Assignment 8 Overview

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20.309: Biological Instrumentation and Measurement

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Assignment details

This assignment has 2 parts:

  1. Part 1: Let's check that you're comfortable with convolution and the lock-in amplifier design;
  2. Part 2: Modify your instrument to include a lock-in amplifier and temperature control.

Submit your work on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment8.pdf.

Note: this list has been updated (11/12/2017) to be consistent with the wiki pages. The contents on the wiki pages for part 1 and 2 of this assignment have not changed.--JS

Pencil.png Here is a checklist of all things you have to turn in:
  1. answers to all questions in Assignment 8, Part 1;
  2. document the changes you made to your instrument.
    • Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
    • It is not necessary to document construction details, unless you built an instrument that was significantly different than the lab manual suggested.
    • Refer to schematics and diagrams in the lab manual instead of copying them into your report. Use reference designators (such as R7, C2) to refer to call out particular components in schematic diagrams.
  3. Turn in the resulting plots used to make your SNR measurement and record your adjusted SNR. How does this SNR compare to the one you took in Assignment 7?
  4. Report instrument settings you used for each trial, including control software parameters.
  5. Plot fluorescence vs. block temperature.
    • The plot should have temperature in °C on the horizontal axis and fraction of double stranded DNA on the vertical axis.
    • Normalize the data so that the fluorescence decreases from 1 at room temperature to 0 at 95C.
    • On the same axes, plot your the fraction of double-stranded DNA predicted by DINAmelt (or any other software of your choice).
  6. Estimate the DNA melting temperature from your plot. Compare with the theoretical Tm.
  7. How does your data compare to the curve you measured in Assignment 7?


Please IGNORE the previous assignment turn in list (below). It was out of date. (11/12/2017) -JS

  1. a technical subsection of a lab report on your apparatus ameliorated with lock-in amplifier and temperature control:
    • Document your instrument design.
      • Describe your apparatus with sufficient detail for another person to replicate your work. Assume the reader is familiar with the concepts of 20.309 and has access to course materials.
      • Detail your electronic and optical subsystems. Include component values, gain values, cutoff frequencies, lens focal lengths, and relevant distances.
      • It is not necessary to document construction details, unless you built an instrument that was significantly different than the lab manual suggested.
      • Refer to schematics and diagrams in the lab manual instead of copying them into your report. Use reference designators (such as R7, C2) to refer to call out particular components in schematic diagrams.
    • Why not include a nice snapshot or two of the instrument? So lovely.
    • Report the signal-to-noise ratio of your instrument.
    • Document the procedure used to gather your data with fluorescein or beater DNA:
      • Refer to procedures in the lab manual. Describe any changes you made.
      • Report instrument settings for each trial, including control software parameters.
    • Plot all of your raw data, fluorescence vs. block temperature, on the smallest number of axes that clearly conveys the dataset. Include only data generated by your own group.

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