Fundamental
limits of biological measurement
(BE.481J,
7.86J, MAS.866)
Spring 2005
Instructors: |
Scott Manalis | scottm@media.mit.edu | E15-422 |
| Peter Sorger | psorger@mit.edu | 68-371 | |
Teaching
Assistants: |
Ben Zeskind | zben@mit.edu | WI-639 |
| Craig Forest | cforest@mit.edu | 3-147 | |
Laboratory
Instructor: |
Maxim Shusteff | shusteff@mit.edu | E15-420 |
Location: |
56-154 | Time: |
Tuesday and Thursday, 1 - 2:30 pm |
| Credit
hours: |
3 - 3 - 6 | Prerequisite: |
Graduate or senior undergraduate |
Description:
|
This
course explores the need for quantitative measurement in biology using
particular biological systems as case studies. The class discusses both
conventional and emerging measurement techniques and devices in coordination
with principles of interpretation. Biological topics include apoptosis
signaling and biological networks, and engineering topics include microsystems
and automation, imaging and diffraction. The course introduces the mathematical
and experimental methodologies necessary for quantitative measurement,
such as wave theory, fourier transform, and noise theory. An essential
aspect of measurement emphasized in the course is understanding the physical
limits and interpretation of data obtained with advanced technologies.
Homework assignments aid in helping students to understand the theories
and limitations and enable them to be applied in real biological problems.
At the conclusion of the course, the class uses home-built atomic force
microscopes to explore the principles taught during the course. |
| Feb
1 | |
Systems Biology and Measurement: The Data Drought (Sorger) | |
| Feb
3 | |
Laboratory measurement today: Lab in a room (Sorger) | |
| Feb
8 | |
Laboratory measurement tomorrow: Lab on a chip (Manalis) | |
| Feb
10 | |
Solid-liquid interface: the electrical double layer (Manalis) | |
| Feb
15 | |
Molecular recognition: binding affinity and thermodynamics (Sorger) | |
| Feb
17 | |
Affinity detection: microarray, Elisa, phosphor affinity chromotography (student presentation) | |
| Feb
22 | |
-no class- (Monday schedule) | |
| Feb
24 | |
Measurement in nature I: Physics of chemoreception (Manalis) | |
| March
1 | |
Measurement in nature II: Mammalian signal transduction (Sorger) | |
| Time
Varying Data (Manalis) Measurement in the time and frequency domain |
||
| March
3 | |
Signal analysis I: Fourier transforms | |
| March
8
| |
Signal analysis II: Correlation, convolution, and filters | |
| March
10
| |
Forces and biological systems (student presentations) | |
|
March
15
| |
Noise, mechanical systems, and ultimate limits of position and force detection | |
| March
17
| |
Random processes and the fluctuation dissipation theorem | |
spring
break |
||
| Spatially
Resolved Data (Sorger) |
||
|
March
29
| |
Microscopy and biological systems (student presentations) | |
| March
31
| |
Introduction to imaging, microscopes diffraction | |
| April
5
| |
Diffraction and Fourier approaches to imaging | |
| April
7
| |
Resolution and detectability | |
| April
12 | |
Diffraction methods in biological measurement (student presentations) | |
| April
14 | |
Crystallography and X-Ray Diffraction (Harrison) | |
| April
19 | |
-no class- | |
| April
21 | |
EM and electron diffraction (Harrison) | |
| April
26 | |
5D data-space and time: super-resolution | |
| Force Measurement Laboratory (Manalis) | ||
| April
28 | |
Instrumentation: filters, amplifiers, data acquisition and signal processing | |
|
May
3 | |
Microcantilevers and thermomechanical noise | |
| May
5 | |
Atomic force microscopy: imaging and applications | |
| May
10 | |
Optical trap I: bead manipulation and calibration (Lang) | |
| May
12 | |
Optical trap II: e-coli flagellum (Lang) | |