Spring 2004 / 3 credits
Instructor: Prof. Stephen
Hagen,
2362 NPB,
Department of Physics, Univ of Florida
phone: (352) 392-4716;
office
hours: Wednesday 2-4 pm
Web Page:
This webpage provides some basic information about the
course. The primary course website is
maintained on the UF WebCT server at http://webct.ufl.edu. Click below to access WebCT:
You will need your gatorlink ID and password to log in. I will assume that you are checking the
WebCT site fairly regularly for announcements and other information.
Prerequisites:
One complete year of an introductory Physics Course (PHY 2048/2049
or PHY 2053/2054 or similar sequence) or permission of the instructor. Calculus will be used occasionally, but the
course is not heavily mathematical.
Meetings: 1216 NPB
Tue. 8th period
(15:00 - 15:50) and Thur. 8th & 9th (15:00 to 16:55, with a break!);
Objectives:
This course aims to introduce the physical principles that underly
a variety of important biological and biophysical phenomena, as well as a
number of valuable laboratory techniques and probes. The course combines physical and biological perspectives in order
to explore a wide range of topics in a way that is not usually possible in
standard undergraduate physical- or biological-science courses. The presentation is aimed at the
undergraduate level and is designed for both bio-oriented and physics-oriented
students.
The course also emphasizes scientific writing and
communication. Through papers and
presentations, students can explore the areas of biophysics that they find most
interesting. The course satisfies a
Gordon Rule communications requirement:
the student will receive credit for 2000 words of writing if the course
is completed with a letter grade of C or higher.
Topics covered:
Rather than using a published textbook, this year
we will read from a selection of articles
mostly derived from Physics Today. These articles are fairly
readable, and we will supplement them in class
with details and discussion. We will also discuss some of the popular
topics from previous years. These
include the applications of dimensionless numbers and scaling laws in biology
(including the famous Kleiber’s law), aspects of molecular biophysics
(including protein and nucleic acid structure, simple polymer-physical
approaches to the study of biomolecules, and the physics behind important
technologies for DNA separation and electrophoresis), the physics of biological
motility (including the hydrodynamics of bacterial motion and the operation of
the bacterial flagellar motor). If time
permits, we can also examine aspects of electromagnetism in biological physics,
including NMR and x-ray crystallographic techniques for studies of biomolecular
structure and dynamics, the physics of vision, as well as rhodopsin and neural
signalling.
Grading
30% Term paper (2500 words, or about 10
pages)
20% Short assignments & homework
20% Final examination (Friday April 30, 2004)
15% Classroom presentation on the topic
of the paper
15% Class participation and discussion
100% Total.
There will be a term paper, short assignments, presentations, and a final exam. The paper is your opportunity to develop and present your own interdisciplinary perspective on an contemporary scientific research problem. Students will have broad freedom to select topics that reflect their own interests, although the goal should be to choose a topic that represents (as nearly as possible) a 50/50 mix of biological and physical science. The final choice of topic must be approved by the instructor. Each student will write an initial draft, which will be carefully reviewed by the instructor and by other students. Written comments will be provided on the draft. These comments - and the grades on the final version - will reflect the suitability of the topic, the level of presentation, the conceptual organization and structure, the adequacy of referencing and bibliographic detail, and the overall adherence to standards of good written communication.
Textbook: (optional) Philip Nelson
Biological Physics: Energy, Information, Life
We will primarily rely on readings that will be posted in
PDF form on the course WebCT page. Nelson's book is optional.
General Expectations:
Class participation includes regular attendance and is definitely
expected. Students who anticipate difficulty in attending class regularly
should contact the instructor in advance.
Homework and other assignments (such as the components of the term
paper) should not be submitted late. If you anticipate a problem in meeting a
deadline you will need to discuss this with me in advance of the deadline.
Students with Disabilities:
Students requesting classroom accommodation must first register
with the Dean of Students Office. The Dean of Students Office will provide
documentation to the student who must then provide this documentation to the
instructor when requesting accommodation.
Academic Honesty:
Students are expected to hold themselves to a high standard of academic
honesty. While completing the registration form at the University of Florida,
every student has signed the following statement: "I understand that the
University of Florida expects its students to be honest in all their academic
work. I agree to adhere to this commitment to academic honesty and understand
that my failure to comply with this commitment may result in disciplinary
action up to and including expulsion from the University."
The issue of plagiarism in writing the term paper is considered to
be especially serious. Any student who submits a plagiarized paper or draft
will receive a failing grade in the course.
If you are unclear as to what constitutes plagiarism, I will be happy to
discuss this with you before you submit your work.