http://pre.aps.org/ Accepted Papers for Physical Review E hourly 1 2012-02-09T20:06:25-05:00 rss@aps.org assocpub@aps.org 2012-02-09T20:06:25-05:00 en Copyright © 2012 the American Physical Society. Personal use only, all commercial or other reuse prohibited Copyright © 2012 the American Physical Society assocpub@aps.org http://pre.aps.org/accepted/E/3f07fY40Mbe1611d57f93586f1587c8fd45fa7ad8 Bottlenecks occur in a wide range of situations from pedestrians, ants, cattle and traffic flow to the transport of granular materials. We examine granular flow across a bottleneck using simulations of monodisperse disks. Contrary to expectations but consistent with previous work, we find that the f... Bottlenecks in granular flow: When does an obstacle increase the flow rate in an hourglass? 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/3f07fY40Mbe1611d57f93586f1587c8fd45fa7ad8 Granular materials Granular materials http://pre.aps.org/accepted/E/bd07bRa8UeaW3017502759129ed26151765dfbb0f Persson's multiscale contact mechanics theory combined with a multiscale Brillouin-Prandl-Tomlinson model is used to show that on the basis of these models "dry friction" [i.e., kinetic friction that remains at exceedingly small velocities (but still above the creep range) close to its value at high... Surface roughness and dry friction 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/bd07bRa8UeaW3017502759129ed26151765dfbb0f Interdisciplinary physics Interdisciplinary physics http://pre.aps.org/accepted/E/9f07eY29Wb618e38325b83095210b83a8db7d7d58 We investigate the onset of irreversibility in a dense granular medium subjected to cyclic shear in a split-bottom geometry. To probe the micro and mesoscale, we image bead trajectories in 3D throughout a series of shear strain oscillations. Though beads lose and regain contact with neighbors during... Onset of irreversibility in cyclic shear of granular packings 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/9f07eY29Wb618e38325b83095210b83a8db7d7d58 Granular materials Granular materials http://pre.aps.org/accepted/E/0d074RfaZ1013a00b71990620344600c7af6dc880 A low density binary mixture of granular gases is considered within the Boltzmann kinetic theory. One component, the intruders, is taken to be dilute with respect to the other, and thermal segregation of the two species is described for a special solution to the Boltzmann equation. This solution has... Thermal segregation of intruders in the Fourier state of a granular gas 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/0d074RfaZ1013a00b71990620344600c7af6dc880 Granular materials Granular materials http://pre.aps.org/accepted/E/66070Rd0Z4d1b503076d202493ced1e8bf99935cd Long-range interacting systems, while relaxing to equilibrium, often get trapped in long-lived quasistationary states which have lifetimes that diverge with the system size. In this work, we address the question of how a long-range system in a quasistationary state (QSS) responds to an external pert... Linear response theory for long-range interacting systems in quasistationary states 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/66070Rd0Z4d1b503076d202493ced1e8bf99935cd Statistical physics Statistical physics http://pre.aps.org/accepted/E/fd07cR61Z3a18c0b19e220943be1d84e384197fdb We introduce a general model which augments the one-dimensional nonlinear Schrödinger (NLS) equation by nonlinear-diffraction terms competing with the linear diffraction. The new terms contain two irreducible parameters and admit a Hamiltonian representation in a form natural for optical media.... Spatial solitons under competing linear and nonlinear diffractions 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/fd07cR61Z3a18c0b19e220943be1d84e384197fdb Classical physics Classical physics http://pre.aps.org/accepted/E/39070R18P0517a0f49dd7b5930b78816531b10560 A recent segregation criterion [V. Garzó, Phys. Rev. E 78, 020301(R) (2008)] based on the thermal diffusion factor L of an intruder in a heated granular gas described by the inelastic Enskog equation is revisited. The sign of L provides a criterion for the transition between the Brazil-nut effe... Segregation of an intruder in a heated granular dense gas 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/39070R18P0517a0f49dd7b5930b78816531b10560 Granular materials Granular materials http://pre.aps.org/accepted/E/e007eR16Zb91a50fe82b77167e4ff2b21f2114855 We study the nonconserved phase ordering dynamics of the d=2,3 random field Ising model, quenched to below the critical temperature. Motivated by the puzzling results of previous work in two and three dimensions, reporting a crossover from power-law to logarithmic growth, together with superuniversa... Crossover in growth law and violation of superuniversality in the random-field Ising model 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/e007eR16Zb91a50fe82b77167e4ff2b21f2114855 Statistical physics Statistical physics http://pre.aps.org/accepted/E/a2070R13Y4210700e87e3956479b55e025e8c9a9f Pattern formation in microbial colonies of competing strains under purely space-limited population growth has recently attracted considerable research interest. We show that the reproduction time statistics of individuals has a significant impact on the sectoring patterns. Generalizing the standard ... Reproduction-time statistics and segregation patterns in growing populations 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/a2070R13Y4210700e87e3956479b55e025e8c9a9f Biological physics Biological physics http://pre.aps.org/accepted/E/25075R1eZff1090eb7967615a2bff950663c5d823 We study the dynamic evolution of geometric structures in a poly-degenerate system represented by a q-state Potts model with non-conserved order parameter that is quenched from its disordered into its ordered phase. The numerical results obtained with Monte Carlo simulations show a strong relation b... Geometrical properties of the Potts model during the coarsening regime 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/25075R1eZff1090eb7967615a2bff950663c5d823 Statistical physics Statistical physics http://pre.aps.org/accepted/E/73077R92Kbd18b00a6b56b223e8b900d8cac80ab5 The probability densities of the mean recurrence time, which is the average time needed for a system to recur to a previously visited neighborhood, are investigated in various dynamical regimes and are found to be in agreement with those of the finite-time Lyapunov exponents. The important advantage... Distinguishing dynamics using recurrence time statistics 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/73077R92Kbd18b00a6b56b223e8b900d8cac80ab5 Chaos and pattern formation Chaos and pattern formation http://pre.aps.org/accepted/E/9e07eR70Wad1720ca6bc98b4baf96f34afaced926 We develop a systematic methodology for classifying the periodic orbits of homogeneous ordered granular chains with no dissipation, under the assumption that all granules oscillate with the same frequency. The analysis is based on the idea of balancing linear momentum for sets of auxiliary models co... Effective particles and classification of the dynamics of homogeneous granular chains with no precompression 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/9e07eR70Wad1720ca6bc98b4baf96f34afaced926 Classical physics Classical physics http://pre.aps.org/accepted/E/4c07eR4eWb51e103c8440a4747bcbf1c1a5e53e7f Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a gen... Soliton concepts and protein structure 2012-02-08T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/4c07eR4eWb51e103c8440a4747bcbf1c1a5e53e7f Biological physics Biological physics http://pre.aps.org/accepted/E/bd079Yc2U021962e09c77e86254a5c630add9a3fd We scrutinize the reliability of covariant and Gram-Schmidt Lyapunov vectors to capture hydrodynamic Lyapunov modes (HLMs) in one-dimensional Hamiltonian lattices. We show that, in contrast with previous claims, HLMs do exist for any energy density so that strong chaos is not essential for the appea... Covariant hydrodynamic Lyapunov modes and strong stochasticity threshold in Hamiltonian lattices 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/bd079Yc2U021962e09c77e86254a5c630add9a3fd Chaos and pattern formation Chaos and pattern formation http://pre.aps.org/accepted/E/5b076NdeX8612209a8b50d949ac01a406e4990c5b We examine numerically vortex families near band edges of the Bloch wave spectrum in the Gross-Pitaevskii equation with a two-dimensional periodic potential and in the discrete nonlinear Schrödinger equation. We show that besides vortex families that terminate at a small distance from the band ... Vortex families near a spectral edge in the Gross-Pitaevskii equation with a two-dimensional periodic potential 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/5b076NdeX8612209a8b50d949ac01a406e4990c5b Classical physics Classical physics http://pre.aps.org/accepted/E/43073YceR3814733400091c5772c3922aa6a45947 Nanoconfined water and surface-structured water impacts a broad range of fields. For water confined between hydrophilic surfaces, measurements and simulations have shown conflicting results ranging from `liquid-like' to `solid-like' behavior, from bulk-like water viscosity to viscosity orders of mag... Dynamics of confined water reconstructed from inelastic x-ray scattering measurements of bulk response functions 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/43073YceR3814733400091c5772c3922aa6a45947 Structured and complex fluids Structured and complex fluids http://pre.aps.org/accepted/E/cf07cRa5R2f1fc02a8e880a869166fff68e4bac46 For a class of integrate-and-fire, pulse-coupled networks with complex topology, we study the dependence of the pulse rate on the underlying architectural connectivity statistics. We derive the distribution of the pulse rate from this dependence and determine when the underlying scale-free architect... Topological effects on dynamics in complex pulse-coupled networks of integrate-and-fire type 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/cf07cRa5R2f1fc02a8e880a869166fff68e4bac46 Interdisciplinary physics Interdisciplinary physics http://pre.aps.org/accepted/E/cf07fRc1S7c1b11f30ce1042e564a67b7c180f937 By means of N-body simulations, we study the evolution of gravity-dominated systems from an early relaxation to a collapse, focusing on the velocity distributions and thermodynamic properties. To simulate the dynamical evolution, we consider self-gravitating small N-body systems enclosed in a spheri... Transition of velocity distributions in collapsing self-gravitating $N$-body systems 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/cf07fRc1S7c1b11f30ce1042e564a67b7c180f937 Statistical physics Statistical physics http://pre.aps.org/accepted/E/de078RabTcc1580e988b7e70a2a82fc69dc651a38 A numerically stable method to solve the discretized Boltzmann-Enskog equation describing the behavior of non ideal fluids under inhomogeneous conditions is presented. The algorithm employed uses a Lagrangian finite-difference scheme for the treatment of the convective term and a forcing term to acc... Stabilized lattice Boltzmann-Enskog method for compressible flows and its application to one- and two-component fluids in nanochannels 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/de078RabTcc1580e988b7e70a2a82fc69dc651a38 Computational physics Computational physics http://pre.aps.org/accepted/E/3107aR5aWb21bc08575179c464c0e59bdd782ed46 I formulate a quantum stochastic thermodynamics for the quantum trajectories of a continuously-monitored forced harmonic oscillator coupled to a thermal reservoir. Consistent trajectory-dependent definitions are introduced for work, heat, and entropy, through engineering the thermal reservoir from a... Quantum-trajectory approach to the stochastic thermodynamics of a forced harmonic oscillator 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/3107aR5aWb21bc08575179c464c0e59bdd782ed46 Statistical physics Statistical physics http://pre.aps.org/accepted/E/42079R3bU4610205d87e0184588b194c5f6a24df8 We present an analysis of the price impact associated with single trades effected by different financial firms. Using data from the Spanish Stock Market, we find a high degree of heterogeneity across different market members, both in the instantaneous impact functions and in the time-dependent marke... Agent-specific impact of single trades in financial markets 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/42079R3bU4610205d87e0184588b194c5f6a24df8 Interdisciplinary physics Interdisciplinary physics http://pre.aps.org/accepted/E/2e07eRacW6817b07862760628844bba77cf5db83a In quantum spin chains at criticality, two types of scaling for the entanglement entropy exist: one comes from conformal field theory (CFT), and the other is for entanglement support of matrix product state (MPS) approximation. On the other hand, the quantum spin-chain models can be mapped onto two-... Holographic entanglement entropy in Suzuki-Trotter decomposition of spin systems 2012-02-07T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/2e07eRacW6817b07862760628844bba77cf5db83a Statistical physics Statistical physics http://pre.aps.org/accepted/E/8a079YdcW2417b34b477192842d69b3e9032e520b The propulsion velocity of active colloids that asymmetrically catalyze a chemical reaction is probed experimentally as a function of their sizes. It is found that over the experimentally accessible range, the velocity decays as a function of size, with a rate that is compatible with an inverse size... Size dependence of the propulsion velocity for catalytic Janus-sphere swimmers 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/8a079YdcW2417b34b477192842d69b3e9032e520b Colloidal dispersions, suspensions, and aggregates Colloidal dispersions, suspensions, and aggregates http://pre.aps.org/accepted/E/61076Y38Zce1b029f8bd3d88c20badc00c3c15ee0 A Monte Carlo method to sample the classical configurational canonical ensemble is introduced. In contrast to the Metropolis algorithm, where trial moves can be rejected, in this approach collisions take place. The implementation is event-driven, i.e., at scheduled times the collisions occur. A uniq... Rejection-free Monte Carlo sampling for general potentials 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/61076Y38Zce1b029f8bd3d88c20badc00c3c15ee0 Computational physics Computational physics http://pre.aps.org/accepted/E/5c079R14X0b1c707f7a1675725bad01afa18616e7 Numerical simulation of two-dimensional bulk instability of the one-dimensional conduction state in an electrolyte confined between a pair of cation-exchange membranes subjected to an external voltage is conducted under an assumption of constant current. By employing variable grids, we resolve the p... Numerical study on the bulk instability of constant-current conduction in cation-exchange membranes 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/5c079R14X0b1c707f7a1675725bad01afa18616e7 Fluid dynamics Fluid dynamics http://pre.aps.org/accepted/E/a507fR0eX881e40eb9a646c6e93a8867354d62130 Cylindrical implosions driven by intense heavy ions beams should be instrumental in a near future to study High Energy Density Matter. By rotating the beam by means of a high frequency wobbler, it should be possible to deposit energy in the outer layers of a cylinder, compressing the material deposi... Harmonic analysis of irradiation asymmetry for cylindrical implosions driven by high-frequency rotating ion beams 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/a507fR0eX881e40eb9a646c6e93a8867354d62130 Plasma physics Plasma physics http://pre.aps.org/accepted/E/dc079R41X5a16101382f8bc01d636e9ccea180f56 The electric-field-driven entry process of flexible charged polymers such as single stranded DNA (ssDNA) into asymmetric nanoscale channels such as a-hemolysin protein channel is studied theoretically and using molecular dynamics simulations. Dependence of the height of the free-energy barrier on th... Electric-field-driven polymer entry into asymmetric nanoscale channels 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/dc079R41X5a16101382f8bc01d636e9ccea180f56 Polymers Polymers http://pre.aps.org/accepted/E/7507cRedYc61860f58bd7f17d8b26e96887f41ceb : We present a modified master equation for a homogeneous gaseous reactive systemwhich includes nonequilibrium corrections due to the reaction-induced perturbation of the particle velocity distribution function. For the Schlögl model, the modified stochastic approach predicts nonequilibrium-ind... Master equation for a bistable chemical system with perturbed particle velocity distribution function 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/7507cRedYc61860f58bd7f17d8b26e96887f41ceb Statistical physics Statistical physics http://pre.aps.org/accepted/E/5f075Y17Y5f1d72f56de0e65c9470c94719c33dae In this Letter we study the jamming transition in complex adaptive networks. We introduce an adaptation mechanism that modifies the weight of the communication channels in order to delay the congestion onset. Adaptivity takes place locally as it is driven by each node of the network. Surprisingly, r... Reciprocal interactions out of congestion-free adaptive networks 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/5f075Y17Y5f1d72f56de0e65c9470c94719c33dae Interdisciplinary physics Interdisciplinary physics http://pre.aps.org/accepted/E/c6077R69Y8d1fc075934713942a5b42555ba6a928 We present a detailed account of a recently proposed phenomenological theory for noncatenated ring polymer melts (Phys. Rev. Lett. 106, 167802 (2011)). A basic assumption lies in the implementation of the noncatenation constraint via the effective excluded-volume effect, from which a geometrical pic... Statistics and geometrical picture of ring polymer melts and solutions 2012-02-06T10:00:00-05:00 Personal use only, all commercial or other reuse prohibited Phys. Rev. E article Physical Review E http://pre.aps.org/accepted/E/c6077R69Y8d1fc075934713942a5b42555ba6a928 Polymers Polymers