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| {{Template:20.309}}
| | *[http://www.openwetware.org/wiki/Image:Schedule_v5.pdf Schedule] |
| <div style="padding: 10px; width: 774px; border: 3px solid #000000;">
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| <table width="100%" border="1" cellpadding="5" cellspacing="0">
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| <tr>
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| <td width="5%" valign="top"><b>WEEK</b></td>
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| <td width="31%" valign="top"><b>LECTURES & RECITATIONS</b></td>
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| <td width="34%" valign="top"><b>LAB</b></td>
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| <td width="30%" valign="top"><b>READINGS & ASSIGNMENTS</b></td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"> </td>
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| <td colspan="3">
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| <div align="center"><b>Electronics</b></div>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b>0</b></td>
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| <td width="31%" valign="top">
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| <p><b>Thu, Sep. 6</b><br>
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| Course Overview & syllabus; Lab Intro & logistics: scheduling, wiki, assignments </p>
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| <p><b>[[Media:20.309lect1.pdf|Fri, Sep. 7 (LECTURE)]]</b><br>
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| Electronics for DNA analysis; dividers, Thevenin's theorem, impedance
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| and loading, RC circuits</p>
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| </td>
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| <td width="34%" valign="top"> </td>
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| <td width="30%" valign="top"> </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 1</b></td>
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| <td width="31%" valign="top">
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| <p><b>Tue, Sep. 11</b><br>
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| RC circuits: transfer functions, Laplace transforms, impedance, RC filters
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| </p>
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| <p><b>[[Media:20.309_lect4.pdf|Thu, Sep. 13]]</b><br>
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| DNA analysis: SNP detection, chemical equilib. - K and deltaG; description
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| of DNA melting lab apparatus
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| </p>
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| <p><b>Fri, Sep. 14 (RECITATION)</b><br>
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| Electronics tutorial
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| </p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Mon, Sep. 10 - Fri, Sep. 14</b><br>
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| <u>Lab manual for Week 1: [[Media:20.309mod0.pdf|Intro to Electronics]].</u><br>
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| Intro to DC measurements, dividers, impedance; photodiode <i>i-v </i>curves,
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| AC measurements, black-box transfer functions;<br>
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| the Wheatstone bridge for temperature measurement </p>
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| </td>
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| <td width="30%" valign="top">
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| <p><b>Readings</b><br>
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| [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/reading_lecture_1.pdf Resistors, capacitors, voltage & current dividers, RC transients.]</p>
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| <p>[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/reading_lecture_2&3.pdf Impedance, frequency response, filters.]</p>
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| <p>This brief [[20.309:DiodePrimer|introduction to diodes]] will be helpful for working on the labs this week.</p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b>2</b></td>
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| <td width="31%" valign="top">
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| <p><b>Tue, Sep. 18</b><br>
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| Feedback: Black's formula, the loop;<br>
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| op-amps: "golden rules" and circuit examples </p>
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| <p><b>[[Media:20.309_lect5.pdf|Thu, Sep. 20]]</b>
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| Fourier series & integrals; Fourier transform (continuous & discrete)
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| </p>
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| <p><b>Fri, Sep. 21 (RECITATION)</b>
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| MATLAB tutorial and Lab Report Guidelines
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| </p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Mon, Sep. 18 - Fri, Sep. 22</b><br>
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| <u>Lab manual for Weeks 2 - 4: [[Media:20.309mod1.pdf|Measuring DNA Melting Curves]].</u><br>
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| Build optics for DNA melting experiment, build photodiode readout circuit;
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| calibrate fluorescence signal </p>
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| </td>
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| <td width="30%" valign="top">
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| <p><b>Readings</b>
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| [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/reading_lecture_4.pdf Operational amplifiers.]</p>
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| <p>[[Media:MatlabIntro.pdf|Matlab Tutorial file 1 (the basics)]]</p>
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| <p>[[Media:MatlabtutorialV2.pdf|Matlab Tutorial file 2 (curve fitting, etc.)]]</p>
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| <p> </p><p><font color=#aa0000>[[Media:HW1.pdf|HOMEWORK SET 1]], DUE.</font></p>
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| </td>
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| </tr>
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| <tr>
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| <td valign="top" width="5%"><b>3</b></td>
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| <td width="31%" valign="top">
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| <p><b>Tue, Sep. 25</b><br>
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| Fourier analysis (cont'd) </p>
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| <p><b>Thu, Sep. 27<br>
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| </b>Signals, noise, Power Spectral Density </p>
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| <p><b>Fri, Sep. 28</b><br>
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| [[20.309:Presentations|Student presentations]] (Session #1)</p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b><i>NO LAB MONDAY SEP. 24 <br>
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| (Student holiday)</i></b></p>
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| <p> <b>Tue, Sep. 25 - Fri, Sep. 28</b><br>
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| <u>Lab manual for Weeks 2 - 4: [[Media:20.309mod1.pdf|Measuring DNA Melting Curves]].</u> <br>
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| Complete DNA melting curves apparatus; test perfect-match, all-mismatch,
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| and single-base mismatch DNA strands </p>
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| </td>
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| <td width="30%" valign="top">
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| <p><b>Readings</b><br>
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| [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/strang.pdf Fourier Transforms.]</p>
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| <p>[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/FFTreference.pdf FFT reference material]</p>
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| <p>[[Media:20309_tutorial_2.pdf|Tutorial 1: Overview of Fourier Transforms]]<br>
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| [[Media:Sampling_example.pdf|Tutorial 2: Sampling and Aliasing]]</p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"> </td>
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| <td valign="middle" colspan="3">
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| <div align="center"><b>Mechanics</b></div>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 4</b></td>
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| <td width="31%" valign="top">
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| <p><b>Tue, Oct. 2</b><br>
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| Correlation/convolution; lock-in amplification & demo; linear systems
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| </p>
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| <p><b>[[Media:20.309_lect6.pdf|Thu, Oct. 4]]</b><br>
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| Scanning probe microscopy (and associated [[Media:criticalband.zip|critical band audio files]])
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| </p>
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| <p><b>Fri, Oct. 5 (RECITATION)</b><br>
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| Intro to AFM lab module
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| </p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Mon, Oct. 1 - Fri, Oct. 5</b><br>
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| <u>Lab manual for weeks 2 - 4: [[Media:20.309mod1.pdf|Measuring DNA Melting Curves]]</u>.<br>
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| wrap up DNA melting curve measurements</p>
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| </td>
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| <td width="30%" valign="top">
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| <p><b>Readings</b><br>
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| <p>One-page handout, with a few [[Media:convclar.pdf| convolution clarification examples]].</p>
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| <p>A helpful link that discusses [http://www.dsptutor.freeuk.com/analyser/guidance.html#leakage spectral leakage]
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| when doing spectral analysis.</p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b>5</b></td>
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| <td width="31%" valign="top">
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| <p><i><b>NO LECTURE</b></i><b><i> TUESDAY, OCT. 9</i></b><i><b> <br>
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| (Columbus Day)</b></i> </p>
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| <p><b>Thu, Oct. 11</b><br>
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| Equipartition theorem and thermal fluctuations</p>
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| <p><b>Fri, Oct. 12</b><br>
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| [[20.309:Presentations|Student presentations]] (Session #2)</p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b><i>NO LAB MON-TUE<br>
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| (Columbus Day Weekend)</i></b> </p>
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| <p><b>Wed, Oct. 10 - Fri, Oct. 12</b><br>
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| AFM alignment and calibration, AFM imaging I </p>
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| <p><u>Lab manual for weeks 5 - 7: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]</u></p>
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| </td>
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| <td width="30%" valign="top">
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| <p><font color=#aa0000>LAB REPORT #1 ([[Media:20.309mod1.pdf|Measuring DNA Melting Curves]]) DUE</font></p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 6</b></td>
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| <td width="31%" valign="top">
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| <p><b>Tue, Oct. 16</b><br>
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| [[20.309:Presentations|Student presentations]] (Session #3)</p>
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| <p><b>[[Media:20.309_ImProcLect1.pdf|Thu, Oct. 18]]</b><br>
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| Image Processing I</p>
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| <p><b>Fri, Oct. 19 (RECITATION)</b><br>
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| Laser Safety Session; AFM data analysis tutorial</p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Oct. 15 - Friday Oct. 19</b><br>
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| AFM imaging II; force spectroscopy </p>
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| <p><u>Lab manual for weeks 5 - 7: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]</u></p>
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| </td>
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| <td width="30%" valign="top">
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| <p> </p>
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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>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"> </td>
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| <td valign="middle" colspan="3">
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| <div align="center"><b>Optics</b></div>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b>7</b></td>
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| <td width="31%" valign="top">
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| <p><b>[[Media:20.309_ImProcLect2.pdf|Tue, Oct. 23]]</b><br>
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| Image processing II</p>
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| <p><b>[[Media:OpticsLect3.pdf|Thu, Oct. 25]]</b><br>
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| Image processing II </p>
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| <p>[[Media:20.309_ImProcLect2_supp.pdf|Supplementary slides to image processing lectures]]</p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Oct. 23 - Friday, Oct. 27</b><br>
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| Thermal fluctuations of microcantilevers: Boltzmann's constant experiment</p>
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| <p><u>Lab manual for weeks 5 - 7: [[Media:20309f06mod2.pdf|The Atomic Force Microscope]]</u></p>
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| <p>Image processing <br>
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| <u>Handout on [[Media:HW3.pdf|Image Processing]]</u></p>
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| </td>
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| <td width="30%" valign="top">
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| <p><b>Readings</b> <br>
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| [http://www.mathworks.com/company/newsletters/digest/sept01/matrix.html Great Matlab Matrix Indexing Tutorial]</p>
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| <p>Image Processing Readings (from Gonzalez & Woods):<br>
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| [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh4.pdf Chapter 4]: histograms, contrast, spatial filtering. <br>
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| [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh8.pdf Chapter 8]: morphological operations <br>
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| [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh7.pdf Chapter 7]: segmentation <br>
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| [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh9.pdf Chapter 9]: recognition & interpretation </p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b>8</b></td>
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| <td width="31%" valign="top">
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| <p><b>[[Media:OpticsLect1.pdf| Tuesday, Oct. 31]]</b><br>
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| Physical optics and optical instrumentation: detectors, noise</p>
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| <p><b>[[Media:OpticsLect2.pdf| Thursday, Nov. 2]]</b><br>
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| Optical instrumentation: sources, lasers</p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Oct. 30 - Friday, Nov. 3</b><br>
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| <u>Optoelectronics: [[Media:HW3.5.pdf | PMT & photon counting]]</u></p>
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| </td>
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| <td width="30%" valign="top">
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| <p><font color=#aa0000>LAB REPORT #2 ([[Media:20309f06mod2.pdf|The Atomic Force Microscope]]) due <b>Monday, Oct. 30 by 12:00 noon.</b>
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| <br> [[Media:HW3.pdf|HOMEWORK SET 3]] due <b>(Friday, Nov. 3 by 12:00noon)</b>.</font></p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 9</b></td>
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| <td width="31%" valign="top">
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| <p><b>[[Media:OpticsLect3.pdf|Tuesday, Nov. 7]]</b><br>
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| Intro to microscopy: geometric optics, lenses, ray tracing </p>
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| <p><b>[[Media:OpticsLect4.pdf|Thursday, Nov. 9]]<br>
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| </b>Interference and diffraction, resolution in microscopy, Fourier optics </p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Nov. 6 - Friday, Nov. 9</b><br>
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| <u>Lab manual for weeks 9-11: [[Media:20.309f06mod3.pdf|Fluorescence microscope construction I]]: white light imaging and Fourier optics </u></p>
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| <p><i><b>NO LAB FRIDAY NOV. 10<br> (Veteran's Day)</b></i></p>
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| </td>
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| <td width="30%" valign="top">
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| <p><b>Readings</b><br>
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| Nice online microscopy references: <br>
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| [http://www.microscopyu.com/index.html "MicroscopyU" from Nikon] and [http://micro.magnet.fsu.edu/primer/index.html Molecular Expressions Optical Microscopy Primer]</p>
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| <p><font color=#aa0000>HOMEWORK SET 3.5 [[Media:HW3.5.pdf|(PMT & photon counting)]] due <b>Tuesday, Nov. 7 in class</b>.</font></p></td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 10</b></td>
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| <td width="31%" valign="top">
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| <p><b>[[Media:OpticsLect5.pdf|Tuesday, Nov. 14]]</b><br>
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| Fluorescence microscopy</p>
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| <p><b>[[Media:20.309_MicroRheolLect1.pdf|Thursday, Nov. 16]]</b><br>
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| Active microrheology</p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Nov. 13 - Friday, Nov. 17</b><br>
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| <u>Lab manual for weeks 9-11: [[Media:20.309f06mod3.pdf|Fluorescence microscope construction II]]: Live-cell
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| imaging & microrheology </u></p>
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| </td>
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| <td width="30%" valign="top">
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| <p> </p>
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| <p><font color=#aa0000><b>Thursday, Nov. 16 @ 8:00pm – Room 56-614</b><br>
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| [[20.309:Presentations|Student Presentations]] (Session #3)</font></p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 11</b></td>
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| <td width="31%" valign="top">
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| <p><b>[[Media:20.309_MicroRheolLect2.pdf|Tuesday, Nov. 21]]</b><br>
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| Passive microrheology & Particle tracking</p>
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| <p><i><b>NO LECTURE THURSDAY, NOV. 23<br>
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| (Thanksgiving)</b></i> </p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Nov. 20 - Wednesday, Nov. 24</b><br>
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| <u>Lab manual for weeks 9-11: [[Media:20.309f06mod3.pdf|Fluorescence microscope construction III]]: Actin cytoskeleton imaging</u></p>
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| <p>Papers referenced in the lab manual:<br>
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| The [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Vukusic_BiolPhotStruct_Nature2003.pdf Vukusic paper] on photonic structures <br> and the [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Mason_ViscoelasticModuli_RheolActa2000.pdf Mason] and [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Lau_MicrorheolStress_PRL2003.pdf Lau] papers on microrheology and the complex viscoelastic modulus.</p>
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| <p><b><i>NO LAB THU-FRI</i><br>
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| <i>(Thanksgiving Weekend)</i></b> </p>
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| </td>
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| <td width="30%" valign="top">
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| <p>MATLAB scripts for calculating [[Media:getMSD_BE309.m|MSD]] and [[Media:getGstar_Mason_BE309.m|G*]]</p>
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| <p>Three papers about peacock feathers:<br>
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| – [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Zi_PeacockColor_PNAS2003.pdf Zi, <i>PNAS</i> (2003)]<br>
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| – [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Yoshioka_PeacockMacroStruct_Forma2002.pdf Yoshioka, <i>Forma</i> (2002)]<br>
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| – [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Kinoshita_StructColorsNature_ChemPhysChem2005.pdf Kinoshita, <i>ChemPhysChem</i> (2005)]</p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 12</b></td>
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| <td width="31%" valign="top">
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| <p><b>[[Media:309TrappingLect.pdf|Tuesday, Nov. 28]]</b><br>
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| Optical trapping</p>
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| <p><b>[[Media:20.309_OpticsLect6.pdf|Thursday, Nov. 30]]<br>
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| </b>Advanced fluorescence microscopy</p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Nov. 27 - Wednesday, Nov. 29</b><br>
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| Fluorescence microscope construction/experiments</p>
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| <p><b>Wednesday, Nov. 29 - Friday, Dec. 1</b><br>
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| <u>Lab manual for weeks 12/13: [[Media:20309f06mod4.pdf|Optical Trapping]]</u></p>
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| <p>Preprint of AJP paper by [http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Appleyard_AJPproof.pdf Appleyard ''et al.''] on the 20.309 traps.</p>
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| </td>
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| <td width="30%" valign="top">
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| <p><font color=#aa0000><b>Thursday, Nov. 30 @ 8:00pm – Room 56-614</b><br>
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| [[20.309:Presentations|Student Presentations]] (Session #4)</font></p>
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| </td>
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| </tr>
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| <tr>
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| <td width="5%" valign="top"><b> 13</b></td>
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| <td width="31%" valign="top">
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| <p><b>[[Media:20.309_3DmicroLect1.pdf|Tuesday, Dec. 5]]</b><br>3D microscopy: Confocal imaging</p>
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| <p><b>[[Media:20.309_3DmicroLect2.pdf|Thursday, Dec. 7]]</b><br>3D microscopy: 2-photon microscopy, 3D image processing </p>
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| </td>
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| <td width="34%" valign="top">
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| <p><b>Monday, Dec. 4 - Wednesday Dec. 6</b><br>
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| <u>Lab manual for weeks 12/13: [[Media:20309f06mod4.pdf|Optical Trapping]]</u></p>
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| <p><b>Thursday, Dec. 7 - Friday, Dec. 8</b><br>
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| 3D Imaging & Visualization: two-photon microscopy</p>
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| </td>
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| <td width="30%" valign="top">
| |
| <p><font color=#aa0000>LAB REPORT #3 ([[Media:20.309f06mod3.pdf|Fluorescence Microscope]]) due <b>Monday, Dec. 4, by 12:00 noon.</b></font></p>
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| </td>
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| </tr>
| |
| <tr>
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| <td width="5%" valign="top"><b>14</b></td>
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| <td width="31%" valign="top"><p> <b>Tuesday, Dec. 12</b><br>
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| [[20.309:Presentations|Student presentations]] (Session #5) </p>
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| <p><b>Thursday, Dec. 14</b><br>
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| End-of-Semester Party</p></td>
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| <td width="34%" valign="top"><p><b>Monday, Dec. 11 - Wednesday, Dec. 13</b><br>
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| 3D Image-stack Visualization, ImageJ</p>
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| </td>
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| <td width="30%" valign="top">
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| <p><font color=#aa0000>LAB REPORT #4 ([[Media:20309f06mod4.pdf|Optical Trapping]]) due <b>Monday, Dec. 11, by 12:00 noon.</b></font></p>
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| <p><font color=#aa0000><b>Tuesday, Dec. 12 (in class)</b><br>
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| [[20.309:Presentations|Student presentations]] (Session #5)</font></p>
| |
| </td>
| |
| </tr>
| |
| </table>
| |
| | |
| </div>
| |
