Department
of Physics
In-vivo Schedule
Week 1
04 Jan Introduce Course, Syllabus, Jargon (Green Tree Snake), Eyeless Gene
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
06 Jan Review Webpage, Other Useful Links, Integrity in Science
More on "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).
Handout of
Take-Home Final Exams for Spring 1997 and Spring 1998.
"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
Start
"Radiation Physics".
"Radiation
Risk and Ethics". By: Jaworowski, Zbigniew. Physics
Today, Sep99, Vol. 52 Issue 9, p24, 6p.
HIFR User Site at ORNL: http://neutrons.ornl.gov/hfir_cns/RW_Trng.pdf
Week 2
11 Jan Continue the discussion of "Radiation
Physics".
Short classroom excercise for HW1
credit, 1 point.
"Radiation" hand-out about effects due to pollution/accidents.
"EMF Handouts" and Contrast of health risks
of radiation to EMF and other.
"Protein Structure Handout" for next lecture.
"How to read a science paper?" disucssion.
13 Jan X-rays (Biophysics Structure)
"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.)
HW 2 Assignment: Due at the start of class on 20 January. Submit via Turnitin.
HW 2 "Template": adh.
Some "biophysics in the news" overview.
Week 3
18 Jan 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.
HW3: In-class, provide definition of "MAD".
Absorption coefficient of water.
20 Jan HW2 due at the start of class via Turnitin.
Return HW3.
Grammar Point of the Day: "Diagramming Sentences"
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.
Hands-on "model" and "imaging" exercise.
Week 4
25 Jan Return HW2 and review grading procedure.
HW4 (5 points): To be submitted at the start of class on Thursday, 3 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.
NMR and MRI (completed).
27 Jan Bio-electromagnetic measurements. The Inverse Problem.
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
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
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
Week 5
01 Feb Microscopes of all flavors, continued. Discussion about the "parts". FRET/TIR/SPR.
HW5 (5 points): Due at the start of class on Thursday, 10 Feb.
From the past 2 years, find an image made using one of the microscopes that we have discussed.
Present the image to the class and describe the method, resolution, and 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 example.
03 Feb HW4 Due at the start of class. Provide hardcopy, one sheet.
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.
Week 6
08 Feb Review the visit to MRI. High magnetic field effects on plants?
FSU: Mice and Magnets, Prof. Tom Houpt and Prof. Jim Smith (thanks to Prof. Tom Mareci for site)
10 Feb HW5 Due at the start of class. To be presented in class. Final discussion on magnetic field effects?
Be prepared to discuss subjects that you would like discussed in class.
Week 7
15 Feb HW5 presentation (one left).
Scanning Probe Microscopy (SPM), especially AFM.
"Scanning Force Microsopy in Biology", C. Bustamante and D. Keller, Physics Today, Dec. 1995, 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.
Discussion of other subjects to cover: neural networks?
17 Feb Professor Steve Hagen, Protein Folding and Lab Tour. Class starts in the regular classroom.
You may want to prepare yourself by visiting Folding@home.
HW6: Due at the start of class. Hardcopy use HW2 format.
Visit the Baker Lab (University of Washington) Contact Order Calculator.
Use the protein that you found in HW2, use the calculator, and report the results on your sheet.
Be prepared to discuss these results with Professor Hagen. As a part of this excercise, you
will need to understand the definition of "contact order".
Week 8
22 Feb Discussion on Contact Order, Mechanical Properties of Proteins, What can the AFM and other techniques provide?
"Stretch Genes", Robert H. Austin, James P. Brody, Edward C. Cox, Thomas Duke and Wayne Volkmuth
Physics Today, Feb. 1997, 32-38.
24 Feb HW 7 (5 pts, In-class): Typical F vs. d sketch (with units) for DNA.
Molecular Evolutionary Biology, A Brief Discussion and Thoughts to Ponder for Spring Break
Deadline for Approving Topic for Term Paper; must be approved by the end of class.
Research presentation about magnetic levitation and high magnetic field effects on gene regulation.
Week 9
No classes Spring Break
Week 10
08 Mar "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.
10 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.
Continue discussion of "Neural Networks".
Begin discussion of "Biomechanics" and "Life at Low Reynolds Numbers"
The "entropy" demo.
"Exposing Life's Limits with Dimensionless Numbers", Steven Vogel, Physics Today, Nov. 1998, 22-27.
Week 11
15 Mar Continue "Biomechanics" and "Life at Low Reymolds Numbers" discussion
"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.
17 Mar Dr. Anna-Lisa Paul,Gene Regulation/Chromatin Structure with Data from a Confocal Microscope and Microarrays.
Week 12
22 Mar Return of Term Paper Drafts (done 15 March)
Review Reynolds Number HW Problem (collect at the start of class).
Review Dr. Paul's presentation. Start "Symmetry of viruses" discussion.
Hoberman sphere motivation of mechanical modelling (time elapsed filming of plants?!).
24 Mar Continue the "Symmetry" discussion. Discuss "Do you believe it" and "peer review" issues.
Some Fact/Fiction example Questions. An example of a possible Final Exam Question.
Leave 30 min. for group discussion for generating 4 possible questions for Final Exam.
Week 13
29 Mar Reading/Writing Day. No class. Professor Meisel available in NPB B133 for consultation, as needed.
31 Mar 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).
Topics to be Discussed: Review of the Course in Preparation for Final Exam.
Week 14
05 Apr Student Presentations
07 Apr Student Presentations
Week 15
12 Apr Student Presentations
14 Apr Student Presentations
Week 16
19 Apr Last Class, Course Evaluations, Return Graded Term Papers, Take-Home Final Handout
21 Apr NO CLASS
Take-Home Final Exam Due: 27 April, 09:30 am 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 9:30 AM, Wednesday, 27 April 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.
End of Page
or Mozilla 1.5