Fall 2007
Physics G731: Biological Physics
| Class meetings: | 10:00-11:40
MW 325 CH
|
| 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:
|
Michael
Holmes
|
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
Some recommended texts are listed below. Although no single textbook
covers the full range of topics for
this course, the textbooks by Daune and by Serdyuk et al. provide the closest match
in terms of level and style. I have asked the bookstore to stock these
two, and
also requested that the library place one copy of each on reserve. In
addition, I recommend that you refer to relevant portions of the
Frauenfelder notes (free online) throughout the semester. I will
distribute my own notes for some parts of the course, and
can recommend all of the following sources for excellent coverage of
certain
topics.
Michel Daune, Molecular
Biophysics: Structure in Motion,
(Oxford University Press, 1999).
Although
slightly dated (the original French version was published in 1993),
this book provides reasonably broad coverage of physical concepts
relevant to the study of biological macromolecules. Its strengths and
weaknesses largely complement either the online Frauenfelder notes or
the new Serdyuk et al. text.
Although coverage of physical methods is weak, Daune provides
considerably more coverage of nucleic acids and polymer
physics. This book provides more detail on biomolecular structure than
many of the texts listed here.
Hans Frauenfelder, Physics of Proteins,
unpublished lecture notes available online.
These are notes for a course that Hans Frauenfelder taught periodically
before his retirement from the
University of Illinois in 1992. They date
well because they emphasize physical fundamentals. These notes 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.
Igor N. Serdyuk, Nathan R.
Zaccai, Joseph Zaccai, Methods in Molecular
Biophysics: Structure, Dynamics, and Function,
(Cambridge University Press, 2007).
This excellent recent text emphasizes the application of experimental techniques from physics to biological macromolecules and assemblies. I have given it a slightly lower recomendation because the coverage is much more extensive than needed for this course and because I have not had time to explore it thoroughly. However, the sections that I have read are authoritative and up-to-date. On a price-per-page basis, it is a bargain, and you will want to have a copy if you work in experimental biomolecular physics.
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 many of the books listed) 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 14)
Assignment 2 (due September 21) solution
Assignment 3 (due September 28) solution
Assignment 4 (due October 5) solution
Assignment 5 (due October 12) solution
Assignment 6 (due October 19) solution
Assignment 7 (due October 26) solution
Assignment 8 (due November 7) with associated
files: Lovellfig7.jpg, helix.pdb, and Ala3.pdb
and solution: pg 1, pg 2,
pg 3, pg 4
Assignment 9 (due November 14) solution
Assignment 10 (due November 21) solution
Assignment 11 (due November 28) solution
Assignment 12 (due December 5) solution
Assignment 13 (due December 10) solution
You may submit either Assignement 12 or 13 for credit. If you submit
both, you will receive the higher of the two scores.
Your grade will be determined by homework problems and by two exams,
with the following weights:
| Homework |
|
| Midterm exam |
|
| Final exam |
|
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?
