WEEK |
LECTURES & RECITATIONS |
LAB |
READINGS & ASSIGNMENTS |
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Electronics
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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
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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
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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
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Readings
see http://www.openwetware.org/wiki/20.309
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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
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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
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HOMEWORK SET 1 DUE (electronics, circuits).
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3 |
Tue, Sep. 25
Fourier analysis (cont'd)
Thu, Sep. 27
Signals, noise, Power Spectral Density
Fri, Sep. 28
Student presentations (Session #1)
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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
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Readings
Fourier Transforms.
FFT reference material
Tutorial 1: Overview of Fourier Transforms
Tutorial 2: Sampling and Aliasing
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Mechanics
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4 |
Tue, Oct. 2
Correlation/convolution; lock-in amplification & demo; linear systems
Thu, Oct. 4
Equipartition theorem and thermal fluctuations
Fri, Oct. 5 (RECITATION)
Intro to AFM lab module
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Mon, Oct. 1 - Fri, Oct. 5
Lab manual for weeks 2 - 4: Measuring DNA Melting Curves.
wrap up DNA melting curve measurements
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Readings
One-page handout, with a few convolution clarification examples.
A helpful link that discusses spectral leakage
when doing spectral analysis.
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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)
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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
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LAB REPORT #1 (Measuring DNA Melting Curves) DUE
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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
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Monday, Oct. 15 - Friday Oct. 19
AFM imaging II; force spectroscopy
Lab manual for weeks 5 - 7: The Atomic Force Microscope
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HOMEWORK SET 2 DUE (signals, digital sampling, SPM).
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Optics
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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)
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Mon, Oct. 22 - Fri, Oct. 26
Thermal fluctuations of microcantilevers: Boltzmann's constant experiment
Lab manual for weeks 5 - 7: The Atomic Force Microscope
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Readings
Great Matlab Matrix Indexing Tutorial
Nice online microscopy references:
"MicroscopyU" from Nikon
and Molecular Expressions Optical Microscopy Primer
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8 |
Tue, Oct. 30
Optical instrumentation I: physics, sources, lasers
Thu, Nov. 1
Optical instrumentation II: detectors, noise; Statistics I
Fri, Nov. 2 (RECITATION)
Intro to Microscopy lab module and design review presentations
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Mon, Oct. 29 - Fri, Nov. 2
Image processing
Handout on Image Processing
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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.
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9 |
Tue, Nov. 6
Statistics II
Thu, Nov. 8
Fluorescence microscopy/spectroscopy
Fri, Nov. 9
Student presentations (Session #5)
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Mon, Nov. 5 - Fri, Nov. 9
Lab manual for weeks 9-11: Fluorescence microscope construction I:
lenses, white light imaging, resolution/alignment, begin fluorescence
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Readings
Nice online microscopy references:
"MicroscopyU" from Nikon
and Molecular Expressions Optical Microscopy Primer
HOMEWORK SET 3 DUE (Image Processing).
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10 |
Tue, Nov. 13
Microrheology & particle tracking
Thu, Nov. 15
Optical trapping I (Prof. Matt Lang guest lecture)
Fri, Nov. 16
Student presentations (Session #6)
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NO LAB MONDAY NOV. 12 (Veteran's Day)
Tue, Nov. 13 - Fri, Nov. 16
Lab manual for weeks 9-11: Fluorescence microscope construction II:
finish construction, live-cell imaging; particle tracking
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MATLAB scripts for calculating MSD and G*
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11 |
Tue, Nov. 20
Optical Trapping II and Intro to Optical Trap lab module
NO LECTURE THU, NOV. 22
NO RECITATION FRI, NOV. 23
(Thanksgiving weekend)
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Mon, Nov. 19 - Wed, Nov. 21
Lab manual for weeks 9-11: Fluorescence microscope construction III:
live-cell imaging, microrheology, actin cytoskeleton staining & imaging
NO LAB THU-FRI
(Thanksgiving Weekend)
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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.
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12 |
Tue, Nov. 27
Interference and diffraction, phase-contrast microscopy
Thu, Nov. 29
Resolution in microscopy, Fourier optics + demo
Fri, Nov. 30
Student presentations (Session #7)
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Mon, Nov. 26 - Fri, Nov. 30
Lab manual for weeks 12 - 13: Optical Trapping
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Readings
AJP paper by Appleyard et al. on the 20.309 traps,
and the wiki page about them.
LAB REPORT #3 (Fluorescence Microscope) DUE.
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13 |
Tue, Dec. 4 3D microscopy: confocal & multiphoton imaging
Thu, Dec. 6 3D microscopy: 3D image processing
Fri, Dec. 7
Student presentations (Session #8)
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Mon, Dec. 3 - Thu Dec. 6
Lab manual for weeks 12 - 13: Optical Trapping
Fri, Dec. 7
Mini-Lab & hands-on demo: 3D Imaging - two-photon microscopy
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14 |
Tue, Dec. 11
TBD & end-of-term party
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Mon, Dec. 10 - Wed, Dec. 12
Mini-Lab & hands-on demo: 3D Imaging - two-photon microscopy
3D Image-stack Visualization, ImageJ
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LAB REPORT #4 (Optical Trapping) DUE.
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