# Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics (Phys Rev E )

Publisher: American Physical Society; American Institute of Physics

## Description

The subtitle of Physical Review E is Statistical, Nonlinear, and Soft Matter Physics. PRE has two parts and sixteen subsections: Part 1: Soft Matter and Biological Physics: Statistical physics of soft matter; Equilibrium and linear transport properties of flluids; Granular materials; Colloidal dispersions, suspensions, and agregates; Structured and complex fluids; Films, interfaces, and crystal growth; Liquid crystals; Polymers; Biological Physics. Part 2: Chaos, Hydrodynamics, Plasmas, and Related Topics: General methods of statistical physics; Chaos and pattern formation; Nonlinear hydrodynamics and turbulence; Plasma physics; Physics of beams; Classical physics, including nonlinear media; Computational physics. Discontinued in 2001. Continued by Physical Review E - Statistical, Nonlinear, and Soft matter Physics (1539-3755)

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• Website
Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics website
• Other titles
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, Statistical physics, plasmas, fluids, and related interdisciplinary topics
• ISSN
1063-651X
• OCLC
26103502
• Material type
Periodical, Internet resource
• Document type
Journal / Magazine / Newspaper, Internet Resource

## Publications in this journal

• ##### Article: Relativistic theory for localized electrostatic excitations in degenerate electron-ion plasmas
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 09/2014; 90:033112.
• ##### Article: Characteristics of angular cross correlations studied by light scattering from two-dimensional microsphere films
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ABSTRACT: Recently the analysis of scattering patterns by angular cross-correlation analysis (CCA) was introduced to reveal the orientational order in disordered samples with special focus to future applications on x-ray free-electron laser facilities. We apply this CCA approach to ultra-small-angle light-scattering data obtained from two-dimensional monolayers of microspheres. The films were studied in addition by optical microscopy. This combined approach allows to calculate the cross-correlations of the scattering patterns, characterized by the orientational correlation function Ψ_{l}(q), as well as to obtain the real-space structure of the monolayers. We show that CCA is sensitive to the orientational order of monolayers formed by the microspheres which are not directly visible from the scattering patterns. By mixing microspheres of different radii the sizes of ordered monolayer domains is reduced. For these samples it is shown that Ψ_{l}(q) quantitatively describes the degree of hexagonal order of the two-dimensional films. The experimental CCA results are compared with calculations based on the microscopy images. Both techniques show qualitatively similar features. Differences can be attributed to the wave-front distortion of the laser beam in the experiment. This effect is discussed by investigating the effect of different wave fronts on the cross-correlation analysis results. The so-determined characteristics of the cross-correlation analysis will be also relevant for future x-ray-based studies.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 07/2014; 90:012309.
• ##### Article: Determination of effective brain connectivity from functional connectivity with application to resting state connectivities
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ABSTRACT: Neural field theory insights are used to derive effective brain connectivity matrices from the functional connectivity matrix defined by activity covariances. The symmetric case is exactly solved for a resting state system driven by white noise, in which strengths of connections, often termed effective connectivities, are inferred from functional data; these include strengths of connections that are underestimated or not detected by anatomical imaging. Proximity to criticality is calculated and found to be consistent with estimates obtainable from other methods. Links between anatomical, effective, and functional connectivity and resting state activity are quantified, with applicability to other complex networks. Proof-of-principle results are illustrated using published experimental data on anatomical connectivity and resting state functional connectivity. In particular, it is shown that functional connection matrices can be used to uncover the existence and strength of connections that are missed from anatomical connection matrices, including interhemispheric connections that are difficult to track with techniques such as diffusion spectrum imaging.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 07/2014; 90(1):012707.
• ##### Article: Decay of a linear pendulum in a collisional gas: Spatially one-dimensional cas
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ABSTRACT: An infinitely wide plate, subject to an external force in its normal direction obeying Hooke's law, is placed in an infinite expanse of a rarefied gas. When the plate is displaced from its equilibrium position and released, it starts in general an oscillatory motion in its normal direction. This is the one-dimensional setting of a linear pendulum considered previously for a collisionless gas and a special Lorentz gas by the present authors [T. Tsuji and K. Aoki, J. Stat. Phys. 146, 620 (2012)]. The motion decays as time proceeds because of the drag force on the plate exerted by the surrounding gas. The long-time behavior of the unsteady motion of the gas caused by the motion of the plate is investigated numerically on the basis of the Bhatnagar-Gross-Krook (BGK) model of the Boltzmann equation with special interest in the rate of the decay of the oscillatory motion of the plate. The result provides numerical evidence that the displacement of the plate decays in proportion to an inverse power of time for large time.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2014;
• ##### Article: Mean force on a finite-sized spherical particle due to an acoustic field in a viscous compressible medium
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ABSTRACT: An analytical expression to evaluate the second-order mean force (acoustic radiation force) on a finite-sized, rigid, spherical particle due to an acoustic wave is presented. The medium in which the particle is situated is taken to be both viscous and compressible. A far-field derivation approach has been used in determining the force, which is a function of the particle size, acoustic wavelength, and viscous boundary-layer thickness. It is assumed that the viscous length scale is negligibly small compared to the acoustic wavelength. The force expression presented here (i) reduces to the correct inviscid behavior (for both small- and finite-sized particles) and (ii) is identical to recent viscous results [M. Settnes and H. Bruus, Phys. Rev. E 85, 016327 (2012)] for small-sized particles. Further, the computed force qualitatively matches the computational fluid dynamics (finite-element) results [D. Foresti, M. Nabavi, and D. Poulikakos, J. Fluid Mech. 709, 581 (2012)] for finite-sized particles. Additionally, the mean force is interpreted in terms of a multipole expansion. Subsequently, considering the fact that the force expansion is an infinite series, the number of terms that are required or adequate to capture the force to a specified accuracy is also provided as a function of the particle size to acoustic wavelength ratio. The dependence of the force on particle density, kinematic viscosity, and bulk viscosity of the fluid is also investigated. Here, both traveling and standing waves are considered.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2014; 89:053008.
• ##### Article: Nucleation, aggregation, annealing, and disintegration of granular clusters
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ABSTRACT: The processes of nucleation, aggregation, annealing, and disintegration of clusters of non-Brownian paramagnetic beads in a vibrofluidized system are experimentally investigated. The interaction among the beads is induced by a magnetic seed composed of two dipoles allocated outside the container cell. We observe a clearly differentiated nucleation stage, whose evolution (nucleation time versus acceleration strength) follows a power law. Thereafter, the beads aggregate forming 2D disordered clusters around the nucleus. Both processes (nucleation and aggregation) are determined by the competition between magnetic forces and the drag produced by a thermal bath created by glass particles. Once the agglomerates reach a final state (shape and length), they are annealed by increasing and decreasing the granular temperature. We found that the fractal dimension and the lacunarity index clearly describe the structural variations of the clusters. Our discussion on this phenomenon is addressed, making a rough analogy with the glass transition in a super-cooled liquid. Finally, we study the disintegration of the clusters as a function of time and the density of the surrounding gas. The question is not if, but how they disintegrate upon removing the external field; we find that the disintegration follows an exponential decay.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2014; 89((5)):052205.
• ##### Article: Bayesian approach to inverse statistical mechanics
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ABSTRACT: Inverse statistical mechanics aims to determine particle interactions from ensemble properties. This article looks at this inverse problem from a Bayesian perspective and discusses several statistical estimators to solve it. In addition, a sequential Monte Carlo algorithm is proposed that draws the interaction parameters from their posterior probability distribution. The posterior probability involves an intractable partition function that is estimated along with the interactions. The method is illustrated for inverse problems of varying complexity, including the estimation of a temperature, the inverse Ising problem, maximum entropy fitting, and the reconstruction of molecular interaction potentials.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2014; 89:052113.
• ##### Article: Ultraslow diffusion in an exactly solvable non-Markovian random walk
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ABSTRACT: We study a one-dimensional discrete-time non-Markovian random walk with strong memory correlations subjected to pauses. Unlike the Scher-Montroll continuous-time random walk, which can be made Markovian by defining an operational time equal to the random-walk step number, the model we study keeps a record of the entire history of the walk. This new model is closely related to the one proposed recently by Kumar, Harbola, and Lindenberg [Phys. Rev. E 82, 021101 (2010)], with the difference that in our model the stochastic dynamics does not stop even in the extreme limit of subdiffusion. Surprisingly, this small difference leads to large consequences. The main results we report here are exact results showing ultraslow diffusion and a stationary diffusion regime (i.e., localization). Specifically, the equations of motion are solved analytically for the first two moments, allowing the determination of the Hurst exponent. Several anomalous diffusion regimes are apparent, ranging from superdiffusion to subdiffusion, as well as ultraslow and stationary regimes. We present the complete phase diffusion diagram, along with a study of the persistence and the statistics in the regions of interest.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2014; 89(5):052110.
• ##### Article: Residence times and boundary-following behavior in animals
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ABSTRACT: Many animals in heterogeneous environments bias their trajectories displaying a preference for the vicinity of boundaries. Here we propose a criterion, relying on recent invariance properties of residence times for microreversible Boltzmann’s walks, that permits detecting and quantifying boundary-following behaviors. On this basis we introduce a boundary-following model that is a nonmicroreversible Boltzmann’s walk and that can represent all kinds of boundary-following distributions. This allows us to perform a theoretical analysis of field-resolved boundary following in animals. Two consequences are pointed out and are illustrated: A systematic procedure can now be used for extraction of individual properties from experimental field measurements, and boundary-curvature influence can be recovered as an emerging property without the need for individuals perceiving the curvature via complex physiological mechanisms. The presented results apply to any memoryless correlated random walk, such as the run-and-tumble models that are widely used in cell motility studies.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2014; 89:052715.
• ##### Article: Localization of Chain Dynamics in Entangled Polymer Melts
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ABSTRACT: The dynamics of polymer melts in both the unentangled and entangled regimes is described by a Langevin equation for the correlated motion of a group of chains, interacting through both intra- and inter-molecular potentials. Entanglements are represented by an intermolecular monomer-monomer confining potential that has no effect on short chains, while interpolymer interactions, responsible for correlated motion and subdiffusive center-of-mass dynamics, are represented by an intermolecular center-of-mass potential derived from the Ornstein-Zernike equation. This potential ensures that the liquid of phantom chains reproduces the compressibility and free energy of the real samples. For polyethylene melts the calculated dynamic structure factor is found to be in quantitative agreement with neutron spin echo experiments of polyethylene melts with chain lengths that span both the unentangled and the entangled regimes. The theory shows a progressive localization of the cooperative chain dynamics at the crossover from the unentangled to the entangled regime, in the spirit of the reptation model.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 05/2014; 89:052603.
• ##### Article: Dynamics of magnetic particles near a surface: Model and experiments on field-induced disaggregation
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ABSTRACT: Magnetic particles are widely used in biological research and bioanalytical applications. As the corresponding tools are progressively being miniaturized and integrated, the understanding of particle dynamics and the control of particles down to the level of single particles become important. Here, we describe a numerical model to simulate the dynamic behavior of ensembles of magnetic particles, taking account of magnetic interparticle interactions, interactions with the liquid medium and solid surfaces, as well as thermal diffusive motion of the particles. The model is verified using experimental data of magnetic field-induced disaggregation of magnetic particle clusters near a physical surface, wherein the magnetic field properties, particle size, cluster size, and cluster geometry were varied. Furthermore, the model clarifies how the cluster configuration, cluster alignment, magnitude of the field gradient, and the field repetition rate play a role in the particle disaggregation process. The simulation model will be very useful for further in silico studies on magnetic particle dynamics in biotechnological tools.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 04/2014; 89:042306.
• ##### Article: Electronic states of DNA and M-DNA studied by optical absorption
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ABSTRACT: To unveil the electronic states of divalent metal ion incorporated M-DNAs, where M is Mg, Mn, Ni, Co, or Fe, optical absorption spectra have been studied in aqueous solutions of single-stranded (SS) 30mer DNA of poly(dA) (adenine), poly(dG) (guanine), poly(dT) (thymine), poly(dC) (cytosine), salmon-sperm DNA (B-DNA), and M-DNA. The absorption spectrum of the double-stranded (DS) B-DNA can be reproduced with the sum of the four absorption spectra of the SS oligo-DNAs in the ratio corresponding to the composition of B-DNA. This observation suggests that the interactions between complementary strands of DS DNA are negligibly weaker than the bandwidths of the optical spectra. In the metal-incorporated M-DNAs, except for Fe-DNA, the absorption spectra show no significant qualitative change from that of B-DNA. Quantitatively, however, the absorption intensity decreases by ≈15% uniquely in a DS poly(dA)-poly(dT) solution with adding MCl2, while nothing happens quantitatively and qualitatively in any SS oligo-DNA and DS poly(dG)-poly(dC) solutions, suggesting some suppression of the electronic excitation only in the Adenine-M-Thymine complex. In contrast, remarkable differences have been observed in Fe-DNA, prepared with FeCl2 and B-DNA. New absorption bands appear in the intragap energy of Fe-DNA, in addition to the suppression of the interband absorption peak of DNA at 4.8 eV. The intragap absorption is attributed to the appearance of Fe3+ species with the same spectral feature as that of FeCl3, that is, purely ionic Fe3+ species. This observation suggests that FeCl2+B-DNA forms Fe-DNA with hydrated Fe3+ ions with ionic bonds. Thus, it is concluded that the charge transfer from Fe2+ to DNA has occurred in Fe-DNA and that the transferred charges are expected to be located in the nearby bases.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 02/2014; 89(2):022719.
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##### Article: Duration of local violations of the second law of thermodynamics along single trajectories in phase space
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ABSTRACT: We define the {\it violation fraction} $\nu$ as the cumulative fraction of time that the entropy change is negative during single realizations of processes in phase space. This quantity depends on both the number of degrees of freedom $N$ and the duration of the time interval $\tau$. In the large-$\tau$ and large-$N$ limit we show that, for ergodic and microreversible systems, the mean value of $\nu$ scales as $\langle\nu(N,\tau)\rangle\sim\big(\tau N^{\frac{1}{1+\alpha}}\big)^{-1}$. The exponent $\alpha$ is positive and generally depends on the protocol for the external driving forces, being $\alpha=1$ for a constant drive. As an example, we study a nontrivial model where the fluctuations of the entropy production are non-Gaussian: an elastic line driven at a constant rate by an anharmonic trap. In this case we show that the scaling of $\langle \nu \rangle$ with $N$ and $\tau$ agrees with our result. Finally, we discuss how this scaling law may break down in the vicinity of a continuous phase transition.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 02/2014; 89:022116.