20.309 development to-do list

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Style principles

  • Model the 20.309 report writing guidelines
  • Use Wikipedia style guidelines except when they are inappropriate
    • Document exceptions here
    • Capitalize only the first letter of the page title, proper nouns, and acronyms
    • Do not use pseudo-namspaces
  • Use HTML for inline equations, LaTex for equations on their own line
  • Each lab should have its own main page with links to all the component pages
  • There should only be a link to the lab main page from the wiki main page
  • Hyperlinks should be meaningful
    • Some seminal visions of hypertext documents envisioned that every word on a page would be a hyperlink. Unfortunately, in HTML all links carry equal emphasis. Thus, readers cannot easily differentiate between low- and high-value links. The bodies of articles on this wiki should include only high-value links. Do not include a link in the body of a page unless you intend that it is to be followed by most of students. Lower value links can be included in separate section at the end of the page that clearly delineates their purpose, with a title such as "See also."

Use these categories:

  • 20.309 general
  • Optical microscopy
  • Optical microscopy lab
  • Electronics signals and systems
  • DNA melting lab
  • AFM
  • Optical trapping
  • Thermally limited measurement lab
  • Lab exercise
  • Image processing

Circuits, signals and systems theory

Task Priority Owner Link Status
Electronics primer 1
Capacitors and inductors (time response) 1
Bode plots and frequency response 1
Modeling real systems (based on Real Electronics lecture) 1
Circuits (based on electronics primer, including C and L) 1
Bode plots 1
Fourier transform, transfer functions 1

Intro to electronics lab

Task Priority Owner Link Status
Rewrite 1

DNA melting lab

Task Priority Owner Link Status
Simulating DNA melting I (include noise/parameter confidence interval plot) 1
Page: Build and test your amplifier
Rewrite lock-in in Matlab 3
Redesign heating block for round, disposable vials

Optics

List of optics pages:

Microscopy lab

Lecture schedule

  • Optics
    • Lecture 1: Course Overview
    • Lecture 2: Introduction to Optics
    • Lecture 3: Lab 1, Eyeballs, and Laser Safety
    • Lecture 4: Limits of Light Microscopy
    • Lecture 5: Optical Detectors
    • Lecture 6: Fluorescence Microscopy
    • Lecture 7: Image Processing I
    • Lecture 8: Image Processing II -- Feeling the Fourier Transform
    • Lecture 9: Phase Microscopy & Microrheology
    • Lecture 10: DNA Melting Lab
    • Lecture 12: Thermodynamics of DNA melting Thurs, October 4
      • Reading: SantaLucia, p. 1460-1462
  • Electronics
    • Lecture 13: Voltage dividers and electrical impedance Fri, October 5
    • Reading: H&H p. 3-24
    • Lecture 14: Statistics and Lab 1 wrap-up Thurs, October 11
      • Reading: HW #4 Due
    • Electronics Lecture 15: Capacitors and RC circuits Fri, October 12
      • Reading: H&H p. 32-35 and 6.002 notes p. 703-718, 993-1004
    • Lecture 15 Input/output impedance
    • Lecture 16: RC Circuits
    • Lecture 16: Transfer Functions and RC filters Tues, October 16
      • Reading: H&H p. 37-40, 46-53
      • 6.002 notes p. 1004-1012, 1030-1054
    • Lecture 17: Feedback I
    • Lecture 17: Feedback and Amplifiers I Thurs, October 18
      • Reading: H&H p. 163-176 and 6.002 notes p. 1185-1191
    • Lecture 18: Modeling Real Systems
    • Lecture 18: Feedback and Amplifiers II Fri, October 19
      • Reading: 6.002 notes p. 1191-1220 Elect Intro Lab Due
    • Lecture 18: Frequency Response of an Optical Table
    • Lecture 19: Real Electronics Tues, October 23
    • EXAM #2 Electronics
  • Signals and Systems
    • Lecture 20: Convolution I: Lock-in amplifier Fri, October 26
      • Reading: Strang p. 263-275, 309-315
    • Lecture 21: Convolution II: Filtering Tues, October 30
      • Reading: Strang p. 316-320
    • Lecture 22: Sampling, Nyquist, and Discrete Transform Thurs, November 1
      • Reading: Tutorial and Press p. 500-504
    • Lecture 23: Power Spectral Density, Noise and Bandwidth Fri, November 2
      • Reading: Press p. 496-500 (on PSD) DNA Melting, pI
    • Lecture 24: Sampling, Nyquist, Discrete Transforms, and all that
    • Lecture 25: Advanced DNA Melting
    • Lecture 26, 27: 3D Microscopy
    • Lecture 28: Ultimate Limits pI
      • Reading: Manalis notes
    • Lecture 29: Ultimate Limits pII
    • Lecture 28: Ultimate limits of detection I Fri, November 16
    • Lecture 29: Ultimate limits of detection II Tues, November 20
      • Reading: Manalis notes DNA Melting, pII
    • Lecture 30: Ultimate limits of detection III Tues, November 27
      • Reading: Manalis notes
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