Physics 174 Student Presentations
Fall, 2011

All papers discussed by groups are available to download from the Sakai class website, under the Resources link. The primary papers are the main papers of interest for the class and represent substantial advances in biophysics. The secondary papers are less-technical survey articles that you should be able to read quickly and easily, to get some background and context.

Please read the Guideline for presentations to get a sense of how to prepare your slides. The 47-minute video Designing effective scientific presentations by Susan McConnell is also helpful.

The following are the dates and papers for student presentations:

• Tuesday, December 6
  • Group 3: Hunter Nisonoff
    • A Pessimistic Estimate of the Time Required for an Eye to Evolve, by Dan-E. Nilsson and Susanne Pelger, Proceedings of the Royal Society: Biology 256:53-58 (1994).

  • Group 4: Tony Phipps
    • Primary paper: Trilobite eyes and the optics of Descartes and Huygens, Euan Clarkson and Riccardo Levi-Setti, Nature 254: 663-667 (1975).
    • Secondary paper: Designing efficient microlens arrays: lessons from Nature, Joanna Aizenberg and Gordon Hendler, J. Material Chemistry 14:2066-2072 (2004).

• Tuesday, November 29
  • Group 6: presented by Willie Zhang
    Challenges and opportunities for structural DNA nanotechnology, A. Pinheiro et al, Nature Nanotechnology, published online November 6, 2011.

  • Group 1: presented by Shaun Thompson
    Dimensionality and Dynamics in the Behavior of C. elegans, Greg Stephens et al, PLoS Computational Biology 4(4):e1000028, pages 1-10.

  • Group 2: presented by Jay Krishnan
    Biomechanics and biophysics of cancer cells, Subra Suresh, Acta Biomaterialia 3:413-438 (2007).

• Tuesday, November 8
  • Group 3: Josh Lewis
    • Primary paper: Ion-Channel Noise Places Limits on the Miniaturization of the Brain's Wiring by A. Faisal et al, Current Biology 15:1143-1149 (2005).
    • Secondary paper: The Limits of Intelligence by Douglas Fox, Scientific American, July, 2011, pages 38-43.

  • Group 4: Dennis Li
    • The Terrestrial Planet Finder, put together a talk based on this website and on the TPF book.

  • Group 5: presented by Yifei Chen
    • Primary paper: Introductory science and mathematics education for 21st-century biologists by W. Bialek and D. Botstein, Science 303:788-790 (2004).
    • Secondary paper: Form Follows Function by John Hopfield, Physics Today, November, 2002, pages 10-11.

• Tuesday, October 25, 2011
  • Group 6: presented by Kevin Chiou
    The Protein Folding Problem by Hue Sun Chan and Ken Dill, Physics Today February 1993: pages 24-32.

  • Group 1: presented by Alex Bloedel
    Exposing Life's Limits with Dimensionless Numbers by Steven Vogel, Physics Today, November 1998, pages 22-27.

  • Group 2: presented by Emily Foltz
    Motile Behavior of Bacteria by Howard Berg, Physics Today January 2000, pages 24-29.

• Tuesday, October 4, 2011
  • Group 3: presented by Shreyen Sen
    • Primary paper: Multimodal fast optical interrogation of neural circuitry by F. Zhang et al, Nature 446:633-641 (2007).
    • Secondary paper: Controlling the Brain with Light by Karl Deisseroth, Scientific American, November, 2010, pages 49-55.

  • Group 4: presented by Will Gilmore
    • Primary paper: Collective dynamics of 'small-world' networks by Duncan Watts and Stephen Strogatz, Nature 393: 440-442 (1998).
    • Secondary paper: Effects of immunization in small-world epidemics by Damian Zanette and Marcelo Kuperman, Physica A 309:445-452 (2002).
    • And a semi-serious paper When Zombies Attack!: Mathematical Modelling of an Outbreak of Zombie Infection, for the class to read when AMC's The Walking Dead is back on TV this October. The paper does leave out the effect of spatial transmission (modern zombies seek out healthy people so simple diffusion doesn't work) so leaves an opportunity for a 174 student to write a paper to complete the analysis.

  • Group 5: presented by Aashiq Dheraj
    • Primary paper: Ten years of tension: single-molecule DNA mechanics by Carlos Bustamante et al, Nature 421:423-427 (2003).
  
  
  
• Tuesday, September 20, 2011
  • Group 1: presented by Jason Klein
    • Primary paper: A synthetic oscillatory network of transcriptional regulators by Michael Elowitz and Stanislas Leibler, Nature 403:335 (2000)
    • Secondary paper: Biology by design: reduction and synthesis of cellular components and behavior by Philippe Marguet et al, Journal of the Royal Society Interface 4:607-623 (2007).

  • Group 2: presented by James Tian
    • Primary paper: Isolation of rare circulating tumour cells in cancer patients by microchip technology by Sunitha Nagrath et al, Nature 450: 1235-1239 (2007).
    • Secondary paper: The origins and the future of microfluidics by George Whitesides, Nature 442:368-373 (2006).