- Final Exam is Wednesday May 1, 2002, 12:30 - 2:30 pm:
- The format is closed book. Please don't bring books, notes, or other materials.
- You are advised to bring a calculator or slide rule.
- There will be 14 questions, for a total of 25 points. You will have some
choice of which questions to answer.
- If you need to talk with me before the exam, please make an appointment by sending me an email.
- (Week of 4-29-2002) On Tuesday we will have a review discussion on
the final exam. Please come prepared to ask questions about the lectures,
readings, and homework.
I have placed most of my own
class notes on the web.
They are for use by students in this course only, and so you will need
a password in order to access them. Please keep in mind that these
notes are provided "as is", with no guarantees: they are a
reference provided for your convenience, and I do not claim they are
error-free, or that they are a perfect record of what transpired in class.
Regarding presentations,
you may be interested to know that the student evaluations of presentations
were highly uniform -- all presentations received an average overall rating
between 4.0 and 5.0 from the class. Based on this fact, I will give the
full credit of 15 points to each student who gave a presentation.
Finally, you should have received an email containing information
about your term paper. Let me know if you didn't get your paper grade yet.
- (Week of 4-15-2002) On Tuesday we will further discuss kinesin, mostly as
an excuse to learn a little about the chemical kinetics of enzymes.
On Thursday we will have a
guest lecture on molecular dynamic simulations.
Please bring your ideas on Thursday, regarding what you want for
a review class on Tuesday April 30. Don't leave it up to me to decide
what would be helpful. I anticipate the final will consist of a number
of short answer questions (25-50 words required to answer). It will be
in closed-book format. You will have some choice of which questions to
answer. You may view an old practice exam at
this location, but I can't promise that this year's exam will be
very similar.
- (Week of 4-8-2002) This week, we discuss the bacterial flagellar motor
and the cytoskeletal motor protein kinesin.
- (Week of 4-1-2002) We will continue our discussion of motility. Again,
please read
Motile Behavior of Bacteria by H. Berg.
Homework #6
is due on Thursday, April 11.
Note that solutions to old homework appear at the bottom of this page.
The grading of homework was discussed in class on 3-28-2002. The
basic idea is that all homework questions are weighted equally, and I
will simply add up all of your points on all the homework. Your
homework grade will be based on the ratio of your total to the
class average. (The average grade will be reasonably high.)
Class on Thursday (4-4-2002) will consist of
- 3:00 - 3:50 pm: Student presentations
- 4:00 - 4:50 pm: Physics Colloquium: Prof. Daniel Purich,
Discovery of the Actoclampin Biomolecular Motor Responsible for
Cell Crawling, in room 1002 NPB
- (Week of 3-25-2002) This week we will discuss motility of biological
systems. Please read
Life at Low Reynolds Number. This classic article by E.M. Purcell
discusses the physics of motion at very small length scales.
Class on 3-28-2002 was diverted to the Physics Colloquium on protein
folding.
It is a remarkably lucky coincidence that the following seminar on
biomotility is being held in the Dept of Biochemistry & Molecular
Biology this week. You are all strongly encouraged to attend:
- Wed., March 27 5:30 p.m., R3-265
- Dr. Daniel Purich
- (Faculty Research Discussion)
- Discovering How Cells Crawl
Remember that Term Papers are due on Friday 3-29-2002.
Finally, the following article is recommended (optional) for any who
are interested in Brownian ratchets in biophysics: Peskin, Odell, & Oster,
Cellular motions and thermal fluctuations: the Brownian ratchet
, Biophys. J.
65 316-324 (1993).
- (Week of 3-18-2002) This week we have a guest lecture from Dr. Anna
Lisa Paul, on chromatin structure.
We will then conclude our discussion of DNA separation. This will lead
us slightly toward the side-topic of Brownian ratchets, which offer
potential as a means for sorting biomolecules.
- (Week of 3-11-2002) Welcome back. This week we resume discussion of
the physics of DNA electrophoresis, and we will learn about some
novel technologies for separation of DNA. One very interesting approach,
which does not rely on gels, is the Brownian ratchet. Please read
this article about the Brownian ratchet approach to DNA separation.
Homework #5 is due next Tuesday, March 19, 2002. Please put it in my
mailbox by 5:00 pm.
Next Tuesday (3/19/02) we will have a guest lecture on chromatin structure,
by
Dr. Anna-Lisa Paul.
- (Week of 3-4-2002) Spring Break! You should have turned in
your draft paper last Friday. I have not yet received papers from
several students.
- (Week of 2-25-2002) This Tuesday we will have a guest lecture by Prof. Andrew
Rinzler of the U.F. Physics Dept. He will speak on the applications of
atomic force microscopy to biological systems. On Thursday we have a guest
lecture by Prof. Mark Meisel, also of U.F. Physics. Prof. Meisel will discuss
magnetic and gravitational field effects on plant growth and gene expression.
Don't miss either talk!
- (Week of 2-18-2002)
This week we continue our discussion of basic polymer-physics approaches
to the study of DNA. We will discuss DNA stretching experiments and begin
discussion of the physics of gel electrophoresis.
Homework #4 is due on Friday February 22, 2002.
- (Week of 2-11-2002) This week we are discussing physical properties
of DNA. We may have a brief in-class writing assignment on the
paper Stretch Genes by R.H.Austin and coauthors (Physics Today,
February 1997).
Please also read sections 4.1, 4.2, 4.4, and 4.5 (on DNA structure and
supercoiling) in Molecular Biophysics: Structures in Motion
(by Michel Daune). I also recommend that you read section 4.3, although
some may find it rather tedious, so I consider it to be optional.
This book is on 2-hr reserve in the Marston Science Library.
- (Week of 2-4-2002) This week we will conclude our discussion of scaling
laws in biology.
Homework #3 is due on Friday February 8, 2002, at 5:00 pm. This
homework is designed to give you practice applying the same kinds
of scaling and dimensional arguments that we have used in class.
We will also begin discussing the physical properties of nucleic acids,
especially DNA. Reading: Stretch Genes, by R.H. Austin and
coauthors, from Physics Today, February 1997. Copies were
distributed in class.
- Special announcement (1-31-2002) Owing to the biological
physics colloquium today at 4:00 pm, we will have only one period of
lecture today (3:00-3:50 pm). You are encouraged to spend the second
period at the colloquium, entitled "The Bifurcation of Species",
by Prof. Ed Spiegel of Columbia University. (Room 1002 NPB)
- (Week of 1-28-2002) This week we will discuss scaling laws and
dimensionless numbers in biology, as mentioned below. In applying these
simple ideas to biological systems, we will appreciate the famous comment:
- There is something fascinating about science. One gets such
wholesale returns of conjecture out of such a trifling investment of fact.
(Mark Twain)
Please be sure
to read the article (by Steven Vogel) that was handed out in class on
1/17/02. A brief in-class writing assignment on this article is a
distinct possibility for 1/29/02.
Homework #2 is due on Friday, February 1, 2002.
- Please note that I am moving up the
deadline for the choice of topic for the term paper -- to February
8th. This is to discourage people from allocating too little time to
the actual research, thinking, and writing phases of the project. I
will take some time in class soon to discuss the
general guidelines for the paper.
- (Week of 1-21-2002) Guest lectures by
Professor Arthur S. Edison, who will discuss
(1) the fundamentals of nuclear magnetic resonance in biology,
(2) multidimensional
NMR, and (3) applications of multidimensional NMR in structural biology.
Prof. Edison may choose to assign a reading assignment or other homework this
week.
- (Week of 1-14-2002) This week we will have an overview of protein
and polypeptide structure. We will also review some important
thermodynamics relevant to protein structure -- free energy etc.
The answers to Homework #1 (due Jan-18-2002) are available
here
Reading (protein structure): M.Daune, Molecular Biophysics, sections 5.1-5.5.1 and 5.6 - 5.6.1
or
van Holde, Principles of Physical Biochemistry, sections 1.5-1.5.3 and
1.5.5 - 1.5.6
- (Week of 1-7-2002) We will start with a brief introduction to address
the question, What is biophysics?
Reading: Harold Varmus (Nobel Laureate & former Director of the National
Institutes of Health),
The Impact of Physics on Biology & Medicine.
- The week of January 28, 2002, we will then begin discussing applications of scaling laws and
dimensionless numbers in biology.
Reading: Steven Vogel, Exposing life's limits with
dimensionless numbers, Physics Today (November 1998).
That is, we will seek to understand what is wrong with the following picture: