20.309J / 2.673J
Laboratory Fundamentals in Biological Engineering II:
Biological Instrumentation and Measurement

Click here for the most updated course information and the Fall 2006 course website.


Laboratory Instructor:



Scott Manalis and Peter So

Maxim Shusteff

2 - 7 - 3

18.03 or Permission of Instructor

Enrollment will be limited to 15-20 students.

Description 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.


Questions and Answers

  • Is enrollment limited?
  • At this time the 20.309 lab can accommodate approx. 15-20 students. The final class size and composition will be determined by the course instructors during the first week of class, with the intention of optimally matching student interests, background, and expectations to the course.

  • How do to sign up for 20.309?
  • You will be able to pre-register for this subject during the spring semester. It will also be helpful to sign up for our mailing list, to receive news and information about scheduling, enrollment, course content, etc. Please e-mail Lab Instructor to be placed on this list.

  • How does 20.309 compare to 20.109?
  • These two subjects are very complementary. 20.109 introduces the fundamentals of "wet" biological engineering laboratory techniques, with a particular focus on manipulating nucleic acid and protein systems. 20.309 emphasizes the "dry" side of BE, building a background in signals, instrumentation, and measurement techniques that are key to modern biological research.

  • Isn't designing and building instruments done by electrical and mechanical engineers?
  • There are many examples in biological research today that requires an understanding of the measurement instruments that are used, and many biologists and engineers who work in bio-applications build and modify their own instruments.

  • How much work is this class really?
  • Since this is a laboratory course, most of your time will be spent working on lab assignments, which are designed to be completed in about 6-8 hrs per week. In Fall 2006, we are implementing a new open lab format, in which students will have the ability to schedule their own hours in the lab, giving them the flexibility to work at their own pace. Instructors will schedule "lab hours" (similar to office hours) each week to provide help and guidance.
    Periodic lab reports will need to be submitted about your experiments.

Please feel free to contact , the 20.309 Lab Instructor, with any questions that have not been answered here.