PHZ 4710: Introduction to Biophysics
updated 04/17/06
Spring 2006
Department of Physics, University of Florida
PHZ 4710
Department
of Physics

In-vivo Schedule:  Note Black is projected and tentative and Red is past material.

 

Week 1

10 Jan    Introduce Course, Syllabus, Review Webpage, Integrity in Science,
                Jargon (Green Tree Snake)
                Eyeless Gene, a "Master Control" Gene:

                   A "Mater Control" Gene of Fly Eyes Shares Its Power, W. Roush

                      in 31 January 1997 issue of Science (Vol 275).

                   On the Path of the Primordial Eye, a "Randon Sample"

                      in 28 March 1997 issue of Science (Vol. 275, p. 1885).
                Biophysics or Biological Physics?  See Biophysical Society Webpage, 

                Division of Biological Physics Webpage of the American Physical Society (APS), 

                both pages are linked to the logos on the left bar.

                See also (Introduction and as much as may interest you at this point):

                Biological Physics, H. Frauenfelder, P.G. Wolynes, and R.H. Austin,

                    Rev. Mod. Phys. 71 (1999) S419-S430.

                    http://prola.aps.org/abstract/RMP/v71/i2/pS419_1

                Harold Varmus Lecture, The Impact of Physics on Biology & Medicine (1999)

                    http://www.mskcc.org/mskcc/html/1812.cfm

 

12 Jan    Review Webpage, Other Useful Links (and UF linkable issues),.
                Read "Science" and/or "Nature" or similar and "biophysics in the news".

                Handout of Take-Home Final Exams for Spring 1997, Spring 1998, Spring 2005.
                "Biophysics vs. Biological Physics" Handout, length scale, ...
                    contrast to Biophys. Soc., DBP of APS, Frauenfelder et al., Varmus, ...

                "A naive physics question" as an example for this course
                DNA Packing Handout
                Start "Radiation Physics".
                  "Radiation Risk and Ethics". By: Jaworowski, Zbigniew. Physics Today, Sep99, Vol. 52 Issue 9, p24, 6p.
                        (available online at, for example, http://cnts.wpi.edu/rsh/Docs/ZJ99_Radrisk.htm)                 

                   HIFR User Site at ORNL: http://neutrons.ornl.gov/hfir_cns/RW_Trng.pdf


Week 2
17 Jan      Continue the discussion of "Radiation Physics".
                "Radiation" hand-out about effects due to pollution/accidents.

                "Techa River" and "Accident in Japan" handout.

                   Reminder to read Z. Jaworowski's article.

                Sketch extension of "Radiation Physics" to Potential Health Risks due to EMFs ("Thought HW on this topic")


19 Jan       Brian Bothner, Montana State Univ., seminar, MBI LG-101A, 4 pm, 23 Jan 06
                "Structure, Function, and Dynamics of Icosahedral Virus Capsid Proteins"
                Grammar Point of the Day:  Abstract circulated, check for "grammar" issues (discussion today or next time, 24 Jan)
                Attend?  Capsid overview Powerpoint presentation?

                 Short classroom excercise for HW1 credit, 1 point.
                   "How to read a science paper?" disucssion.
                   Final comments/discussion on Z. Jaworowski's article.
                "EMF Handouts" and Contrast of health risks of radiation to EMF and other.
               
                "Protein Structure Handout" for this lecture.
                HW 2 Assignment: Due at the start of class on 26 January.  Submit via Turnitin.
                   HW 2 "Template":  adh.

                                   
Week 3
24  Jan          Grammar Point of the Day:  Bothner Abstract: check for "grammar" issues.  (It is "HW 3".)
                    
                    "X rays in molecular biophysics". By: Hendrickson, Wayne A.. Physics Today, Nov. 1995, Vol. 48 Issue 11, p42, 7p.
                   "Determination of macromolecular structures from anomalous diffraction of synchrotron radiation". Wayne A. Hendrickson.
                          Science Oct 4, 1991 v254 n5028 p51(8).
                   Crystallography 101:  An Introductory Course by Bernhard Rupp (Lawrence Livermore National Laboratory).
                        A Great Website full of information. (Note: sometimes this server goes down.)
                 
                     REMINDER:  HW 2 Assignment: Due at the start of class on 26 January.  Submit via Turnitin.
                   HW 2 "Template":  adh.
       

26  Jan         HW2 due at the start of class via Turnitin.
                   
                    Grammar Points of the Day:  "That versus Which"   and "Dangling Preposition" .
                   Consider the following sentences:
                    "Acetylcholine is a neurotransmitter which functions in the synapses between nerve cells and muscle cells."
                     "This enzyme breaks up acetylcholine into acetic acid and choline which will be reassembled by the neuron for later release."
                      "To prevent this neurotransmitter from building up and interfering with proper communication between neuron and muscle,
                                the acetylcholine must be “cleaned up” after each muscle cell stimulation."
                    Finish X-rays.                          
                      Primers about Synchrotrons and related:  see  http://www.lightsources.org/cms/?pid=1000681


Week 4
31  Jan         Return HW1 (1 pt), HW2 (5 pts), HW3 (1pt), and review grading procedure.                          

Grammar Point of the Day:  "Diagramming Sentences"

Absorption coefficient of water. (Handout)

Note Thursday, Guest Lecturer.

Address Question:  Is all of biophysics related to electromagnetic effects/interactions?
Try this one (powerpoint overview in class):
"Origin of icosahedral symmetry in viruses", R. Zandi et al., Proc. Natl. Acad. Sci. USA 101 (2004) 15556-15560.
"Viruses and the physics of soft condensed matter",  Proc. Natl. Acad. Sci. USA 101 (2004) 15549-15550.
"Thermodynamics explains the symmetry of spherical viruses", Physics Today, Dec. 2004, 27-29.
Try this one:  HW5 without any electromagnetic waves being used!  A challenge!

HW4 (5 points): 
To be submitted at the start of class on Tuesday, 7 February. 
Find 5 grammatical “errors” in “science or technical” writing.  Submit a hardcopy of the examples
with bibliographic citations and provide your suggested corrections.  You should only need to use
one sheet of paper.  Use HW2 as Word document template with respect to formatting
(e.g. 12 pt font, location of name and UFID, et cetera).  If you need a target rich environment,
try Science 307 (2005), 14 January 2005 issue.

HW5 (5 points): 
Due at the start of class on Thursday, 9 Feb.
From the past 2 years, find a "biophysics" related image.  Challenge: electromagnetic waves used?
Present the image to the class and describe the "biophysics", e.g. method, resolution, and/or importance of the image.
(Green text is the correction mentioned in class.)
You should use the presentation format that you intend to use for your "presentation". 
Your discussion should be between 1 to 2 minutes. 
See Meisel's examples: (2005) and (2006).

                   Do's and Don'ts of Poster Presentation, Stephen Block,  Biophys. J. 71(61): 3527-3529 (1996)
                   Garland Grit --- The personal side of giving talks
                   Professor Wilkens, Ohio State: One page guides...
                  Projecting Information, Michael Stumpf, Science 30 January 2004; 303: 630
                   Norvig.com: Gettysburg Powerpoint Presentation
                   http://www.edwardtufte.com/tufte/powerpoint
 

02  Feb         Dr. Anna-Lisa Paul,
                    Gene Regulation/Chromatin Structure with Data from a Confocal Microscope and Microarrays.
                   An Example of an Image/Movie:
                        Isoform Specific Subcellular Localization among 14-3-3 Proteins in Arabidopsis
                            Appears to be Driven by Client Interactions, Mol. Biol. Cell,  Paul et al. 10.1091/mbc.E04-09-0839
                         The Supplemental Material

Week 5
07 Feb           HW4 (5 points):  Due at the start of class on Tuesday, 7 February, TODAY!  Hardcopy due, one sheet.
                      Finish Virus discussion.
                    "Electrophoresis Model"
                    All types of Microscopes.  Alphabet Soup.
                   Molecular Expressions: Exploring the World of Optics and Microscopy
                      A great website run by a FSU/NHMFL group with interactive explanations.
                   Beating the diffraction limit and the road to the perfect lens?
                      See: http://physicsweb.org/articles/world/17/5/3
                     

09 Feb            HW5 (5 points):  Due at the start of class on Thursday, 9 Feb, TODAY!  Give presentation in class today.
                        Microscopes of all flavors, continued.  Discussion about the "parts".  FRET/TIR/SPR.

Week 6
14 Feb            FRET
                      High magnetic field effects on plants?
                      FSU: Mice and Magnets, Prof. Tom Houpt and Prof. Jim Smith (thanks to Prof. Tom Mareci for site)

16 Feb            High magnetic field effects on plants? (continued)
                         Hands-on "model" and "imaging" exercise.

                   

Week 7
21 Feb          Start NMR and MRI.
                   Reference material:
                   "The second revolution in medical imaging", C.N. Guy, Contemporary Physics 37 (1996) 14-45.
                   "Dynamic magnetic resonance imaging of human brain activity during primary sensory stimulation",
                            K.K. Kwong et al., Proc. Natl. Acad. Sci. USA 89 (1992) 5675-5679.
      
                    Be prepared to discuss subjects that you would like discussed in class.  
23 Feb           Continue: 2D-NMR and MRI.

Week 8

28 Feb         Bio-electromagnetic measurements.  The Inverse Problem.  (see handout)

02 Mar        Deadline for Approving Topic for Term Paper; must be approved by the end of class.
                   Begin discussion of "Biomechanics" and "Life at Low Reynolds Numbers"
                   The "entropy/mixing" demo, an explanation is available here.
                   "Exposing Life's Limits with Dimensionless Numbers", Steven Vogel, Physics Today, Nov. 1998, 22-27.
                   March 2006:  this article is available here in pdf format.
                     
Week 9
07 Mar      Continue "Life at Low Reynolds Numbers".  Reynolds Number HW Problem.
                     
09 Mar         Deadline for Providing First Draft of Term Paper (optional),
                        submit electronic version by 3 pm via Turnitin and
                         submit hardcopy to Meisel at the start of class at 3 pm (sharp).
                   Arrange Schedule/Order for Student Presentations.
                    Molecular Evolutionary Biology, A Brief Discussion and Thoughts to Ponder for Spring Break
                        Reference: Prof. Peter Schuster, University of Vienna (his webpage is loaded with great material!)
              

Week 10
14 Mar      No classes Spring Break
16 Mar      No classes Spring Break


Week 11
21 Mar         Professor Steve Hagen, Protein Folding and Life is the "Slow Mixing Lane". 
                         You may want to prepare yourself by visiting Folding@home and
                         "The World's Longest Running Physics Experiment": the Pitch Drop Experiment

23 Mar       Presentations by Prof. Hagen continue, and Lab Tour (Class starts in the regular classroom.).


Week 12
28 Mar         Return of Term Paper Drafts (done 15 March) and Reynolds Number HW, Review "editorial issues" et al.
               
30 Mar         Professor Ani Petkova, "Molecular biophysicist's view of misfolding proteins
                         (or what can we learn about Alzheimer's disease from solid state NMR and electron microscopy?)"

Week 13
04 Apr         Review guidelines for oral presentations and related material.

06 Apr         Term Papers Due by the start of class,
                        submit electronic version by 3 pm via Turnitin and
                         submit hardcopy to Meisel at the start of class at 3 pm (sharp).
                  
                    Scanning Probe Microscopy (SPM), especially AFM.
                         "Scanning Force Microsopy in Biology", C. Bustamante and D. Keller, Physics Today, Dec. 1995, 32-38.
                         "Stretch Genes", Robert H. Austin, James P. Brody, Edward C. Cox, Thomas Duke and Wayne Volkmuth
                              Physics Today, Feb. 1997, 32-38. 
                        "The Manipulation of Single Biomolecules", T. Strick et al., Physcis Today, Oct. 2001, 46-51.
                         "Ten years of tension: single-molecule DNA mechanics", C. Bustamante, Z. Bryant, and S.B. Smith,
                               Nature 421 (2003) 423-427.

Week 14
11 Apr         Student Presentations
13 Apr         Student Presentations 

Week 15
18 Apr         Student Presentations
20 Apr         Review of the Course in Preparation for Final Exam.
                   Note:
                   D. Manoussaki, E.K. Dimitriadis, and R.S. Chadwick, Phys. Rev. Lett. 96 (2006) 088701
                            "Cochlea's Graded Curvature Effect on Low Frequency Waves"
                                      
                    "Intrinsic Low Temperature Paramagnetism in B-DNA"
                   S. Nakamae, M. Cazayous, A. Sacuto, P. Monon, and H. Bouchiat
                   Phys. Rev. Lett. 94 (2005) 248102.
                   URL: http://link.aps.org/abstract/PRL/v94/e248102


Week 16
25 Apr         Last Class, Return Graded Term Papers, Take-Home Final Handout
27 Apr         NO CLASS

Take-Home Final Exam Due (Exam Group 4D): 
Thursday, 04 May 2006, 17:00 hrs (5:00 pm) to Turnitin.

Follow the Instructions at the top of the Handout.
You may want to recall the following points.  Please provide references as needed, if you use them.  Use HW2 as the template.  Please submit to Turnitin by 5 pm, Thursday, 04 May 2005.  Please note that late papers will receive a letter grade reduction for every day (mod one day) that they are late.  Please note, once the work is submitted, you cannot resubmit it.  In other words, all submissions are final.
Temporary Storage of old text:

Leave 30 min. for group discussion for generating 4 possible questions for Final Exam.

 "Neural Networks" Discussion
                      Neurons: see The Mind Project                    
                      Neural Networks, course by Genevieve Orr at Willamette University
                     Neural Java: Neural Networks Tutorial with Java Applets  by  LAMI at  EPFL.

Class will be in a remote site,
                            meet in the lobby of the McKnight Brain Institute (MBI) at 3 pm SHARP.
                      Tour the lab facilities of Professor Tom Mareci, NMR & MRI, brain structure-function.
                        Not certain where MBI is?  Use the campus map.

End of Page

Turnitin
Biophysical Society
APS DBP




      


 
  
 
 
 











 


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