20.309: Difference between revisions
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==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. | |||
[[Old Announcement| Announcement Archives]] | |||
<!-- | |||
*Lecture notes for Fluorescence Spectroscopy II & III are posted. | |||
*Office Hours Monday from 2:00-4:00 PM to answer questions about PSET #7 | |||
*Lecture note for Fluorescence Spectroscopy I is posted. | |||
*A corrected, updated schedule is posted again: [http://openwetware.org/wiki/Image:Schedule_v6.pdf schedule]. There may be an additional homework 9 for extra credit. | |||
*Lectures notes for ImageProcessing I & II are posted | |||
*Lecture notes for Fluorescence spectroscopy I is posted. | |||
*Note that we have updated the course [http://www.openwetware.org/images/8/84/Schedule_v5.pdf schedule]. | |||
*Lecture Note for Optoelectronics III posted. | |||
*Lecture Note for Optoelectronics II posted. Reminder: Quiz tomorrow (focus only on Optics & Microscopy lectures) | |||
*Lecture Note for Optoelectronics I posted. Homework 7 posted. | |||
*Fluorescence microscopy starts today. This week: build your microscope and characterize the white light path. | |||
*'''Preliminary''' lab manual for fluorescence microscopy is [http://scripts.mit.edu/~20.309/wiki/index.php?title=20.309/Labs/Fluorescence_Optical_Microscope here]. Please note there will be changes. | |||
*Lecture Note for Optics & Microscopy IV is now online. Please note that there will be a quiz tomorrow. | |||
*Lecture Note for Optics & Microscopy III is now online. | |||
*Lecture Notes for Optics & Microscopy I & II and Problem Set #6 are now online. Due to some posting problems, Problem Set #6 is due on October 28. See updated schedule. | |||
*Problem Set #5 will be extended to October 24, part (e): 10ms (not 10us) | |||
*[[Media:Thermal Noise Lecture.pdf|DNA melting report and thermal noise lab slides from Friday 10/04 lecture]] | |||
*DNA data analysis slides from Tuesday 9/30 lecture are now posted [[Media:DNA Analysis Advice v2.pdf|here]] | |||
*Slides for Friday 9/26 lecture are now posted [[Media:Sampling Lecture.pdf|here]] | |||
*Sign up for your presentation (with [[20.309:Presentations|this link]]) by September 23 to avoid being randomly assigned. | |||
*[[20.309:Updates for DNA Melting Module|Updates for the DNA melting module]] | |||
--> | |||
*New lab hours: | |||
{| class="wikitable" border="1" style="margin: 1em auto 1em auto" | |||
|+'''Lab Opening Hours''' | |||
|- | |||
|Monday||10:00-7:00 | |||
|- | |||
|Tuesday||1:00-11:00 | |||
|- | |||
|Wednesday||10:00-9:00 | |||
|- | |||
|Thursday||1:00-9:00 | |||
|- | |||
|Friday||1:00-7:00 | |||
|} | |||
==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 and readings== | |||
===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: <code>attach 20.309</code> and then <code>cd ~20.309</code>. | |||
The full AFS path to the readings folder is: <code>\\afs\athena.mit.edu\course\20\20.30\Students\Readings</code>. | |||
You can also download the file directly at [http://www.media.mit.edu/nanoscale/courses/BE309/private/reading.pdf this link]. The login and password will be provided in lecture. | |||
(Due to copyright restrictions, this file cannot be posted on Openwetware.) | |||
==This Week== | |||
{{Template:20.309Week | |||
|StartDate=10/6 | |||
|EndDate=10/10 | |||
|Lecture1=Mechanical Systems | |||
|Lecture2=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_15.pdf Ultimate limits of force and position detection] | |||
|Recitation=[[20.309:Presentations|Student Presentations]] | |||
|Optional reading= | |||
|Lab= | |||
*DNA Melting lab | |||
|Homework= | |||
*Homework #5 due on Oct 24 at noon | |||
|Lab= | |||
*Module 2: Thermal noise measurement | |||
}} | |||
==Week 4== | |||
{{Template:20.309Week | |||
|StartDate=9/29 | |||
|EndDate=10/3 | |||
|Lecture1=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_9.pdf Convolution] | |||
|Lecture2=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_10.pdf Application of Convolution Theorem] | |||
|Recitation=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_dna.pdf Lab 1 Requirements and Intro to Lab 2] | |||
|Optional reading= | |||
|Lab= | |||
*DNA Melting lab | |||
|Homework= | |||
*Homework #4 due on Oct 7 [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw4.pdf SOLUTIONS] | |||
|Lab= | |||
*Module 1: [[20.309:Measuring_DNA_Melting_Curves|DNA Melting Lab]] FINAL WEEK | |||
}} | |||
==Week 3== | |||
{{Template:20.309Week | |||
|StartDate=9/15 | |||
|EndDate=9/20 | |||
|Lecture1=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_8.pdf Intro to Fourier Analysis] [http://www.media.mit.edu/nanoscale/courses/BE309/private/quizzes/quiz_2_sol.pdf Quiz #2 Solutions] | |||
|Lecture2=Power Spectral Density, Noise and Bandwidth (blackboard) | |||
|Recitation=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/samp.pdf Sampling and Discrete Analysis] | |||
|Optional reading= | |||
|Lab= | |||
*DNA Melting lab | |||
|Homework= | |||
*Homework #3 due on Sept 30 [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw3.pdf SOLUTIONS] | |||
|Lab= | |||
*Module 1: [[20.309:Measuring_DNA_Melting_Curves|DNA Melting Lab]] | |||
}} | |||
==Week 2== | |||
{{Template:20.309Week | |||
|StartDate=9/15 | |||
|EndDate=9/20 | |||
|Lecture1=Op-amps and negative feedback (blackboard) [http://www.media.mit.edu/nanoscale/courses/BE309/private/quizzes/quiz_1_sol.pdf Quiz #1 Solutions] | |||
|Lecture2=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_7.pdf Op-amp applications] | |||
|Recitation=The reality of op-amps | |||
|Optional reading= | |||
|Lab= | |||
*DNA Melting lab | |||
|Homework= | |||
*Homework #2 due on Sept 23 [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw2.pdf SOLUTIONS] | |||
|Lab= | |||
*Module 1: [[20.309:Measuring_DNA_Melting_Curves|DNA Melting Lab]] | |||
}} | |||
==Week 1== | |||
{{Template:20.309Week | |||
|StartDate=9/8 | |||
|EndDate=9/12 | |||
|Lecture1=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_3.pdf RC Circuits] | |||
|Lecture2=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_4.pdf Filters] | |||
|Recitation=[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_5.pdf Thermodynamics of DNA melting] | |||
|Optional reading= | |||
*[[20.309:DiodePrimer|Introduction to diodes]] | |||
|Lab= | |||
*Lab opens 9/8 | |||
|Homework= | |||
*[[20.309:Homeworks/Homework1|Homework #1]] (also available in the course [[Media:packet.pdf|PDF file]]) [http://www.media.mit.edu/nanoscale/courses/BE309/private/hw/hw1.pdf SOLUTIONS] | |||
|Lab= | |||
*Module 0: Introduction to Electronics | |||
}} | |||
==Week 0== | |||
{{Template:20.309Week | |||
|StartDate=9/4 | |||
|EndDate=9/5 | |||
|Lecture2= | |||
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/Lecture_1_intro.pdf Course overview] | |||
|Recitation= | |||
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/lect08/lect_2.pdf Voltage dividers and electrical impedance] | |||
|Lab= | |||
*Lab opens 9/8 | |||
}} | |||
<!-- | |||
{| width="100%" | {| width="100%" | ||
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==Announcements== | ==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: | |||
<code> | |||
dlmwrite('subtracted_traj_sum30.txt',1E6*[differentialTrajectoryX;differentialTrajectoryY]','\t') | |||
GetMSD_BE309 | |||
GetGstar_Mason_BE309 | |||
</code> | |||
to compute G(ω) | |||
'''November 20, 2007''' | '''November 20, 2007''' | ||
*You may find this [[Media:MicroRheologyTutorial.pdf|microrheology tutorial]] useful. But, then again, you may not. | *You may find this [[Media:MicroRheologyTutorial.pdf|microrheology tutorial]] useful. But, then again, you may not. | ||
Line 15: | Line 202: | ||
'''November 6, 2007''' | '''November 6, 2007''' | ||
*Here's a [[Media:microscope.ppt | link]] to the presentation | *Here's a [[Media:microscope.ppt | link]] to the presentation on microscope design that Lissa gave. | ||
*And here are the [[20.309:assembly|pictures]] | *And here are the [[20.309:assembly|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! | *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: | *It is ''strongly recommended'' that you: | ||
Line 35: | Line 222: | ||
*Thanksgiving holiday | *Thanksgiving holiday | ||
|Readings= | |Readings= | ||
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Vukusic_BiolPhotStruct_Nature2003.pdf Vukusic paper] on photonic structures | |||
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Mason_ViscoelasticModuli_RheolActa2000.pdf Mason paper] | |||
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/papers/Lau_MicrorheolStress_PRL2003.pdf Lau] paper on microrheology and the complex viscoelastic modulus | |||
|Lab= | |Lab= | ||
*[[Media:20.309f06mod3.pdf|Building Fluorescence Microscopes]] week 3 | *[[Media:20.309f06mod3.pdf|Building Fluorescence Microscopes]] week 3 | ||
Line 41: | Line 231: | ||
}} | }} | ||
==Next | ==Next week== | ||
{{Template:20.309Week | {{Template:20.309Week | ||
|StartDate=11/26 | |StartDate=11/26 | ||
Line 53: | Line 243: | ||
*Student presentations | *Student presentations | ||
|Readings= | |Readings= | ||
*[http://scitation.aip.org/journals/doc/AJPIAS-ft/vol_75/iss_1/5_1.html Appleyard] paper on the 20.309 optical traps | |||
*[[Optical_Trap|Optical trap wiki page]] | |||
|Lab= | |||
*Complete [[Media:20.309f06mod3.pdf|fluorescence microscopy]] by Wednesday | |||
*Begin [[20.309/Labs/Optical trapping|optical trapping]] | |||
}} | |||
==Week after next== | |||
{{Template:20.309Week | |||
|StartDate=12/4 | |||
|EndDate=12/9 | |||
|Lecture1= | |||
*Confocal microscopy | |||
|Lecture2= | |||
*Two photon microscopy | |||
|Recitation= | |||
*Student presentations | |||
|Readings= | |||
*[http://scitation.aip.org/journals/doc/AJPIAS-ft/vol_75/iss_1/5_1.html Appleyard] paper on the 20.309 optical traps | |||
*[[Optical_Trap|Optical trap wiki page]] | |||
|Lab= | |Lab= | ||
*Complete [[Media:20.309f06mod3.pdf|fluorescence microscopy]] by Wednesday | *Complete [[Media:20.309f06mod3.pdf|fluorescence microscopy]] by Wednesday | ||
Line 271: | Line 481: | ||
[[20.309:Measuring DNA Melting Curves|Lab manual for DNA Melting]] (weeks 2-4, due 10/12) | [[20.309:Measuring DNA Melting Curves|Lab manual for DNA Melting]] (weeks 2-4, due 10/12) | ||
--> | |||
<!-- | <!-- | ||
<div style="color: #aaaaaa;"> | <div style="color: #aaaaaa;"> |
Latest revision as of 14:34, 4 December 2008
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.
- New lab hours:
Monday | 10:00-7:00 |
Tuesday | 1:00-11:00 |
Wednesday | 10:00-9:00 |
Thursday | 1:00-9:00 |
Friday | 1:00-7:00 |
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 and readings
Course packet
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: attach 20.309
and then cd ~20.309
.
The full AFS path to the readings folder is: \\afs\athena.mit.edu\course\20\20.30\Students\Readings
.
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.)
This Week
10/6-10/10 | |
---|---|
Lecture & Recitation | |
Tuesday |
Mechanical Systems |
Thursday | |
Friday | |
Optional reading | |
Homework | |
| |
Lab | |
|
Week 4
9/29-10/3 | |
---|---|
Lecture & Recitation | |
Tuesday | |
Thursday | |
Friday | |
Optional reading | |
Homework | |
| |
Lab | |
|
Week 3
9/15-9/20 | |
---|---|
Lecture & Recitation | |
Tuesday | |
Thursday |
Power Spectral Density, Noise and Bandwidth (blackboard) |
Friday | |
Optional reading | |
Homework | |
| |
Lab | |
|
Week 2
9/15-9/20 | |
---|---|
Lecture & Recitation | |
Tuesday |
Op-amps and negative feedback (blackboard) Quiz #1 Solutions |
Thursday | |
Friday |
The reality of op-amps |
Optional reading | |
Homework | |
| |
Lab | |
|
Week 1
9/8-9/12 | |
---|---|
Lecture & Recitation | |
Tuesday | |
Thursday | |
Friday | |
Optional reading | |
Homework | |
| |
Lab | |
|
Week 0
9/4-9/5 | |
---|---|
Lecture & Recitation | |
Tuesday |
|
Thursday | |
Friday | |
Optional reading | |
| |
Homework | |
| |
Lab | |
|