------------------------%
% MSD TRACKS ANALYSIS
%-------------------------------------------%
function [] = MSDfunction(tracks,Ndots,Nsteps,D,Dn,L,dT,k,Scale,MSDtest)
SPACE_UNITS = 'µm';
TIME_UNITS = 's';
N_PARTICLES = Ndots;
N_TIME_STEPS = Nsteps;
N_DIM = 2;
oD = D; % raw µm^2/s
D = D*Scale; % to-scale µm^2/s
oDn = Dn; % raw µm^2/s
Dn = Dn*Scale; % to-scale µm^2/s
oL = L; % raw µm
L = L*Scale; % to-scale µm
dTbase = dT; % raw time-step
dT = dT*Scale; % to-scale time-step
k = k; % stdv of step distribution
ma = msdanalyzer(2, SPACE_UNITS, TIME_UNITS);
ma = ma.addAll(tracks);
disp(ma)
figure
ma.plotTracks;
ma.labelPlotTracks;
ma = ma.computeMSD;
ma.msd;
t = (0 : N_TIME_STEPS)' * dT;
[T1, T2] = meshgrid(t, t);
all_delays = unique( abs(T1 - T2) );
figure
ma.plotMSD;
cla
ma.plotMeanMSD(gca, true)
mmsd = ma.getMeanMSD;
t = mmsd(:,1);
x = mmsd(:,2);
dx = mmsd(:,3) ./ sqrt(mmsd(:,4));
errorbar(t, x, dx, 'k')
[fo, gof] = ma.fitMeanMSD;
plot(fo)
ma.labelPlotMSD;
legend off
ma = ma.fitMSD;
good_enough_fit = ma.lfit.r2fit > 0.8;
Dmean = mean( ma.lfit.a(good_enough_fit) ) / 2 / ma.n_dim;
Dstd = std( ma.lfit.a(good_enough_fit) ) / 2 / ma.n_dim;
Dheader1 = ['Raw Unscaled Values'];
Dhead1 = [' D Dn L'];
Ddat1 = [oD oDn oL];
disp(' ')
disp(Dheader1)
disp(Dhead1)
disp(Ddat1)
yourtesthead = ['YOU ARE TESTING DIFFUSION FOR:'];
if MSDtest(1)
yourtest = [' D: original diffusion rate'];
elseif MSDtest(2)
yourtest = [' Dn: new diffusion rate'];
elseif MSDtest(3)
yourtest = [' L: step length'];
else
yourtest = [' generic diffusion rate'];
end
disp(yourtesthead)
disp(yourtest)
disp(' ')
fprintf('Estimation of raw D coefficient from MSD:\n')
fprintf('D = %.3g ± %.3g (mean ± std, N = %d)\n', ...
Dmean, Dstd, sum(good_enough_fit));
% Retrieve instantaneous velocities, per track
trackV = ma.getVelocities;
% Pool track data together
TV = vertcat( trackV{:} );
% Velocities are returned in a N x (nDim+1) array: [ T Vx Vy ...]. So the
% velocity vector in 2D is:
V = TV(:, 2:3);
% Compute diffusion coefficient
varV = var(V);
mVarV = mean(varV); % Take the mean of the two estimates
Dest = mVarV / 2 * dT;
Dheader2 = ['Scaling to model...'];
Dhead2 = [' D Dn L'];
Ddat2 = [D Dn L];
disp(' ')
disp(Dheader2)
disp(Dhead2)
disp(Ddat2)
fprintf('Estimation from velocities histogram:\n')
fprintf('Tested D = %.3g %s, compare to scaled Des value of %.3g %s\n', ...
Dest, [SPACE_UNITS '²/' TIME_UNITS], D, [SPACE_UNITS '²/' TIME_UNITS]);
% printf('D.psd target value was %.3g %s\n', ...
% Dest, msdDpsd, [SPACE_UNITS '²/' TIME_UNITS]);
end
SI Fig. 3 - Title
Text Text Text
SI Fig. 4 - Title
Text Text Text
SI Fig. 5 - Title
Text Text Text