Difference between revisions of "Limits of Detection:Report Requirements"

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==Guidelines==
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* Before you go to the lab, read the [http://measure.mit.edu/~20.309/wiki/images/2/27/Optical_Trapping_Lab_Manual.pdf optical trapping lab manual] and the the [http://measure.mit.edu/~20.309/wiki/index.php?title=Lab_Manual:Atomic_Force_Microscopy_(AFM) Atomic Force Microscopy lab manual]
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#Carefully read sections in the Optical Trapping and Atomic Force Microscopy lab manuals, as guided by your TA. It would be a good idead to read as much as possible from the manuals before your lab sessions with the TA.
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*Attend an optical trap lab session.
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#Gather data as a group, but complete these deliverables <b>individually</b>. This includes both your code and your written report.
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*Attend an AFM lab session.
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#Upload your code and report as <b>separate</b> documents on Stellar. (Include your name in the filename as usual.)
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*Submit your report in PDF format to Stellar.  
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#Write no more than one paragraph when comments are requested. That means your report will be only three paragraphs long, plus graphs.
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*Name the file: <lastname>DetectionLimitReport.pdf. (Substitute your surname for "<lastname>")
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#Include plots of your raw data and any additional plots to support your answers.
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*The report should be answer-book style, like a problem set.
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*Include computer code in an appendix at the end of the file. Do not submit code separately.
  
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==Deliverables==
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'''''You will gather data as a group; however, reports must be individually authored. Everything in your report, including computer code, must be entirely your own work.'''''
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<br/>
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<center>'''Answer the following questions:'''</center>
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#Optical trap calibration
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##Plot QPD responsivity, ''R<sub>QPD</sub>'', versus power.
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##What is your estimate of the trap stiffness as a function of power as determined by the three different calibration methods (equipartition, PSD roll-off, and Stokes drag)? Plot stiffness versus power for each method on the same set of axes.
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##*For the PSD method: plot a representative power spectrum and the corresponding model fit on the same set of axes.
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##*For the Stokes method: plot a representative force or displacement versus velocity dataset and the corresponding regression model on the same set of axes.
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##Which method is superior? Explain why.
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##What is the minimum detectable force as a function of power and bandwidth?
  
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===Optical trap exercise===
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#AFM
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After working with your TA to gather data, work through Section 4 of the Optical Trapping lab manual and include the following in your Limits of Detection report.
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##What is the responsivity of the AFM? Plot the z-scan data and linearized response on one set of axes with distance units on the horizontal axis and output voltage on the vertical axis. Over what range of displacements is the detector response reasonably approximated by a line?
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#Report your results for trap stiffness by each of the three methods at the same power level: equipartition, PSD roll-off, and Stokes drag.
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##What is the stiffness of the cantilever you measured? Plot the spectrum you measured and the model fit on one set of axes.
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#Comment on which method you believe to be the best and provide support using concepts that we've discussed in class and in lab both recently and throughout the semester.
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##How does the stiffness computed from the cantilever's material properties compare to the value measured by the Sader method?
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#Report the minimum detectable force in a 100 Hz bandwidth, at your power level.
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##What is the smallest force you could measure using that cantilever?
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#Submit all code used to arrive at your results.
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===Atomic force microscope exercise===
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{{Template:20.309 bottom}}
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#Report your results for cantilever stiffness
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#Report the minimum detectable force in a 100 Hz bandwidth if one were to use the cantilever you measured.
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#Comment on how this value compares to typical forces in biological systems (e.g. antibody/antigen binding, DNA hybridization, interdomain forces in proteins, etc.)? Use whatever knowledge you may have, or find one or two examples, but don't spend long doing literature searches.
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#Comment on how you could modify the cantilever to detect smaller forces and state what you believe to be the smallest detectable force using a silicon nitride cantilever. Which parameters most affect the minimum detectable force? I.e. for smaller forces, do you need a cantilever that's shorter? thinner? wider? Comment on which parameter variations will have the greatest effect. Do you see any constraints on these parameters?
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#Submit all code used to arrive at your results.
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Latest revision as of 20:20, 10 April 2014

20.309: Biological Instrumentation and Measurement

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  • Before you go to the lab, read the optical trapping lab manual and the the Atomic Force Microscopy lab manual
  • Attend an optical trap lab session.
  • Attend an AFM lab session.
  • Submit your report in PDF format to Stellar.
  • Name the file: <lastname>DetectionLimitReport.pdf. (Substitute your surname for "<lastname>")
  • The report should be answer-book style, like a problem set.
  • Include computer code in an appendix at the end of the file. Do not submit code separately.

You will gather data as a group; however, reports must be individually authored. Everything in your report, including computer code, must be entirely your own work.

Answer the following questions:
  1. Optical trap calibration
    1. Plot QPD responsivity, RQPD, versus power.
    2. What is your estimate of the trap stiffness as a function of power as determined by the three different calibration methods (equipartition, PSD roll-off, and Stokes drag)? Plot stiffness versus power for each method on the same set of axes.
      • For the PSD method: plot a representative power spectrum and the corresponding model fit on the same set of axes.
      • For the Stokes method: plot a representative force or displacement versus velocity dataset and the corresponding regression model on the same set of axes.
    3. Which method is superior? Explain why.
    4. What is the minimum detectable force as a function of power and bandwidth?
  1. AFM
    1. What is the responsivity of the AFM? Plot the z-scan data and linearized response on one set of axes with distance units on the horizontal axis and output voltage on the vertical axis. Over what range of displacements is the detector response reasonably approximated by a line?
    2. What is the stiffness of the cantilever you measured? Plot the spectrum you measured and the model fit on one set of axes.
    3. How does the stiffness computed from the cantilever's material properties compare to the value measured by the Sader method?
    4. What is the smallest force you could measure using that cantilever?
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