Possible Paper Topics

In principle, this project is not supposed to take longer than would preparation for a final exam.
The object is to demonstrate mastery of some recent research article at a level that could be used to explain to your peers in a roughly one hour lecture in (some future) class. In practice, this means finding some suitable punchline from the article, explaining why it's interesting and/or important, and outlining some minimal path to that result, providing any necessary background material necessary to understand the details along the way (with references, obtained either via literature search or web search). This can usually be done in about five typed pages (or more, handwritten), or in any other self-contained manner sufficient to convey to the instructor your mastery of the material.
The intent of the exercise is for the student to learn substantially more than would be possible just from preparing for a final exam, with the possibility for the instructor to assess the suitability of the topic for use in some future version of the course.

• Lipid Bilayers
  • Dan, N. Safran S. A. Spontaneous curvature of mixed-copolymer bilayers. Europhys. Lett. 1993; 21(9):975-980.
  • S. Gruner, Stability of Lyotropic Phases with Curved Interfaces, J. Phys. Chem 93, 7562 (1989)
  • Tobias Baumgart, Samuel T. Hess, and Watt W. Webb, Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension, Nature 425, p821 (23 Oct 2003)
• Physical Limits
  • Physical limits to biochemical signaling (W. Bialek and S. Setayeshgar, 2003)
    
  • H. C. Berg and E. M. Purcell, Biophysical Journal 20, 193 (1977)
  • E. M. Purcell, Life at low Reynolds number, Am J Phys 45, 3-11 (and E. M. Purcell, The efficiency of propulsion by a rotating flagellum, PNAS 94, 11307 (1997))
• Genomics
  • Information theory in molecular biology (Christoph Adami (KGI, Caltech), 2004)
  • On the Way to Protein Alphabet: Informational Classification of Amino Acids in Comparison to Other Classifications (A.N. Gorban, M. Kudryashev, T. Popova, 2005)
  • Divergence and Shannon information in genomes (Hong-Da Chen, Chang-Heng Chang, Li-Ching Hsieh and Hoong-Chien Lee, 2004)
    
  • M Djordjevic, A.M. Sengupta, B.I. Shraiman, A biophysical approach to transcription factor binding site discovery, Genome Res. 2003 Nov;13(11):2381-90
  • Exons, introns and DNA thermodynamics (Enrico Carlon, Mehdi Lejard Malki, Ralf Blossey, 2004)
  • Self consistent proteomic field theory of stochastic gene switches (Aleksandra M. Walczak, Masaki Sasai and Peter G. Wolynes, 2004)
  • The long reach of DNA sequence heterogeneity in diffusive processes (Michael Slutsky, Mehran Kardar and Leonid A. Mirny, 2003)
• Allometric Scaling
  • Geoffrey B. West, William H. Woodruff, and James H. Brown Allometric scaling of metabolic rate from molecules and mitochondria to cells and mammals PNAS 99, suppl.1, 2473-2478 (February 19, 2002)
  • G.B.West, The Origin of Universal Scaling Laws in Biology, Physica A 263, 104-113 (1999)
  • (for overview see also nytimes article "Of Mice and Elephants: A Matter of Scale", 12 Jan 1999, copy1 or copy2)
• Virus Structure
  • Thermodynamics Explains the Symmetry of Spherical Viruses, Physics Today, Dec 2004, p.27
  • Viral self-assembly as a thermodynamic process (Robijn F. Bruinsma, William M. Gelbart, David Reguera, Joseph Rudnick, 2002)
    
  • Virus shapes and buckling transitions in spherical shells (Jack Lidmar, Leonid Mirny, and David R. Nelson, 2003) and Spherical Crystallography: Virus Buckling and Grain Boundary Scars (David R. Nelson, 2003)
• Motors and Ratchets
  • Fluctuations in type IV pilus retraction (Martin Linden, Emil Johansson, Ann-Beth Jonsson, Mats Wallin, 2005)
    
  • Pump process of the rotatory molecular motor and its energy efficiency (Hiroshi Miki, Masatoshi Sato, and Mahito Kohmoto, 2004)
    
  • Brownian motors in a ring and type IV pilus retraction (Martin Linden, Tomi Tuohimaa, Ann-Beth Jonsson and Mats Wallin, 2004)
    
  • Elastic lever arm model for myosin V (Andrej Vilfan, 2005)
  • Dynamics of Molecular Motors and Polymer Translocation with Sequence (Yariv Kafri, David K. Lubensky, David R. Nelson, 2003) and Dynamics of Molecular Motors with Finite Processivity on Heterogeneous (Yariv Kafri, David K. Lubensky and David R. Nelson, 2004)
  • A Multiscale Approach to Brownian Motors (G.A. Pavliotis, 2005)
  • On Myosin II dynamics in the presence of external loads (A. Buonocore, L. Caputo, Y. Ishii, E. Pirozzi, T. Yanagida and L. M., 2005)
  • Motoring oil drops, (Yutaka Sumino et al., Self-Running Droplet: Emergence of Regular Motion from Nonequilibrium Noise, Phys. Rev. Lett. 94, 068301
  • A.E. Ruckenstein et al., A ratchet mechanism of transcription elongation and its control, Cell. 2005 Jan 28;120(2):183-93.
  • Winning an Uphill Battle (Ioan Kosztin and Klaus Schulten, Fluctuation-Driven Molecular Transport Through an Asymmetric Membrane Channel, Phys. Rev. Lett. 93, 238102)
  • Heat Flow and Efficiency in a Microscopic Engine (Baoquan Ai, Liqiu Wang, Huizhang Xie, Lianggang Liu, 2005)
  • Dynamic Properties of Motor Proteins with Two Subunits (Anatoly B. Kolomeisky and Hubert Phillips III, 2005)
• Molecular Zippers
  • Mechanical unfolding of RNA hairpins (Changbong Hyeon and D. Thirumalai, 2005)
    
  • Force Unfolding Single RNAs: from Equilibrium to Far-from Equilibrium (Fei Liu and Zhong-can Ou-Yang, 2005)
    
  • Statistical Physics of Unzipping DNA (David R. Nelson, 2003)
• DNA translocation
  • Amit Meller, Lucas Nivon, Eric Brandin, Jene Golovchenko, and Daniel Branton, Rapid nanopore discrimination between single polynucleotide molecules, PNAS 97(3): 1079-1084 (1 Feb 2000)
  • A. Meller, D. Branton,Single molecule measurements of DNA transport through a nanopore, Electrophoresis 23, 2583-2591 (2002)
  • Fast DNA translocation through a solid-state nanopore (Arnold J. Storm et al., 2004)
    
  • S. Howorka et al, Sequence-specific detection of individual DNA strands using engineered nanopores, Nature Biotechnology 19, 636-639 (Jul 2001)
• Gene Microarrays
  • G Bhanot, Y Louzoun, J Zhu, C DeLisi, The importance of thermodynamic equilibrium for high throughput gene expression arrays, Biophysical Journal 84, 124-135 (2003)
  • Y Tu, G Stolovitzky, U Klein, Quantitative noise analysis for gene expression microarray experiments, PNAS 99, 14031-14036 (29 Oct, 2002)
  • On The Reconstruction of Interaction Networks with Applications to Transcriptional Regulation (Adam A. Margolin, Ilya Nemenman, et al, 2004), ARACNE: An algorithm for the reconstruction of gene regulatory networks (Adam A. Margolin, Ilya Nemenman, et al 2004)
• Molecular Networks
  • F. Li, T. Long, Y. Lu, Q. Ouyang, and C. Tang, The Yeast Cell-Cycle Network Is Robustly Designed, PNAS 101, 4781 (2004)
  • Marie Csete and John Doyle, Bow ties, metabolism and disease, Trends in Biotech 22, 447 (Sep 2004)
  • A.M. Sengupta, M. Djordjevic, B.I. Shraiman, Free in PMC Specificity and robustness in transcription control networks, PNAS 99, 2072-2077 (19 Feb 2002)
  • Optimal Path to Epigenetic Switching (David Marin Roma, Ruadhan A. O'Flanagan, Andrei E. Ruckenstein, et al. 2004)
  • On The Reconstruction of Interaction Networks with Applications to (Margolin et al., 2004); ; see also ARACNE: An algorithm for the reconstruction of gene regulatory networks (Margolin et al., 2004)