20.309:Course Information

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20.309: Biological Instrumentation and Measurement


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Course meetings

Lecture: T/R 12:00n-1:00pm (4-237)

Recitation: F 12:00n-1:00pm (4-231)

Lab: open scheduling, approximately 6 hours per week (16-352)

Lab hours and scheduling

The lab will be open approximately 40 hour per week. Students are responsible for scheduling sufficient time in the lab to complete assignments before the deadline. Generally, the opening hours will be:

Lab Opening Hours
Monday 10:00 AM - 6:00 PM
Tuesday 1:00 PM - 9:00 PM
Wednesday 1:00 PM - 9:00 PM
Thursday 10:00 AM - 6:00 PM
Friday 10:00 AM - 6:00 PM

You must sign up at least 24 hours before coming to the lab. Use the LAB SIGNUP link above in the title bar.

The lab is located in room 16-352.

Lab attendance is mandatory and there will be no make-up labs.

Lab phone: 617-324-1634


The chief hazards present in the 20.309 Lab come from laser radiation, chemical and biological materials, and electric equipment. Some simple precautions will make your time in the lab much safer.

Get to know the 20.309 Safety Page. Read the safety precautions in each lab manual.

Overview of laboratory modules


DNA Melting Apparatus

Resistive networks, filters, and op-amp circuits for measurement

The first part of the course focuses on electronics. Over a series of labs, we will build several types of commonly used electronic circuits and combine them implement a system for measuring DNA melting curves. This section will also provide an introduction to computer control and data acquisition, including LabVIEW and MATLAB software.

Ultimate limits for force and position detection

Microcantilevers, precision measurement, and thermomechanical noise

Force sensors such as the optical tweezers and atomic force microscope (AFM) provide a unique means for investigating single biomolecules. Examples include the real-time monitoring of enzymatic activity with the optical tweezers and the direct measurement of forces required to unfold individual protein domains with the AFM. At the heart of these force sensors is an ultrasensitive displacement detector that resolves the position of compliant structure (i.e. microcantilever or optically trapped mircobead) with nanometer, or in some cases, sub-nanometer resolution. The performance of the force sensor is determined by the mechanical properties of the structure (spring constant, resonant frequency, damping, etc) and the resolution of the displacement detector. In this lab, we will measure the thermomechanical motion of a microcantilever sensor, estimate its detection limit, and compare to theoretical calculations.


Fluorescence Microscope

Fluorescent microscopy, image processing, and optical traps

Approximately half of the semester is devoted to optical microscopy and imaging. The lectures will cover geometric optics, Fourier optics, and optical instrumentation design, the fundamentals of image processing and 3D microscopy. In the labs, we will build microscopes for white light and fluorescent imaging and apply them to studying cellular mechano-transduction based on particle tracking and immunolabeling. We will also use optical traps for high sensitivity measurements of bacterial flagella torque generation, and get some hands-on experience with two-photon and confocal microscopes.

Lab facilities

Lab stations

There are 8 lab stations in room 16-352. Each station is equipped with:

  1. anti-vibration optical table
  2. analog oscilloscope
  3. triple output power supply
  4. function generator
  5. instrumentation amplifier
  6. toolbox
  7. computer workstation with data acquisition card

Station number 3 is reserved for instructor use at all times.


Lab stations are equipped with PCs running Windows XP. Each PC has a data acquisition card that is connected by a long cable to a signal breakout box at the lab station. MatLab and LabVIEW software are installed on all lab PCs.

Lab PCs are members of the WIN.MIT.EDU domain. Press ctrl-alt-delete to log on. Make sure the Log On To: dropdown menu is set to ATHENA.MIT.EDU (Kerberos Realm). Use your Athena username and password.

The first time you log on, a Windows profile for storing all of your files and settings will be created in your home directory. From then on, your My Documents and Desktop folders will be available on whichever machine you log on to.

Store files in your My Documents folder. Do not keep large files on your desktop. (Use a shortcut to large items instead.) This will dramatically decrease the amount of time it takes to log in. (If you are curious why this is so, see: http://web.mit.edu/win/user_profiles.html.)

Your Windows home directory will be mounted on H:. In addition, your Athena home directory will be mounted on U: and /mit/afs will be mounted on Z:.

IS&T maintains a help page for the WIN domain at http://web.mit.edu/win/help.html.

Course locker

The 20.309 course locker and wiki contain virtually every computer file you will need for the course. To access the locker on an Athena workstation, type attach 20.309 and then cd /mit/20.309. Use the Desktop or Start Menu shortcut to access the locker from any PC in the lab. You can also access the locker with SecureFX.


  • 40%: Lab module assignments

You will work in pairs throughout the semester (and in some cases groups of three), but you will submit individual lab reports. Please see the section on lab reports below. Lab partners must be different for each module with the exception of the project lab.

  • 10%: Class presentation

You will each give a 10 minute presentation on a selected lab module, relevant journal paper, or research experience.

  • 20%: Homework assignments

These will include questions related to lecture material, lab modules, and selected journal articles.

  • 15%: Quizzes

These are intended to help you prepare for the experiment you are performing and will cover key concepts from lectures and lab modules. To prepare, be familiar with the homework and the current lab module. The questions will be straightforward and will take the first 10 minutes of class. It is important to arrive to class on time since the quiz will begin at 12:05 pm. Although there will not be make-up quizzes, your lowest score of the semester will be dropped.

  • 15% Lab performance and overall participation

Your preparation for each lab module is essential as well as participation in lectures and your peer’s presentations.


The lectures are intended to introduce the key concepts behind the labs. An underlying theme throughout all the lectures will be on signals analysis (e.g. Fourier transforms, power spectral density, convolution theorem, etc.) as applied to electrical, mechanical and optical systems.

In some cases, the lectures will be closely related to ongoing lab modules, and in other cases, the lectures will develop material that will be used in a future lab module.


Many of the Friday recitations will be similar to lectures in that new material will be introduced. Occasionally there will be lab demonstrations. The remainder of the recitations will be used for student presentations. In order to make time for each student to give a 10 minute presentation, the class will be split into two groups so that sessions can run in parallel. For last names beginning with A-L, presentations will be in 4-231, and 4-153 will be used for M-Z.


All assignments will be due by 12:05 pm on the days designated in the schedule. Late assignments (those that arrive after 12:05) will not be accepted. Solutions will be posted in afternoon.

You are encouraged to seek advice from the instructors, TAs and other students, however, the work that is turned in must be your own.

We will not accept late assignments for any reason (accept ones that are excused by the Dean’s office). However, we will omit the one lowest homework grade for the calculation of the term homework grade (20%). Students are encouraged to use this to their benefit and to accommodate special situations such as interview travel.

Lab assignment

There are four laboratory sections that require a dedicated assignment: DNA Melting, Ultimate limits of detection, Fluorescent microscopy, and the Project lab. The first three will be similar in form to problem sets (as opposed to formal lab reports) and will focus on presentation, analysis and interpretation of laboratory measurements. Guidelines for the fourth (Project lab) will be announced later in the semester.

It is important that data is presented properly. This includes:

  • Plots must have a brief, informative title. Axes must be labeled with a description, including units, and be legible when printed.
  • Images must have a scale.
  • Use tables appropriately. If a table can be replaced by one or two sentences, do so.
  • Do not use screen captures for line plots and avoid screen captures for images. Instead, plot the data files with your own scripts (using Matlab or your favorite plotting program).


We will have weekly problem sets until the project labs begin. The problem sets are designed to help you solidify concepts presented in lecture and also to prepare for upcoming labs.

Class Presentation

Presentations will be on a research paper (in some cases two related papers) from the list under ‘Student Presentations’. You should look through these papers and enter your name next to paper that interests you the most (edit the wiki page to do this). This should be done by Tuesday, September 23 to avoid being randomly assigned by the instructors. It is also an option to present on your own research experience (e.g. a fruitful UROP) or a paper that is not on the list (but related to the overall themes of 20.309). If you’re interested in this option, make sure to discus this with an instructor before Sept 23.

Your presentation time is 10 minutes and it's very important that you do not go over this time. We will have a few minutes for questions and discussion. It's also important that all non-presenters read the papers carefully before the session as this will make the discussion much more interesting.

Your presentation should provide background to motivate why the research was conducted, describe the key results of the paper (not necessarily all of the results) and the essence of the measurement method, and explain the significance of the results to the general field. Remember that 10 minutes will not be nearly enough time to discuss every aspect of the paper so you will need to identify the most important aspects to include in your presentation.

Make sure to upload a Powerpoint or PDF file of your presentation to the wiki site 12 hours in advance of your presentation so that all files can be launched from a single laptop. Individual laptops will not be allowed since there is no time allotted for connecting between talks.

Feel free to see 20.309 staff outside of class to discuss any questions or ideas that you might have about the paper.