20.309:Schedule: Difference between revisions

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       <p><b>Readings</b><br>
       <p><b>Readings</b>
       [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/reading_lecture_4.pdf Operational amplifiers.]</p>
       [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/reading_lecture_4.pdf Operational amplifiers.]</p>
       <p><font color=#aa0000>[[Media:HW1.pdf|''HOMEWORK SET 1'']], due Friday, 9/22 by 12:00 noon.</font></p>
       <p>&nbsp;</p><p><font color=#aa0000>[[Media:HW1.pdf|''HOMEWORK SET 1'']], due Friday, 9/22 by 12:00 noon.</font></p>
       <p>[[Media:hw1sol.pdf|Homework Set 1 SOLUTIONS]] and [[Media:hw1matlab.zip|associated Matlab files]].</p>
       <p>[[Media:hw1sol.pdf|Homework Set 1 SOLUTIONS]] and [[Media:hw1matlab.zip|associated Matlab files]].</p>
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       <p><b>Thursday, Sep. 28<br>
       <p><b>Thursday, Sep. 28<br>
         </b>Fourier analysis (cont'd) </p>
         </b>Fourier analysis (cont'd) </p>
       <p><b><font color=#aa0000>Thursday, Sep. 28 @ 7:00pm &ndash; Room 56-614</font><br>
       <p><font color=#aa0000><b>Thursday, Sep. 28 @ 7:00pm &ndash; Room 56-614</b><br>
         </b>[[20.309:Presentations|Student presentations]]</p>
         [[20.309:Presentations|Student presentations]] (Session #1)</font></p>
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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><b><font color=#aa0000>Thursday, Sep. 28 @ 7:00pm &ndash; Room 56-614</font><br>
         <p><font color=#aa0000><b>Thursday, Sep. 28 @ 7:00pm &ndash; Room 56-614</b><br>
         </b>[[20.309:Presentations|Student presentations]]</p>
         [[20.309:Presentations|Student presentations]] (Session #1)</font></p>
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    <p><font color=#aa0000>[[Media:HW2.pdf|''HOMEWORK SET 2'']], due Wednesday, 10/11 by 12:00 noon.</font></p>
     <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]  
     A helpful link that discusses [http://www.dsptutor.freeuk.com/analyser/guidance.html#leakage spectral leakage]  
       when doing spectral analysis.<br>
       when doing spectral analysis.<br>
     See also the [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/FFTreference.pdf FFT reference] reading</p></td>
     See also the [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/FFTreference.pdf FFT reference] reading</p>
    <p>&nbsp;</p>
    <p>LAB REPORT #1 ([[Media:20.309mod1.pdf|Measuring DNA Melting Curves]]) due <b>Friday, Oct. 6 by 12:00 noon</b>.</p>
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       <p>''Lab Manual for weeks 4-6: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]''</p>
       <p>''Lab Manual for weeks 4-6: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]''</p>
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     <td width="30%" valign="top">&nbsp;</td>
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    <p><font color=#aa0000>[[Media:HW2.pdf|''HOMEWORK SET 2'']], due <b>Wednesday, 10/11 by 12:00 noon</b>.</font></p></td>
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       <p>''Lab Manual for weeks 4-6: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]''</p>
       <p>''Lab Manual for weeks 4-6: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]''</p>
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     <td width="30%" valign="top">&nbsp;</td>
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    <p>&nbsp;</p>
    <p><font color=#cc0000>Thursday, Sep. 28 (in class) <br>
    [[20.309:Presentations|Student Presentations]] (Session #2)</font></p></td>
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Revision as of 08:26, 3 October 2006

20.309: Biological Instrumentation and Measurement

Home        Course Information        Schedule        People        Student Presentations        LAB SIGNUP       

WEEK LECTURES LAB READINGS & ASSIGNMENTS
 
Electronics
0

Thursday, Sep. 7
Course Overview, procedures, syllabus, scheduling

Friday, Sep. 8, 3:00-4:00PM
Lab orientation and tour, safety, introduction to electronics

  
1

Tuesday, Sep. 12
Electronics for DNA analysis; dividers, Thevenin's theorem, impedance and loading, RC circuits

Thursday, Sep. 14
RC circuits: transfer functions, Laplace transforms, impedance, RC filters

Monday, Sep. 11 9:30-10:30AM
Lab orientation and tour, safety, introduction to electronics

Monday, Sep. 11 - Friday Sep. 15
Lab manual for Week 1: Intro to Electronics.
Intro to DC measurements, dividers, impedance, photodiode i-v curves, AC measurements, 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

Tuesday, Sep. 19
Feedback: Black's formula, the loop;
op-amps: "golden rules" and circuit examples

Friday, Sep. 22
DNA analysis: SNP detection, chemical equilib. - K and deltaG; description of DNA melting lab apparatus

Monday, Sep. 18 - Friday Sep. 22
Lab manual for Weeks 2 & 3: Measuring DNA Melting Curves.
Build optics for DNA melting experiment, build photodiode readout circuit; calibrate fluorescence signal

Matlab Tutorial file 1 (the basics)

Matlab Tutorial file 2 (curve fitting, etc.)

Readings Operational amplifiers.

 

HOMEWORK SET 1, due Friday, 9/22 by 12:00 noon.

Homework Set 1 SOLUTIONS and associated Matlab files.
3

Tuesday, Sep. 26
Fourier series, integrals, Fourier transform (continuous/discrete)

Thursday, Sep. 28
Fourier analysis (cont'd)

Thursday, Sep. 28 @ 7:00pm – Room 56-614
Student presentations (Session #1)

NO LAB MONDAY SEP. 25
(Student holiday)

Tuesday, Sep. 26 - Friday, Sep. 29
Lab manual for Weeks 2 & 3: 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

Thursday, Sep. 28 @ 7:00pm – Room 56-614
Student presentations (Session #1)
 
Mechanics
4

Tuesday, Oct. 3
Scanning probe microscopy

Thursday, Oct. 5
Signals, noise, Power Spectral Density

Monday, Oct. 2 - Friday, Oct. 6
AFM alignment and calibration, AFM imaging I

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

Readings
A helpful link that discusses spectral leakage when doing spectral analysis.
See also the FFT reference reading

 

LAB REPORT #1 (Measuring DNA Melting Curves) due Friday, Oct. 6 by 12:00 noon.
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 imaging II; force spectroscopy

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

HOMEWORK SET 2, due Wednesday, 10/11 by 12:00 noon.
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 4-6: The Atomic Force Microscope

 

Thursday, Sep. 28 (in class)
Student Presentations (Session #2)
 
Optics
7

Tuesday, Oct. 24
Physical optics and optical instrumentation: detectors, noise

Thursday, Oct. 26
Optical instrumentation: sources, lasers

Monday, Oct. 23 - Friday, Oct. 27
Optoelectronics: PMT, & photon counting; digital lock-in detection of DNA fluorescence

 
8

Tuesday, Oct. 31
Image processing I

Thursday, Nov. 2
Image processing II

Monday, Oct. 30 - Friday, Nov. 3
Image processing

 
9

Tuesday, Nov. 7
Intro to microscopy: geometric optics, lenses, ray tracing

Thursday, Nov. 9
Fluorescence spectroscopy

Monday, Nov. 6 - Friday, Nov. 10
Fluorescence microscope construction I: lenses, white light imaging

 
10

Tuesday, Nov. 14
interference and diffraction, phase-contrast miscroscopy

Thursday, Nov. 16
Resolution in microscopy; Fourier optics

Monday, Nov. 13 - Friday, Nov. 17
Fluorescence microscope construction II, fluorescence imaging, live-cell imaging & microrheology

 
11

Tuesday, Nov. 21
interference and diffraction, phase-contrast miscroscopy

NO LECTURE THURSDAY, NOV. 23
(Thanksgiving)

Monday, Nov. 20 - Wednesday, Nov. 24
Light-scattering microscope and Fourier optics

NO LAB THU-FRI
(Thanksgiving Weekend)

 
12

Tuesday, Nov. 28
Optical trapping

Thursday, Nov. 30
3D microscopy

Monday, Nov. 27 - Friday, Dec. 1
Optical trapping

 

  
13

Tuesday, Dec. 5
3D image processing

Thursday, Dec. 7

Monday, Dec. 4 - Friday, Dec. 8
3D Imaging & Visualization; confocal & two-photon microscopy, ImageJ

 
14 Tuesday, Dec. 12
Student presentations (Group #5) 		   
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