Fall 2006
Physics G731: Biological Physics
| Class meetings: | 10:00-11:40
MW
325 Churchill |
| Instructor:
Office: |
Prof. J. Timothy Sage
106 Dana I am generally available when I am in my office. However, you
can count on finding me during "official" office hours. |
| Grader:
Office: |
Dr.
Alexander
Barabanschikov
358 Egan |
This course is intended to reduce the barrier that many physicists
encounter
when they first move into biological science. Some of you are
considering
pursuing thesis research in this area, and I hope that this course will
help you to make an informed decision. Those of you who specialize in
other areas for your
Ph. D. may spend part of your later career working on biological or
medical
problems.
At the end of the semester, I expect you to be able to
No single textbook covers the full range of topics for
this course. I will distribute my own notes for part of the course, and
recommend the following sources for excellent coverage of certain
topics. I recommend that you refer to relevant portions of the
Frauenfelder notes throughout the course, and obtain one of the
other books. I have requested that the library place the Daune and
Nelson
books on reserve.
Hans Frauenfelder, Physics of Proteins,
unpublished lecture notes available online.
These are notes for a course Hans Frauenfelder taught periodically
before his retirement from the
University of Illinois in 1992. These notes date
well because they emphasize physical fundamentals. They provide better
coverage of experimental topics than the books listed below, but less
on mathematical modelling. Coverage of nucleic acids is limited. There
are some typos and missing
chapters,
but the target audience is the same as this course: readers looking to
apply a background in physics to important problems in biology.
Michel Daune, Molecular
Biophysics: Structure in Motion,
(Oxford University Press, 1999).
This is a good complement to the Frauenfelder notes. Although
slightly dated (the original French version was published in 1993),
there is considerably more coverage of nucleic acids and polymer
physics. This book provides more detail on biomolecular structure than
the other texts listed here.
Phillip Nelson, Biological Physics: Energy, Information Life, (W. H. Freeman, 2003).
This is an excellent, physically motivated textbook, but is written at an undergraduate level. As a result, it spends significant time introducing ideas that should already be familiar to graduate students in physics. For example, I will use relevant ideas from statistical physics, such as Gibbs' free energy and Boltzmann factors, and you can refer to Nelson's book if you feel that you need a more detailed review than what I present in class. Kim Sneppen and Giovanni
Zocchi, Physics in Molecular
Biology, (Cambridge
University Press, 2005).
Basic topics in statistical physics and molecular biology selected
to build up to more specialized discussions of molecular motors,
genetic regulation, protein networks and evolution. Although the focus
is narrower than the above books, I find this book unusually readable
because of the concise presentation, coupled to example exercises
(absent in Frauenfelder and Daune) and references for further reading.
You can find much more extensive coverage of biological and
biochemical topics than will be presented in this course in several
books that are available online at the NCBI
Bookshelf at the NIH. These virtual textbooks are excellent
resources as references, but you may want to purchase the actual
textbook if you plan to read large sections. The following are
particularly relevant to this class:
Alberts, Bruce; Johnson,
Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter. Molecular Biology of the Cell, (Garland Science, 2002).
Berg, Jeremy M.; Tymoczko, John
L.; and Stryer, Lubert. Biochemistry, (W.
H. Freeman, 2002).
Brown, T.A. Genomes,
(Garland Science, 2002).
Problem sets will be distributed throughout the semester (no more
than
once a week).
Assignment 1 (due September 20)
Assignment
2 (due September 27)--partial
solution
Assignment
3 (due October 4)
Assignment
4 (due October 11)
Assignment
5 (due October 18)--partial
solution
Assignment
6 (due October 27)
Assignment
7 (due November 10)--with associated files Lovell7.jpg
and ramassgt.pdb
Assignment
8 (due November 17)
Assignment
9 (due November 29)
Assignment
10 (due December 8)
Assignment
11 (due December 13)
Your grade will be determined by homework problems, exams, and, if you
choose,
presentation
of a short paper summarizing a topic of current research in biological
physics. You will choose between two options for the detailed breakdown
of your
grade:
| Homework |
|
| Midterm exam |
|
| Final exam |
|
| Homework (drop two) |
|
| Midterm exam |
|
| Research presentation |
|
In track II, a substantial element of your course grade
will be a report on a specific topic of current research in biological
physics. The topic of the research presentation is to be chosen by you,
with
the approval of the instructor. I will post some possible
topics, but
you are encouraged to suggest your own.
In addition, I expect regular attendance and participation in class
meetings--poor
attendance can lower your grade.
Cellular Organization and Biological Macromolecules
Basic Physics at the Cellular and Molecular Level
------->What makes "soft" matter soft?
Molecular Interactions and Macromolecular Structure
------->How do complex biomolecules self-assemble?
Physical Techniques
------->Where are the atoms, and when?
Biomolecular Dynamics
------->How does the machinery work?
