Physical Review E – July 2007
Volume 76, Issue 1

Part 1 - Statistical, Soft Matter, and Biological Physics

Part 2 - Nonlinear and Plasma Physics, Fluid Dynamics, and Related Topics

Part 1 - Statistical, Soft Matter, and Biological Physics

RAPID COMMUNICATIONS

Statistical physics

•
Epidemic size and probability in populations with heterogeneous infectivity and susceptibility
Joel C. Miller
Published 10 July 2007 (4 pages)
010101(R) [View PDF (119 kB)]
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Time-dependent couplings and crossover length scales in nonequilibrium surface roughening
Marc Pradas, Juan M. López, and A. Hernández-Machado
Published 11 July 2007 (4 pages)
010102(R) [View PDF (1,825 kB)]
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Phase transition in a stochastic prime-number generator
Bartolo Luque, Lucas Lacasa, and Octavio Miramontes
Published 18 July 2007 (4 pages)
010103(R) [View PDF (224 kB)]

Colloidal dispersions, suspensions, and aggregates

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Slow dynamics and aging in colloidal gels studied by x-ray photon correlation spectroscopy
Andrei Fluerasu, Abdellatif Moussaïd, Anders Madsen, and Andrew Schofield
Published 2 July 2007 (4 pages)
010401(R) [View PDF (1,432 kB)]
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Reversible clustering under the influence of a periodically modulated binding rate
Ronny Straube and Martin Falcke
Published 26 July 2007 (4 pages)
010402(R) [View PDF (206 kB)]

Structured and complex fluids

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Simulations of dynamics and viscoelasticity in highly entangled solutions of semiflexible rods
Shriram Ramanathan and David C. Morse
Published 6 July 2007 (4 pages)
010501(R) [View PDF (616 kB)]

Polymers

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Polymer translocation through a nanopore: A showcase of anomalous diffusion
J. L. A. Dubbeldam, A. Milchev, V. G. Rostiashvili, and T. A. Vilgis
Published 13 July 2007 (4 pages)
010801(R) [View PDF (395 kB)]

Biological physics

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Solution of an infection model near threshold
David A. Kessler and Nadav M. Shnerb
Published 16 July 2007 (4 pages)
010901(R) [View PDF (114 kB)]

ARTICLES

Statistical physics

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Phase diagram of the 1-in-3 satisfiability problem
Jack Raymond, Andrea Sportiello, and Lenka Zdeborová
Published 2 July 2007 (22 pages)
011101 [View PDF (404 kB)]
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Cavity approximation for graphical models
T. Rizzo, B. Wemmenhove, and H. J. Kappen
Published 3 July 2007 (9 pages)
011102 [View PDF (194 kB)]
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Invaded cluster algorithm for a tricritical point in a diluted Potts model
I. Balog and K. Uzelac
Published 3 July 2007 (7 pages)
011103 [View PDF (127 kB)]
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Ehrenfest urn revisited: Playing the game on a realistic fluid model
Enrico Scalas, Edgar Martin, and Guido Germano
Published 6 July 2007 (6 pages)
011104 [View PDF (211 kB)]
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Spin-dynamics simulations of the XY vector Blume-Emery-Griffiths model in three dimensions
J. A. Plascak, Shan-Ho Tsai, and D. P. Landau
Published 9 July 2007 (10 pages)
011105 [View PDF (724 kB)]
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Inferring Markov chains: Bayesian estimation, model comparison, entropy rate, and out-of-class modeling
Christopher C. Strelioff, James P. Crutchfield, and Alfred W. Hübler
Published 12 July 2007 (14 pages)
011106 [View PDF (472 kB)]
See Also: Publisher's Note
•
Scaling of Hamiltonian walks on fractal lattices
Sunčica Elezović-Hadžić, Dušanka Marčetić, and Slobodan Maletić
Published 12 July 2007 (17 pages)
011107 [View PDF (473 kB)]
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Parameter-dependent thermal conductivity of one-dimensional ϕ4 lattice
Nianbei Li and Baowen Li
Published 13 July 2007 (6 pages)
011108 [View PDF (163 kB)]
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Numerical method for solving stochastic differential equations with Poissonian white shot noise
Changho Kim, Eok Kyun Lee, Peter Hänggi, and Peter Talkner
Published 13 July 2007 (10 pages)
011109 [View PDF (198 kB)]
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Rigorous confidence intervals for critical probabilities
Oliver Riordan and Mark Walters
Published 17 July 2007 (8 pages)
011110 [View PDF (389 kB)]
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Quantum mechanical heat transport in disordered harmonic chains
Christopher Gaul and Helmut Büttner
Published 17 July 2007 (12 pages)
011111 [View PDF (317 kB)]
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Motion of a colloidal particle in an optical trap
Branimir Lukić, Sylvia Jeney, Željko Sviben, Andrzej J. Kulik, Ernst-Ludwig Florin, and László Forró
Published 19 July 2007 (9 pages)
011112 [View PDF (278 kB)]
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Generalized Casimir forces in nonequilibrium systems
R. Brito, U. Marini Bettolo Marconi, and R. Soto
Published 19 July 2007 (5 pages)
011113 [View PDF (110 kB)]
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Fluctuation-dissipation relation for stochastic dynamics without detailed balance
Mário J. de Oliveira
Published 19 July 2007 (4 pages)
011114 [View PDF (81 kB)]
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Inference and optimization of real edges on sparse graphs: A statistical physics perspective
K. Y. Michael Wong and David Saad
Published 20 July 2007 (22 pages)
011115 [View PDF (473 kB)]
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Gravitational dynamics of an infinite shuffled lattice: Particle coarse-graining, nonlinear clustering, and the continuum limit
T. Baertschiger, M. Joyce, A. Gabrielli, and F. Sylos Labini
Published 23 July 2007 (21 pages)
011116 [View PDF (5,539 kB)]
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Projected single-spin-flip dynamics in the Ising model
A. L. C. Ferreira and Raúl Toral
Published 23 July 2007 (10 pages)
011117 [View PDF (244 kB)]
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Non-Markovian approach to globally coupled excitable systems
T. Prager, M. Falcke, L. Schimansky-Geier, and M. A. Zaks
Published 24 July 2007 (13 pages)
011118 [View PDF (604 kB)]
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Supercritical series expansion for the contact process in heterogeneous and disordered environments
C. J. Neugebauer and S. N. Taraskin
Published 24 July 2007 (14 pages)
011119 [View PDF (448 kB)]
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Critical behavior of the particle mass spectra in a family of gelling systems
A. A. Lushnikov
Published 25 July 2007 (9 pages)
011120 [View PDF (164 kB)]
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Interplay of critical Casimir and dispersion forces
Daniel Dantchev, Frank Schlesener, and S. Dietrich
Published 26 July 2007 (24 pages)
011121 [View PDF (559 kB)]
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Return times for stochastic processes with power-law scaling
Piero Olla
Published 27 July 2007 (9 pages)
011122 [View PDF (531 kB)]
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State-dependent diffusion: Thermodynamic consistency and its path integral formulation
A. W. C. Lau and T. C. Lubensky
Published 27 July 2007 (17 pages)
011123 [View PDF (294 kB)]
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Diffusion in channeled structures. III. Quantum corrections induced by lattice vibrations
Benoit Palmieri and David Ronis
Published 27 July 2007 (22 pages)
011124 [View PDF (679 kB)]
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Diffusion process with two reflecting barriers in a time-dependent potential
Elisabeth Mayr, Michael Schulz, Peter Reineker, Thomas Pletl, and Petr Chvosta
Published 30 July 2007 (11 pages)
011125 [View PDF (235 kB)]
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Statistical behavior of domain systems
Diego Luis González and Gabriel Téllez
Published 31 July 2007 (8 pages)
011126 [View PDF (488 kB)]
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Shocks in asymmetric simple exclusion processes of interacting particles
Sutapa Mukherji
Published 31 July 2007 (9 pages)
011127 [View PDF (154 kB)]
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Fluctuations of the partial filling factors in competitive random sequential adsorption from binary mixtures
Arsen V. Subashiev and Serge Luryi
Published 31 July 2007 (13 pages)
011128 [View PDF (303 kB)]

Equilibrium and linear transport properties of fluids

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Entropy, local order, and the freezing transition in Morse liquids
Somendra Nath Chakraborty and Charusita Chakravarty
Published 13 July 2007 (9 pages)
011201 [View PDF (214 kB)]
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Self-consistent molecular dynamics formulation for electric-field-mediated electrolyte transport through nanochannels
A. V. Raghunathan and N. R. Aluru
Published 17 July 2007 (12 pages)
011202 [View PDF (380 kB)]

Granular materials

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Force transmission in a packing of pentagonal particles
Emilien Azéma, Farhang Radjaï, Robert Peyroux, and Gilles Saussine
Published 13 July 2007 (13 pages)
011301 [View PDF (1,919 kB)]

Colloidal dispersions, suspensions, and aggregates

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Low temperature behavior and glass line in the symmetrical colloidal electrolyte
Jose B. Caballero and Antonio M. Puertas
Published 10 July 2007 (9 pages)
011401 [View PDF (361 kB)]
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Effective nonadditive pair potential for lock-and-key interacting particles: The role of the limited valence
Julio Largo, Piero Tartaglia, and Francesco Sciortino
Published 13 July 2007 (4 pages)
011402 [View PDF (522 kB)]
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Fundamental-measure density functional for the fluid of aligned hard hexagons: Further insights in fundamental measure theory
José A. Capitán and José A. Cuesta
Published 18 July 2007 (9 pages)
011403 [View PDF (163 kB)]
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Evidence of the early stage of porphyrin aggregation by enhanced Raman scattering and fluorescence spectroscopy
Norberto Micali, Valentina Villari, Andrea Romeo, Maria Angela Castriciano, and Luigi Monsù Scolaro
Published 18 July 2007 (6 pages)
011404 [View PDF (464 kB)]
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Formation of magnetic filaments: A kinetic study
F. Martínez-Pedrero, M. Tirado-Miranda, A. Schmitt, and J. Callejas-Fernández
Published 18 July 2007 (9 pages)
011405 [View PDF (259 kB)]
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Physical age of soft-jammed systems
G. Ovarlez and P. Coussot
Published 19 July 2007 (7 pages)
011406 [View PDF (648 kB)]
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Density scaling laws for the structure of granular deposits
Daniel Rodríguez-Pérez, Jose L. Castillo, and J. Carlos Antoranz
Published 25 July 2007 (5 pages)
011407 [View PDF (356 kB)]
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Aggregation of liposomes in presence of La3+ : A study of the fractal dimension
Juan Sabín, Gerardo Prieto, Juan M. Ruso, Paula Messina, and Félix Sarmiento
Published 30 July 2007 (7 pages)
011408 [View PDF (744 kB)]
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Incoherent light transport in an anisotropic random medium: A probe of human erythrocyte aggregation and deformation
C. Baravian, F. Caton, J. Dillet, G. Toussaint, and P. Flaud
Published 31 July 2007 (7 pages)
011409 [View PDF (406 kB)]

Structured and complex fluids

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Charging dynamics of the electric double layer in porous media
Hidetsugu Sakaguchi and Reisei Baba
Published 2 July 2007 (7 pages)
011501 [View PDF (1,244 kB)]
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Do short-time fluctuations predict the long-time dynamic heterogeneity in a supercooled liquid?
J. A. Rodriguez Fris, L. M. Alarcón, and G. A. Appignanesi
Published 2 July 2007 (6 pages)
011502 [View PDF (391 kB)]
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Evidence for three-dimensional unstable flows in shear-banding wormlike micelles
Lydiane Bécu, Domitille Anache, Sébastien Manneville, and Annie Colin
Published 5 July 2007 (12 pages)
011503 [View PDF (1,236 kB)]
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Characterization of the potential energy landscape of an antiplasticized polymer
Robert A. Riggleman, Jack F. Douglas, and Juan J. de Pablo
Published 6 July 2007 (8 pages)
011504 [View PDF (438 kB)]
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Ultraslow relaxation of hydrogen-bonded dynamic clusters in glass-forming aqueous glucose solutions: A light scattering study
D. L. Sidebottom
Published 10 July 2007 (7 pages)
011505 [View PDF (1,098 kB)]
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Small-angle x-ray scattering measurements of the microstructure of liquid helium mixtures adsorbed in aerogel
L. B. Lurio, N. Mulders, M. Paetkau, M. H. W. Chan, and S. G. J. Mochrie
Published 12 July 2007 (10 pages)
011506 [View PDF (485 kB)]
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Revisiting the slow dynamics of a silica melt using Monte Carlo simulations
Ludovic Berthier
Published 16 July 2007 (12 pages)
011507 [View PDF (475 kB)]
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Dynamic glass transition in two dimensions
M. Bayer, J. M. Brader, F. Ebert, M. Fuchs, E. Lange, G. Maret, R. Schilling, M. Sperl, and J. P. Wittmer
Published 20 July 2007 (12 pages)
011508 [View PDF (647 kB)]
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Analysis of a heterodyne-detected transient-grating experiment on a molecular supercooled liquid. I. Basic formulation of the problem
A. Azzimani, C. Dreyfus, R. M. Pick, P. Bartolini, A. Taschin, and R. Torre
Published 24 July 2007 (6 pages)
011509 [View PDF (123 kB)]
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Analysis of a heterodyne-detected transient-grating experiment on a molecular supercooled liquid. II. Application to m -toluidine
A. Azzimani, C. Dreyfus, R. M. Pick, P. Bartolini, A. Taschin, and R. Torre
Published 24 July 2007 (10 pages)
011510 [View PDF (1,025 kB)]
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Model energy landscapes of low-temperature fluids: Dipolar hard spheres
Dmitry V. Matyushov
Published 24 July 2007 (7 pages)
011511 [View PDF (231 kB)]
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Scaling behavior in corrosion and growth of a passive film
F. D. A. Aarão Reis and Janusz Stafiej
Published 24 July 2007 (7 pages)
011512 [View PDF (144 kB)]
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Nucleation of lamellar domains from a sponge phase under shear flow: Shape selection of nuclei in a nonequilibrium steady state
Hideyuki Miyazawa and Hajime Tanaka
Published 27 July 2007 (9 pages)
011513 [View PDF (618 kB)]
•
Route to calculate the length scale for the glass transition in polymers
D. Cangialosi, A. Alegría, and J. Colmenero
Published 27 July 2007 (5 pages)
011514 [View PDF (170 kB)]

Films, interfaces, and crystal growth

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Linear stability analysis for step meandering instabilities with elastic interactions and Ehrlich-Schwoebel barriers
Dong-Hee Yeon, Pil-Ryung Cha, John S. Lowengrub, Axel Voigt, and K. Thornton
Published 11 July 2007 (15 pages)
011601 [View PDF (1,335 kB)]
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Evaporatively driven morphological instability
Robert W. Style and J. S. Wettlaufer
Published 16 July 2007 (6 pages)
011602 [View PDF (267 kB)]
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Localization in disordered media, anomalous roughening, and coarsening dynamics of faceted surfaces
Ivan G. Szendro, Juan M. López, and Miguel A. Rodríguez
Published 20 July 2007 (9 pages)
011603 [View PDF (1,507 kB)]
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Crystal growth in a three-phase system: Diffusion and liquid-liquid phase separation in lysozyme crystal growth
M. C. R. Heijna, W. J. P. van Enckevort, and E. Vlieg
Published 20 July 2007 (7 pages)
011604 [View PDF (639 kB)]
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Contact lines for fluid surface adhesion
Markus Deserno, Martin Michael Müller, and Jemal Guven
Published 26 July 2007 (10 pages)
011605 [View PDF (189 kB)]
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Topological defects in the crystalline state of one-component plasmas of nonuniform density
A. Mughal and M. A. Moore
Published 27 July 2007 (18 pages)
011606 [View PDF (1,824 kB)]
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Surface instability of confined elastic bilayers: Theory and simulations
Gaurav Tomar, Ashutosh Sharma, Vijay Shenoy, and Gautam Biswas
Published 30 July 2007 (8 pages)
011607 [View PDF (439 kB)]

Liquid crystals

•
Frustration in smectic layers of polar Gay-Berne systems
W. Józefowicz and L. Longa
Published 11 July 2007 (11 pages)
011701 [View PDF (612 kB)]
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Coupled director and polarization fluctuations in suspensions of ferroelectric nanoparticles in nematic liquid crystals
Martin Čopič, Alenka Mertelj, Olexandr Buchnev, and Yuri Reznikov
Published 11 July 2007 (5 pages)
011702 [View PDF (142 kB)]
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Stability of biaxial nematic phase for systems with variable molecular shape anisotropy
Lech Longa, Grzegorz Pająk, and Thomas Wydro
Published 13 July 2007 (6 pages)
011703 [View PDF (532 kB)]
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Possible model of an antiferroelectric twist grain boundary phase
J. G. Meier, M. Nobili, T. Carlsson, P. Rudquist, A. S. Petrenko, J. W. Goodby, M. Brunet, and S. T. Lagerwall
Published 13 July 2007 (9 pages)
011704 [View PDF (445 kB)]
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Influence of charge and flexibility on smectic phase formation in filamentous virus suspensions
Kirstin R. Purdy and Seth Fraden
Published 17 July 2007 (8 pages)
011705 [View PDF (331 kB)]
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Unconventional elasticity in smectic- A elastomers
Olaf Stenull and T. C. Lubensky
Published 18 July 2007 (11 pages)
011706 [View PDF (263 kB)]
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Coulomb-like interaction in nematic emulsions induced by external torques exerted on the colloids
V. M. Pergamenshchik and V. O. Uzunova
Published 19 July 2007 (8 pages)
011707 [View PDF (194 kB)]
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Solitary wave propagation in antiferroelectric liquid crystal cells and the quadrupolar term in the interlayer interaction
Jang-Kun Song, Atsuo Fukuda, and J. K. Vij
Published 20 July 2007 (5 pages)
011708 [View PDF (464 kB)]
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Temperature-induced sign reversal of biaxiality observed by conoscopy in some ferroelectric Sm-C* liquid crystals
Jang-kun Song, A. D. L. Chandani, Atsuo Fukuda, J. K. Vij, Ichiro Kobayashi, and A. V. Emelyanenko
Published 20 July 2007 (13 pages)
011709 [View PDF (835 kB)]
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Poisson-bracket approach to the dynamics of bent-core molecules
William Kung and M. Cristina Marchetti
Published 20 July 2007 (14 pages)
011710 [View PDF (216 kB)]
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Waves at surfactant-laden liquid-liquid crystal interface
S. V. Lishchuk
Published 20 July 2007 (16 pages)
011711 [View PDF (268 kB)]
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Glassy orientational dynamics of rodlike molecules near the isotropic-nematic transition
Biman Jana, Dwaipayan Chakrabarti, and Biman Bagchi
Published 25 July 2007 (6 pages)
011712 [View PDF (531 kB)]
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Quantitative analysis of the x-ray diffraction intensities of undulated smectic phases in bent-core liquid crystals
C. L. Folcia, J. Ortega, and J. Etxebarria
Published 25 July 2007 (7 pages)
011713 [View PDF (193 kB)]

Polymers

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Translocation and insertion of an amphiphilic polymer
Satoshi Tsuchiya and Akihiko Matsuyama
Published 2 July 2007 (6 pages)
011801 [View PDF (355 kB)]
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Dynamic scattering of semirigid macromolecules
I. A. Nyrkova and A. N. Semenov
Published 9 July 2007 (13 pages)
011802 [View PDF (226 kB)]
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Intramolecular long-range correlations in polymer melts: The segmental size distribution and its moments
J. P. Wittmer, P. Beckrich, H. Meyer, A. Cavallo, A. Johner, and J. Baschnagel
Published 12 July 2007 (18 pages)
011803 [View PDF (433 kB)]
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Free energy and extension of a semiflexible polymer in cylindrical confining geometries
Yingzi Yang, Theodore W. Burkhardt, and Gerhard Gompper
Published 19 July 2007 (7 pages)
011804 [View PDF (305 kB)]
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DNA stretch during electrophoresis due to a step change in mobility
Patrick T. Underhill and Patrick S. Doyle
Published 19 July 2007 (7 pages)
011805 [View PDF (195 kB)]
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Static conformation and dynamics of single DNA molecules confined in nanoslits
Po-Keng Lin, Chi-Cheng Fu, Y.-L. Chen, Yan-Ru Chen, Pei-Kuen Wei, C. H. Kuan, and W. S. Fann
Published 23 July 2007 (8 pages)
011806 [View PDF (275 kB)]
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Molecular-dynamics simulation study of the glass transition in amorphous polymers with controlled chain stiffness
Monica Bulacu and Erik van der Giessen
Published 26 July 2007 (11 pages)
011807 [View PDF (1,156 kB)]
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Laser-induced structures in a polymer blend in the vicinity of the phase boundary
A. Voit, A. Krekhov, and W. Köhler
Published 26 July 2007 (11 pages)
011808 [View PDF (474 kB)]
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Coarse-graining intramolecular hydrodynamic interaction in dilute solutions of flexible polymers
R. Prabhakar, E. M. Sevick, and D. R. M. Williams
Published 31 July 2007 (12 pages)
011809 [View PDF (299 kB)]
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Molecular dynamics simulation of diffusion of gases in a carbon-nanotube–polymer composite
Seong Y. Lim, Muhammad Sahimi, Theodore T. Tsotsis, and Nayong Kim
Published 31 July 2007 (15 pages)
011810 [View PDF (1,322 kB)]

Biological physics

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Generalized theory of site-specific DNA-protein interactions
R. Murugan
Published 2 July 2007 (9 pages)
011901 [View PDF (193 kB)]
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Speed of reaction diffusion in embryogenesis
Karen M. Page, Nicholas A. M. Monk, and Philip K. Maini
Published 5 July 2007 (15 pages)
011902 [View PDF (375 kB)]
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Bending rigidity of mixed phospholipid bilayers and the equilibrium radius of corresponding vesicles
M. M. A. E. Claessens, B. F. van Oort, F. A. M. Leermakers, F. A. Hoekstra, and M. A. Cohen Stuart
Published 11 July 2007 (6 pages)
011903 [View PDF (128 kB)]
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Intermittent dynamics underlying the intrinsic fluctuations of the collective synchronization patterns in electrocortical activity
Pulin Gong, Andrey R. Nikolaev, and Cees van Leeuwen
Published 11 July 2007 (7 pages)
011904 [View PDF (263 kB)]
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Spiking synchronization of ion channel clusters on an axon
Shangyou Zeng, Yi Tang, and Peter Jung
Published 11 July 2007 (7 pages)
011905 [View PDF (193 kB)]
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Raman intensity and spectra predictions for cylindrical viruses
Eric C. Dykeman, Otto F. Sankey, and Kong-Thon Tsen
Published 11 July 2007 (12 pages)
011906 [View PDF (1,316 kB)]
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Dynamics of the Davydov-Scott monomer in a thermal bath: Comparison of the full quantum and semiclassical approaches
J. Cuevas, P. A. S. Silva, F. R. Romero, and L. Cruzeiro
Published 12 July 2007 (8 pages)
011907 [View PDF (1,011 kB)]
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Complex population dynamics as a competition between multiple-time-scale phenomena
Ioana Bena, Michel Droz, Janusz Szwabiński, and Andrzej Pȩkalski
Published 16 July 2007 (14 pages)
011908 [View PDF (467 kB)]
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Opening rates of DNA hairpins: Experiment and model
Jeungphill Hanne, Giovanni Zocchi, Nikolaos K. Voulgarakis, Alan R. Bishop, and Kim Ø. Rasmussen
Published 16 July 2007 (8 pages)
011909 [View PDF (743 kB)]
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Frustration, drift, and antiphase coupling in a neural array
Oliver Weihberger and Sonya Bahar
Published 16 July 2007 (9 pages)
011910 [View PDF (681 kB)]
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Analysis of structures causing instabilities
Thomas Wilhelm
Published 17 July 2007 (8 pages)
011911 [View PDF (124 kB)]
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Coupled composition-deformation phase-field method for multicomponent lipid membranes
Chloe M. Funkhouser, Francisco J. Solis, and K. Thornton
Published 17 July 2007 (15 pages)
011912 [View PDF (15,834 kB)]
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Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing
Jaegil Kim, John E. Straub, and Thomas Keyes
Published 18 July 2007 (8 pages)
011913 [View PDF (833 kB)]
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Dynamic and static light scattering analysis of DNA ejection from the phage λ
David Löf, Karin Schillén, Bengt Jönsson, and Alex Evilevitch
Published 20 July 2007 (11 pages)
011914 [View PDF (1,536 kB)]
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Theoretical study of kinetics of zipping phenomena in biomimetic polymers
Arthi Jayaraman, Erik E. Santiso, Carol K. Hall, and Jan Genzer
Published 24 July 2007 (5 pages)
011915 [View PDF (123 kB)]
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Gap junctions mediate large-scale Turing structures in a mean-field cortex driven by subcortical noise
Moira L. Steyn-Ross, D. A. Steyn-Ross, M. T. Wilson, and J. W. Sleigh
Published 24 July 2007 (16 pages)
011916 [View PDF (2,030 kB)]
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Representing perturbed dynamics in biological network models
Gautier Stoll, Jacques Rougemont, and Felix Naef
Published 25 July 2007 (6 pages)
011917 [View PDF (2,374 kB)]
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Stress fluctuations and motion of cytoskeletal-bound markers
Carina Raupach, Daniel Paranhos Zitterbart, Claudia T. Mierke, Claus Metzner, Frank A. Müller, and Ben Fabry
Published 25 July 2007 (12 pages)
011918 [View PDF (857 kB)]
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Evolution of microorganism locomotion induced by starvation
G. J. Sibona
Published 25 July 2007 (9 pages)
011919 [View PDF (197 kB)]
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Effects of dielectric discontinuities on two charged plates
Y. S. Jho, G. Park, C. S. Chang, P. A. Pincus, and M. W. Kim
Published 26 July 2007 (8 pages)
011920 [View PDF (310 kB)]
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Balancing torques in membrane-mediated interactions: Exact results and numerical illustrations
Martin Michael Müller, Markus Deserno, and Jemal Guven
Published 26 July 2007 (16 pages)
011921 [View PDF (499 kB)]
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Inverted catenoid as a fluid membrane with two points pulled together
Pavel Castro-Villarreal and Jemal Guven
Published 27 July 2007 (9 pages)
011922 [View PDF (233 kB)]
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Nonlinear drift-diffusion model of gating in the fast Cl channel
S. R. Vaccaro
Published 30 July 2007 (6 pages)
011923 [View PDF (127 kB)]
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Simple stochastic model for the evolution of protein lengths
C. Destri and C. Miccio
Published 30 July 2007 (12 pages)
011924 [View PDF (245 kB)]
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Liposome-induced DNA compaction and reentrant condensation investigated by dielectric relaxation spectroscopy and dynamic light scattering techniques
S. Zuzzi, C. Cametti, G. Onori, and S. Sennato
Published 30 July 2007 (11 pages)
011925 [View PDF (792 kB)]
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Model for Osteosarcoma-9 as a potent factor in cell survival and resistance to apoptosis
Ekaterini Vourvouhaki, Carla Carvalho, and Paulo Aguiar
Published 31 July 2007 (10 pages)
011926 [View PDF (595 kB)]

BRIEF REPORTS

Statistical physics

•
Theoretical test of Jarzynski’s equality for reversible volume-switching processes of an ideal gas system
Jaeyoung Sung
Published 18 July 2007 (3 pages)
012101 [View PDF (68 kB)]
•
Universality class of the two-dimensional site-diluted Ising model
P. H. L. Martins and J. A. Plascak
Published 31 July 2007 (4 pages)
012102 [View PDF (341 kB)]

Biological physics

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Improving an all-atom force field
Sandipan Mohanty and U. H. E. Hansmann
Published 18 July 2007 (4 pages)
012901 [View PDF (102 kB)]
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Magnetization of circular DNA
Seongjin Kim, Juyeon Yi, and M. Y. Choi
Published 19 July 2007 (4 pages)
012902 [View PDF (324 kB)]

COMMENTS

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Comment on “Correlations between isobaric and isochoric fragilities and thermodynamical scaling exponent for glass-forming liquids”
R. Casalini and C. M. Roland
Published 18 July 2007 (2 pages)
013501 [View PDF (47 kB)]
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Reply to “Comment on ‘Correlations between isobaric and isochoric fragilities and thermodynamical scaling exponent for glass-forming liquids’   ”
A. Grzybowski, K. Grzybowska, J. Zioło, and M. Paluch
Published 18 July 2007 (2 pages)
013502 [View PDF (36 kB)]
•
Comment on “Characterization of the tunneling conductance across DNA bases”
Johan Lagerqvist, Michael Zwolak, and Massimiliano Di Ventra
Published 9 July 2007 (3 pages)
013901 [View PDF (92 kB)]
•
Reply to “Comment on ‘Characterization of the tunneling conductance across DNA bases’ ”
Radomir Zikic, Predrag S. Krstić, X.-G. Zhang, Miguel Fuentes-Cabrera, Jack Wells, and Xiongce Zhao
Published 9 July 2007 (2 pages)
013902 [View PDF (39 kB)]

Part 2 - Nonlinear and Plasma Physics, Fluid Dynamics, and Related Topics

RAPID COMMUNICATIONS

Interdisciplinary physics

•
Emergence of self-sustained patterns in small-world excitable media
Sitabhra Sinha, Jari Saramäki, and Kimmo Kaski
Published 9 July 2007 (4 pages)
015101(R) [View PDF (246 kB)]
•
Partitioning and modularity of graphs with arbitrary degree distribution
Jörg Reichardt and Stefan Bornholdt
Published 10 July 2007 (4 pages)
015102(R) [View PDF (141 kB)]

Chaos and pattern formation

•
Quantum resonances and ratchets in free-falling frames
Itzhack Dana and Vladislav Roitberg
Published 13 July 2007 (4 pages)
015201(R) [View PDF (107 kB)]
•
Fractal conductance fluctuations of classical origin
H. Hennig, R. Fleischmann, L. Hufnagel, and T. Geisel
Published 16 July 2007 (4 pages)
015202(R) [View PDF (558 kB)]

Fluid dynamics

•
Controlling the stability transfer between oppositely traveling waves and standing waves by inversion-symmetry-breaking perturbations
A. Pinter, M. Lücke, and Ch. Hoffmann
Published 6 July 2007 (4 pages)
015301(R) [View PDF (191 kB)]

ARTICLES

Interdisciplinary physics

•
Ensemble approach to the analysis of weighted networks
S. E. Ahnert, D. Garlaschelli, T. M. A. Fink, and G. Caldarelli
Published 2 July 2007 (5 pages)
016101 [View PDF (95 kB)]
•
Numerical study of drying process and columnar fracture process in granule-water mixtures
Akihiro Nishimoto, Tsuyoshi Mizuguchi, and So Kitsunezaki
Published 3 July 2007 (11 pages)
016102 [View PDF (1,554 kB)]
•
Lattice model for self-assembly with application to the formation of cytoskeletal-like structures
Shannon F. Stewman and Aaron R. Dinner
Published 11 July 2007 (9 pages)
016103 [View PDF (420 kB)]
•
Synchronization in time-varying networks: A matrix measure approach
Maoyin Chen
Published 11 July 2007 (10 pages)
016104 [View PDF (919 kB)]
•
Hysteresis phenomena of the intelligent driver model for traffic flow
Wang Dahui, Wei Ziqiang, and Fan Ying
Published 12 July 2007 (7 pages)
016105 [View PDF (1,670 kB)]
•
Self-emergence of knowledge trees: Extraction of the Wikipedia hierarchies
Lev Muchnik, Royi Itzhack, Sorin Solomon, and Yoram Louzoun
Published 13 July 2007 (12 pages)
016106 [View PDF (1,502 kB)]
•
Activity-dependent neural network model on scale-free networks
Gian Luca Pellegrini, Lucilla de Arcangelis, Hans J. Herrmann, and Carla Perrone-Capano
Published 17 July 2007 (9 pages)
016107 [View PDF (524 kB)]
•
Statistical analysis of financial returns for a multiagent order book model of asset trading
Tobias Preis, Sebastian Golke, Wolfgang Paul, and Johannes J. Schneider
Published 20 July 2007 (13 pages)
016108 [View PDF (654 kB)]
•
Relation between volatility correlations in financial markets and Omori processes occurring on all scales
Philipp Weber, Fengzhong Wang, Irena Vodenska-Chitkushev, Shlomo Havlin, and H. Eugene Stanley
Published 24 July 2007 (8 pages)
016109 [View PDF (414 kB)]
•
Relationship between microscopic dynamics in traffic flow and complexity in networks
Xin-Gang Li, Zi-You Gao, Ke-Ping Li, and Xiao-Mei Zhao
Published 25 July 2007 (7 pages)
016110 [View PDF (618 kB)]

Chaos and pattern formation

•
Propagation and refraction of chemical waves generated by local periodic forcing in a reaction-diffusion model
Renwu Zhang, Lingfa Yang, Anatol M. Zhabotinsky, and Irving R. Epstein
Published 2 July 2007 (5 pages)
016201 [View PDF (446 kB)]
•
Fingering instabilities of a reactive micellar interface
Thomas Podgorski, Michael C. Sostarecz, Sylvain Zorman, and Andrew Belmonte
Published 2 July 2007 (6 pages)
016202 [View PDF (360 kB)]
•
Doubly diversity-induced resonance
Martin Gassel, Erik Glatt, and Friedemann Kaiser
Published 3 July 2007 (7 pages)
016203 [View PDF (911 kB)]
•
Transitions to amplitude death in a regular array of nonlinear oscillators
Junzhong Yang
Published 9 July 2007 (5 pages)
016204 [View PDF (938 kB)]
•
Survival versus collapse: Abrupt drop of excitability kills the traveling pulse, while gradual change results in adaptation
Masanobu Tanaka, Hiroki Nagahara, Hiroyuki Kitahata, Valentin Krinsky, Konstantin Agladze, and Kenichi Yoshikawa
Published 10 July 2007 (6 pages)
016205 [View PDF (215 kB)]
•
Spiral waves in linearly coupled reaction-diffusion systems
Hujiang Yang and Junzhong Yang
Published 10 July 2007 (8 pages)
016206 [View PDF (1,978 kB)]
•
Adaptive coupling and enhanced synchronization in coupled phase oscillators
Quansheng Ren and Jianye Zhao
Published 10 July 2007 (6 pages)
016207 [View PDF (623 kB)]
•
Fractal dimension in dissipative chaotic scattering
Jesús M. Seoane, Miguel A. F. Sanjuán, and Ying-Cheng Lai
Published 10 July 2007 (6 pages)
016208 [View PDF (570 kB)]
•
Estimating system parameters from chaotic time series with synchronization optimized by a genetic algorithm
Chao Tao, Yu Zhang, and Jack J. Jiang
Published 11 July 2007 (5 pages)
016209 [View PDF (774 kB)]
•
Distinguishing quasiperiodic dynamics from chaos in short-time series
Y. Zou, D. Pazó, M. C. Romano, M. Thiel, and J. Kurths
Published 13 July 2007 (12 pages)
016210 [View PDF (12,313 kB)]
•
Multiresonant control of two-dimensional dynamical systems
I. Barth and L. Friedland
Published 19 July 2007 (8 pages)
016211 [View PDF (3,079 kB)]
•
Wave chaos in rotating optical cavities
Takahisa Harayama, Satoshi Sunada, and Tomohiro Miyasaka
Published 23 July 2007 (4 pages)
016212 [View PDF (911 kB)]
•
Comparing the coherence resonance curves invoked by different types of forcing
J. Escalona, Gerardo J. Escalera Santos, and P. Parmananda
Published 23 July 2007 (4 pages)
016213 [View PDF (77 kB)]
•
Fermi acceleration in the randomized driven Lorentz gas and the Fermi-Ulam model
A. K. Karlis, P. K. Papachristou, F. K. Diakonos, V. Constantoudis, and P. Schmelcher
Published 23 July 2007 (17 pages)
016214 [View PDF (545 kB)]
•
Semiclassical expansion of the smooth part of the density of states, with application to the hydrogen atom in a uniform magnetic field
Hervé Kunz, Thierry Schüpbach, and Marc-André Dupertuis
Published 23 July 2007 (9 pages)
016215 [View PDF (207 kB)]
•
Stability properties of the N∕4 ( π∕2 -mode) one-mode nonlinear solution of the Fermi-Pasta-Ulam- β system
M. Leo and R. A. Leo
Published 24 July 2007 (8 pages)
016216 [View PDF (161 kB)]
•
Dynamics of hexagonal patterns in a self-focusing Kerr cavity
Damià Gomila and Pere Colet
Published 25 July 2007 (10 pages)
016217 [View PDF (906 kB)]
•
Chaotic phase synchronization in scale-free networks of bursting neurons
C. A. S. Batista, A. M. Batista, J. A. C. de Pontes, R. L. Viana, and S. R. Lopes
Published 30 July 2007 (10 pages)
016218 [View PDF (1,836 kB)]
•
Controlled destruction of chaos in the multistable regime
B. K. Goswami
Published 31 July 2007 (7 pages)
016219 [View PDF (560 kB)]
•
From phase space to frequency domain: A time-frequency analysis for chaotic time series
Junfeng Sun, Yi Zhao, Tomomichi Nakamura, and Michael Small
Published 31 July 2007 (8 pages)
016220 [View PDF (1,211 kB)]

Fluid dynamics

•
Shear turbulence on a sparse spectral grid
F. De Lillo and Bruno Eckhardt
Published 3 July 2007 (7 pages)
016301 [View PDF (352 kB)]
•
Multiple resonant scattering of water waves by a two-dimensional array of vertical cylinders: Linear aspects
Yile Li and Chiang C. Mei
Published 9 July 2007 (23 pages)
016302 [View PDF (893 kB)]
•
Hydromagnetic instability in plane Couette flow
Alfio Bonanno and Vadim Urpin
Published 9 July 2007 (6 pages)
016303 [View PDF (235 kB)]
•
Enhanced mixing in laminar flows using ultrahydrophobic surfaces
Jia Ou, Geoffrey R. Moss, and Jonathan P. Rothstein
Published 12 July 2007 (10 pages)
016304 [View PDF (626 kB)]
•
Supercomplex wave-vortex multiscale phenomena induced in laser-matter interactions
S. Lugomer, Y. Fukumoto, B. Farkas, T. Szörényi, and A. Toth
Published 12 July 2007 (15 pages)
016305 [View PDF (1,548 kB)]
•
Marangoni convection in binary mixtures
Jie Zhang, Robert P. Behringer, and Alexander Oron
Published 16 July 2007 (7 pages)
016306 [View PDF (531 kB)]
•
Modeling the dynamics of a free boundary on turbulent thermal convection
Jin-Qiang Zhong and Jun Zhang
Published 16 July 2007 (12 pages)
016307 [View PDF (978 kB)]
•
Producing swimmers by coupling reaction-diffusion equations to a chemically responsive material
C. M. Pooley and Anna C. Balazs
Published 18 July 2007 (7 pages)
016308 [View PDF (315 kB)]
•
Fluctuating interface in a dilute sedimenting suspension
Evgeny S. Asmolov
Published 18 July 2007 (10 pages)
016309 [View PDF (559 kB)]
•
Traveling waves in a magnetized Taylor-Couette flow
Wei Liu, Jeremy Goodman, and Hantao Ji
Published 19 July 2007 (4 pages)
016310 [View PDF (3,368 kB)]
•
Vorticity structuring and velocity rolls triggered by gradient shear bands
Suzanne M. Fielding
Published 23 July 2007 (8 pages)
016311 [View PDF (234 kB)]
See Also: Publisher's Note
•
Spin coating of non-Newtonian fluids with a moving front
J. P. F. Charpin, M. Lombe, and T. G. Myers
Published 24 July 2007 (9 pages)
016312 [View PDF (332 kB)]
•
Epicyclic orbits in a viscous fluid about a precessing rod: Theory and experiments at the micro- and macro-scales
Elizabeth L. Bouzarth, Adam Brooks, Roberto Camassa, Hao Jing, Terry Jo Leiterman, Richard M. McLaughlin, Richard Superfine, Jonathan Toledo, and Leandra Vicci
Published 25 July 2007 (5 pages)
016313 [View PDF (376 kB)]
•
Multiple flow transitions in a box heated from the side in low-Prandtl-number fluids
D. Henry and H. BenHadid
Published 27 July 2007 (9 pages)
016314 [View PDF (559 kB)]
•
Prediction of fluid occupancy in fractures using network modeling and x-ray microtomography. I: Data conditioning and model description
Zuleima T. Karpyn and Mohammad Piri
Published 31 July 2007 (13 pages)
016315 [View PDF (1,363 kB)]
•
Prediction of fluid occupancy in fractures using network modeling and x-ray microtomography. II: Results
Mohammad Piri and Zuleima T. Karpyn
Published 31 July 2007 (11 pages)
016316 [View PDF (2,861 kB)]

Plasma physics

•
Giant electromagnetic vortex and MeV monoenergetic electrons generated by short laser pulses in underdense plasma near quarter critical density region
Alexei Zhidkov, Koshichi Nemoto, Takuya Nayuki, Yuji Oishi, and Takashi Fuji
Published 5 July 2007 (8 pages)
016401 [View PDF (1,096 kB)]
•
Existence of multisite intrinsic localized modes in one-dimensional Debye crystals
V. Koukouloyannis and I. Kourakis
Published 9 July 2007 (10 pages)
016402 [View PDF (371 kB)]
•
Memory and persistence correlation of microstructural fluctuations in two-dimensional dusty plasma liquids
Yu-Hsuan Huang and Lin I
Published 10 July 2007 (6 pages)
016403 [View PDF (922 kB)]
•
Probing instabilities in arc plasma devices using binary gas mixtures
S. Ghorui, M. Vysohlid, J. V. R. Heberlein, and E. Pfender
Published 19 July 2007 (13 pages)
016404 [View PDF (1,458 kB)]
•
Influence of damping on proton energy loss in plasmas of all degeneracies
Manuel D. Barriga-Carrasco
Published 20 July 2007 (7 pages)
016405 [View PDF (395 kB)]
•
Relativistic statistical thermodynamics of dense photon gas
Levan N. Tsintsadze, Yasuaki Kishimoto, Dirk K. Callebaut, and Nodar L. Tsintsadze
Published 30 July 2007 (7 pages)
016406 [View PDF (121 kB)]

Classical physics

•
Spatial coherence of the thermal electromagnetic field in the vicinity of a dielectric slab
Wah Tung Lau, Jung-Tsung Shen, Georgios Veronis, and Shanhui Fan
Published 10 July 2007 (11 pages)
016601 [View PDF (577 kB)]
•
Self-bending of dark and gray photorefractive solitons
M. I. Carvalho, M. Facão, and D. N. Christodoulides
Published 10 July 2007 (8 pages)
016602 [View PDF (257 kB)]
•
Polarization-dependent tunneling of light in gradient optics
A. Shvartsburg, V. Kuzmiak, and G. Petite
Published 12 July 2007 (11 pages)
016603 [View PDF (628 kB)]
•
Bandwidth control of forbidden transmission gaps in compound structures with subwavelength slits
Diana C. Skigin, Hung Loui, Zoya Popovic, and Edward F. Kuester
Published 16 July 2007 (6 pages)
016604 [View PDF (265 kB)]
•
Dynamics of a curved Fermi-Pasta-Ulam chain: Effects of geometry, long-range interaction, and nonlinear dispersion
Ranja Sarkar and Bishwajyoti Dey
Published 17 July 2007 (12 pages)
016605 [View PDF (285 kB)]
•
Surface-plasmon-induced optical magnetic response in perforated trilayer metamaterial
T. Li, H. Liu, F. M. Wang, J. Q. Li, Y. Y. Zhu, and S. N. Zhu
Published 23 July 2007 (5 pages)
016606 [View PDF (808 kB)]
•
Creeping solitons in dissipative systems and their bifurcations
Wonkeun Chang, Adrian Ankiewicz, Nail Akhmediev, and J. M. Soto-Crespo
Published 26 July 2007 (8 pages)
016607 [View PDF (4,658 kB)]
•
Theoretical approach to photoinduced inhomogeneous anisotropy in bacteriorhodopsin films
P. Acebal, L. Carretero, S. Blaya, A. Murciano, and A. Fimia
Published 30 July 2007 (8 pages)
016608 [View PDF (217 kB)]
•
Particle plasmons of metal nanospheres: Application of multiple scattering approach
Ruey-Lin Chern, Xing-Xiang Liu, and Chien-Cheng Chang
Published 30 July 2007 (9 pages)
016609 [View PDF (2,711 kB)]

Computational physics

•
Stochastic analysis and simulation of spin star systems
Heinz-Peter Breuer and Francesco Petruccione
Published 6 July 2007 (8 pages)
016701 [View PDF (140 kB)]
•
Lattice Boltzmann method for thermal flow simulation on standard lattices
Nikolaos I. Prasianakis and Iliya V. Karlin
Published 9 July 2007 (11 pages)
016702 [View PDF (499 kB)]
•
Choosing weights for simulated tempering
Sanghyun Park and Vijay S. Pande
Published 16 July 2007 (5 pages)
016703 [View PDF (267 kB)]
•
Entropic effects in large-scale Monte Carlo simulations
Cristian Predescu
Published 18 July 2007 (13 pages)
016704 [View PDF (246 kB)]
•
Symmetric four-dimensional polytope and visualization method in four, eight, and sixteen dimensions using Hopf maps
Eric Lewin Altschuler and Antonio Pérez-Garrido
Published 18 July 2007 (6 pages)
016705 [View PDF (253 kB)]
•
Data-based parameter estimation of generalized multidimensional Langevin processes
Illia Horenko, Carsten Hartmann, Christof Schütte, and Frank Noe
Published 19 July 2007 (9 pages)
016706 [View PDF (512 kB)]
•
Lattice Boltzmann simulation of dense gas flows in microchannels
Yong Shi, T. S. Zhao, and Zhaoli Guo
Published 23 July 2007 (8 pages)
016707 [View PDF (188 kB)]
•
Numerical methods for the stochastic Landau-Lifshitz Navier-Stokes equations
John B. Bell, Alejandro L. Garcia, and Sarah A. Williams
Published 26 July 2007 (12 pages)
016708 [View PDF (401 kB)]
•
Control of density fluctuations in atomistic-continuum simulations of dense liquids
E. M. Kotsalis, J. H. Walther, and P. Koumoutsakos
Published 30 July 2007 (7 pages)
016709 [View PDF (242 kB)]

BRIEF REPORTS

Interdisciplinary physics

•
Enhancing the transmission efficiency by edge deletion in scale-free networks
Guo-Qing Zhang, Di Wang, and Guo-Jie Li
Published 13 July 2007 (4 pages)
017101 [View PDF (130 kB)]

Chaos and pattern formation

•
Finite-size Lyapunov exponent for Levy processes
R. Parashar and J. H. Cushman
Published 11 July 2007 (4 pages)
017201 [View PDF (96 kB)]
•
Transversal dynamics of a non-locally-coupled map lattice
S. E. de S. Pinto, I. L. Caldas, A. M. Batista, S. R. Lopes, and R. L. Viana
Published 11 July 2007 (4 pages)
017202 [View PDF (2,816 kB)]
•
Formation of white-eye patterns with microdischarge in an air dielectric-barrier-discharge system
Yafeng He, Lifang Dong, Weili Liu, Hongfang Wang, Zengchao Zhao, and Weili Fan
Published 13 July 2007 (4 pages)
017203 [View PDF (382 kB)]
•
Stabilized Kuramoto-Sivashinsky equation: A useful model for secondary instabilities and related dynamics of experimental one-dimensional cellular flows
P. Brunet
Published 13 July 2007 (4 pages)
017204 [View PDF (671 kB)]
•
Soliton turbulence in the complex Ginzburg-Landau equation
Hidetsugu Sakaguchi
Published 23 July 2007 (4 pages)
017205 [View PDF (177 kB)]

Fluid dynamics

•
Micronanostructures of the scales on a mosquito’s legs and their role in weight support
C. W. Wu, X. Q. Kong, and Diane Wu
Published 5 July 2007 (4 pages)
017301 [View PDF (464 kB)]

Plasma physics

•
Diffusive radiation in one-dimensional Langmuir turbulence
G. D. Fleishman and I. N. Toptygin
Published 10 July 2007 (4 pages)
017401 [View PDF (128 kB)]
•
Effect of positron space charge on operation of an antihydrogen trap
C. A. Ordonez
Published 16 July 2007 (3 pages)
017402 [View PDF (75 kB)]

ERRATA

•
Erratum: Symmetry-based determination of space-time functions in nonequilibrium growth processes [Phys. Rev. E 74, 061604 (2006)]
Andreas Röthlein, Florian Baumann, and Michel Pleimling
Published 2 July 2007 (2 pages)
019901(E) [View PDF (269 kB)]
•
Publisher's Note: Inferring Markov chains: Bayesian estimation, model comparison, entropy rate, and out-of-class modeling [Phys. Rev. E 76, 011106 (2007)]
Christopher C. Strelioff, James P. Crutchfield, and Alfred W. Hübler
Published 23 July 2007 (1 page)
019902(E) [View PDF (18 kB)]
•
Publisher's Note: Griffiths singularities and algebraic order in the exact solution of an Ising model on a fractal modular network [Phys. Rev. E 75, 061104 (2007)]
Michael Hinczewski
Published 26 July 2007 (1 page)
019903(E) [View PDF (19 kB)]
•
Publisher's Note: Vorticity structuring and velocity rolls triggered by gradient shear bands [Phys. Rev. E 76, 016311 (2007)]
Suzanne M. Fielding
Published 31 July 2007 (1 page)
019904(E) [View PDF (19 kB)]