Course Meeting Times

Lectures: 2 sessions / week, 1 hour / session

Labwork: Self-scheduled sessions, 6 to 8 hours / week expected

Course Overview

20.309 is an intensive laboratory that teaches the principles and practices of making quantitative measurements using advanced instrumentation. The field of Biological Engineering employs a broad set of measurement techniques and instruments, and students studying the discipline must develop a strong understanding to use them effectively. Students must know not only how to use these tools, but should learn their underlying physical principles, and how they are designed. The approach of 20.309 is highly hands-on and we believe students learn best by building and doing the experiments in the lab. Lectures provide the broader underpinnings in measurement principles that support the experiments. Topics include light and fluorescence microscopies, electro-mechanical probes, application of statistics, probability, and noise analysis to experimental data, and Fourier techniques.

The course content is organized into modules, each focused on a major piece of apparatus or a group of experiments. In Fall 2006, the four main modules are:

  • Electronics for measuring DNA melting curves
  • Micromechanics and the atomic force microscope
  • Fluorescence optical microscopy
  • Optical trapping

We emphasize design and building – several of the setups, such as the DNA melting experiment and optical microscope are build by students from scratch. Going beyond simply using the instruments provides students with the confidence to "turn the knobs" on these systems to make the types of measurements that modern research requires.





Students must complete several homework assignments. These will include questions related to lecture material, lab modules, and selected journal articles.

Oral Presentations

Five class sessions are devoted to student oral presentations. Each student will each give a 12 minute presentation on a lab module or a journal article of their choice.


Quizzes will be given during lab sessions, and 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.


20.309 is an "open format" lab. Generally, students should aim to sign up for 6-8 hours of lab time per week, which should be enough to accomplish the week's goals. Students are responsible for scheduling their own hours. 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).

Four written reports on the labs will comprise 50% of the course grade. You will be working in pairs throughout the semester, but you will be submitting individual lab reports.

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.


Written reports for lab modules 50%
Oral presentation 15%
Homework assignments 15%
Lab quizzes 10%
Oral participation during lectures, student presentations and laboratory modules 10%


Course Calendar

Part I: Electronics (Instructor - Scott Manalis)
0 0 Course overview, procedures, syllabus, scheduling Lab orientation and tour, safety, introduction to electronics  
1 1-2

Electronics for DNA analysis; dividers, Thevenin's theorem, impedance and loading, RC circuits

RC circuits: transfer functions, Laplace transforms, impedance, RC filters

Lab orientation and tour, safety, introduction to electronics (cont.)

Module 0: introduction to electronics

2 3-4

Feedback: Black's formula, the loop; Op-amps: "Golden Rules" and circuit examples

DNA analysis: SNP detection, chemical equilibrium - K and DeltaG; description of DNA melting lab apparatus

Module 1: measuring DNA melting curves

Part I: build optics for DNA melting experiment, build photodiode readout circuit; calibrate fluorescence signal

Homework 1 due in Lec #4
3 5-6

Fourier series, integrals, Fourier transform (continuous/discrete)

Fourier analysis (cont.)

Evening session: student presentations 1

Module 1: measuring DNA melting curves (cont.)

Part II: complete DNA melting curves apparatus; test perfect-match, all-mismatch, and single-base mismatch DNA strands

Student presentations 1 due
Part II: Mechanics (Instructor - Scott Manalis)


Scanning probe microscopy

Signals, noise, power spectral density

Module 2: atomic force microscope

Part I: AFM alignment and calibration, AFM imaging I

Lab report 1 due one day after Lec #8
5 9 Correlation/convolution, lock-in amplification, linear systems

Module 2: atomic force microscope (cont.)

Part II: AFM imaging II; force spectroscopy

Homework 2 due one day before Lec #9


Equipartition theorem and thermal fluctuations

Student presentations 2

Module 2: atomic force microscope (cont.)

Part III: thermal fluctuations of microcantilevers: Boltzmann's constant experiment

Students presentations 2 due
Part III: Optics (Instructor - Peter So)


Image processing I

Image processing II

Image processing with MATLAB® (linked to homework 3)  


Physical optics and optical instrumentation: detectors, noise

Optical instrumentation: sources, lasers

Optoelectronics: PMT and photon counting (linked to homework 3.5)

Lab report 2 due one day before Lec #14

Homework 3 due one day after Lec #15



Introduction to microscopy: geometric optics, lenses, ray tracing

Interference and diffraction, resolution in microscopy, Fourier optics

Module 3: fluorescence microscope construction

Part I: White light imaging and Fourier optics

Homework 3.5 due in Lec #16
10 18-19

Fluorescence microscopy

Active microrheology

Evening session: student presentations 3

Module 3: fluorescence microscope construction (cont.)

Part II: live-cell imaging and microrheology

Students presentations 3 due
11 20 Passive microrheology and particle tracking

Module 3: fluorescence microscope construction (cont.)

Part III: actin cytoskeleton imaging

12 21-22

Optical trapping [Instructor: Prof. Matt Lang]

Advanced fluorescence microscopy

Evening session: student presentations 4

Module 3: fluorescence microscope construction (cont.) and experiments

Module 4: optical trapping

Student presentations 4 due
13 23-24

3D microscopy: confocal imaging

3D microscopy: two-photon microscopy, 3D image processing

Module 4: optical trapping (cont.)

3D imaging and visualization: two-photon microscopy

Lab report 3 due one day before Lec #23
14 25 Student presentations 5

3D image-stack visualization, imageJ

Lab report 4 due one day before Lec #25

Student presentations 5 due