Gluckstern Lectures in Biological Physics, Spring 2011:

"The Physics of DNA" (Gluckstern Lecturer: Dr. Rudi Podgornik)

Final Project:
Schedule of Project Presentations, which includes UPDATED topics (rev. 4/15/2011)

The final project of this 1-credit course has two components: a 15-minute, in-class oral presentation and a 1-page written document. Each project will be the work of an individual student (as opposed to a group collaboration), but of course you may seek help from the instructors or from other resources.

For your final project, choose one of the papers (below) to read, and then choose a topic or sub-topic of that article as your area of focus. The topic could be one or more experiments, could be a theoretical model, or some conbination thereof. Your presentation and written document will be based on this selection, so you might need to read a bit before you finally decide on your topic. You will probably also need to refer to other sources for background information, such as cited works, a statistical mechanics textbook, Rudi Podgornik's notes, etc.

For the in-class presentation:

• Select a date at your earliest convenience from among these options: April 7, April 14, April 21 or April 28. If you choose an early date, you have the advantage of (i) wrapping it up well before exams and (ii) not having your topic 'scooped' by another person.
• Prepare to deliver a presentation that will last no longer than 12 minutes plus an additional 3 minutes for discussion. During your presentation, provide for the class a summary of your topic. You should assume that the audience knows general concepts of physics (as you do), and some general information about DNA (as you do, now). But do not assume the audience has knowledge of any information that is specific to your topic.
• If you cannot possibly summarize your topic in 12 minutes, then it means your topic is too large; try choosing a sub-section of your topic.
• As part of your presentation, include one slide that briefly...
  • identifies the conclusion(s) of the body of work, and...
  • identifies the limitations of the work (For example, are assumptions or approximations made and are they too restrictive?), and...
  • identifies an area for possible future improvement (but you need not say how this might be accomplished).
• Plan on using a computer and the projector. If you need to borrow a computer, please ask Prof. Parsegian or Dinsmore in advance.
• It can be challenging to say everything you need to say in just 12 minutes. As a guide, we suggest that you plan on no more than 10 slides. (A few good slides are more effective than too many.) Each slide should have one major point with supporting details. Use schematic illustrations whenever possible (which you may copy from the literature if you cite appropriately). Use bullets and descriptive phrases rather than complete sentences. Be sure to practice the talk aloud, and preferably in front of a friendly audience that will offer suggestions. For the presentation, DO NOT JUST READ FROM YOUR SLIDES. Practice until it comfortably lasts 12 minutes.

For the written document (due in class, on the last Thursday of classes, 4/28) :

• In one page of text, identify the conclusions and offer critical analysis of the work contained within your chosen topic. Note that you cannot attempt a full summary of the work; that will be contained in your presentation.
• You may include figures. If you do so, please put the figure(s) and descriptive caption(s) on a separate page and do not include them in the page count.
• You must include references. Cite them in text as appropriate and list them on a separate page (not including them in the page count).
• Include a copy of the slides that you used for your oral presentation. If you revise them, then please include the revision as well as the originally presented version.

Please ask Prof. Parsegian and/or Prof. Dinsmore if you have questions or need some advice about the presentation or the written document.

Here is a list of articles, from which you should choose one (or a part of one).

Original Research Articles:

1. "Effects of Salts on Internal DNA Pressure and Mechanical Properties of Phage Capsids," A. Evilevitch, W. H. Roos, I. L. Ivanovska, M. Jeembaeva, Bengt Jonsson, and G. J. L. Wuite (2011) [J. Mol. Biol., 6 pages].
2. "The nucleosome: A transparent, slippery, sticky and yet stable DNA-protein complex," H. Schiessel (2006) [Eur. Phys. J. E, 12 pages].
3. "The physics behind the larger scale organization of DNA in eukaryotes," Marc Emanuel, Nima Hamedani Radja, Andreas Henriksson and Helmut Schiessel (2009) [Phys. Biol., 11 pages].

   Review articles:

4. "Stretching of macromolecules and proteins," T R Strick, M-N Dessinges, G Charvin, N H Dekker, J-F Allemand, D Bensimon and V Croquette (2003) [Rep. Prog. Phys., 45 pages].
5. "Materials Science of DNA,"Y.-W. Kwon, C. H. Lee, D.-H. Choi and J.-Il Jin (2009) [J. Mater. Chem., 28 pages].
6. "Theoretical and Computational Treatments of DNA and RNA Molecules," H. Zhou, Y. Zhang, Z.-H. Ou-Yang (2011) [preprint, 143 pages].
7. "21st century: what is life from the perspective of physics?" G. R. Ivanitskii (2010) [Uspekhi Fizicheskikh Nauk, Russian Academy of Sciences; reviews of topical problems, 31 pages].
8. "Biophysics of the DNA molecule," M. D. Frank-Kamenetskii (1997) [Physics Reports, 48 pages].
9. "The Discovery of the DNA Double Helix," Aaron Klug (2004) [J. Mol. Biol., 24 pages].
10. "Theory and computational modeling of the 30 nm chromatin fiber," J. Langowski and H. Schiessel (2011) [preprint; 33 pages].
11. "Ordered Phases of DNA in vivo and in vitro," F. Livolant (1991) [Physica A, 21 pages].
12. "The DNA double helix - the untold story," J. E. Lydon (2003) [Liqu. Crystals Today, 10 pages].
13. "Nonlinear dynamics and statistical physics of DNA," M. Peyrard (2004) [Nonlinearity, 40 pages].
14. "Tail Bridging vs. Patchiness: Models for the Interaction of Nucleosomes (a Ph.D. thesis)," F. Muhlbacher (2004) [Ph. D. thesis, 133 pages].
15. "Physical virology," W. H. Roos, R. Bruinsma, and G. J. L. Wuite (2010) [Nat. Phys., 11 pages].
16. "Structure and interactions of biological helices," A. Kornyshev, D. J. Lee, S. Leikin, A. Wynveen (2007) [Rev. Mod. Phys., 54 pages].
17. "Force spectroscopy of single DNA and RNA molecules," Mark C Williams and Ioulia Rouzina (2002) [Curr. Opinion Structural Biol., 7 pages].
18. "The physics of chromatin," Helmut Schiessel (2003) [J. Phys:CM, 76 pages].
19. "Optical Tweezers: Measuring Piconewton Forces, M. C. Williams (2011) [preprint; 14 pages].
20. "Evidence for water structuring forces between surfaces," Christopher Stanley and Donald C Rau (2011) [preprint; 26 pages].
21. - new addition - "Interactions in Macromolecular Complexes Used as Nonviral Vectors for Gene Delivery," Rudolf Podgornik, D. Harries, J. DeRouchey, H. H. Strey, and V. A. Parsegian (2004) [book chapter; 42 pages].

    Journalism/Popular Press:

22. - even newer addition(4/4) - "Nanopore sequencing: Towards the 15-minute genome," (author unknown), from the March 10, 2011 issue of The Economist. (If you choose this one, be sure to explore the scientific background with an intellectually critical eye.)