PHZ 4710: Introduction to Biophysics

updated 04/23/07

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In-vivo Schedule:  Note Black is projected and tentative, Red is for Deadlines, and Green is past material.

 

Week 1

09 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

 

11 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://www.riskworld.com/nreports/1999/jaworowski/NR99aa01.htm)                 

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

Week 2
16 Jan      True start 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.

18 Jan      "Radiation Physics" continued.
               
               Grammar Point of the Day:  Abstract circulated, check for "grammar" issues, review Science for common errors.
                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.
                Sketch extension of "Radiation Physics" to Potential Health Risks due to EMFs ("Thought HW on this topic")
                                   
Week 3
23  Jan         "Protein Structure Handout" for this lecture.
                     HW2 Assignment: Due by the start of class on 30 January.  Submit via Turnitin.
                       HW2 "Template":  adh.

                   HW3 (5 points):  Due at the start of class on Thursday, 1 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.
                        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).

                    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."

                   HW4 (5 points):  To be submitted by the start of class on Tuesday, 6 February.   Submit via Turnitin.
                    Find 5 grammatical “errors” in “science or technical” writing, with bibliographic citations (consistent sytle)
                        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.
                   
                   Start X-rays: form, function, dynamics(?).
                    "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.)
                 
                    

25  Jan         Return HW1 (1 point).
                      Continue discussion of X-rays.                          
                      Primers about Synchrotrons and related:  see  http://www.lightsources.org/cms/?pid=1000681

Week 4
30  Jan         HW2 due by the start of class via Turnitin.

01  Feb        HW3 (5 points):  Due at the start of class TODAY.  Be ready to do it.
                      Start Virus discussion.

Week 5
06 Feb           HW4 (5 points):  Due TODAY by the start of class.   Submit via Turnitin.
                      Guest Lecture:  Professor Steve Hagen (protein folding and unfolding, how to study it, energy landscapes).
                      From last year (but may be substantially different than this year):
                      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
                      "HW5" (4 points) was in-class exercise.

08 Feb            HW3 (5 points):  Make-up time for anyone with technical problems.
                        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

Week 6
13 Feb            HW3 (5 points):  Make-up time for anyone with technical problems or excused absences.
                     
                      Writing Tip of the Week:  "APPENDIX A: WRITING A BETTER SCIENTIFIC ARTICLE"
                                                            Karie Friedman, Review of Modern Physics, http://rmp.aps.org/rmpguapa.pdf
                        Microscopes of all flavors, continued.  Discussion about the "parts".  FRET/TIR/SPR.
                     

15 Feb            Short lecture, remaining time is "reading" for TOPIC!
                      Be prepared to discuss subjects that you would like discussed in class.  
                   
Week 7
20 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.  

22 Feb           Continue: 2D-NMR and MRI.  Hands-on "model" and "imaging" exercise.

Week 8

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

01 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" by E.M. Purcell, (link to PDF via UF machines?)
                    American Journal of Physics -- January 1977 -- Volume 45, Issue 1, pp. 3-11 (READ)
                   
                    "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. (READ)
                     
Week 9
06 Mar      Continue "Life at Low Reynolds Numbers". 
                The "entropy/mixing" demo, an explanation is available here.
                                   Reynolds Number HW Problem.
                     
08 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).
                  
                    Reynolds Number HW Problem DUE (hardcopy at start of class).

                    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
13 Mar      No classes Spring Break
15 Mar      No classes Spring Break


Week 11
20 Mar         Return of Term Paper Drafts (done 15 March) and Reynolds Number HW, Review "editorial issues" et al.

                   Noise and Stochastic Processes in Biology
                   Read before class: 
22 Mar       Finish "motivation", Reference:
                   Anna-Lisa Paul , Robert J Ferl  and Mark W Meisel
                    High magnetic field induced changes of gene expression in arabidopsis
                    BioMagnetic Research and Technology 2006, 4:7 (doi:10.1186/1477-044X-4-7)
                            Published   22 December 2006  Open  Access

                    Continue with "Noise and Stochastic Processes in Biology" (see 20 Mar))


Week 12
27 Mar       Review guidelines for oral presentations and related material.

                    "Science in the News": plus movies!
                   From Swimming to Walking with a Salamander Robot Driven by a Spinal Cord Model
                    A. J. Ijspeert, A. Crespi, D. Ryczko, and J.-M. Cabelguen
                    Science 9 March 2007 315: 1416-1420
                       Link to movies in Supporting Online Material.
  
                    Stochastic synchronization of electroreceptors in the paddlefish
                    A. B. Neiman, D. F. Russell, X. Pei, W. Wojtenek, J. Twitty, E. Simonotto,
                        B. A. Wettring, E. Wagner, L. A. Wilkens and F. Moss
                          http://www.phy.ohiou.edu/~neiman/synchronization/      
                  
                      For further consideration:
                      1.  "What do you think?":  see paddlefish video and materials at:
                            http://www.umesc.usgs.gov/aquatic/fish/paddlefish/video.html
                      2.  YouTube "paddlefish" and "daphnia" search yields:
                            A.  Paddlefish Feeding
                            B.  Paddlefish at the Shedd
                            C.  Daphnia (Pulga de Agua)
                      3.  Daphnia at the previously cited
                                 Molecular Expressions: Exploring the World of Optics and Microscopy
                      4.  Coupled Oscillators
                            A.  http://www.walter-fendt.de/ph14e/cpendula.htm
                            B.  http://qbx6.ltu.edu/s_schneider/physlets/main/coupledosc.shtml


29 Mar         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"

                   "Science in the News" Folding@Home going to be available on PS3!

                   Discussion from 27 March continued (first period).
                   Second Period:  Last chance to test "presentation technology";
                         plus "extended office hour" about paper and presentation.

Week 13
03 Apr         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

05 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).
                  
                    Start (required reading):
                   The Bacterial Condensin MukBEF Compacts DNA into a Repetitive, Stable Structure
                            R. B. Case, Y.-P. Chang, S.B. Smith, J. Gore, N.R. Cozzarelli, C. Bustamante
                      Science 9 July 2004:  Vol. 305. no. 5681, pp. 222 - 227

                    (suggested additional reading):
                    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.

                      Course Evaluations
                      HW in class: Potential Questions for Final
                      Last checks of AV-computer links for presentations

Week 14
10 Apr         Student Presentations 1-4
12 Apr         Student Presentations  5-12

Week 15
17 Apr         Student Presentations 13-16
19 Apr         Student Presentations 17-19
                    Turkey trots?
                    Brownian ratchets?
                    Review of the Course in Preparation for Final Exam.
                                                      
Week 16
24 Apr         Last Class, Return Graded Term Papers, Take-Home Final Handout
26 Apr         NO CLASS

Take-Home Final Exam Due (Exam Group 3D): 
Thursday, 03 May 2007, 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, 03 May 2007.  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.

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