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. 4 Scanning probe microscopy (and associated critical band audio files) 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. 10 (Columbus Day) Thursday, Oct. 12 Correlation/convolution, lock-in amplification, linear systems	NO LAB MON-TUE (Columbus Day Weekend) Wednesday, Oct. 11 - Friday, Oct. 13 AFM alignment and calibration, AFM imaging I AFM imaging II; force spectroscopy Lab manual for weeks 4-6: The Atomic Force Microscope	Readings   LAB REPORT #1 (Measuring DNA Melting Curves) DUE
6	Tuesday, Oct. 17 Equipartition theorem and thermal fluctuations Thursday, Oct. 19 Student Presentations (Session #2)	Monday, Oct. 16 - Friday Oct. 20 Thermal fluctuations of microcantilevers: Boltzmann's constant experiment Lab manual for weeks 5 - 7: The Atomic Force Microscope	Lab Exercise on Sampling and Aliasing   HOMEWORK SET 2, due Wednesday, 10/11 by 12:00 noon. Thursday, Oct. 19 (in class) Student Presentations (Session #2)
	Optics
7	Tuesday, Oct. 24 Image processing I Thursday, Oct. 26 Image processing II Supplementary slides to image processing lectures	Monday, Oct. 23 - Friday, Oct. 27 Image processing Handout on Image Processing	Readings Great Matlab Matrix Indexing Tutorial Image Processing Readings (from Gonzalez & Woods): Chapter 4: histograms, contrast, spatial filtering. Chapter 8: morphological operations Chapter 7: segmentation Chapter 9: recognition & interpretation
8	Tuesday, Oct. 31 Physical optics and optical instrumentation: detectors, noise Thursday, Nov. 2 Optical instrumentation: sources, lasers	Monday, Oct. 30 - Friday, Nov. 3 Optoelectronics: PMT & photon counting	LAB REPORT #2 (The Atomic Force Microscope) due Monday, Oct. 30 by 12:00 noon. HOMEWORK SET 3 due (Friday, Nov. 3 by 12:00noon).
9	Tuesday, Nov. 7 Intro to microscopy: geometric optics, lenses, ray tracing Thursday, Nov. 9 Interference and diffraction, resolution in microscopy, Fourier optics	Monday, Nov. 6 - Friday, Nov. 9 Lab manual for weeks 9-11: Fluorescence microscope construction I: white light imaging and Fourier optics NO LAB FRIDAY NOV. 10 (Veteran's Day)	Readings Nice online microscopy references: "MicroscopyU" from Nikon and Molecular Expressions Optical Microscopy Primer HOMEWORK SET 3.5 (PMT & photon counting) due Tuesday, Nov. 7 in class.
10	Tuesday, Nov. 14 Fluorescence microscopy Thursday, Nov. 16 Active microrheology	Monday, Nov. 13 - Friday, Nov. 17 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)