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Physical Review EPhysical Review E, interdisciplinary in scope, focuses on many-body phenomena, including recent developments in quantum and classical chaos and soft matter physics. It has sections on statistical physics, equilibrium and transport properties of fluids, liquid crystals, complex fluids, polymers, chaos, fluid dynamics, plasma physics, classical physics, and computational physics. In addition, the journal features sections on two rapidly growing areas: biological physics and granular materials. More...
Statistical physics
Seung Ki Baek, Hiroyuki Shima, and Beom Jun Kim
We study low-temperature properties of the XY spin model on a negatively curved surface. Geometric curvature of the surface gives rise to frustration in local spin configuration, which results in the formation of high-energy spin clusters scattered over the system. Asymptotic behavior of the spin-...
[Phys. Rev. E 79, 060106
] Published Mon Jun 22, 2009
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Fei Liu and Zhong-can Ou-Yang
Using Feynman-Kac and Cameron-Martin-Girsanov formulas, we find a generalized integral fluctuation theorem (GIFT) for general diffusion processes by constructing a time-invariable integral. The existing integral fluctuation theorems can be derived as its specific cases. We interpret the origin of th...
[Phys. Rev. E 79, 060107
] Published Mon Jun 22, 2009
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Alberto Enciso, Federico Finkel, and Artemio González-López
We show that the density of energy levels of a wide class of finite-dimensional quantum systems tends to a Gaussian distribution as the number of degrees of freedom increases. Our result is based on a variant of the central limit theorem which is especially suited to models whose partition function ...
[Phys. Rev. E 79, 060105
] Published Fri Jun 19, 2009
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P. Zhang and B. Shen
We study the thermoacoustic wave propagation and reflection near the liquid-gas critical point. Specifically, we perform a numerical investigation of the acoustic responses in a near-critical fluid to thermal perturbations based on the same setup of a recent ultrasensitive interferometry measurement...
[Phys. Rev. E 79, 060103
] Published Thu Jun 18, 2009
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Valentin Blickle, Jakob Mehl, and Clemens Bechinger
We study the relaxation of a single colloidal sphere which is periodically driven between two nonequilibrium steady states. Experimentally, this is achieved by driving the particle along a toroidal trap imposed by scanned optical tweezers. We find that the relaxation time after which the probability...
[Phys. Rev. E 79, 060104
] Published Thu Jun 18, 2009
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Adam Lipowski and Dorota Lipowska
We study a two-lane model of two species of particles that perform biased diffusion. Extensive numerical simulations show that when bias q is strong enough, oppositely drifting particles form some clusters that block each other. Coarsening of such clusters is very slow and their size increases log...
[Phys. Rev. E 79, 060102
] Published Wed Jun 17, 2009
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Bo Li, Sheng-Hao Li, and Huan-Qiang Zhou
A systematic analysis is performed for quantum phase transitions in a two-dimensional anisotropic spin-1/2 antiferromagnetic XYX model in an external magnetic field. With the help of an innovative tensor network algorithm, we compute the fidelity per lattice site to demonstrate that the field-indu...
[Phys. Rev. E 79, 060101
] Published Mon Jun 1, 2009
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Carl T. West, Tomaz Prosen, and Tsampikos Kottos
We study the Loschmidt echo F(t) for a class of dynamical systems showing critical chaos. Using a kicked rotor with singular potential as a prototype model, we found that the classical echo shows a gap (initial drop) 1−Fg , where Fg scales as Fg(α,ϵ,η)=fcl(χcl≡η3−α/ϵ) ; α is th...
[Phys. Rev. E 79, 050107
] Published Fri May 29, 2009
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Granular materials
S. A. Galindo-Torres, F. Alonso-Marroquín, Y. C. Wang, D. Pedroso, and J. D. Muñoz Castaño
We investigate the macroscopic properties of frictionless nonconvex particles using molecular dynamics. The calculations are based on a simple and efficient method to simulate complex-shaped interacting bodies. The particle shape is represented by Minkowski operators. A multicontact time-continuous ...
[Phys. Rev. E 79, 060301
] Published Mon Jun 22, 2009
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Colloidal dispersions, suspensions, and aggregates
J. Guery, J. Baudry, D. A. Weitz, P. M. Chaikin, and J. Bibette
The permeability of solids has long been associated with a diffusive process involving activated mechanism as originally envisioned by Eyring. Tensile stress can affect the activation energy but definitive experiments of the diffusion rate of species through a stressed solid are lacking. Here we use...
[Phys. Rev. E 79, 060402
] Published Mon Jun 29, 2009
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L. Fornasari, F. Mantegazza, M. L. Jimenez, M. Buscaglia, and T. Bellini
Binary mixtures of larger and smaller colloids having charges of equal sign display unusual response to low-frequency electric fields. We show here that the previously reported negative torque acting on rodlike particles when in presence of a sea of smaller particles is accompanied by a field-induce...
[Phys. Rev. E 79, 060401
] Published Tue Jun 9, 2009
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Structured and complex fluids
Kang Kim and Shinji Saito
A multitime probing of density fluctuations is introduced to investigate hidden time scales of heterogeneous dynamics in glass-forming liquids. Molecular-dynamics simulations for simple glass-forming liquids are performed and a three-time correlation function is numerically calculated for general ti...
[Phys. Rev. E 79, 060501
] Published Fri Jun 12, 2009
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Liquid crystals
Surajit Dhara, Jin Ki Kim, Soon Moon Jeong, Reiri Kogo, Fumito Araoka, Ken Ishikawa, and Hideo Takezoe
We report a strong discontinuous orientational transition (anchoring transition) of liquid-crystal molecules with a large transverse dipole moment. A perfluoropolymer was used as an alignment layer and the transition was observed from planar to homeotropic with decreasing temperature in the nematic ...
[Phys. Rev. E 79, 060701
] Published Tue Jun 2, 2009
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Polymers
Noboru Osaka, Hitoshi Endo, Toshihiko Nishida, Takuya Suzuki, Huan-jun Li, Kazutoshi Haraguchi, and Mitsuhiro Shibayama
Microphase separation in poly( N -isopropylacrylamide)(PNIPA)-clay nanocomposite hydrogels (NC gels) is investigated by means of contrast-variation small-angle neutron scattering (CV-SANS) and dynamic light scattering (DLS). By using CV-SANS, it is revealed that microphase separation occurs in NC ge...
[Phys. Rev. E 79, 060801
] Published Mon Jun 15, 2009
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Biological physics
Alexey K. Mazur
A promising method for measuring intramolecular distances in solution uses small-angle x-ray scattering interference between gold nanocrystal labels [Mathew-Fenn , Science 322, 446 (2008)]. When applied to double-stranded DNA, it revealed that the DNA length fluctuations are strikingly strong and co...
[Phys. Rev. E 80, 010901
] Published Thu Jul 2, 2009
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Thomas Butler, Nigel Goldenfeld, Damien Mathew, and Zaida Luthey-Schulten
A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, eff...
[Phys. Rev. E 79, 060901
] Published Wed Jun 17, 2009
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Olaf J. Rolinski, Katherine Scobie, and David J. S. Birch
We present a description of fluorescence decay kinetics in complex environments based on gamma functions rather than the conventional approach using exponentials. The gamma function description is tested in measurements on the temperature dependence of the protein human serum albumin (HSA), N-acetyl...
[Phys. Rev. E 79, 050901
] Published Thu May 28, 2009
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Interdisciplinary physics
Attila Fekete, Gábor Vattay, and Márton Pósfai
In this Rapid Communication we present an analytic study of sampled networks in the case of some important shortest-path sampling models. We present analytic formulas for the probability of edge discovery in the case of an evolving and a static network model. We also show that the number of discover...
[Phys. Rev. E 79, 065101
] Published Tue Jun 23, 2009
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Chaos and pattern formation
M. Zeitler, A. Daffertshofer, and C. C. A. M. Gielen
We studied the dynamics of synchronization in asymmetrically coupled neural oscillators with time delay. Stability analysis revealed that symmetric excitatory coupling results in synchrony at multiple phase relations. Asymmetry yields two saddle-node bifurcations of the stable states when coupling i...
[Phys. Rev. E 79, 065203
] Published Thu Jun 11, 2009
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Adilson E. Motter and Katrin Gelfert
We study the behavior of dynamical systems under time reparameterizations, which is important not only to characterize chaos in relativistic systems but also to probe the invariance of dynamical quantities. We first show that time transformations are locally equivalent to metric transformations, a r...
[Phys. Rev. E 79, 065202
] Published Tue Jun 9, 2009
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V. Flunkert, O. D’Huys, J. Danckaert, I. Fischer, and E. Schöll
We theoretically study chaos synchronization of two lasers which are delay coupled via an active or a passive relay. While the lasers are synchronized, their dynamics is identical to a single laser with delayed feedback for a passive relay and identical to two delay-coupled lasers for an active rela...
[Phys. Rev. E 79, 065201
] Published Thu Jun 4, 2009
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Fluid dynamics
Nicholas Guttenberg and Nigel Goldenfeld
We use momentum-transfer arguments to predict the friction factor f in two-dimensional turbulent soap film flows with rough boundaries (an analog of three-dimensional pipe flow) as a function of Reynolds number Re and roughness r , considering separately the inverse energy cascade and the forward...
[Phys. Rev. E 79, 065306
] Published Thu Jun 25, 2009
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Håkan Wedin, Alessandro Bottaro, and Masato Nagata
A nonlinear streamwise traveling-wave solution is obtained by homotopy for square duct flow. For a particular symmetry of the perturbations, this wave comes into existence at about Reb=600 (based on half-duct width and bulk speed) for a streamwise wave number α=0.85 . The resulting four-vortex m...
[Phys. Rev. E 79, 065305
] Published Thu Jun 18, 2009
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Karnig O. Mikaelian
We present a model for nonlinear hydrodynamic instabilities of interfaces and the formation of bubbles driven by time-dependent accelerations g(t) . To obtain analytic solutions, we map the equation for the bubble amplitude η(t) onto the Schrödinger equation and solve it as an initial value (Î...
[Phys. Rev. E 79, 065303
] Published Tue Jun 16, 2009
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V. P. Ruban
Formation of giant waves in sea states with two spectral maxima centered at close wave vectors k0±Δk/2 in the Fourier plane is numerically simulated using the fully nonlinear model for long-crested water waves [V. P. Ruban, Phys. Rev. E 71, 055303(R) (2005)]. Depending on an angle θ between t...
[Phys. Rev. E 79, 065304
] Published Tue Jun 16, 2009
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J. M. McDonough
Outline of the derivation and mathematical and physical interpretations are presented for a discrete dynamical system known as the “poor man’s Navier-Stokes equation.” Numerical studies demonstrate that velocity fields produced by this dynamical system are similar to those seen in laboratory e...
[Phys. Rev. E 79, 065302
] Published Wed Jun 3, 2009
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G. Boffetta, A. Mazzino, S. Musacchio, and L. Vozella
Turbulence induced by Rayleigh-Taylor instability is a ubiquitous phenomenon with applications ranging from atmospheric physics and geophysics to supernova explosions and plasma confinement fusion. Despite its fundamental character, a phenomenological theory has been proposed only recently and sever...
[Phys. Rev. E 79, 065301
] Published Mon Jun 1, 2009
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Classical physics
Po-Ru Loh, Ardavan F. Oskooi, Mihai Ibanescu, Maksim Skorobogatiy, and Steven G. Johnson
We demonstrate that the ratio of group to phase velocity has a simple relationship to the orientation of the electromagnetic field. In nondispersive materials, opposite group and phase velocity corresponds to fields that are mostly oriented in the propagation direction. More generally, this relation...
[Phys. Rev. E 79, 065601
] Published Thu Jun 11, 2009
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Computational physics
V. Martin-Mayor and D. Yllanes
We propose a cluster simulation algorithm for statistical ensembles with fixed order parameter. We use the tethered ensemble, which features Helmholtz’s effective potential rather than Gibbs’s free energy and in which canonical averages are recovered with arbitrary accuracy. For the D=2,3 Isin...
[Phys. Rev. E 80, 015701
] Published Thu Jul 2, 2009
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Satoshi Morita, Sei Suzuki, and Tota Nakamura
A quantum-thermal annealing method using a cluster-flip algorithm is studied in the two-dimensional spin-glass model. The temperature (T) and the transverse field (Γ) are decreased simultaneously with the same rate along a linear path on the T-Γ plane. We found that the additional pulse of t...
[Phys. Rev. E 79, 065701
] Published Fri Jun 5, 2009
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Recently published articles in Physical Review E. See the current issue for more. Biological physics
Alexey K. Mazur
[Phys. Rev. E 80, 010901
] Published Thu Jul 2, 2009
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Sebastian Meßlinger, Benjamin Schmidt, Hiroshi Noguchi, and Gerhard Gompper
The dynamics of two-dimensional viscous vesicles in shear flow, with different fluid viscosities ηin and ηout inside and outside, respectively, is studied using mesoscale simulation techniques. Besides the well-known tank-treading and tumbling motions, an oscillatory swinging motion is observe...
[Phys. Rev. E 80, 011901
] Published Thu Jul 2, 2009
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P. A. Tass, A. N. Silchenko, C. Hauptmann, U. B. Barnikol, and E.-J. Speckmann
In computational models it has been shown that appropriate stimulation protocols may reshape the connectivity pattern of neural or oscillator networks with synaptic plasticity in a way that the network learns or unlearns strong synchronization. The underlying mechanism is that a network is shifted f...
[Phys. Rev. E 80, 011902
] Published Thu Jul 2, 2009
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Abdorreza Samarbakhsh and Jack. A. Tuszynski
The so-called shooting-bead method is a fast and easy experimental technique for evaluating cantilever stiffness and flexural rigidity of semiflexible to semirigid rodlike biological and nano-filaments based on the measurement of just two distances. In this paper we have derived the shooting-bead fo...
[Phys. Rev. E 80, 011903
] Published Thu Jul 2, 2009
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A. Hočevar and P. Ziherl
The salient feature of one-cell-thick epithelia is their en face view, which reveals the polygonal cross section of the close-packed prismatic cells. The physical mechanisms that shape these tissues were hitherto explored using theories based on cell proliferation, which were either entirely topolog...
[Phys. Rev. E 80, 011904
] Published Thu Jul 2, 2009
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Marco Baiesi, Lorenzo Bongini, Lapo Casetti, and Lorenzo Tattini
In systems characterized by a rough potential-energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and splitting of metastable states, have nontrivial effects on such ne...
[Phys. Rev. E 80, 011905
] Published Thu Jul 2, 2009
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Lorenzo Bongini, Lapo Casetti, Roberto Livi, Antonio Politi, and Alessandro Torcini
A method for reconstructing the potential energy landscape of simple polypeptidic chains is described. We show how to obtain a faithful representation of the energy landscape in terms of a suitable directed graph. Topological and dynamical indicators of the graph are shown to yield an effective esti...
[Phys. Rev. E 79, 061925
] Published Tue Jun 30, 2009
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Statistical physics
T. Nakajima and K. Hukushima
A one-step replica-symmetry-breaking solution for finite-connectivity spin-glass models with K body interaction is constructed at finite temperature using the replica method and thermodynamic constraints. In the absence of external fields, this construction provides a general extension of replica ...
[Phys. Rev. E 80, 011103
] Published Thu Jul 2, 2009
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A. D. Viñales, K. G. Wang, and M. A. Despósito
The diffusive behavior of a harmonic oscillator driven by a Mittag-Leffler noise is studied. Using the Laplace analysis we derive exact expressions for the relaxation functions of the particle in terms of generalized Mittag-Leffler functions and its derivatives from a generalized Langevin equation. ...
[Phys. Rev. E 80, 011101
] Published Wed Jul 1, 2009
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Jana Gevertz and S. Torquato
Understanding the transport properties of a porous medium from a knowledge of its microstructure is a problem of great interest in the physical, chemical, and biological sciences. Using a first-passage time method, we compute the mean survival time τ of a Brownian particle among perfectly absorbi...
[Phys. Rev. E 80, 011102
] Published Wed Jul 1, 2009
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Granular materials
Peter Eshuis, Ko van der Weele, Enrico Calzavarini, Detlef Lohse, and Devaraj van der Meer
The limits of granular hydrodynamics are explored in the context of the one-dimensional granular system introduced by Du, Li, and Kadanoff [Phys. Rev. Lett. 74, 1268 (1995)]. The density profile of the characteristic steady state, in which a single particle commutes between the driving wall and a de...
[Phys. Rev. E 80, 011302
] Published Thu Jul 2, 2009
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Philip A. Reynolds, Duncan J. McGillivray, Andrew J. Jackson, and John W. White
We measured ultra-small-angle neutron scattering (USANS) from polymethylmethacrylate spheres tamped down in air. Two slightly polydisperse pure sphere sizes (1.5 and 7.5 μm diameters) and five mixtures of these were used. All were loose packed (packing fractions of 0.3–0.6) with nongravitatio...
[Phys. Rev. E 80, 011301
] Published Wed Jul 1, 2009
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Colloidal dispersions, suspensions, and aggregates
D. Lacoste, C. Brangbour, J. Bibette, and J. Baudry
We study the thermal expansion of chains formed by self-assembly of magnetic colloidal particles in a magnetic field. Using video microscopy, complete positional data of all the particles of the chains is obtained. By changing the ionic strength of the solution and the applied magnetic field, the in...
[Phys. Rev. E 80, 011401
] Published Wed Jul 1, 2009
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Liquid crystals
Jürgen Schmidtke and Harry J. Coles
We discuss the partial demixing of a chiral nematic mixture of a chiral and an achiral compound, induced by inhomogeneous confinement between substrates. While the effect is tiny in low molar mass mixtures, it is predicted to be noticeable in polymeric systems. The potential of the effect for improv...
[Phys. Rev. E 80, 011702
] Published Thu Jul 2, 2009
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Erfan Kadivar
The prewetting phenomena in a nematic liquid crystal confined to a droplet embedded in a spherical solid surface are discussed. This paper is based on Landau–de Gennes theory and Nobili-Durand surface energy. By using a Maxwell construction, we find that the first-order boundary-layer transition i...
[Phys. Rev. E 80, 011701
] Published Wed Jul 1, 2009
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Computational physics
V. Martin-Mayor and D. Yllanes
[Phys. Rev. E 80, 015701
] Published Thu Jul 2, 2009
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Interdisciplinary physics
Jing Wang, Feng Fu, Te Wu, and Long Wang
In real situations, people are often faced with the option of voluntary contribution to achieve a collective goal, for example, building a dam or a fence, in order to avoid an unfavorable loss. Those who do not donate, however, can free ride on others’ sacrifices. As a result, cooperation is diffi...
[Phys. Rev. E 80, 016101
] Published Wed Jul 1, 2009
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Ryosuke Nishi, Hiroshi Miki, Akiyasu Tomoeda, and Katsuhiro Nishinari
Heavy traffic congestion occurs daily at merging sections on a highway. For relieving this congestion, possibility of alternative configuration of vehicles on multiple-lane road at a merging area is discussed in this paper. This is the configuration where no vehicles move aside on the other lane. It...
[Phys. Rev. E 79, 066119
] Published Tue Jun 30, 2009
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Gourab Ghoshal, Vinko Zlatić, Guido Caldarelli, and M. E. J. Newman
In the last few years we have witnessed the emergence, primarily in online communities, of new types of social networks that require for their representation more complex graph structures than have been employed in the past. One example is the folksonomy, a tripartite structure of users, resources, ...
[Phys. Rev. E 79, 066118
] Published Mon Jun 29, 2009
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Fluid dynamics
A. Widom, J. Swain, J. Silverberg, S. Sivasubramanian, and Y. N. Srivastava
A water bridge refers to an experimental “flexible cable” made up of pure de-ionized water, which can hang across two supports maintained with a sufficiently large voltage difference. The resulting electric fields within the de-ionized water flexible cable maintain a tension that sustains the wa...
[Phys. Rev. E 80, 016301
] Published Thu Jul 2, 2009
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Irene M. Mazzitelli and Detlef Lohse
We investigate by direct numerical simulations the flow that rising bubbles cause in an originally quiescent fluid. We employ the Eulerian-Lagrangian method with two-way coupling and periodic boundary conditions. In order to be able to treat up to 288000 bubbles, the following approximations and sim...
[Phys. Rev. E 79, 066317
] Published Tue Jun 30, 2009
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Gijs Katgert, Andrzej Latka, Matthias E. Möbius, and Martin van Hecke
We probe the flow of two-dimensional (2D) foams, consisting of a monolayer of bubbles sandwiched between a liquid bath and glass plate, as a function of driving rate, packing fraction, and degree of disorder. First, we find that bidisperse, disordered foams exhibit strongly rate-dependent and inhomo...
[Phys. Rev. E 79, 066318
] Published Tue Jun 30, 2009
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Plasma physics
Anupam Karmakar, Naveen Kumar, Alexander Pukhov, O. Polomarov, and Gennady Shvets
We present comprehensive two-dimensional (2D) particle-in-cell (PIC) simulations on the transport of a relativistic electron beam in a plasma in the context of fast ignition fusion. The 2D PIC simulations are performed by constructing two different simulation planes and have shown the complete stabi...
[Phys. Rev. E 80, 016401
] Published Thu Jul 2, 2009
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J. Myatt, J. A. Delettrez, A. V. Maximov, D. D. Meyerhofer, R. W. Short, C. Stoeckl, and M. Storm
Expressions for the yield of electron-positron pairs, their energy spectra, and production rates have been obtained in the interaction of multi-kJ pulses of high-intensity laser light interacting with solid targets. The Bethe-Heitler conversion of hard x-ray bremsstrahlung [D. A. Gryaznykh, Y. Z. Ka...
[Phys. Rev. E 79, 066409
] Published Tue Jun 30, 2009
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Papers recently accepted for publication in Physical Review E (view more). Statistical physics
Relaxation through an asymmetric fluctuating potential barrier
A. Wozinski and J. Iwaniszewski
We revise the problem of thermally activated crossing of a fluctuating potential barrier, laying stress on the asymmetry of the barrier. Considering as a working model a paradigmatic triangular dichotomously varying potential landscape we find an untypical dependence of the mean first-passage time on the correlation time t of fluctuations. Namely, in the range of small t an additional maximum appears. We propose a qualitative explanation of this feature emphasizing the relevance of dynamics in the vicinity of the barrier top, i.e. recrossing, which generally has not been recognized by this time in this particular context. Moreover, we observe that addition of fast barrier fluctuations of some finite intensity need not to increase the relaxation rate, as has been indicated many times in extensive studies related to the resonant activation phenomenon. Our findings are confirmed numerically for some other systems.
Accepted Thu Jul 2, 2009
Fluctuation relation and heterogeneous superdffusion in glassy transport
Mauro Sellitto
Current fluctuations and related steady state fluctuation relation are investigated in simple coarse-grained lattice-gas analogs of a non-Newtonian fluid driven by a constant and uniform force field, in two regimes of small entropy production. Non-Gaussian current fluctuations and deviations from fluctuation relation are observed and related to the existence of growing amorphous correlations and heterogeneous anomalous diffusion regimes.
Accepted Thu Jul 2, 2009
Shuttling heat across one dimensional homogenous nonlinear lattices with a Brownian heat motor
Nia Linbei, Fei Zhan, Peter Hanggi and Bao Liwen
We investigate directed thermal heat flux across 1D homogenous nonlinear lattices when no net thermal bias is present on average. A nonlinear lattice of Fermi-Pasta-Ulam-type or Lennard-Jones-type system is connected at both ends to thermal baths which are held at the same temperature on temporal average. We study two different modulations of the heat bath temperatures, namely: (i) a symmetric, harmonic ac-driving of temperature of one heat bath only and (ii) a harmonic mixing drive of temperature acting on both heat baths. While for case (i) an adiabatic result for the net heat transport can be derived in terms of the temperature dependent heat conductivity of the nonlinear lattice a similar such transport approach fails for the harmonic mixing case (ii). Then, for case (ii), not even the sign of the resulting Brownian motion induced heat flux can be predicted a priori. A non-vanishing heat flux (including a non-adiabatic reversal of flux) is detected which is the result of an induced dynamical symmetry breaking mechanism in conjunction with the nonlinearity of the lattice dynamics. Computer simulations demonstrate that the heat flux is robust against an increase of lattice sizes. The observed ratchet effect for such directed heat currents is quite sizable for our studied class of homogenous nonlinear lattice structures, thereby making this setup accessible for experimental implementation and verification.
Accepted Tue Jun 30, 2009
Granular materials
Magnetically driven surface mixing by far from-equilibrium magnetic granular layer
M. Belkin, A. Snezhko, I. S. Aranson and W. K. Kwok
Magnetic micro-particles suspended on the surface of liquid and energized by vertical alternating magnetic field exhibit complex collective behavior. Various immobile and self-propelled self-assembled structures have been observed. Here we report on experimental studies of mixing and surface diffusion processes in this system. We show that the pattern-induced surface flows have properties of quasi-two-dimensional turbulence. Correspondingly, the surface advection of tracer particle exhibits properties of Brownian diffusion.
Accepted Thu Jul 2, 2009
Colloidal dispersions, suspensions, and aggregates
Hierarchical self assembly of asymmetric amphiphatic spherical colloidal particles
William L. Miller and Angelo Cacciuto
From dumbbells to FCC crystals, we study the self-assembly pathway of amphiphatic, spherical colloidal particles as a function of the size of the hydrophobic region using molecular dynamics simulations. Specifically, we analyze how local inter-particle interactions correlate to the final self-assembled aggregate and how they affect the dynamical pathway of structure formation. We present a detailed diagram separating the many phases that we find for different sizes of the hydrophobic area, and uncover a narrow region where particles self-assemble into hollow, faceted cages that could potentially find interesting engineering applications.
Accepted Wed Jul 1, 2009
Liquid crystals
Rheodielectric study on shear induced structural change in the smectic-A phase of 4-n-octyl-4\prime-cyanobiphenyl (8CB)
K. Negita and H. Kaneko
Simultaneous measurements of rheological and dielectric properties are made to investigate shear-induced structural change in the smectic A phase of 8CB (4-n-octyl-4'-cyanobiphenyl). With increasing the shear rate, the fluidity changes from non-Newtonian to Newtonian flow via an unstable flow region, accompanied by a characteristic change in the dielectric permittivity. In the non-Newtonian flow region, a dielectric dispersion, which can be ascribed to an undulation motion of smectic layer, is recognized. On the basis of these results, it is suggested that with increasing the shear rate the undulation changes to a chaotic structure, which is followed by a more simple structure with the layer normal along the neutral axis, and that these structural changes are responsible for the fluidity change.
Accepted Tue Jun 30, 2009
Biological physics
Asymmetric elastic rod model for DNA
B. Eslami Mossallam and M. R. Ejtehadi
In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure of the DNA molecule. We will show that the model can explain the high flexibility of DNA at small length scales, as well as kink formation at high deformation limit.
Accepted Thu Jul 2, 2009
Noisy swimming at low Reynolds numbers
Jorn Dunkel and Irwin M. Zaid
Small organisms (e.g., bacteria) and artificial microswimmers move due to a combination of active swimming and passive Brownian motion. Considering a simplified linear three-sphere swimmer, we study how the swimmer size regulates the interplay between self-driven and diffusive behavior at low Reynolds number. Starting from the Kirkwood-Smoluchowski equation and its corresponding Langevin equation, we derive formulas for the orientation correlation time, the mean velocity and the mean square displacement in three space dimensions. The validity of the analytical results is illustrated through numerical simulations. Tuning the swimmer parameters to values that are typical of bacteria, we find three characteristic regimes: (i) Brownian motion at small times, (ii) quasi-ballistic behavior at intermediate time scales, and (iii) quasi-diffusive behavior at large times due to noise-induced rotation. Our analytical results can be useful for a better quantitative understanding of optimal foraging strategies in bacterial systems, and they can help to construct more efficient artificial microswimmers in fluctuating fluids.
Accepted Tue Jun 30, 2009
Modeling synchronized calling behavior of Japanese tree frogs
Ikkyu Aihara
We experimentally observed synchronized calling behavior of male Japanese tree frogs Hyla japonica: namely, while isolated single frogs called nearly periodically, a pair of interacting frogs called synchronously almost in anti-phase or in-phase. In this study, we propose two types of phase-oscillator models on different degrees of approximations which can quantitatively explain the phase and frequency property in the experiment. Moreover, it should be noted that, although the second model is obtained by fitting to the experimental data of the two synchronized states, that can also explain the transitory dynamics in the interactive calling behavior, namely the shift from a transient in-phase state to a stable anti-phase state. We also discuss the biological relevance of the estimated parameter values to calling behavior of Japanese tree frogs, and the possible biological meanings of the synchronized calling behavior.
Accepted Tue Jun 30, 2009
Role of cooperative binding on noise expression
P. S. Gutierrez, D. Monteoliva and L. Diambra
The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing transitions between discrete chemical states and the small size of biological compartments. In this paper, we propose a stochastic model for gene expression regulation including several binding sites, considering elementary reactions only. The model is used to investigate the role of cooperativity on the intrinsic fluctuations of gene expression, by means of master equation formalism. We found that the Hill coefficient and the level of noise increases as the interaction energy between activators increases. Additionally, we show that the model allows to distinguish between two cooperative binding mechanisms.
Accepted Tue Jun 30, 2009
Chaos and pattern formation
Coherence resonance in a unijunction transistor relaxation oscillator
Md. Nurujjaman, P. S. Bhattacharya, A. N.Sekar Iyengar and Sandip Sarkar
The phenomenon of coherence resonance (CR) is investigated in an unijunction transistor relaxation oscillator (UJT-RO) and quantified by estimating the normal variance (NV). Depending upon the measuring points two types of NV curves have been obtained. We have observed that the degradations in coherency at higher noise amplitudes in our system is probably the result of direct interference of coherent oscillations and the stochastic perturbation. Degradation of coherency may be minimal if this direct interference of noise and coherent oscillations is eliminated.
Accepted Wed Jul 1, 2009
Splitting instability of cellular structures in the Ginzburg Landau model under feedback control
Hidetsugu Sakaguchi
We study numerically a Ginzburg-Landau type equation for micelles in two dimensions. The domain size and the interface length of a cellular structure are controlled by two feedback terms. The deformation and the successive splitting of the cellular structure are observed when the controlled interface length is increased. The splitting instability is further investigated using coupled mode equations to understand the bifurcation structure.
Accepted Wed Jul 1, 2009
Diffusion and localization for the Chirikov typical map
Klaus M. Frahm and Dima L. Shepelyansky
We consider the classical and quantum properties of the "Chirikov typical map", proposed by Boris Chirikov in 1969. This map is obtained from the well known Chirikov standard map by introducing a finite number T of random phase shift angles. These angles induce a random behavior for small time scales (t < T) and a T-periodic iterated map which is relevant for larger time scales (t > T). We identify the classical chaos border kc ~ T-3/2 << 1 for the kick parameter k and two regimes with diffusive behavior on short and long time scales. The quantum dynamics is characterized by the effect of Chirikov localization (or dynamical localization). We find that the localization length depends in a subtle way on the two classical diffusion constants in the two time-scale regime.
Accepted Tue Jun 30, 2009
Control of stochastic multistable systems: Experimental demonstration
B. K. Goswami, S. Euzzor, K. Al Naimee, A. Geltrude, R. Meucci and F. T. Arecchi
Stochastic disturbances and spikes (sudden sharp fluctuations of any system parameter), commonly observed among natural and laboratory-scale systems, can perturb the multistable dynamics significantly and become a serious impediment when the device is designed for a certain dynamical behaviour. We experimentally demonstrate that suitable periodic modulation of any system parameter may efficiently control such stochastic multistability related problems. The control mechanism is verified individually with two standard models (namely, an analog circuit of Lorenz equations and a cavity-loss modulated CO2 laser), against three externally introduced disturbing signals, (namely, white Gaussian noise, pink noise and train of spikes). Indeed, with both the systems, it has been observed that the modulation is capable to significantly control untoward jumps to coexisting attractors that otherwise would have occurred due to either of the disturbances. These results establish the robustness and wide applicability of this novel control mechanism in resolving stochastic multistability related problems.
Accepted Tue Jun 30, 2009
Fluid dynamics
Alignment of velocity and vorticity and the intermittent distribution of helicity in isotropic turbulence
Yeontaek Choi, ByungGu Kim and Changhoon Lee
We provide an observation suggesting a strong correlation between helicity and enstrophy in fluid turbulence. Helicity statistics were obtained in a direct numerical simulation of forced isotropic turbulence. An investigation of coherent structures revealed that intermittently large local helicity was found in the core region of the coherent rotational structures, thus showing a strong correlation with local enstrophy, not dissipation. Statistics regarding the relative helicity and the correlation between velocity and vorticity conditioned on different levels of enstrophy clearly suggest that velocity and vorticity tend to be aligned in the core of the coherent structures.
Accepted Thu Jul 2, 2009
Microcolumn formation between electrodes in a narrow channel from metallic colloidal suspension through induced charge electrophoresis
Hideyuki Sugioka
It is desirable to achieve the self-organization of a microcolumn between electrodes in a flow channel because the microcolumn can be used as a biosensor with high sensitivity. A direct simulation of a dispersed system of metallic particles in water is performed to show that a microcolumn between electrodes is formed by the application of an ac electric field. By the multi-physics coupled simulation technique between fluidics and electrostatics based on the boundary element method along with the double layer approximation, we find that microcolumns are formed by the growth of clusters perpendicular to the electrodes under the condition that the number density of particles is larger than the percolation threshold. Further, we propose a simple model that efficiently explains the time dependence of the probability of the formation of a microcolumn by considering standard collision theory and percolation theory. By this analysis, we can greatly contribute to developments in studies on the self-organization of microcolumns and biosensors.
Accepted Thu Jul 2, 2009
Miscible ferrofluid patterns in a radial magnetic field
ChingYao Chen, Y. S. Yang and Jose A. Miranda
Pattern formation in a miscible ferrofluid system is experimentally investigated. The experiment is performed by immersing a thin ferrofluid droplet in a cylindrical container, overfilling it with a nonmagnetic miscible fluid, and applying an in-plane radial magnetic field. Visually striking patterns are obtained whose morphologies change from circular at zero field to complex starburst-like structures at finite field. The evolution of miscible ferrofluid droplets of various initial diameters, subjected to different magnetic field strengths is considered. Proper rescaling of the experimental data indicates that the time evolution of the droplets' area increments obeys a universal 4/3 power law behavior at long times.
Accepted Wed Jul 1, 2009
Heat transport in rotating convection without Ekman layers
S. Schmitz and A. Tilgner
Numerical simulation of rotating convection in plane layers with free slip boundaries show that the convective flows can be classified according to a quantity constructed from the Reynolds, Prandtl and Ekman numbers. Three different flow regimes appear: Laminar flow close to the onset of convection, turbulent flow in which the heat flow approaches the heat flow of non-rotating convection, and an intermediate regime in which the heat flow scales according to a power law independent of thermal diffusivity and kinematic viscosity.
Accepted Wed Jul 1, 2009
Turbulent transport and dynamo in sheared magnetohydrodynamics turbulence with a nonuniform magnetic field
Nicolas Leprovost and Eunjin Kim
We investigate three-dimensional magnetohydrodynamics turbulence in the presence of velocity and magnetic shear (i.e. with both a large-scale shear flow and a non-uniform magnetic field). By assuming a turbulence driven by an external forcing with both helical and non-helical spectra, we investigate the combined effect of these two shears on turbulence intensity and turbulent transport represented by turbulent diffusivities (turbulent viscosity, a and b effect) in Reynolds-averaged equations. We show that turbulent transport (turbulent viscosity and diffusivity) is quenched by a strong flow shear and a strong magnetic field. For a weak flow shear, we further show that the magnetic shear increases the turbulence intensity while decreasing the turbulent transport. In the presence of a strong flow shear, the effect of the magnetic shear is found to oppose the effect of flow shear (which reduces turbulence due to shear stabilization) by enhancing turbulence and transport, thereby weakening the strong quenching by flow shear stabilization. In the case of a strong magnetic field (compared to flow shear), magnetic shear increases turbulence intensity and quenches turbulent transport.
Accepted Wed Jul 1, 2009
Experimental determination of heat transfer coefficient in the slip regime and its anomalously low value
Anwar Demsis, Bhaskar Verma, S. V. Prabhu and Amit Agrawal
n this paper, the measurement of heat transfer coefficient in rarefied gases is presented; these are among the first heat transfer measurements in the slip flow regime. The experimental setup is validated by comparing friction factor in the slip regime and heat transfer coefficient in the continuum regime. Experimental results suggest that the Nusselt number is a function of Reynolds and Knudsen numbers in the slip flow regime. The measured values for Nusselt numbers are smaller than that predicted by theoretical or simulation results, and can become a few orders of magnitude smaller than the theoretical values in the continuum regime. The results are repeatable and expected to be useful for further experimentation and modeling of flow in the slip and transition regimes.
Accepted Wed Jul 1, 2009
Aerodynamic performance due to forewing and hindwing interaction in gliding dragonfly flight
Jie Zhang and XiY Luun
Aerodynamic performance due to forewing and hindwing interaction in gliding dragonfly flight has been studied using a multi-block lattice Boltzmann method. We find that the interactions between forewing and hindwing effectively enhance the total lift force and reduce the drag force on the wings compared to two independent wings. The interaction mechanism may be associated with the triangular camber effect by modulating the relative arrangement of the forewing and hindwing. The results obtained in this Brief Report provide physical insight into the understanding of aerodynamic behaviors for gliding dragonfly flight.
Accepted Tue Jun 30, 2009
Plasma physics
Finite dissipation and intermittency in magnetohydrodynamics
P. D. Mininni and A. Pouquet
We present an analysis of data stemming from numerical simulations of decaying magnetohydrodynamic (MHD) turbulence up to grid resolution of 15363 points and up to Taylor Reynolds number of ~ 1200. The initial conditions are such that the initial velocity and magnetic fields are helical and in equipartition, while their correlation is negligible. Analyzing the data at the peak of dissipation, we show that the dissipation in MHD seems to asymptote to a constant as the Reynolds number increases, thereby strengthening the possibility of fast reconnection events in the solar environment for very large Reynolds numbers. Furthermore, intermittency of MHD flows, as determined by the spectrum of anomalous exponents of structure functions of the velocity and the magnetic field, is stronger than for fluids, confirming earlier results; however, we also find that there is a measurable difference between the exponents of the velocity and those of the magnetic field, reminiscent of recent solar wind observations. Finally, we discuss the spectral scaling laws that arise in this flow.
Accepted Thu Jul 2, 2009
Magnetization of a warm plasma by the nonstationary ponderomotive force of an electromagnetic wave
Nitin Shukla, P. K. Shukla and L. Stenflo
It is shown that magnetic fields can be generated in a warm plasma by the non-stationary ponderomotive force of a large amplitude electromagnetic wave. In the present paper, we derive simple and explicit results that can be useful for understanding the origin of the magnetic fields that are produced in intense laser-plasma interaction experiments.
Accepted Thu Jul 2, 2009
Classical Physics
Model for the soliton potential interaction in the {\varphi}^{4} model
Ensieh Hakimi and Kurosh Javidan
An improved model for the soliton-potential scattering is presented. This model is constructed with a better approximation for adding the potential to the lagrangian through the metric of background space-time. The results of the model are compared with other models and the differences are discussed.
Accepted Tue Jun 30, 2009
Computational physics
Calculating thermodynamics properties of quantum systems by a non Markovian Monte Carlo procedure
Yanier Crespo, Alessandro Laio, Giuseppe E. Santoro and Erio Tosatti
We present a history-dependent Monte Carlo scheme for the efficient calculation of the free-energy of quantum systems, inspired by Wang-Landau and metadynamics. In the two-dimensional quantum Ising model, chosen here for illustration, the accuracy of free energy, critical temperature, and specific heat is demonstrated as a function of simulation time, and successfully compared with the best available approaches. The approach is based on a path integral formulation of the quantum problem, and can be applied without modifications to quantum hamiltonians of any level of complexity. The combination of high accuracy and performance with a much broader applicability is a major advance with respect to other available methods.
Accepted Thu Jul 2, 2009
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