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Dr. Stephen J. Hagen
Physics 4710 - Introduction to Biophysics
Spring 2002


CLICK HERE FOR SPRING 2003 WEB PAGE


Table of Contents




Course Objective:

Introduction to Biophysics is a one-semester course designed to introduce biological physics at the undergraduate level. The course is not designed to teach either "physics for biologists" or "biology for physicists." Instead, it presents an overview of a range of topics that lie at the interface of physics and biology. It emphasizes examples of important biophysical research problems and techniques that require an interdisciplinary approach, and therefore are usually not discussed or presented in standard introductory physics, biology, or biochemistry courses.

The course is open to undergraduate students from both the physical and biological sciences.

Specific Information:

  • Syllabus for Spring 2002, with information on prerequisites, suggested textbooks, course objectives, grading, etc.
  • Calendar (tentative) for Spring 2002
  • Biological physics web links
  • Web page from previous term -- Spring 2001, including description of topics, readings, special events, presentations, papers, etc.
  • Guidelines for the term paper. I apologize for the tedious character of these guidelines.
  • Class composition (Spring 2002): Undergraduate physics majors (7), undergraduate non-physics majors* (5), graduate physics (2).

    *includes biochemistry, chemistry, engineering, and other fields.

Paper & presentation topics and dates (all dates are Thursdays):

  • See the Abstracts summarizing these papers.
  • March 14th: Physics-based constraints for life on Europa, David Elm
  • March 14th: Tensegrity -- developing a mechanical/chemical theory for cellular function, Rani Hasan
  • March 21st: Physical principles of glomerular and tubule function in the kidney, Justin Brooten
  • March 21st: Fluorescent nanocrystals as biological probes, Ed Grant
  • March 28th: Validity of Kleiber's Law, Dennis Warner
  • March 28th: Nonlinear electrical behavior of the heart following heart attack, Ales Necas
  • April 2nd: AFM unzipping of DNA molecules, Preston Aleshire
  • April 4th: Physical and biological aspects of metachrosis, Nancy Huang
  • April 4th: Forced unfolding of single biomolecules, Rebecca Boren
  • April 11th: Investigating cellular phones and cancer: RF radiation and thermal heating, Danny Colvin
  • April 11th: Sensitivity of mammalian vestibular endorgans to air- and bone- conducted sound, Sam Choe
  • April 18th: Charge-reversal of Colloids in the Electrostatic Interactions of DNA-lipid Complexes, Frank Raucci
  • April 18th: The physical effects of foramen, of varying diameter, on cortical bone, Daniel Zahrly
Important Dates:
  • Friday February 8, 2002 -- Term paper topic must be approved
  • Friday March 1, 2002 -- Draft version of term paper is due at 5:00 pm
  • March 2-10, 2002 -- UF Spring Break
  • Tuesday March 19, 2002 -- Guest lecture, Dr. Anna-Lisa Paul
  • Friday March 29, 2002 -- Final version of term paper is due at 5:00 pm
  • Thursday April 18, 2002 -- Guest lecture, Dr. Adrian Roitberg
  • Wednesday May 1, 2002 -- Final Exam 12:30 - 2:30 pm
Announcements:
  • 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:

Solutions to Homework Assignments:

Histogram of (Cumulative) Homework scores to date appears below. Your final grade for homework will be calculated according to your position within this histogram. (If you don't know your cumulative score, send me a request by email. Those who submitted abstracts for HW#4 received 1 homework point. It should have been more, and I will increase this to 5 points when I calculate final HW grades.)




 

 
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