20.309:Course Information

Course Meetings

Lecture: T/R 12:00n-1:00pm (56-180)

Recitation: F 12:00n-1:00pm (56-162)

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 AM - 9:00 PM
Wednesday	1:00 AM - 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. There will be no make-up labs, except extraordinary circumstances.

Lab phone: 617-324-1634

Safety

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

Electronics

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.

Mechanics

Scanning probe microscopy

We will learn to configure and use "home-built" atomic force microscopes (AFMs) for imaging surfaces with nanometer-scale resolution, conducting sensitive force measurements, and exploring the ultimate detection limits of microcantilevers. Such instruments are essential for investigating the mechanics of single biomolecules, cellular adhesion and modulus, as well as the physical properties of biomaterials. The goal of these labs is to gain hands-on experience with these instruments in the lab and understand the basic principles that they use to achieve exquisite sensitivity.

Optics

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 report guidelines

A report will be due at the end of each lab module. Each lab manual will list requirements for its write-up and give guidelines for the length of the report. Your report should:

• summarize the question(s) you aimed to answer or measurement(s) you made
• summarize what experiments you performed to that end
• detail the collected data and the experimental results
• explain how you interpreted your results, what conclusions you drew and why

Authorship and collaboration

In 20.309, you will usually work with a partner in the lab. However, every student is responsible for writing and submitting his or her own individual lab report. You should always acknowledge the partner with whom you worked. On occasion, you may need to use data collected by someone else, in which case you must acknowledge that you were not the one to collect it.

Other Things to Remember

DO:

1. Follow the Report Requirements section at the end of each lab module.
2. Describe any procedures you followed that were different from what's suggested in the pre-lab handout.
3. Present data concisely and clearly: a series of curves all being compared to each other should all appear on the same graph. A caption or explanation of the graph should make evident the meaning of what's plotted.
4. Label the axes of graphs and the columns of tables. (Include units.)

DON'T:

1. Rehash all the details of the lab procedures if you followed them exactly as described in your pre-lab handout. A short summary is suffcient.
2. Strive for sheer volume of data. If you're including pages of nearly-identical plots, with little discussion of what they mean, something is wrong. A single ¯gure that's well-thought-out is worth a dozen that aren't.

Grading

• 50%: Written reports for lab modules

You will be working in pairs throughout the semester, but you will be submitting individual lab reports.

• 15%: Oral presentation

You will each give a 12 minute presentation on a selected lab module or a relevant journal paper.

• 15%: Homework assignments

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

• 10%: Lab quizzes

These are intended to help you prepare for the experiment you are performing. The questions will be straightforward and should take about 5 minutes before you begin working on each lab.

• 10% Participation during lectures and laboratory modules

Your participation is essential to learning during the semester. This includes attendance at lectures and your peers' presentations.

Lab Report Grading

1. Presentation of Data (10 pts.)
   • all figures have clear purpose, have a figure number and caption, and are discussed in text
   • data plots:
     • appropriately chosen/organized (e.g. curves overlaid or compared, when appropriate, correct scales, etc.)
       
     • axes labeled with quantities/units
       
     • quality of data
   • no "data dumping" or screen captures (unless explicitly specified)
2. Analysis/discussion (10 pts.)
   • demonstrates understanding of key concepts/methods
   • coherent, logical reasoning, clear thought process
   • show key numeric parameters; include important calculations and results
   • appropriate data processing applied, described and justified
   • draw conclusions supported by the data
3. Overall quality (5 pts.)
   • report typed, well-organized, length appropriate say what you need to – not more or less
   • report requirements met
   • sufficient time spent in the lab
   • citation of any material that isn't your own (e.g. things you looked up on the web, in literature; data from others in the class; be sure to list with whom you worked on the lab)

Two examples of excellent lab reports are available here and here.