PHZ 4710: Introduction to Biophysics

Spring 2003 / 3 credits

Instructor: Prof. Stephen Hagen,

2360 NPB, Department of Physics, Univ of Florida

email: sjhagen [at] ufl.edu

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: http://webct.ufl.edu

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:

This year we will use the new textbook by Philip Nelson. 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

25% Term paper (2500 words, or about 10 pages)

25% Short assignments & homework

20% Final examination

15% Classroom presentation on the topic of the paper

15% Class participation and discussion

100% Total.

The term paper forms an important part of the course: it 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: Philip Nelson, Biological Physics: Energy, Information, Life

Nelson’s book is available as a 2-volume photocopy from Target Copy (22 NW 13th St., 376-3826).

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.

You are welcome to collaborate with other students when you do the homework. Please just let me know who your collaborators are.

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.