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==Announcements==


'''Lab phone:''' 617-324-1634
*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.




<font color=#aa0000>'''CURRENT QUIZ: #6'''</font>
[[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%"
|-bgcolor="#FF8888" align="center"
|'''Lab Report #3 is Due 12/4'''
|}


==Announcements==
==Announcements==
'''Nov. 20:''' New materials posted today include the [[Media:ImgProcSolns.zip|Image Processing Solutions]], MATLAB files for calculating  [[Media:getMSD_BE309.m|MSD]] and [[Media:getGstar_Mason_BE309.m|G*]], and three papers on the optical properties of peacock feathers. All are accessible from the [[20.309:Schedule|Schedule]] page.
'''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(&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 [[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!
*It is ''strongly recommended'' that you:
#prepare a decent sketch of your design; and
#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: <code>attach 20.309; cd /mit/20.309/Students</code> or use [http://itinfo.mit.edu/product.php?name=securefx&platform=Windows SecureFX] from a non-Athena computer.
 
==This Week==
{{Template:20.309Week
|StartDate=11/19
|EndDate=11/23
|Lecture1=
*Steve forgets to give lecture on optical traps. Best lecture of the year.
|Lecture2=
*Thanksgiving holiday. (Second best lecture of the year.)
|Recitation=
*Thanksgiving holiday
|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=
*[[Media:20.309f06mod3.pdf|Building Fluorescence Microscopes]] week 3
*Actin imaging
*Microrheology
}}
 
==Next week==
{{Template:20.309Week
|StartDate=11/26
|EndDate=11/30
|Lecture1=
*Fourier optics
|Lecture2=
*Fourier optics lecture 2
*Fourier optics demo
|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=
*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=
*Complete [[Media:20.309f06mod3.pdf|fluorescence microscopy]] by Wednesday
*Begin [[20.309/Labs/Optical trapping|optical trapping]]
}}
 
==Week 10==
{{Template:20.309Week
|StartDate=11/12
|EndDate=11/16
|Lecture1=
*Microrheology and particle tracking
|Lecture2=
*Optical trapping (Professor Lang guest lecture)
|Recitation=
*Student Presentations
|Readings=
*[http://www.microscopyu.com/index.html "MicroscopyU" from Nikon]
*[http://micro.magnet.fsu.edu/primer/index.html Molecular Expressions Optical Microscopy Primer]
|Lab=
*[[Media:20.309f06mod3.pdf|Building Fluorescence Microscopes]] week 2
*Complete construction
*Fluorescence
*Live cell imaging
*Particle tracking
}}
 
==Week 9==
{{Template:20.309Week
|StartDate=11/5
|EndDate=11/9
|Lecture1=
*Fluorescence spectroscopy & microscopy
|Lecture2=
*Advanced fluorescence microscopy
|Recitation=
*[[20.309:Presentations#Nov_9:_Optical_Microscopy:_Biomechanics|Student presentations]]
|Readings=
From Gonzalez & Woods:
*[[Media:20.309_ImProcLect2_supp.pdf|Supplementary slides to image processing lectures]]
*[http://www.mathworks.com/company/newsletters/digest/sept01/matrix.html Matlab Matrix Indexing Tutorial]
*[http://www.microscopyu.com/index.html Nikon "MicroscopyU"]
*[http://micro.magnet.fsu.edu/primer/index.html Molecular Expressions Optical Microscopy Primer]
|Homework=
[[20.309:Homeworks/Homework 3|Homework #3]] due Tuesday
|Lab=
*[[Media:20.309f06mod3.pdf|Building Fluorescence Microscopes]] week 1
*Microscope construction
*White light imaging
*Alignment
*Resolution
}}
 
==Week 8==
{{Template:20.309Week
|StartDate=10/29
|EndDate=11/2
|Lecture1=
*Geometric optics
*Ray tracing
*Optical microscopy
|Lecture2=
*Optical microscopy
*[[20.309:Presentations#Nov_2:_Optical_Microscopy:_Imaging|Student presentation]]
|Recitation=
*[[20.309:Presentations#Nov_2:_Optical_Microscopy:_Imaging|Student presentations]]
*Fluorescence microscope design review presentations
|Readings=
From Gonzalez & Woods:
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh4.pdf Chapter 4]: histograms, contrast, spatial filtering
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh8.pdf Chapter 8]: morphological operations
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh7.pdf Chapter 7]: segmentation
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/GonzalezWoodsCh9.pdf Chapter 9]: recognition & interpretation
|Homework=
[[20.309:Homeworks/Homework 3|Homework #3]]
}}
 
==Week 7==
{{Template:20.309Week
|StartDate=10/22
|EndDate=10/27
|Lecture1=
*[[Media:20.309_ImProcLect2.pdf|Image processing II]]
|Lecture2=
*Optical Instruments I: Physics, Noises, Detectors
|Recitation=
*Optical Instruments II: Detectors, Lamps, Lasers
|Readings=
*[[Media:20.309_ImProcLect2_supp.pdf|Supplementary slides to image processing lectures]]
*[http://www.mathworks.com/company/newsletters/digest/sept01/matrix.html Matlab Matrix Indexing Tutorial]
*[http://www.microscopyu.com/index.html Nikon "MicroscopyU"]
*[http://micro.magnet.fsu.edu/primer/index.html Molecular Expressions Optical Microscopy Primer]
|Lab=
*Complete [[Media:20309f06mod2.pdf|Atomic Force Microscopy]] lab
}}
 
==Week 6==
{{Template:20.309Week
|StartDate=10/15
|EndDate=10/19
|Lecture1=
*Atomic force microscopy
|Lecture2=
*Image processing
|Recitation=
*MANDATORY: Laser safety training
*Image processing in MatLAB
|Readings=
*Atomic force microscopy [[Media:20309f06mod2.pdf|lab manual]]
|Lab=
*AFM alignment and calibration
*AFM thermal noise measurement
|Homework=[[Media:20309HW2.pdf|Homework Set #2]] (due 10/18 at lecture)
}}
 
==Week 5==
{{Template:20.309Week
|StartDate=10/8
|EndDate=10/12
|Lecture1=
*No lecture (holiday)
|Lecture2=
*Equipartition theorem and thermal fluctuations
|Recitation=
*Scanning probe microscopy student [[20.309:Presentations#Oct_12:_Scanning_probe_microscopy_I|presentations]]
|Readings=
*Atomic force microscopy [[Media:20309f06mod2.pdf|lab manual]]
|Lab=
*DNA Melting lab report due
*AFM alignment and calibration
*AFM imaging I
|Homework=[[Media:20309HW2.pdf|Homework Set #2]] (due 10/18 at lecture)
}}
 
==Week 4==
{{Template:20.309Week
|StartDate=10/1
|EndDate=10/5
|Lecture1=
*PSD and signal-to-noise
*Convolution
|Lecture2=
*Convolution Theorem
*Application to lock-in detection
|Recitation=
*Introduction to AFM lab module
|Readings=
*One-page handout: [[Media:convclar.pdf| convolution clarification examples]]
*[http://www.dsptutor.freeuk.com/analyser/guidance.html#leakage Spectral leakage]
*[[20.309:Presentations#Oct_12:_Scanning_probe_microscopy_I|Papers]] for presentation 10/12
|Homework=
*[[Media:20309HW2.pdf|Homework Set #2]] (due 10/16)
|Lab=
*Complete [[20.309:Measuring_DNA_Melting_Curves|DNA melting]] experiment
}}
 
==Week 3(9/25-9/28)==
===Lecture & recitation===
 
====Tuesday====
*Fourier analysis (cont'd)
 
====Thu, Sep. 27====
*Signals, noise, Power Spectral Density
 
====Friday====
*[[20.309:Presentations#Sept_28:_Nucleic_acid_technologies|Student presentations (Session #1)]]
 
===Readings===
 
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/strang.pdf Fourier Transforms.]
*[http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/FFTreference.pdf FFT reference material]
*[[Media:20309_tutorial_2.pdf|Tutorial 1: Overview of Fourier Transforms]]
*[[Media:Sampling_example.pdf|Tutorial 2: Sampling and Aliasing]]
*[[20.309:Presentations#Sept_28:_Nucleic_acid_technologies|Papers]] for presentations on Friday.
 
===Homework===
 
<font color=#aa0000>[[20.309:Homeworks/Homework1|Homework Set #1]] (due 9/25)</font>
 
 
===Lab===
 
*[[20.309:Measuring DNA Melting Curves|Lab manual for DNA Melting]] (weeks 2-4, due 10/12)
*DNA thermodynamics: [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/20.309_DNAmelt_PNAS_1998.pdf SantaLucia, PNAS 1998.]
 
==Week 2 (9/17-9/21)==
===Lecture & recitation===
 
====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: [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/lect_4_horowitz_opamp.pdf Art of Electronics (Hayes and Horowitz)]
*Supplemental: [http://www.media.mit.edu/nanoscale/courses/BE309/private/readings/lect_4_6002.pdf MIT 6.002 notes]
*[[Media:MatlabIntro.pdf|Matlab Tutorial file 1 (the basics)]]
*[[Media:MatlabtutorialV2.pdf|Matlab Tutorial file 2 (curve fitting, etc...)]]
 
===Homework===
 
<font color=#aa0000>[[20.309:Homeworks/Homework1|Homework Set #1]] (due 9/25)</font>
 
===Lab===
 
[[20.309:Measuring DNA Melting Curves|Lab manual for DNA Melting]] (weeks 2-4, due 10/12)


'''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 [[20.309:Schedule|Schedule]] page).  It is another hybrid lab/HW set and will be weighted as half a homework, since it is very short.


-->
<!--
<div style="color: #aaaaaa;">
<div style="color: #aaaaaa;">


=== Old Announcements ===
== 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 [http://www.leadcodecs.com/Download/eval.htm 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 [[20.309:Schedule|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 [[20.309:Schedule|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 [[20.309:Presentations|Presentations]] Page now has a large selection of papers to choose from for those who have not yet presented.
'''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 [[20.309:Presentations|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 [[20.309:Overview|General Info]] Page.  The Lab/Homework on [[Media:HW3.pdf|Image Processing]] is posted.  
'''Oct. 24:''' Lab report guidelines and grading rubric are posted on the [[20.309:Overview|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. 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.
Line 27: Line 507:
'''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.
'''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:''' [[Media:hw1sol.pdf|Solutions]] to Homework Set #1 have been posted.
'''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. 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.
Line 45: Line 525:
'''Aug. 28, 2006:''' All interested students who have not pre-registered yet should contact Lab Instructor [[User:Shusteff | 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.
'''Aug. 28, 2006:''' All interested students who have not pre-registered yet should contact Lab Instructor [[User:Shusteff | 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.
</div>
</div>
 
-->
==Welcome==
'''20.309J/2.673J: Biological Engineering II: Biological Instrumentation and Measurement'''<br>
'''Fall 2006'''
 
'''Units:''' 2-7-3
 
'''Lecture:'''  T/R 12:00n-1:00pm (56-180)
 
'''Lab:''' 16-352 (open scheduling)

Latest revision as of 14:34, 4 December 2008

20.309: Biological Instrumentation and Measurement

Home        Course Information        Schedule        People        Student Presentations        LAB SIGNUP       


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:
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

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

Ultimate limits of force and position detection

Friday

Student Presentations

Optional reading
Homework
  • Homework #5 due on Oct 24 at noon
Lab
  • Module 2: Thermal noise measurement

Week 4

9/29-10/3
Lecture & Recitation
Tuesday

Convolution

Thursday

Application of Convolution Theorem

Friday

Lab 1 Requirements and Intro to Lab 2

Optional reading
Homework
Lab

Week 3

9/15-9/20
Lecture & Recitation
Tuesday

Intro to Fourier Analysis Quiz #2 Solutions

Thursday

Power Spectral Density, Noise and Bandwidth (blackboard)

Friday

Sampling and Discrete Analysis

Optional reading
Homework
Lab

Week 2

9/15-9/20
Lecture & Recitation
Tuesday

Op-amps and negative feedback (blackboard) Quiz #1 Solutions

Thursday

Op-amp applications

Friday

The reality of op-amps

Optional reading
Homework
Lab

Week 1

9/8-9/12
Lecture & Recitation
Tuesday

RC Circuits

Thursday

Filters

Friday

Thermodynamics of DNA melting

Optional reading
Homework
Lab
  • Module 0: Introduction to Electronics

Week 0

9/4-9/5
Lecture & Recitation
Tuesday
  • No lecture
Thursday
Friday
Optional reading
  • No optional readings this week
Homework
  • None assigned
Lab
  • Lab opens 9/8



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