20.309:Course Information

General Lab Guidelines

20.309 is an "open format" lab. The lab is open Mon-Fri from 9:00am to 5:00pm, and students are responsible for scheduling their own hours, enough to complete the necessary assignments. Instructors and TAs will always be present in the lab, but will only be available to answer questions and help you work on your experiments during scheduled hours. (However, if an emergency arises or an injury occurs, get an instructor's attention immediately).

Use the "LAB SIGNUP" link above in the title bar to go to the signup schedules.

Please also read this Lab Guidelines Document regarding safety, lab notebooks, and other issues.

Lab attendance is mandatory and there are no make-up labs. A family crisis or severe illness requiring attention from the infirmary and prohibiting you from all your coursework are acceptable reasons for missing lab. In these exceptional circumstances, every effort will be made to accommodate you.

Lab Grading Rubric

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)

1. 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

1. 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)

Overview of Laboratory Modules

Electronics

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

During the first part of the course we will focus 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.

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. You

• 10%: Oral participation during lectures and laboratory modules

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