Soft Matter Journal Club

The soft matter journal club will usually meet Wednesdays over lunch in the soft matter nook. Generically, any topic is fair game, though the general focus will remain on systems in soft condensed matter theory, non-equilibrium statistical mechanics, and complex fluids. As always, papers are selected based on the interest of journal club members. Please email me with any future paper suggestions.

• Potential Future Papers
• 2008
• 2007
• 2006

Upcoming Paper Selectors:

For December 17: Sabetta Matsumoto
For January 7: Bryan Chen
For January 14: Tom Haxton

• December 10, 12pm
  • "Conical defects in growing sheets"
    M. M. Miller, M. B. Amar, and J. Guven
    arXiv:0807.1814.
    paper suggested by Anton Souslov
    
• December 3, 12pm
  • "Compressing nearly hard sphere fluids increases glass fragility"
    L. Berthier and T. A. Witten
    arXiv:0810.4405.
    paper suggested by Ning Xu
    
• November 26, 12pm
  • "Stochastic Gene Expression in a Single Cell"
    M.B. Elowitz, A.J. Levine, E.D. Siggia, P.S. Swain
    Science 297, 1183 (2002).
    paper suggested by Xiaoming Mao
    
• November 5, 12 pm
  • "Nature's Microfluidic Transporter: Rotational Cytoplasmic Streaming at High Peclet Numbers"
    J. van de Meent, I. Tuval, R. E. Goldstein
    PRL 101, 178102 (2008).
    paper suggested by Gareth Alexander
    
• October 29, 12 pm
  • "Linked and Knotted Beams of Light"
    W. T. M. Irvine and D. Bouwmeester
    Nature Physics 4, 716 (2008).
    paper suggested by Vincenzo Vitelli
    
• September 24, 12 pm
  • "Localized and Extended Deformations of Elastic Shells"
    A. Vaziri and L. Mahadevan
    PNAS 105(23), 7913 (2008).
    paper suggested by Ed Banigan
    
• August 25, 12 pm
  • "Experimental Study of the Fluctuation Theorem in a Nonequilibrium Steady State"
    G. M. Wang, J. C. Reid, D. M. Carberry, D. R. M. Williams, E. M. Sevick, et al.
    PRE 71 046142 (2005).
  • "Experimental Demonstration of Violations of the Second Law of Thermodynamics for Small Systems and Short Time Scales"
    G. M. Wang, E. M. Sevick, E. Mittag, D. J. Searles, and D. J. Evans
    PRL 89 050601 (2002).
    papers for week six of Andrea's reading course
    
• August 18, 12 pm
  • "Fluctuation Theorems"
    E. M. Sevick, R. Prabhakar, S. R. Williams, and D. J. Searles
    Annu. Rev. Phys. Chem. 59 603 (2008).
    paper for week five of Andrea's reading course
    
• August 6, 12 pm
  • "Phenomenological Energetics for Molecular Motors"
    T. Harada
    EPL 70(1) 49 (2005).
  • "Restoring a Fluctuation-Dissipation Theorem in a Nonequilibrium Steady State"
    T. Speck and U. Seifert
    EPL 74(3) 391 (2006).
    papers for week four of Andrea's reading course
    
• July 28, 12 pm
  • Introduction to Modern Statistical Mechanics
    D. Chandler
    Oxford University Press, 1987 pp. 252 - 257.
  • "Correlation Functions and Relaxation Properties in Chaotic Dynamics and Statistical Mechanics"
    M. Falcioni, S. Isola, and A. Vulpiani
    PRA 144(6,7) 341 (1990).
    papers for week three of Andrea's reading course
    
• July 21, 12 pm
  • "Equilibrium Information from Nonequilibrium Measurements in an Experimental Test of Jarzynski's Equality"
    J. Liphardt, S. Dumont, S. B. Smith, I. Tinoco Jr., and C. Bustamante
    SCIENCE 296, 1832 (2002).
  • "A Note on the Jarzynski Equality"
    E. G. D. Cohen and D. Mauzerall
    JSTAT P07006 (2004).
  • "Nonequilibrium Work Theorem for a System Strongly Coupled to a Thermal Environment"
    C. Jarzynski
    JSTAT P09005 (2004).
    papers for week two of Andrea's reading course
    
• July 14, 12 pm
  • "Nonequilibrium Equality for Free Energy Differences"
    C. Jarzynski
    PRL 78, 2690 (1997).
    paper for week one of Andrea's reading course
    
• July 7, 12 pm
  • "Scaling of Sound Emission Energy and Fracture Behavior of Cellular Solid Foods"
    M. B. J. Meinders and T. van Vliet
    PRE 77, 036116 (2008).
    paper suggested by Wouter Ellenbroek
    
• June 30, 12 pm
  • "Entropy Maximization in the Force Network Ensemble for Granular Solids"
    B. P. Tighe, A. R. T. van Eerd, and T. J. H. Vlugt
    arxiv:0803.0907v1
    paper suggested by Tom Haxton
    
• June 23, 12 pm
  • "Static Equilibria of Rigid Bodies: Dice, Pebbles, and the Poincaré-Hopf Theorem"
    P. L. Várkonyi and G. Domokos
    J. Nonlinear Sci. 16, 255 (2006).
    
  • "Mono-monostatic Bodies: The Answer to Arnold's Question"
    The Mathematical Intelligencer 28(4), (2006).
    paper suggested by Bryan Chen
    
• June 16, 12 pm
  • "Paradoxical Pop-ups: Why Are They Hard to Catch?"
    M. K. McBeath, A. M. Nathan, A. T. Bahill, and D. G. Baldwin
    arxiv:0803.4357v1
    paper suggested by Carl Modes
    
• June 2, 12 pm
  • "Universality of Synchrony: Critical Behavior in a Discrete Model of Stochastic Phase-Coupled Oscillators"
    K. Wood, C. Van den Broeck, R. Kawai, and K. Lindenberg
    PRL 96, 145701 (2006).
    paper suggested by Yair Shokef
    
• May 22, 12 pm
  • "Force Fluctuations and Polymerization Dynamics of Intracellular Microtubules"
    C. P. Brangwynne, F. C. MacKintosh, and D. A. Weitz
    PNAS 104(41), 16128 (2007).
    paper suggested by Sujit Datta
    
• May 7, 12 pm
  • "Giant Hexagonal Superstructures in Diblock-Copolymer Membranes"
    C. K. Haluska, W. T. Góźdź, H.-G. Döbereiner, S. Förster, and G. Gompper
    PRL 89(23), 238302 (2002).
    paper suggested by Sabetta Matsumoto
    
• April 30, 12 pm
  • "Soft Glassy Rheology of Supercooled Molecular Liquids"
    R. Zondervan, T. Xia, H. van der Meer, C. Storm, F. Kulzer, W. van Saarloos, and M. Orrit
    PNAS 105(13), 4993 (2008).
    paper suggested by Wouter Ellenbroek
    
• April 23, 12 pm
  • "Non-Affine Rubber Elasticity for Stiff Polymer Networks"
    C. Heussinger, B. Schaefer, and E. Frey
    arXiv:cond-mat/0703095
    paper suggested by Anton Souslov
    
• April 16, 12 pm
  • "Mechanics of Climbing and Attachment in Twining Plants"
    A. Goriely and S. Neukirch
    PRL 97, 184302 (2006).
    
  • "String Theory for Plants"
    Physical Review Focus for PRL 97, 184302 (2006).
    paper suggested by Jesse Kinder
    
• April 9, 12 pm
  • "Jamming Transition and New Percolation Universality Classes in Particulate Systems with Attraction"
    G. Lois, J. Blawzdziewicz, and C.S. O'Hern
    PRL 100, 028001 (2008).
    paper suggested by Tom Haxton
    
• April 2, 12 pm
  • "Asymmetric Exclusion Processes with Constrained Dynamics"
    M. Sellitto
    arXiv:0803.2287v1 [cond-mat].
    paper suggested by Yair Shokef
    
• March 26, 12 pm
  • "Analytic Results for the Three-sphere Swimmer at Low Reynolds Number"
    R. Golestanian and A. Ajdari
    PRE 77, 036308 (2008).
    paper suggested by Wouter Ellenbroek
    
• March 19, 12 pm
  • "Swarming and Swirling in Self-Propelled Polar Granular Rods"
    A. Kudrolli, G. Lumay, D. Volfson, and L.S. Tsimring
    PRL 100, 058001 (2008).
    paper suggested by Ning Xu
    
• March 5, 12 pm
  • "Generalization of Distance to Higher Dimensional Objects"
    S. S. Plotkin
    PNAS 104(38), 14899 (2007).
    paper suggested by Bryan Chen
    
• February 27, 12 pm
  • "Toroidal Crystals"
    L. Giomi and M. J. Bowick
    arXiv:0801.3484v1 [cond-mat].
    paper suggested by Carl Modes
    
• February 20, 12 pm
  • "Nonequilibrium Green's Function Approach to Phonon Transport in Defective Carbon Nanotubes"
    T. Yamamoto and K. Watanabe
    PRL 96, 255503 (2006).
    paper suggested by Vincenzo Vitelli
    
• February 13, 12 pm
  • "Phonons in a one-dimensional microfluidic crystal"
    T. Beatus , T. Tlusty, and R. Bar-ziv
    Nature Physics 2, 743 (2006).
    paper suggested by Yair Shokef
    
• January 30, 12 pm
  • "Effect of Curvature and Twist on the Conformations of a Fluctuating Ribbon"
    D. A. Kessler and Y. Rabin
    J. Chem. Phys. 118(2), 897 - 904 (2003).
    paper suggested by Sabetta Matsumoto
    

• December 12, 12 pm
  • "Interaction Ruling Animal Collective Behaviour Depnds on Topological Rather than Metric Distance: Evidence from a Field Study"
    M. Ballerini, N. Cabibbo, R. Candelier, A Cavagna, E. Cisbani, I. Giardina, V. Lecomte, A. Orlandi, G. Parisi, A. Procaccini, M. Viale, V. Zdravkovic
    arXiv:0709.1916v1[q-bio.PE]
    
• December 5, 12 pm
  • "Topological Theory of Reptation"
    A. L. Kholodenko
    Physics Letters A 159, 437 - 441 (1991).
    
• November 28, 12 pm
  • "Self-Motile Colloidal Particles: From Directed Propulsion to Random Walk"
    N. R. Howse, R. A. L. Jones, A. J. Ryan, T. Gough, R. Vafabakhsh, and R. Golestanian
    PRL 99, 048102 (2007).
    
• November 14, 12 pm
  • "Spontaneous Formation of Ordered Structures in Thin Films of Metals Suported on an Elastomeric Polymer"
    N. Bowden, S. Brittain, A. G. Evans, J. W. Hutchinson, and G. M. Whitesides
    Nature 393, 146 - 149 (1998).
    
• November 7, 12 pm
  • "Ultrasound Propagation in Externally Stressed Granular Media"
    X. Jia, C. Caroli, and B. Velicky
    PRL 82(9), 1863 - 1866 (1999).
    
• October 17, 12 pm
  • "Entropy and Temperature of a Static Granular Assembly: an Ab Initio Approach"
    S. Henkes, C. S. O'Hern, and B. Chakraborty
    PRL 99, 038002 (2007).
    
• October 10, 12 pm
  • "Shape Selection in Chiral Self-Assembly"
    R. L. B. Selinger, J. V. Selinger, A. P. Malanoski, and J. M. Schnur
    PRL 93, 158103 (2004).
    
• October 3, 12 pm
  • "Spatial Structures and Dynamics of Kinetically Constrained Models of Glasses"
    C. Toninelli, G. Biroli, and D. S. Fisher
    PRL 92, 185504 (2004).
    
• September 26, 12 pm
  • "Critical Exponents and Scaling Relations for Self-Organized Critical Phenomena"
    C. Tang and P. Bak
    PRL 60, 2347 - 2350 (1988).
    
• September 19, 12 pm
  • "The Dynamics of Granular Ripples Formed by Rolling Wheels"
    N. Taberlet, S. W. Morris, and J. N. McElwaine
    PRL 99, 068003 (2007).
    
• September 12, 12 pm
  • "A General Model for the Origin of Allometric Scaling Laws in Biology"
    G. B. West, J. H. Brown, and B. J. Enquist
    Science 276, 122 - 126 (1997).
    
• August 23, 12 pm
  • "On Being the Right Size"
    J. B. S. Haldane
    (1928).
    
• August 15, 12 pm
  • "On the Mechanism of Water Holding in Meat: The Swelling and Shrinking of Myofibrils"
    G. Offer and J. Trinick
    Meat Science 8, 245 - 281 (1983).
    
• August 8, 12 pm
  • "Structural Properties of Crumpled Cream Layers"
    M. A. F. Gomes, C. C. Donato, S. L. Campello, R. E. de Souza, and R. Cassia-Moura
    J. Phys. D: Appl. Phys. 40, 3665 - 3669 (2007).
    
• August 1, 12 pm
  • "Formation and Physical Properties of Milk Protein Gels"
    J. A. Lucey
    J. Dairy Sci. 85, 281 - 294 (2002).
    
• July 9, 12 pm
  • "The 'Cheerios' effect"
    D. Vella and L. Mahadevan
    Am. J. Phys. 73, 817-825 (2005).
    
• May 21, 12 pm
  • "The physics of ice cream"
    C. Clarke
    Phys. Ed. 30, 248-253 (2003).
    
  • "Relationship between ice recrystallisation rates and the glass transition in frozen sugar solutions"
    S. Ablett, C.J. Clarke, M.J. Izzard, and D.R. Martin
    J. Sci. Food Arg. 82, 1855-1859 (2002).
    
• May 15, 12 pm
  • "Tempering of Chocolate in a Scraped Surface Heat Exchanger"
    C. Liosel, G. Keller, G. Lecq, B. Launay. and M. Ollivon
    J. Food Sci. 62, 773-780 (1997).
    
• May 2, 12 pm
  • "Ground Red Peppers: Capsaicinoids Content, Scoville Scores, and Discrimination by an Electronic Nose"
    F. Korel, N. Bagdatlioglu, M.O. Balaban, and Y. Hisil
    J. Agric. Food Chem. 50, 3257-3261 (2002).
    
• April 25, 12 pm
  • Principles of condensed matter physics
    P.M. Chaikin & T.C. Lubensky
    Do Problem 2.1 and look at Problem 2.2
    
• April 18, 12 pm
  • "State Transitions and the Continuum Limit for a 2D Interacting, Self-Propelled Particle System"
    Y. Chuang, M.R. D'Orsogna, D. Marthaler, A.L. Bertozzi, and L.S. Chayes
    ArXiv:nlin.AO/0606031 v1 (11 June 2006).
    
• April 11, 12 pm
  • "Pre-vitrification by viscosity feedback"
    T. Geszti
    J. Phys. C 16, 5805 (1983).
    
• April 4, 12 pm
  • "Phase Diagram of Patchy Colloids: Towards Empty Liquids"
    E. Bianchi, J. Largo, P. Tartaglia, E. Zaccarelli, and F. Sciortino
    PRL 97, 168301 (2006).
    
• March 28, 12 pm
  • "Correlated Random Networks"
    J. Berg and M. Lässig
    PRL 89, 228701 (2002).
    
• March 21, 12 pm
  • "Proteins with Selected Sequences Fold into Unique Native Conformation"
    E. I. Shakhnovich
    PRL 72, 3907 (1994).
    
• March 14, 12 pm
  • "Why does water change the pitch of a singing wineglass the way it does?"
    Y.-Y. Chen
    Am. J. Phys. 73, 1045 (2005).
    
• February 28, 12 pm
  • "Monte Carlo study of hard pentagons"
    T. Schilling, S. Pronk, B. Mulder, and D. Frenkel
    PRE 71, 036138 (2005).
• February 21, 12 pm
  • "Dynamic Scaling of Growing Interfaces"
    M. Kardar, G. Parisi, and Y.C. Zhang
    PRL 56, 889 (1986).
• February 14, 12 pm
  • "Phonons in an Entropic Crystal"
    Z. Cheng, J. Zhu, W.B. Russel, and P.M. Chaikin
    PRL 85, 1460 (2000).
• February 7, 12 pm
  • "Quasicrystals: A New Class of Ordered Structures"
    D. Levine and P.J. Steinhardt
    PRL 53, 2477 (1984).
• January 31, 12 pm
  • "Stick-slip dynamics around a topological defect in free-standing smectic films"
    A. Eremin, C. Bohley, and R. Stannarius
    PRE 74, 040701(R) (2006).
• January 24, 12 pm
  • "Pushmepullyou: an efficient micro-swimmer"
    J.E. Avron, O. Kenneth, and D.H. Oaknin
    New Journal of Physics 7 (2005) 234.
• January 17, 12 pm
  • "The topological theory of defects in ordered media"
    N.D. Mermin
    Rev. Mod. Phys. 51, 591 (1979).
    Discussion will cover pages 619-648.
    
• January 10, 12 pm
  • "The topological theory of defects in ordered media"
    N.D. Mermin
    Rev. Mod. Phys. 51, 591 (1979).
    Pages 591-619 will be discussed.

2006:

• December 14, 12 pm
  • "The relationship between fragility, configurational entropy and the potential energy landscape of glass-forming liquids"
    S. Sastry
    Nature 409, 164 (2001).
• December 7, 12 pm
  • "Reverse Brazil Nut Problem: Competition between Percolation and Condensation"
    D. Hong and V. Quinn
    PRL 86, 3423 (2001).
• November 16, 12 pm
  • "Nonequilibrium clustering of self-propelled rods"
    F. Peruani, A. Deutsch, and M Bär
    PRE 74, 030904 (2006).
    
• November 9, 12 pm
  • "Evolution of a vibrational wave packet on a disordered chain"
    P.B. Allen and J. Kelner
    Am. J. Phys. 66, 497 (1998).
    
• October 26, 12 pm
  • "Equivalence of Cellular Automata to Ising Models and Directed Percolation"
    E. Domany and W. Kinzel
    PRL 53, 311 (1984).
    
• October 19, 12 pm
  • "Two Dimensional Mechanics for Insect Hovering"
    ZJ Wang
    PRL 85, 2216 (2000).
  • "Falling Paper: Navier-Stokes Solutions, Model of Fluid Forces, and Center of Mass Elevation"
    U. Pesavento and ZJ Wang
    PRL 93, 144501 (2004).
  • For Reference: "Dissecting insect flight"
    ZJ Wang
    Annu. Rev. Fluid. Mech. 37, 183 (2005).
    
• October 12, 12 pm
  • "Nonequilibrium Equality for Free Energy Differences"
    C. Jarzynski
    PRL 78, 2690 (1997).
• October 4, 12 pm
  • "Renormalization Group Theory for Global Asymptotic Analysis"
    L. Chen, N. Goldenfeld, and Y. Oono
    PRL 73, 1311 (1994).
    
• September 28, 12 pm
  • "Breakdown of Energy Equipartition in a 2D Binary Vibrated Granular Gas"
    K. Feitosa and N. Menon
    PRL 88, 198301 (2002).
  • "Lack of energy equipartition in homogeneous heated binary granular mixtures"
    A. Barrat and E. Trizac
    Granular Matter 4, 57-63 (2002).
    
• September 21, 12 pm
  • Wrap up of papers from previous week.
  • For Reference: "Effect of random defects on the critical behaviour of Ising models"
    A.B. Harris
    J. Phys. C 7, 1671 (1974).
• September 14, 12 pm
  • "Random-Field Instability of the Ordered State of Continuous Symmetry"
    Y. Imry and S. Ma
    PRL 35, 1399 (1975).
  • "On the theory of the phase transition in the two-dimensional planar spin model"
    A.P. Young
    J. Phys. C 11, L453 (1978).
• September 7, 12 pm
  • "Ordering, metastability and phase transitions in two-dimensional systems"
    J.M. Kosterlitz and D.J. Thouless
    J. Phys. C 6, 1181 (1973).
  • For Reference: "The critical properties of the two-dimensional xy model"
    J.M. Kosterlitz
    J. Phys. C 7, 1046 (1974).

Possible future papers:

• "Saddles in the Energy Landscape Probed by Supercooled Liquids"
  L. Angelani, R. Di Leonardo, G. Ruocco, A. Scala, and F. Sciortino
  PRL 85, 5356 (2000).
• "Energy Landscape of a Lennard-Jones Liquid: Statistics of Stationary Points"
  K. Broderix, K. K. Bhattacharya, A. Cavagna, A. Zippelius, and I. Giardina
  PRL 85, 5360 (2000).
• "Artificial ‘spin ice’ in a geometrically frustrated lattice of nanoscale ferromagnetic islands"
  
• R.F. Wang, C. Nisoli, R.S. Freitas, J. Li, W. McConville, B.J. Cooley, M.S. Lund, N. Samarth, C. Leighton, V. H. Crespi & P. Schiffer
  Nature 439 , 303 (2006).
• "The Instantaneous Normal Modes of Liquids"
  R. M. Stratt
  Acc. Chem. Res. 28, 201 (1995).
• "Mechanical model of an earthquake fault"
  J.M. Carlson and J.S. Langer
  Phys. Rev. A 40, 6470 (1989).
• "How the Venus flytrap snaps"
  Y. Forterre, J.M. Skotheim, J. Dumais, and L. Mahadevan
  Nature 433, 421 (2005).
  
• "Collective dynamics of 'small-world' networks"
  D.J. Watts and S.H. Strogatz
  Nature 393, 440 (1998).
  
• "Real-Space Imaging of Nucleation and Growth in Colloidal Crystallization"
  U. Gasser, E.R. Weeks, A. Schofield, P.N. Pusey, and D.A. Weitz
  Science 292, 258 (2001).
• "Optimal Swimming at Low Reynolds Numbers"
  J.E. Avron, O. Gat, and O. Kenneth
  PRL 93, 186001 (2004).
  
• "Nonequilibrium work theorem for a system strongly coupled to a thermal environment"
  C. Jarzynski
  J. Stat. Mech.: Theor. Exp. (2004) P09005.
  
• "Studies of Non Linear Problems"
  E. Fermi, J. Pasta, and S. Ulam
  Document LA-1940 (May 1955) 266, 978.
  
• "Non-equilibrium work relations."
  J. Kurchan
  arXiv:cond-mat/0511073 v1 3 Nov 2005.
  
• "Statistical mechanics, Euler's equation, and Jupiter's Red Spot"
  J. Miller, P.B. Weichman, and M.C. Cross
  PRA 45, 2328 (1992).
• "The Theory of Microphase Separation in Block Copolymers"
  L. Leibler
  Macromolecules 13, 1602 (1980).
• "Statistical Dynamics of Classical Systems"
  P.C. Martin, E.D. Siggia, H.A. Rose
  Phys. Rev. A 8, 423 (1973).
• "Equations of state and renormalization-group recursion relations"
  J. Rudnick and D.R. Nelson
  Phys. Rev. B 13, 2208 (2005).
• "Soft Condensed Matter Physics"
  T.C. Lubensky
  arXiv:cond-mat/9609215 v1 20 Sep 1996
  
• "Practical Applicability of the Jarzynski Relation in Statistical Mechanics: A Pedagogical Example"
  R.C. Lua and A.Y. Grosberg
  J. Phys. Chem. B 109, 6805 (2005).
• "Theory of Powders"
  S.F. Edwards and R.B.S. Oakeshott
  Physica A 157, 1080 (1989).
• "Temperature probes in binary granular gases"
  A. Barrat, V. Loreto and A. Puglisi
  Physica A 334, 513 (2004).
• "Fluctuation-dissipation relations in driven granular gases"
  A. Puglisi, A. Baldassarri, and V. Loreto
  PRE 66, 061305 (2002).
• "Clustering Instability in Dissipative Gases"
  I. Goldhirsch and G. Zanetti
  PRL 70, 1619 (1993).
• "Crumpling a Thin Sheet"
  K. Matan, R.B. Williams, T.A. Witten and S.R. Nagel
  PRL 88, 076101 (2002).
• "Weak chaos and fractional dynamics in an optically driven colloidal ring"
  Y. Roichman, G. Zaslavsky, D.G. Grier
  cond-mat/0605686
• "Observation of Flux Reversal in a Symmetric Optical Thermal Ratchet"
  S.H. Lee, K. Ladavac, M. Polin, D.G. Grier
  cond-mat/0411731

For further paper suggestions see the following other Soft Matter Journal Club Websites:

• Dave Weitz's Group Journal Club
• Eric Weeks' Group Journal Club

Last updated: October 28, 2008 by Carl Modes