20.309

Announcements

 * For lab demo tomorrow, we will meet on the 2nd floor of NE47 (500 Technology Square) across the street from the McGovern Center (Brain and Cog building). We will divide the class into two groups.  People with last names from A-L, please come at 12:00 and people with last names from M-Z please come at 12:30.
 * Lecture notes for 3D Microscopy II: Multiphoton Microscopy posted.
 * Lecture notes for 3D Microscopy I: Confocal Microscopy posted.
 * Thank you for reminding me that I have forgotten to give you the images to process for the Fourier problem in HW8. They are now posted in MATLAB file format.  I have also included the Perlman paper that I mentioned in the homework and hopefully it makes the last problem clearer.  Good luck.
 * Lecture note for Advanced Fluorescence Microscopy II posted.
 * Lecture note for Advanced Fluorescence Microscopy I posted.
 * Homework 8 posted, due right before Thanksgiving.

Announcement Archives


 * New lab hours:

Course Documents
Documents This includes documents related to psets, quizes, labs, and lectures

Deadlines Update

 * Student presentations Tuesday 11/25
 * PSET #8 DUE Monday, 12/1 at 12:00 PM. No exceptions. (note change ONCE again)
 * Thanksgiving holiday 11/27-28
 * 12/9 will be the last day to work in the lab on your final project
 * Final project poster will be due at 4:59 PM on 12/10
 * Very informal poster session and class party at 5:00 PM on 12/10

Course packet
[[Media:packet.pdf|20.309 course packet]] (schedule, reading assignments, lab modules, and homework: 3.5 MB pdf file)

Readings
Readings for the first half of the course are available in a single (32 MB pdf) file, located in the readings folder of the course locker. The course locker is available on all lab machines, Project Athena machines, and via AFS.

To access the locker from a Project Athena machine, type:  and then.

The full AFS path to the readings folder is:.

You can also download the file directly at this link. The login and password will be provided in lecture.

(Due to copyright restrictions, this file cannot be posted on Openwetware.)

Week 0
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Announcements
November 27, 2007
 * Heejin's MATLAB scripts for calculating [[Media:getMSD_BE309.m|MSD]] and [[Media:getGstar_Mason_BE309.m|G*]]
 * If you are using SimpleTracker, use the commands:

to compute G(&omega;)

November 20, 2007
 * You may find this [[Media:MicroRheologyTutorial.pdf|microrheology tutorial]] useful. But, then again, you may not.
 * A limited number (2) of optical traps will be set up on Monday. With a little luck, all 6 will be set up by Friday.

November 6, 2007
 * Here's a [[Media:microscope.ppt | link]] to the presentation on microscope design that Lissa gave.
 * And here are the fancy pictures that Sergio presented.
 * Here is the best piece of advice you will receive on [[Media:20.309f06mod3.pdf|Lab Module 3]]: design your microscope before you begin constructing it!
 * It is strongly recommended that you:
 * 1) prepare a decent sketch of your design; and
 * 2) run it by Heejin or Jae Won before you begin construction.
 * Heejin and/or Jae Won will be in the lab Tuesday from 3:30-5:30, Wednesday from 3:00-6:00, Thursday from 1:00-6:00, and Friday 1:00-5:00
 * Access the course locker from Athena terminals by typing:  or use SecureFX from a non-Athena computer.

Tuesday

 * Fourier analysis (cont'd)

Thu, Sep. 27

 * Signals, noise, Power Spectral Density

Friday

 * Student presentations (Session #1)

Readings

 * Fourier Transforms.
 * FFT reference material
 * [[Media:20309_tutorial_2.pdf|Tutorial 1: Overview of Fourier Transforms]]
 * [[Media:Sampling_example.pdf|Tutorial 2: Sampling and Aliasing]]
 * Papers for presentations on Friday.

Homework
Homework Set #1 (due 9/25)

Lab

 * Lab manual for DNA Melting (weeks 2-4, due 10/12)
 * DNA thermodynamics: SantaLucia, PNAS 1998.

Tuesday

 * Feedback
 * Black's formula
 * op-amps: "golden rules" and circuit examples

Thursday

 * Fourier series & integrals
 * Fourier transform (continuous & discrete)

Friday

 * Review of ideal elements and circuit modeling
 * Modeling a battery with the ideal elements
 * Real vs. ideal op-amps
 * Ugly op-amp example

Readings

 * Primary: Art of Electronics (Hayes and Horowitz)
 * Supplemental: MIT 6.002 notes
 * [[Media:MatlabIntro.pdf|Matlab Tutorial file 1 (the basics)]]
 * [[Media:MatlabtutorialV2.pdf|Matlab Tutorial file 2 (curve fitting, etc...)]]

Homework
Homework Set #1 (due 9/25)

Lab
Lab manual for DNA Melting (weeks 2-4, due 10/12)

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Old Announcements
Dec. 1: If you are having trouble opening the bead movies on your home computer and need a codec, it can be downloaded from the LEAD Multimedia Website. Select the LEAD MCMP/MJPEG Video Codec on the left column and install with the evaulation version.

Nov. 28: Heejin has provided a solution set for the PMT assignment, as well as a MATLAB script for summing multiple frames for bead tracking.

Nov. 20: New materials posted today include the Image Processing Solutions, MATLAB files for calculating MSD and G*, and three papers on the optical properties of peacock feathers. All are accessible from the Schedule page.

Nov. 7: The [[Media:20.309f06mod3.pdf|Fluorescence Microscope lab manual]] is online.

Oct. 30: [[Media:HW3.5.pdf|The PMT lab/homework handout]] has been posted (see Schedule page). It is another hybrid lab/HW set and will be weighted as half a homework, since it is very short.

Oct. 26: Helpful readings on Image Processing and the slides from Prof. So's lectures are posted on the Schedule Page (see Week 7). In addition, the Presentations Page now has a large selection of papers to choose from for those who have not yet presented.

Oct. 24: Lab report guidelines and grading rubric are posted on the General Info Page. The Lab/Homework on [[Media:HW3.pdf|Image Processing]] is posted.

Oct. 16: A Lab Exercise on [[Media:20309mod2.5.pdf|Sampling and Aliasing]] has been posted, doing which should help with doing some of the AFM experiments.

Oct. 1: [[Media:20309f06mod2.pdf|Lab Module 2: The Atomic Force Microscope]] is now available. It covers three weeks, and is of a rather large size. It's highly advisable to start reading through it early.

Sep. 26: Solutions to Homework Set #1 have been posted.

Sep. 18: [[Media:20.309mod1.pdf|Lab Module 1: Measuring DNA Melting Curves]] has been posted. Please aim to finish the circuit construction and most of the optics assembly by Sep. 22, so that you can spend most of the week of Sep. 25 running melting curves and optimizing your setup.

Sep. 13: Marcio has posted MATLAB tutorial files [[Media:MatlabIntro.pdf|one]] and [[Media:MatlabtutorialV2.pdf|two]] (also available on the Schedule page).

Sep. 11: Pizza Dinner, 6 pm Monday at the 4th floor Stata faculty lunch room. The Stata Pub will be the alternate location.

[[Media:HW1.pdf|HOMEWORK SET 1]] has been posted on the Schedule page, and will be due on Friday, Sep. 22 at 12:00 noon.

Sep. 8: Lab orientation sessions will take place Friday, Sep. 8 from 3pm to 4pm and Monday, Sep. 11 from 9:30am to 10:30am. Attendance at  either one of these is mandatory for all enrolled. Please also read over the [[Media:309LabHandout.pdf|Laboratory Guidelines Document]].

Sep. 6: All students who intend to enroll should email a brief statement of your interest (a few paragraphs) to Prof. Scott Manalis scottm AT media DOT mit DOT edu by 5:00pm on Thursday Sep. 7. You should mention your background and (research) interests, any relevant prior coursework in mechanics, electronics, or optics, why you're interested in 20.309, and what you hope to get out of it.

Aug. 30: The lab schedule this semester will be open-format, meaning that there will be very few fixed lab hours. The lab will be open 9am to 5pm and students will sign up for the lab hours that work for them each week, about a week in advance, so you can plan each week as your schedule permits. Keeping regular lab hours will be a good idea, but you won't be locked into it.

Aug. 28, 2006: All interested students who have not pre-registered yet should contact Lab Instructor Maxim Shusteff, if you have not already done so, and attend the first lecture on Thursday, Sep. 7, 2006 at 12:00noon in 56-180. -->