20.309:Schedule

WEEK	LECTURES & RECITATIONS	LAB	READINGS & ASSIGNMENTS
	Electronics
0	Thu, Sep. 6 Course Overview & syllabus; Lab Intro & logistics: scheduling, wiki, assignments Fri, Sep. 7 (LECTURE) Electronics for DNA analysis; dividers, Thevenin's theorem, impedance and loading, RC circuits
1	Tue, Sep. 11 RC circuits: transfer functions, Laplace transforms, impedance, RC filters Thu, Sep. 13 DNA analysis: SNP detection, chemical equilib. - K and deltaG; description of DNA melting lab apparatus Fri, Sep. 14 (RECITATION) Electronics tutorial	Mon, Sep. 10 - Fri, Sep. 14 Lab manual for Week 1: Intro to Electronics. Intro to DC measurements, dividers, impedance; photodiode i-v curves, AC measurements, black-box transfer functions; the Wheatstone bridge for temperature measurement	Readings Resistors, capacitors, voltage & current dividers, RC transients. Impedance, frequency response, filters. This brief introduction to diodes will be helpful for working on the labs this week.
2	Tue, Sep. 18 Feedback: Black's formula, the loop; op-amps: "golden rules" and circuit examples Thu, Sep. 20 Fourier series & integrals; Fourier transform (continuous & discrete) Fri, Sep. 21 (RECITATION) MATLAB tutorial and Lab Report Guidelines	Mon, Sep. 18 - Fri, Sep. 22 Lab manual for Weeks 2 - 4: Measuring DNA Melting Curves. Build optics for DNA melting experiment, build photodiode readout circuit; calibrate fluorescence signal	Readings Operational amplifiers. Matlab Tutorial file 1 (the basics) Matlab Tutorial file 2 (curve fitting, etc.)   HOMEWORK SET 1, DUE.
3	Tue, Sep. 25 Fourier analysis (cont'd) Thu, Sep. 27 Signals, noise, Power Spectral Density Fri, Sep. 28 Student presentations (Session #1)	NO LAB MONDAY SEP. 24 (Student holiday) Tue, Sep. 25 - Fri, Sep. 28 Lab manual for Weeks 2 - 4: Measuring DNA Melting Curves. Complete DNA melting curves apparatus; test perfect-match, all-mismatch, and single-base mismatch DNA strands	Readings Fourier Transforms. FFT reference material Tutorial 1: Overview of Fourier Transforms Tutorial 2: Sampling and Aliasing
	Mechanics
4	Tue, Oct. 2 Correlation/convolution; lock-in amplification & demo; linear systems Thu, Oct. 11 Equipartition theorem and thermal fluctuations Fri, Oct. 5 (RECITATION) Intro to AFM lab module	Mon, Oct. 1 - Fri, Oct. 5 Lab manual for weeks 2 - 4: Measuring DNA Melting Curves. wrap up DNA melting curve measurements	Readings One-page handout, with a few convolution clarification examples. A helpful link that discusses spectral leakage when doing spectral analysis.
5	NO LECTURE TUESDAY, OCT. 9 (Columbus Day) Thu, Oct. 11 Scanning probe microscopy (and associated critical band audio files) Fri, Oct. 12 Student presentations (Session #2)	NO LAB MON-TUE (Columbus Day Weekend) Wed, Oct. 10 - Fri, Oct. 12 AFM alignment and calibration, AFM imaging I Lab manual for weeks 5 - 7: The Atomic Force Microscope	LAB REPORT #1 (Measuring DNA Melting Curves) DUE
6	Tue, Oct. 16 Student presentations (Session #3) Thu, Oct. 18 Image Processing I Fri, Oct. 19 (RECITATION) Laser Safety Session; AFM data analysis tutorial	Monday, Oct. 15 - Friday Oct. 19 AFM imaging II; force spectroscopy Lab manual for weeks 5 - 7: The Atomic Force Microscope	HOMEWORK SET 2, DUE.
	Optics
7	Tue, Oct. 23 Image processing II Supplementary slides to image processing lectures Thu, Oct. 25 Intro to microscopy: geometric optics, lenses, ray tracing Fri, Oct. 26 Image processing tutorial & Student presentations (Session #4)	Mon, Oct. 22 - Fri, Oct. 26 Thermal fluctuations of microcantilevers: Boltzmann's constant experiment Lab manual for weeks 5 - 7: The Atomic Force Microscope	Readings Great Matlab Matrix Indexing Tutorial Nice online microscopy references: "MicroscopyU" from Nikon and Molecular Expressions Optical Microscopy Primer
8	Tue, Oct. 30 Optical instrumentation I: physics, sources, lasers Thu, Nov. 1 Optical instrumentation II: detectors, noise; Statistics I	Mon, Oct. 29 - Fri, Nov. 2 Image processing Handout on Image Processing	Readings Image Processing Readings (from Gonzalez & Woods): Chapter 4: histograms, contrast, spatial filtering. Chapter 8: morphological operations Chapter 7: segmentation Chapter 9: recognition & interpretation LAB REPORT #2 (The Atomic Force Microscope) DUE.
9	Tue, Nov. 6 Statistics II Thursday, Nov. 9 Interference and diffraction, resolution in microscopy, Fourier optics	Mon, Nov. 5 - Fri, Nov. 9 Lab manual for weeks 9-11: Fluorescence microscope construction I: white light imaging and Fourier optics	HOMEWORK SET 3 (Image Processing) DUE.
10	Tuesday, Nov. 14 Fluorescence microscopy Thursday, Nov. 16 Active microrheology	NO LAB MONDAY NOV. 12 (Veteran's Day) Tue, Nov. 13 - Fri, Nov. 16 Lab manual for weeks 9-11: Fluorescence microscope construction II: Live-cell imaging & microrheology	Thursday, Nov. 16 @ 8:00pm – Room 56-614 Student Presentations (Session #3)
11	Tuesday, Nov. 21 Passive microrheology & Particle tracking NO LECTURE THURSDAY, NOV. 23 (Thanksgiving)	Monday, Nov. 20 - Wednesday, Nov. 24 Lab manual for weeks 9-11: Fluorescence microscope construction III: Actin cytoskeleton imaging Papers referenced in the lab manual: The Vukusic paper on photonic structures and the Mason and Lau papers on microrheology and the complex viscoelastic modulus. NO LAB THU-FRI (Thanksgiving Weekend)	MATLAB scripts for calculating MSD and G* Three papers about peacock feathers: – Zi, PNAS (2003) – Yoshioka, Forma (2002) – Kinoshita, ChemPhysChem (2005)
12	Tuesday, Nov. 28 Optical trapping Thursday, Nov. 30 Advanced fluorescence microscopy	Monday, Nov. 27 - Wednesday, Nov. 29 Fluorescence microscope construction/experiments Wednesday, Nov. 29 - Friday, Dec. 1 Lab manual for weeks 12/13: Optical Trapping Preprint of AJP paper by Appleyard et al. on the 20.309 traps.	Thursday, Nov. 30 @ 8:00pm – Room 56-614 Student Presentations (Session #4)
13	Tuesday, Dec. 5 3D microscopy: Confocal imaging Thursday, Dec. 7 3D microscopy: 2-photon microscopy, 3D image processing	Monday, Dec. 4 - Wednesday Dec. 6 Lab manual for weeks 12/13: Optical Trapping Thursday, Dec. 7 - Friday, Dec. 8 3D Imaging & Visualization: two-photon microscopy	LAB REPORT #3 (Fluorescence Microscope) due Monday, Dec. 4, by 12:00 noon.
14	Tuesday, Dec. 12 Student presentations (Session #5) Thursday, Dec. 14 End-of-Semester Party	Monday, Dec. 11 - Wednesday, Dec. 13 3D Image-stack Visualization, ImageJ	LAB REPORT #4 (Optical Trapping) due Monday, Dec. 11, by 12:00 noon. Tuesday, Dec. 12 (in class) Student presentations (Session #5)