Spring 2012:Leanna Morinishi Lab 1

Lab 1: Optical Trapping

What I wanted to accomplish

• Complete a button that takes in data from a tethered microbead and adjusts the stage position to center it on the tether
  • Try to get nicer calibration data
  • Function that finds the center
  • Feed in recorded data in a simulation
• Look at the properties of the tether, to calculate the persistence and contour lengths

How I did it

• Typing?

Code

If you measured DNA tethers, provide estimates of the persistence and contour lengths. (This will require a calibration with .97 micron polystyrene microspheres.) If you haven't done much curve fitting or you would like some help understanding the theory, stop by during lab open hours and Prof. Nagle or I will get you pointed in the right direction.

Centering Function

function pushbuttonDNATetherCenter_Callback(hObject, eventdata, handles)
    dnaTetherCentering(handles, uiSettings)

function DNATetherCentering(handles, uiSettings)
    accuracy = 1;
    accuracyY = 1;
    setParams = false;
    xcenter = false;
    ycenter = false;
    while accuracy < 4;
        if ~setParams
            xaxisPiezoDriver = handles.PiezoDriverDescriptorList{1};
            yaxisPiezoDriver = handles.PiezoDriverDescriptorList{2};
            handles.SamplesToSave = uiSettings.numberofSeconds*uiSettings.sampleRate;

            Amplitude = uiSettings.stageOscillationAmplitude;
            waveformFreq = round(uiSettings.sampleRate / uiSettings.stageOscillationFrequency);
            time = linspace(0:length(numberOfSamples)-1,numberOfSamples);
            centeringcycle = Amplitude*sin(2*pi*waveformFreq * time)';
            waveform = [centeringcycle zeros(length(centeringcycle),1)]; 
            numberOfSamples = sampleRate * duration; %set sampleRate and duration;

            set(handles.DaqInput.ObjectHandle,'SampleRate',400);
            set(handles.DaqInput.ObjectHandle,'Trigger','Manual');
            set(handles.DaqInput.ObjectHandle,'SamplesPerTrigger',numberOfSamples);

            set(handles.DaqOutput.ObjectHandle,'Trigger','Manual');
            set(handles.DaqOutput.ObjectHandle,'RepeatOutput',3);
    % 
            setParams = true;
        end
        start(handles.DaqInput.ObjectHandle);
        data = getdata(handles.DaqInputHandle);
        Trigger(handles.DaqInput.Output.ObjectHandle);
        putdata(handles.DaqOutput.ObjectHandle,waveform);
        start(handles.DaqOutput.ObjectHandle);
        Trigger(handles.DaqOutput.ObjectHandle);
        waveform = findCenter(data, xcenter, ycenter, waveform);
        stop(handles.DaqInput.ObjectHandle);
        stop(handles.DaqOutput.ObjectHandle);
    end
        
        
    function waveform = findCenter(data, xcenter, ycenter, waveform)

        [quantizedXAxisx BinnedDatax StandardDeviationx Countx] = BinData( ...
         data, 'XColumn', 3, 'YColumn', 1);
        [quantizedXAxisy BinnedDatay StandardDeviationy County] = BinData( ...
         data, 'XColumn', 4, 'YColumn', 2);
        data = [BinnedDatax' BinnedDatay' quantizedXAxisx' quantizedXAxisy']; % qpdx qpdy piezx piezy

        centeredPosition = (positionOfMaxVoltage + positionOfMinVoltage)/2;
        fprintf('The position of the stage is %d',centeredPosition);

        if ~xcenter && ~ycenter
            [MaxValue MaxVoltageIndex] = max(data(:,1));
            positionOfMaxVoltage = centeringcycle(MaxVoltageIndex(1));
            [MinValue MinVoltageIndex] = min(data(:,1));
            positionOfMinVoltage = centeringcycle(MinVoltageIndex(1));
            centeredPosition = (positionOfMaxVoltage + positionOfMinVoltage)/2;
            invoke(handles.PiezoDriverDescriptorList{1}.DriverActiveXControl,...
             'SetPosOutput', 0, centeredPosition);
            xcenter = true;
            waveform = [zeros(length(centeringcycle),1) centeringcycle ]; 

        elseif xcenter && ~ycenter
            [MaxValue MaxVoltageIndex] = max(data(:,2));
            positionOfMaxVoltage = centeringcycle(MaxVoltageIndex(1));
            [MinValue MinVoltageIndex] = min(data(:,2));
            positionOfMinVoltage = centeringcycle(MinVoltageIndex(1));
            centeredPosition = (positionOfMaxVoltage + positionOfMinVoltage)/2;
            invoke(handles.PiezoDriverDescriptorList{2}.DriverActiveXControl,...
             'SetPosOutput', 0, centeredPosition);
            fprintf('The position of the stage is %d',centeredPosition);
            waveform = [ centeringcycle zeros(length(centeringcycle),1)]; 
            if accuracyY == 4;
               centeredPosition = mean(CheckaccuracyYposition);
               invoke(handles.PiezoDriverDescriptorList{2}.DriverActiveXControl,...
                'SetPosOutput', 0, centeredPosition);
            end
            CheckaccuracyYposition(accuracyY) = centeredPosition;
            accuracyY = accuracyY + 1;
            ycenter = true;

        elseif xcenter && ycenter 
            [MaxValue MaxVoltageIndex] = max(data(:,1));
            positionOfMaxVoltage = centeringcycle(MaxVoltageIndex(1));
            [MinValue MinVoltageIndex] = min(data(:,1));
            positionOfMinVoltage = centeringcycle(MinVoltageIndex(1));
            centeredPosition = (positionOfMaxVoltage + positionOfMinVoltage)/2;
            CheckaccuracyXposition(accuracy) = centeredPosition;
            waveform = [ centeringcycle zeros(length(centeringcycle),1)];
            % center to mean value of all checkaccuracyXposition
            if accuracy == 4;
               centeredPosition = mean(CheckaccuracyXposition);
               invoke(handles.PiezoDriverDescriptorList{1}.DriverActiveXControl,...
                'SetPosOutput', 0, centeredPosition);
            end
            accuracy = accuracy +1;
            ycenter = false;
        end

Persistence and Contour Length Estimation

Y = 1;          % Young's modulus
I = 1;          % moment of inertia
T = 293;        % Temperature K
k_B = 1.38e-23; % Boltzmann's constant (m^2 kg)/(s^2 K)
x = 10;         % end to end extension of DNA tether

% k_x = 2*pi*D*f_fluid*(x_fluid/x_bead);
% x_bead

l_p = 45;       % persistence length nm (Y * I)/(k_B * T);
l_c = 1180;     % contour length nm

datax = load('pretty nice DNA tether 20mw 1.txt');

datax(:,3) = datax(:,3)*2.22; % 2.22 um/V
datax(:,1) = datax(:,1)/(.5); % .5 V/um

location = [1 1];

edgesx = linspace(min(datax(:,3)), max(datax(:,3)), 1e3);
[l, whichbinx] = histc(datax(:,3), edgesx);
binmeansx = zeros(1, length(edgesx-1));

for i = 1:length(edgesx)-1
    flagmembers = (whichbinx == i);
    members = datax(flagmembers,1);
    binmeansx(i) = mean(members);
end

smoothedx = smooth(binmeansx,200);
[xmin xminindex] = min(smoothedx);
[xmax xmaxindex] = max(smoothedx);
middlex = ceil(mean([xminindex xmaxindex]));

x_stage = edgesx(xmaxindex:xminindex); %, smoothedx(xmaxindex:xminindex)
x_bead = 1e3*abs(smoothedx(middlex) - smoothedx(xmaxindex:xminindex))';

y = x_bead*5e-5; % 5e-5 N/um
myFunction = @ (x, xdata)  forceApplied(Y, I, T, x_bead, x(1), x(2));
 
beta = nlinfit(x_bead, y, myFunction, [45, 1180]);

figure()
semilogx(x_bead, forceApplied(Y, I, T, x_bead, beta(1), beta(2)))
ylabel('Force [pN]')
xlabel('Tether Extension [nm]')
title(['DNA Tether Stretching - L_p: ', num2str(beta(1)), ' L_c: ', num2str(beta(2))])</nowiki