20.309:Schedule

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       [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/strang.pdf Fourier Transforms.]</p>
       [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/strang.pdf Fourier Transforms.]</p>
       <p>[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/FFTreference.pdf FFT reference material]</p>
       <p>[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/FFTreference.pdf FFT reference material]</p>
 +
      <p>[[Media:20309_tutorial_2.pdf|Tutorial 1: Overview of Fourier Transforms]]<br>
 +
      [[Media:Sampling_example.pdf|Tutorial 2: Sampling and Aliasing]]</p>
     </td>
     </td>
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       <p><b>Mon, Oct. 1 - Fri, Oct. 5</b><br>
       <p><b>Mon, Oct. 1 - Fri, Oct. 5</b><br>
-
       AFM alignment and calibration, AFM imaging I </p>
+
       <u>Lab manual for weeks 2 - 4: [[Media:20.309mod1.pdf|Measuring DNA Melting Curves]]</u>.<br>
-
      <p><u>Lab manual for weeks 2 - 4: [[Media:20.309mod1.pdf|Measuring DNA Melting Curves]]</u>.<br>
+
       wrap up DNA melting curve measurements</p>
       wrap up DNA melting curve measurements</p>
     </td>
     </td>
     <td width="30%" valign="top">
     <td width="30%" valign="top">
     <p><b>Readings</b><br>
     <p><b>Readings</b><br>
-
    A helpful link that discusses [http://www.dsptutor.freeuk.com/analyser/guidance.html#leakage spectral leakage]  
+
    <p>One-page handout, with a few [[Media:convclar.pdf| convolution clarification examples]].</p>
-
       when doing spectral analysis.<br>
+
    <p>A helpful link that discusses [http://www.dsptutor.freeuk.com/analyser/guidance.html#leakage spectral leakage]  
-
    See also the [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/FFTreference.pdf FFT reference] reading</p>
+
       when doing spectral analysis.</p>
     </td>
     </td>
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         (Columbus Day Weekend)</i></b> </p>
         (Columbus Day Weekend)</i></b> </p>
       <p><b>Wednesday, Oct. 11 - Friday, Oct. 13</b><br>
       <p><b>Wednesday, Oct. 11 - Friday, Oct. 13</b><br>
-
        AFM imaging II; force spectroscopy </p>
+
      <p> AFM alignment and calibration, AFM imaging I </p>
 +
      <p>AFM imaging II; force spectroscopy </p>
       <p><u>Lab manual for weeks 4-6: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]</u></p>
       <p><u>Lab manual for weeks 4-6: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]</u></p>
     </td>
     </td>
     <td width="30%" valign="top">
     <td width="30%" valign="top">
     <p><b>Readings</b><br>
     <p><b>Readings</b><br>
-
    [[Media:20309_tutorial_2.pdf|Tutorial 1: Overview of Fourier Transforms]]<br>
 
-
    [[Media:Sampling_example.pdf|Tutorial 2: Sampling and Aliasing]]</p>
 
-
    <p>One-page handout, with a few [[Media:convclar.pdf| convolution clarification examples]].</p>
 
     <p>&nbsp;</p>
     <p>&nbsp;</p>
     <p><font color=#aa0000>LAB REPORT #1 ([[Media:20.309mod1.pdf|Measuring DNA Melting Curves]]) DUE</font></p>
     <p><font color=#aa0000>LAB REPORT #1 ([[Media:20.309mod1.pdf|Measuring DNA Melting Curves]]) DUE</font></p>
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       <p><b>Monday, Oct. 16 - Friday Oct. 20</b><br>
       <p><b>Monday, Oct. 16 - Friday Oct. 20</b><br>
         Thermal fluctuations of microcantilevers: Boltzmann's constant experiment</p>
         Thermal fluctuations of microcantilevers: Boltzmann's constant experiment</p>
-
       <p><u>Lab manual for weeks 4-6: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]</u></p>
+
       <p><u>Lab manual for weeks 5 - 7: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]</u></p>
     </td>
     </td>
     <td width="30%" valign="top">
     <td width="30%" valign="top">

Revision as of 15:21, 28 August 2007

20.309: Biological Instrumentation and Measurement

Home        Course Information        Schedule        People        Student Presentations        LAB SIGNUP       

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
<p>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
<p> AFM alignment and calibration, AFM imaging I

AFM imaging II; force spectroscopy

Lab manual for weeks 4-6: The Atomic Force Microscope

Readings
<p> 

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)

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