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Meeting:
Prerequisite:
Credit
Hours:
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Tuesdays
and Thursdays, 1:00 pm- 2:30 pm
56-154 (note room change)
Permission of instructor
3 - 3 - 6
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Introduction
to physical principles that govern the ultimate limits for measuring
force, charge, and optical signals in biological systems. Lecture
material will be motivated by recent experiments in three areas
of biology: detecting single molecule forces, engineering biomolecular
microarrays, and imaging cells with fluorescent probes. Topics include
wave theory, diffraction and imaging, equipartition theorem, dissipative
systems, and noise analysis. Lab modules cover DNA manipulation,
force spectroscopy and single molecule measurements. Parallel introductory
tracks will be offered to accommodate students with both engineering
and biology backgrounds.
In
each case sufficient background material is presented to comprehend
the topic under discussion. The course is intended for graduate
students in physics, engineering, chemistry or biology who are interested
in participating in interdisciplinary research. Grades will be based
on a combination of class presentations, problem sets, and laboratory
notebooks.
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Feb
3 |
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Introduction
and Case Study: DNA Microarrays (Manalis and Sorger) |
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Feb
5 |
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Binding
affinity and thermodynamics (Sorger) |
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Feb
10 |
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The
electrical double layer and electrokinetic transport (Manalis) |
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Feb
12 |
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Surface
functionality and nucleic acid structure (Manalis and Sorger) |
Feb
19 | |
Microarray
applications (student presentations) |
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Foundations
(Parallel tracks) |
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Feb
24 |
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Fourier
Analysis
(Manalis).......................Building
a DNA Microarray (Albeck) |
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Feb
26 |
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Corr,
Conv, and Filters
(Manalis)..............Cell biology (Sorger) |
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March
2 |
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Nano-
and Microfabrication (Manalis)........Genetics
and molecular biology (Sorger) |
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Mechanical
and Electronic Detection (Manalis) |
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March
4 |
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Forces
and biological systems (student presentations) |
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March
9 |
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Noise,
mechanical systems, and ultimate limits of position and force detection |
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March
11 |
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Random
processes and the fluctuation dissipation theorem |
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March
16 |
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Applications
of force detection to nuclear magnetic resonance |
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March
18 |
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Detecting
charge: the single electron transistor |
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March
30 |
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TBA |
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Optical
Sensing and Microscopy (Sorger) |
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April
1 |
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Microscopy
and biological systems (student presentations) |
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April
6
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Introduction
to imaging and microscopes |
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April
8
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Diffraction
and Fourier approaches to imaging |
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April
13|
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Resolution
and detectability |
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Diffraction and Imaging (Sorger) |
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April
15 |
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Diffraction
methods in biological measurement (student presentations) |
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April
22 |
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Current
developments |
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April
27 |
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Crystallography
and X-Ray Diffraction (Harrison) |
April
29 | |
EM
and electron diffraction (Harrison) |
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Measurement
Laboratory (Manalis) |
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May
4 |
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Microcantilever
I: thermomechanical properties |
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May
6 |
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Microcantilever
II: force spectroscopy |
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May
11 |
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Microcantilever
II continued |
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May
13 |
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Lab
presentations |
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