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Preview: Recent Articles in Phys. Rev. E

Recent Articles in Phys. Rev. E

Recent articles in Physical Review E

Published: 2017-12-13T02:02:44+00:00


Permutation entropy with vector embedding delays


Author(s): Douglas J. Little and Deb M. Kane

Permutation entropy (PE) is a statistic used widely for the detection of structure within a time series. Embedding delay times at which the PE is reduced are characteristic timescales for which such structure exists. Here, a generalized scheme is investigated where embedding delays are represented b...

[Phys. Rev. E 96, 062205] Published Tue Dec 12, 2017

Solution x-ray scattering and structure formation in protein dynamics


Author(s): Alexandr Nasedkin, Jan Davidsson, Antti J. Niemi, and Xubiao Peng

We propose a computationally effective approach that builds on Landau mean-field theory in combination with modern nonequilibrium statistical mechanics to model and interpret protein dynamics and structure formation in small- to wide-angle x-ray scattering (S/WAXS) experiments. We develop the method...

[Phys. Rev. E 96, 062405] Published Tue Dec 12, 2017

Simple scaling laws for the evaporation of droplets pinned on pillars: Transfer-rate- and diffusion-limited regimes


Author(s): Ruth Hernandez-Perez, José L. García-Cordero, and Juan V. Escobar

The evaporation of droplets can give rise to a wide range of interesting phenomena in which the dynamics of the evaporation are crucial. In this work, we find simple scaling laws for the evaporation dynamics of axisymmetric droplets pinned on millimeter-sized pillars. Different laws are found depend...

[Phys. Rev. E 96, 062803] Published Tue Dec 12, 2017

Lattice Boltzmann heat transfer model for permeable voxels


Author(s): Gerald G. Pereira, Bisheng Wu, and Shakil Ahmed

We develop a gray-scale lattice Boltzmann (LB) model to study fluid flow combined with heat transfer for flow through porous media where voxels may be partially solid (or void). Heat transfer in rocks may lead to deformation, which in turn can modulate the fluid flow and so has significant contribut...

[Phys. Rev. E 96, 063108] Published Tue Dec 12, 2017

Critical behavior of the two-dimensional icosahedron model


Author(s): Hiroshi Ueda, Kouichi Okunishi, Roman Krčmár, Andrej Gendiar, Seiji Yunoki, and Tomotoshi Nishino

In the context of a discrete analog of the classical Heisenberg model, we investigate the critical behavior of the icosahedron model, where the interaction energy is defined as the inner product of neighboring vector spins of unit length pointing to the vertices of the icosahedron. The effective cor...

[Phys. Rev. E 96, 062112] Published Mon Dec 11, 2017

Dissipation, lag, and drift in driven fluctuating systems


Author(s): Diego Frezzato

This work deals with thermostated fluctuating systems subjected to driven transformations of the internal energetics. The main focus is on generally multidimensional systems with continuous configurational degrees of freedom over which overdamped Markovian fluctuations take place (diffusive regime o...

[Phys. Rev. E 96, 062113] Published Mon Dec 11, 2017

Quasimonochromatic exact solutions to Maxwell's equations with finite total energy and arbitrary frequencies in the vacuum


Author(s): Xiaolu Ma (马晓路) and Richard S. Thompson

We analyze a family of exact finite energy solutions to Maxwell's equations. These solutions are a subset of the modified-power-spectrum solutions found by Ziolkowski [Phys. Rev. A 39, 2005 (1989)]. There are three characteristic parameters in the solutions: ${q}_{1},{q}_{2}$, and ${k}_{0}$. ${q}_{1...

[Phys. Rev. E 96, 062114] Published Mon Dec 11, 2017

Solution of the Riemann problem for polarization waves in a two-component Bose-Einstein condensate


Author(s): S. K. Ivanov, A. M. Kamchatnov, T. Congy, and N. Pavloff

We provide a classification of the possible flows of two-component Bose-Einstein condensates evolving from initially discontinuous profiles. We consider the situation where the dynamics can be reduced to the consideration of a single polarization mode (also denoted as “magnetic excitation”) obeying ...

[Phys. Rev. E 96, 062202] Published Mon Dec 11, 2017

Coupled Lorenz oscillators near the Hopf boundary: Multistability, intermingled basins, and quasiriddling


Author(s): Thierry T. Wontchui, Joseph Y. Effa, H. P. Ekobena Fouda, Sangeeta R. Ujjwal, and Ram Ramaswamy

We investigate the dynamics of coupled identical chaotic Lorenz oscillators just above the subcritical Hopf bifurcation. In the absence of coupling, the motion is on a strange chaotic attractor and the fixed points of the system are all unstable. With the coupling, the unstable fixed points are conv...

[Phys. Rev. E 96, 062203] Published Mon Dec 11, 2017

Synchronization of coupled active rotators by common noise


Author(s): Anastasiya V. Dolmatova, Denis S. Goldobin, and Arkady Pikovsky

We study the effect of common noise on coupled active rotators. While such a noise always facilitates synchrony, coupling may be attractive (synchronizing) or repulsive (desynchronizing). We develop an analytical approach based on a transformation to approximate angle-action variables and averaging ...

[Phys. Rev. E 96, 062204] Published Mon Dec 11, 2017

Energetics in a model of prebiotic evolution


Author(s): B. F. Intoy and J. W. Halley

Previously we reported [A. Wynveen et al., Phys. Rev. E 89, 022725 (2014)] that requiring that the systems regarded as lifelike be out of chemical equilibrium in a model of abstracted polymers undergoing ligation and scission first introduced by Kauffman [S. A. Kauffman, The Origins of Order (Oxfor...

[Phys. Rev. E 96, 062402] Published Mon Dec 11, 2017

Fluctuation correlation models for receptor immobilization


Author(s): B. Fourcade

Nanoscale dynamics with cycles of receptor diffusion and immobilization by cell-external-or-internal factors is a key process in living cell adhesion phenomena at the origin of a plethora of signal transduction pathways. Motivated by modern correlation microscopy approaches, the receptor correlation...

[Phys. Rev. E 96, 062403] Published Mon Dec 11, 2017

Elucidating distinct ion channel populations on the surface of hippocampal neurons via single-particle tracking recurrence analysis


Author(s): Grzegorz Sikora, Agnieszka Wyłomańska, Janusz Gajda, Laura Solé, Elizabeth J. Akin, Michael M. Tamkun, and Diego Krapf

Protein and lipid nanodomains are prevalent on the surface of mammalian cells. In particular, it has been recently recognized that ion channels assemble into surface nanoclusters in the soma of cultured neurons. However, the interactions of these molecules with surface nanodomains display a consider...

[Phys. Rev. E 96, 062404] Published Mon Dec 11, 2017

Swimming efficiency in a shear-thinning fluid


Author(s): Herve Nganguia, Kyle Pietrzyk, and On Shun Pak

Micro-organisms expend energy moving through complex media. While propulsion speed is an important property of locomotion, efficiency is another factor that may determine the swimming gait adopted by a micro-organism in order to locomote in an energetically favorable manner. The efficiency of swimmi...

[Phys. Rev. E 96, 062606] Published Mon Dec 11, 2017

Electromagnetic-radiation absorption by water


Author(s): P. Lunkenheimer, S. Emmert, R. Gulich, M. Köhler, M. Wolf, M. Schwab, and A. Loidl

Why does a microwave oven work? How does biological tissue absorb electromagnetic radiation? Astonishingly, we do not have a definite answer to these simple questions because the microscopic processes governing the absorption of electromagnetic waves by water are largely unclarified. This absorption...

[Phys. Rev. E 96, 062607] Published Mon Dec 11, 2017

Optical band gap in a cholesteric elastomer doped by metallic nanospheres


Author(s): Julio C. Hernández and J. Adrián Reyes

We analyzed the optical band gaps for axially propagating electromagnetic waves throughout a metallic doped cholesteric elastomer. The composed medium is made of metallic nanospheres (silver) randomly dispersed in a cholesteric elastomer liquid crystal whose dielectric properties can be represented ...

[Phys. Rev. E 96, 062701] Published Mon Dec 11, 2017

Bending energy of buckled edge dislocations


Author(s): Raz Kupferman

The study of elastic membranes carrying topological defects has a longstanding history, going back at least to the 1950s. When allowed to buckle in three-dimensional space, membranes with defects can totally relieve their in-plane strain, remaining with a bending energy, whose rigidity modulus is sm...

[Phys. Rev. E 96, 063002] Published Mon Dec 11, 2017

Collapse transition in polymer models with multiple monomers per site and multiple bonds per edge


Author(s): Nathann T. Rodrigues and Tiago J. Oliveira

We present results from extensive Monte Carlo simulations of polymer models where each lattice site can be visited by up to $K$ monomers and no restriction is imposed on the number of bonds on each lattice edge. These multiple monomer per site (MMS) models are investigated on the square and cubic la...

[Phys. Rev. E 96, 062111] Published Fri Dec 08, 2017

Influence of topology in the mobility enhancement of pulse-coupled oscillator synchronization


Author(s): A. Beardo, L. Prignano, O. Sagarra, and A. Díaz-Guilera

In this work we revisit the nonmonotonic behavior (NMB) of synchronization time with velocity reported for systems of mobile pulse-coupled oscillators (PCOs). We devise a control parameter that allows us to predict in which range of velocities NMB may occur, also uncovering the conditions allowing u...

[Phys. Rev. E 96, 062306] Published Fri Dec 08, 2017

Influence of ligand-receptor interactions on force-extension behavior within the freely jointed chain model


Author(s): Milad Radiom and Michal Borkovec

We study the influence of receptor-ligand interactions on the force response of single polymer chains theoretically. The extension of the chain is modeled in terms of freely jointed chain or elastic freely jointed chain (EFJC) models. The situation involving noninteracting bonds is solved exactly, w...

[Phys. Rev. E 96, 062501] Published Fri Dec 08, 2017

Maximum of an Airy process plus Brownian motion and memory in Kardar-Parisi-Zhang growth


Author(s): Pierre Le Doussal

We obtain several exact results for universal distributions involving the maximum of the ${\mathrm{Airy}}_{2}$ process minus a parabola and plus a Brownian motion, with applications to the one-dimensional Kardar-Parisi-Zhang (KPZ) stochastic growth universality class. This allows one to obtain (i) t...

[Phys. Rev. E 96, 060101(R)] Published Thu Dec 07, 2017

Kinetics of doublet formation in bicomponent magnetic suspensions: The role of the magnetic permeability anisotropy


Author(s): M. T. Lopez-Lopez, F. Nogueras-Lara, L. Rodriguez-Arco, N. Guigo, N. Sbirrazzuoli, A. Yu. Zubarev, S. Lacis, and P. Kuzhir

Micron-sized particles (microbeads) dispersed in a suspension of magnetic nanoparticles, i.e., ferrofluids, can be assembled into different types of structures upon application of an external magnetic field. This paper is devoted to theoretical modeling of a relative motion of a pair of microbeads (...

[Phys. Rev. E 96, 062604] Published Thu Dec 07, 2017

Clogging of soft particles in two-dimensional hoppers


Author(s): Xia Hong, Meghan Kohne, Mia Morrell, Haoran Wang, and Eric R. Weeks

Using experiments and simulations, we study the flow of soft particles through quasi-two-dimensional hoppers. The first experiment uses oil-in-water emulsion droplets in a thin sample chamber. Due to surfactants coating the droplets, they easily slide past each other, approximating soft frictionless...

[Phys. Rev. E 96, 062605] Published Thu Dec 07, 2017

Forced underwater laminar flows with active magnetohydrodynamic metamaterials


Author(s): Dean Culver and Yaroslav Urzhumov

Theory and practical implementations for wake-free propulsion systems are proposed and proven with computational fluid dynamic modeling. Introduced earlier, the concept of active hydrodynamic metamaterials is advanced by introducing magnetohydrodynamic metamaterials, structures with custom-designed ...

[Phys. Rev. E 96, 063107] Published Thu Dec 07, 2017

Mechanisms of cooperation and competition of two-species transport in narrow nanochannels


Author(s): Wolfgang Rudolf Bauer

Flow of particles of two different species through a narrow channel with solely two discrete spatial positions is analyzed with respect to the species' capability to cooperate or compete for transport. The origin of the latter arises from particle-channel and interparticle interactions within the ch...

[Phys. Rev. E 96, 062109] Published Wed Dec 06, 2017

Entropy production in systems with random transition rates close to equilibrium


Author(s): Daniel M. Busiello, Jorge Hidalgo, and Amos Maritan

We study the entropy production of systems out of equilibrium using random networks. We focus on systems with a finite number of states described by a master equation close to equilibrium. The dynamics are mapped into a network of states (nodes) connected by transition rates (links). Using this fram...

[Phys. Rev. E 96, 062110] Published Wed Dec 06, 2017

Quantification of tension to explain bias dependence of driven polymer translocation dynamics


Author(s): P. M. Suhonen, J. Piili, and R. P. Linna

Motivated by identifying the origin of the bias dependence of tension propagation, we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here, the motion of flexible polymer chains through a narrow pore is simulated using Lan...

[Phys. Rev. E 96, 062401] Published Wed Dec 06, 2017

Diffusiophoresis in nonadsorbing polymer solutions: The Asakura-Oosawa model and stratification in drying films


Author(s): Richard P. Sear and Patrick B. Warren

This article discusses the physics of stratification of colloidal particles and smaller polymer molecules in drying liquid films. The authors focus on the motion of colloidal particles in response to a concentration gradient of polymer molecules, and include the effect of solvent backflow. Their model provides an explanation for the depletion of colloidal particles at the top surface.

[Phys. Rev. E 96, 062602] Published Wed Dec 06, 2017

Equation of state of polydisperse hard-disk mixtures in the high-density regime


Author(s): Andrés Santos, Santos B. Yuste, Mariano López de Haro, and Vitaliy Ogarko

A proposal to link the equation of state of a monocomponent hard-disk fluid to the equation of state of a polydisperse hard-disk mixture is presented. Event-driven molecular dynamics simulations are performed to obtain data for the compressibility factor of the monocomponent fluid and of 26 polydisp...

[Phys. Rev. E 96, 062603] Published Wed Dec 06, 2017

Onset of fractional-order thermal convection in porous media


Author(s): Hamid Karani, Majid Rashtbehesht, Christian Huber, and Richard L. Magin

The macroscopic description of buoyancy-driven thermal convection in porous media is governed by advection-diffusion processes, which in the presence of thermophysical heterogeneities fail to predict the onset of thermal convection and the average rate of heat transfer. This work extends the classic...

[Phys. Rev. E 96, 063105] Published Wed Dec 06, 2017

Effect of an external field on capillary waves in a dipolar fluid


Author(s): Jason P. Koski, Stan G. Moore, Gary S. Grest, and Mark J. Stevens

The role of an external field on capillary waves at the liquid-vapor interface of a dipolar fluid is investigated using molecular dynamics simulations. For fields parallel to the interface, the interfacial width squared increases linearly with respect to the logarithm of the size of the interface ac...

[Phys. Rev. E 96, 063106] Published Wed Dec 06, 2017

Publisher's Note: Constant-pressure nested sampling with atomistic dynamics [Phys. Rev. E 96, 043311 (2017)]


Author(s): Robert J. N. Baldock, Noam Bernstein, K. Michael Salerno, Lívia B. Pártay, and Gábor Csányi

[Phys. Rev. E 96, 069901] Published Wed Dec 06, 2017

First- and second-order quantum phase transitions of a $q$-state Potts model in fractal lattices


Author(s): Hangmo Yi

Quantum phase transitions of a $q$-state Potts model in fractal lattices are studied using a continuous-time quantum Monte Carlo simulation technique. For small values of $q$, the transition is found to be second order and critical exponents of the quantum critical point are calculated. The dynamic ...

[Phys. Rev. E 96, 062105] Published Tue Dec 05, 2017

Bayesian inference with information content model check for Langevin equations


Author(s): Jens Krog and Michael A. Lomholt

Bayesian inference can be used as a method to analyze statistical data from single-particle-tracking experiments. The authors develop a complementary test to judge the quality of the fit, and they present results on how their scheme applies to a theoretical example of position-dependent mobility.

[Phys. Rev. E 96, 062106] Published Tue Dec 05, 2017

Diverging, but negligible power at Carnot efficiency: Theory and experiment


Author(s): Viktor Holubec and Artem Ryabov

We discuss the possibility of reaching the Carnot efficiency by heat engines (HEs) out of quasistatic conditions at nonzero power output. We focus on several models widely used to describe the performance of actual HEs. These models comprise quantum thermoelectric devices, linear irreversible HEs, m...

[Phys. Rev. E 96, 062107] Published Tue Dec 05, 2017

Geometrical interpretation of dynamical phase transitions in boundary-driven systems


Author(s): Ohad Shpielberg

Dynamical phase transitions are defined as nonanalytic points of the large deviation function of current fluctuations. We show that for boundary-driven systems, many dynamical phase transitions can be identified using the geometrical structure of an effective potential of a Hamiltonian, recovered fr...

[Phys. Rev. E 96, 062108] Published Tue Dec 05, 2017

Three faces of node importance in network epidemiology: Exact results for small graphs


Author(s): Petter Holme

We investigate three aspects of the importance of nodes with respect to susceptible-infectious-removed (SIR) disease dynamics: influence maximization (the expected outbreak size given a set of seed nodes), the effect of vaccination (how much deleting nodes would reduce the expected outbreak size), a...

[Phys. Rev. E 96, 062305] Published Tue Dec 05, 2017

Thermalized formulation of soft glassy rheology


Author(s): Robert S. Hoy

We present a version of soft glassy rheology that includes thermalized strain degrees of freedom. It fully specifies systems' strain-history-dependent positions on their energy landscapes and therefore allows for quantitative analysis of their heterogeneous yielding dynamics and nonequilibrium defor...

[Phys. Rev. E 96, 063001] Published Tue Dec 05, 2017

Dynamics of nonspherical microbubble oscillations above instability threshold


Author(s): Matthieu Guédra, Sarah Cleve, Cyril Mauger, Philippe Blanc-Benon, and Claude Inserra

Time-resolved dynamics of nonspherical oscillations of micrometer-sized bubbles are captured and analyzed using high-speed imaging. The axisymmetry of the bubble shape is ensured with certainty for the first time from the recordings of two synchronous high-speed cameras located at ${90}^{∘}$. The te...

[Phys. Rev. E 96, 063104] Published Tue Dec 05, 2017

Inverse Ising problem in continuous time: A latent variable approach


Author(s): Christian Donner and Manfred Opper

We consider the inverse Ising problem: the inference of network couplings from observed spin trajectories for a model with continuous time Glauber dynamics. By introducing two sets of auxiliary latent random variables we render the likelihood into a form which allows for simple iterative inference a...

[Phys. Rev. E 96, 062104] Published Mon Dec 04, 2017

Mirror node correlations tuning synchronization in multiplex networks


Author(s): Anil Kumar, Murilo S. Baptista, Alexey Zaikin, and Sarika Jalan

We show that the degree-degree correlations have a major impact on global synchronizability (GS) of multiplex networks, enabling the specification of synchronizability by only changing the degree-degree correlations of the mirror nodes while maintaining the connection architecture of the individual ...

[Phys. Rev. E 96, 062301] Published Mon Dec 04, 2017

Controlling percolation with limited resources


Author(s): Malte Schröder, Nuno A. M. Araújo, Didier Sornette, and Jan Nagler

Connectivity, or the lack thereof, is crucial for the function of many man-made systems, from financial and economic networks over epidemic spreading in social networks to technical infrastructure. Often, connections are deliberately established or removed to induce, maintain, or destroy global conn...

[Phys. Rev. E 96, 062302] Published Mon Dec 04, 2017

Allison mixture and the two-envelope problem


Author(s): Kang Hao Cheong, David B. Saakian, and Rubina Zadourian

In the present study, we have investigated the Allison mixture, a variant of the Parrondo's games where random mixing of two random sequences creates autocorrelation. We have obtained the autocorrelation function and mutual entropy of two elements. Our analysis shows that the mutual information is n...

[Phys. Rev. E 96, 062303] Published Mon Dec 04, 2017

Scarcity of crossing dependencies: A direct outcome of a specific constraint?


Author(s): Carlos Gómez-Rodríguez and Ramon Ferrer-i-Cancho

The structure of a sentence can be represented as a network where vertices are words and edges indicate syntactic dependencies. Interestingly, crossing syntactic dependencies have been observed to be infrequent in human languages. This leads to the question of whether the scarcity of crossings in la...

[Phys. Rev. E 96, 062304] Published Mon Dec 04, 2017

Instabilities in rapid directional solidification under weak flow


Author(s): Katarzyna N. Kowal, Stephen H. Davis, and Peter W. Voorhees

We examine a rapidly solidifying binary alloy under directional solidification with nonequilibrium interfacial thermodynamics viz. the segregation coefficient and the liquidus slope are speed dependent and attachment-kinetic effects are present. Both of these effects alone give rise to (steady) cell...

[Phys. Rev. E 96, 062802] Published Mon Dec 04, 2017

Rheology of dense granular flows for elongated particles


Author(s): Dániel B. Nagy, Philippe Claudin, Tamás Börzsönyi, and Ellák Somfai

We study the rheology of dense granular flows for frictionless spherocylinders by means of 3D numerical simulations. As in the case of spherical particles, the effective friction $μ$ is an increasing function of the inertial number $I$, and we systematically investigate the dependence of $μ$ on the ...

[Phys. Rev. E 96, 062903] Published Mon Dec 04, 2017

Numerical study of two disks settling in an Oldroyd-B fluid: From periodic interaction to chaining


Author(s): Tsorng-Whay Pan and Roland Glowinski

In this article, we present a numerical study of the dynamics of two disks sedimenting in a narrow vertical channel filled with an Oldroyd-B fluid. Two kinds of particle dynamics are observed: (i) a periodic interaction between the two disks, and (ii) the formation of a two-disk chain. For the perio...

[Phys. Rev. E 96, 063103] Published Mon Dec 04, 2017

Computational framework for particle and spin simulations based on the stochastic Galerkin method


Author(s): J. Slim, F. Rathmann, and D. Heberling

An implementation of the polynomial chaos expansion is introduced as a fast solver of the equations of beam and spin motion of charged particles in electromagnetic fields. We show that, based on the stochastic Galerkin method, our computational framework substantially reduces the required number of ...

[Phys. Rev. E 96, 063301] Published Mon Dec 04, 2017

Fast inverse nonlinear Fourier transformation using exponential one-step methods: Darboux transformation


Author(s): V. Vaibhav

This paper considers the non-Hermitian Zakharov-Shabat (ZS) scattering problem which forms the basis for defining the $\mathrm{SU}(2)$ nonlinear Fourier transformation (NFT). The theoretical underpinnings of this generalization of the conventional Fourier transformation are quite well established in...

[Phys. Rev. E 96, 063302] Published Mon Dec 04, 2017

Improved thermal lattice Boltzmann model for simulation of liquid-vapor phase change


Author(s): Qing Li, P. Zhou, and H. J. Yan

In this paper, an improved thermal lattice Boltzmann (LB) model is proposed for simulating liquid-vapor phase change, which is aimed at improving an existing thermal LB model for liquid-vapor phase change [S. Gong and P. Cheng, Int. J. Heat Mass Transfer 55, 4923 (2012)]. First, we emphasize that th...

[Phys. Rev. E 96, 063303] Published Mon Dec 04, 2017

Numerical solution of modified differential equations based on symmetry preservation


Author(s): Ersin Ozbenli and Prakash Vedula

In this paper, we propose a method to construct invariant finite-difference schemes for solution of partial differential equations (PDEs) via consideration of modified forms of the underlying PDEs. The invariant schemes, which preserve Lie symmetries, are obtained based on the method of equivariant ...

[Phys. Rev. E 96, 063304] Published Mon Dec 04, 2017

Antiswarming: Structure and dynamics of repulsive chemically active particles


Author(s): Wen Yan and John F. Brady

The authors investigate collective behavior of repulsive Brownian particles. Simulations and analytical studies reveal that chemically active repulsive particles, when confined to a constant-volume domain, may undergo a liquid-to-crystal phase transition analogous to that found for positive ions in one-component plasmas. Experimental tests of the predictions appear to be feasible.

[Phys. Rev. E 96, 060601(R)] Published Fri Dec 01, 2017

Observation of structural universality in disordered systems using bulk diffusion measurement


Author(s): Antonios Papaioannou, Dmitry S. Novikov, Els Fieremans, and Gregory S. Boutis

We report on an experimental observation of classical diffusion distinguishing between structural universality classes of disordered systems in one dimension. Samples of hyperuniform and short-range disorder were designed, characterized by the statistics of the placement of micrometer-thin parallel ...

[Phys. Rev. E 96, 061101(R)] Published Fri Dec 01, 2017

Convex hulls of random walks in higher dimensions: A large-deviation study


Author(s): Hendrik Schawe, Alexander K. Hartmann, and Satya N. Majumdar

The distribution of the hypervolume $V$ and surface $∂V$ of convex hulls of (multiple) random walks in higher dimensions are determined numerically, especially containing probabilities far smaller than $P={10}^{−1000}$ to estimate large deviation properties. For arbitrary dimensions and large walk l...

[Phys. Rev. E 96, 062101] Published Fri Dec 01, 2017

Flows, scaling, and the control of moment hierarchies for stochastic chemical reaction networks


Author(s): Eric Smith and Supriya Krishnamurthy

Stochastic chemical reaction networks (CRNs) are complex systems that combine the features of concurrent transformation of multiple variables in each elementary reaction event and nonlinear relations between states and their rates of change. Most general results concerning CRNs are limited to restri...

[Phys. Rev. E 96, 062102] Published Fri Dec 01, 2017

Complete analysis of ensemble inequivalence in the Blume-Emery-Griffiths model


Author(s): V. V. Hovhannisyan, N. S. Ananikian, A. Campa, and S. Ruffo

We study inequivalence of canonical and microcanonical ensembles in the mean-field Blume-Emery-Griffiths model. This generalizes previous results obtained for the Blume-Capel model. The phase diagram strongly depends on the value of the biquadratic exchange interaction $K$, the additional feature pr...

[Phys. Rev. E 96, 062103] Published Fri Dec 01, 2017

Quantum effects and quantum chaos in multidimensional tunneling


Author(s): J. Zamastil and D. Šimsa

The ground-state energy splitting due to tunneling in two-dimensional double wells of the form $V(x,y)=\frac{{({x}^{2}−{R}^{2})}^{2}}{8{R}^{2}}+\frac{{x}^{2}−{R}^{2}}{{R}^{2}}γy+\frac{{ω}^{2}}{2}{y}^{2}$ is calculated. Several results are reported. First, we give a systematic WKB expansion of the sp...

[Phys. Rev. E 96, 062201] Published Fri Dec 01, 2017

Experimental investigation of mesoscopic heterogeneous motion of laser-activated self-propelling Janus particles in suspension


Author(s): Chong-Wai Io, Tzu-Yin Chen, Jai-Wei Yeh, and Sin-Cen Cai

The mesoscopic collective motion of self-propelling active particle suspension is experimentally investigated. The active particles are silica micro spheres with Au hemisphere coating, and their propelling strength is activated by laser irradiation. The suspension is driven from equilibrium to near ...

[Phys. Rev. E 96, 062601] Published Fri Dec 01, 2017

Effect of temperature on the dynamics and geometry of reactive-wetting interfaces around room temperature


Author(s): Meital Harel and Haim Taitelbaum

The temperature effect on the dynamics and geometry of a mercury droplet (∼150 μm) spreading on a silver substrate (4000 Å) was studied. The system temperature was controlled by a heating stage in the temperature range of −15 °C  T  25 °C, and the spreading process was monitored using an optical mic...

[Phys. Rev. E 96, 062801] Published Fri Dec 01, 2017

Dynamic induced softening in frictional granular materials investigated by discrete-element-method simulation


Author(s): Laure Lemrich, Jan Carmeliet, Paul A. Johnson, Robert Guyer, and Xiaoping Jia

A granular system composed of frictional glass beads is simulated using the discrete element method. The intergrain forces are based on the Hertz contact law in the normal direction with frictional tangential force. The damping due to collision is also accounted for. Systems are loaded at various st...

[Phys. Rev. E 96, 062901] Published Fri Dec 01, 2017

Response of jammed packings to thermal fluctuations


Author(s): Qikai Wu, Thibault Bertrand, Mark D. Shattuck, and Corey S. O'Hern

We focus on the response of mechanically stable (MS) packings of frictionless, bidisperse disks to thermal fluctuations, with the aim of quantifying how nonlinearities affect system properties at finite temperature. In contrast, numerous prior studies characterized the structural and mechanical prop...

[Phys. Rev. E 96, 062902] Published Fri Dec 01, 2017

Logarithmic scaling for fluctuations of a scalar concentration in wall turbulence


Author(s): Hideaki Mouri, Takeshi Morinaga, Toshimasa Yagi, and Kazuyasu Mori

Within wall turbulence, there is a sublayer where the mean velocity and the variance of velocity fluctuations vary logarithmically with the height from the wall. This logarithmic scaling is also known for the mean concentration of a passive scalar. By using heat as such a scalar in a laboratory expe...

[Phys. Rev. E 96, 063101] Published Fri Dec 01, 2017

Cooling beyond the boundary value in supercritical fluids under vibration


Author(s): D. Sharma, A. Erriguible, and S. Amiroudine

Supercritical fluids when subjected to simultaneous quench and vibration have been known to cause various intriguing flow phenomena and instabilities depending on the relative direction of temperature gradient and vibration. Here we describe a surprising and interesting phenomenon wherein temperatur...

[Phys. Rev. E 96, 063102] Published Fri Dec 01, 2017

Infection dynamics on spatial small-world network models


Author(s): Bryan Iotti, Alberto Antonioni, Seth Bullock, Christian Darabos, Marco Tomassini, and Mario Giacobini

The study of complex networks, and in particular of social networks, has mostly concentrated on relational networks, abstracting the distance between nodes. Spatial networks are, however, extremely relevant in our daily lives, and a large body of research exists to show that the distances between no...

[Phys. Rev. E 96, 052316] Published Thu Nov 30, 2017

Laser-excited motion of liquid crystals confined in a microsized volume with a free surface


Author(s): A. V. Zakharov and P. V. Maslennikov

The thermally excited vortical flow in a microsized liquid crystal (LC) volume with a free LC-air interface has been investigated theoretically based on the nonlinear extension of the Ericksen-Leslie theory, with accounting the entropy balance equation. Analysis of the numerical results show that du...

[Phys. Rev. E 96, 052705] Published Thu Nov 30, 2017

Thermodynamic theory of dislocation-enabled plasticity


Author(s): J. S. Langer

The thermodynamic theory of dislocation-enabled plasticity is based on two unconventional hypotheses. The first of these is that a system of dislocations, driven by external forces and irreversibly exchanging heat with its environment, must be characterized by a thermodynamically defined effective t...

[Phys. Rev. E 96, 053005] Published Thu Nov 30, 2017

Exact relations for energy transfer in self-gravitating isothermal turbulence


Author(s): Supratik Banerjee and Alexei G. Kritsuk

Self-gravitating isothermal supersonic turbulence is analyzed in the asymptotic limit of large Reynolds numbers. Based on the inviscid invariance of total energy, an exact relation is derived for homogeneous (not necessarily isotropic) turbulence. A modified definition for the two-point energy corre...

[Phys. Rev. E 96, 053116] Published Thu Nov 30, 2017

Current quantization and fractal hierarchy in a driven repulsive lattice gas


Author(s): Pietro Rotondo, Alessandro Luigi Sellerio, Pietro Glorioso, Sergio Caracciolo, Marco Cosentino Lagomarsino, and Marco Gherardi

Driven lattice gases are widely regarded as the paradigm of collective phenomena out of equilibrium. While such models are usually studied with nearest-neighbor interactions, many empirical driven systems are dominated by slowly decaying interactions such as dipole-dipole and Van der Waals forces. M...

[Phys. Rev. E 96, 052141] Published Wed Nov 29, 2017

Inverse Bremsstrahlung current drive


Author(s): Vadim R. Munirov and Nathaniel J. Fisch

The generation of current from electron-ion Bremsstrahlung absorption is one of the open problems in plasma physics. In this paper, the authors extend previous results for the current generated by colliding electrons and ions in the presence of incoming photons. Understanding the mechanisms behind this plasma current can have important consequences for astrophysical systems and inertial confinement fusion.

[Phys. Rev. E 96, 053211] Published Wed Nov 29, 2017

Computation of the asymptotic states of modulated open quantum systems with a numerically exact realization of the quantum trajectory method


Author(s): V. Volokitin, A. Liniov, I. Meyerov, M. Hartmann, M. Ivanchenko, P. Hänggi, and S. Denisov

Quantum systems out of equilibrium are presently a subject of active research, both in theoretical and experimental domains. In this work, we consider time-periodically modulated quantum systems that are in contact with a stationary environment. Within the framework of a quantum master equation, the...

[Phys. Rev. E 96, 053313] Published Wed Nov 29, 2017

Detection of transition times from single-particle-tracking trajectories


Author(s): Takuma Akimoto and Eiji Yamamoto

In heterogeneous environments, the diffusivity is not constant but changes with time. It is important to detect changes in the diffusivity from single-particle-tracking trajectories in experiments. Here, we devise a novel method for detecting the transition times of the diffusivity from trajectory d...

[Phys. Rev. E 96, 052138] Published Tue Nov 28, 2017

Response and correlation functions of nonlinear systems in equilibrium states


Author(s): Lubo Xu (续路波) and Lei Wang (王雷)

In this paper, we study systematically a serial of correlation functions in some one-dimensional nonlinear lattices. Due to the energy conservation law, they are implicitly interdependent. Various transport coefficients are thus also connected. In the studies of the autocorrelations of local energy ...

[Phys. Rev. E 96, 052139] Published Tue Nov 28, 2017

Transient subdiffusion from an Ising environment


Author(s): G. Muñoz-Gil, C. Charalambous, M. A. García-March, M. F. Garcia-Parajo, C. Manzo, M. Lewenstein, and A. Celi

We introduce a model in which a particle performs a continuous-time random walk (CTRW) coupled to an environment with Ising dynamics. The particle shows locally varying diffusivity determined by the geometrical properties of the underlying Ising environment, that is, the diffusivity depends on the s...

[Phys. Rev. E 96, 052140] Published Tue Nov 28, 2017

Rayleigh-Taylor instability and vortex rings in coupled Gross-Pitaevskii equations


Author(s): Hidetsugu Sakaguchi and Hiroomi Chono

The Rayleigh-Taylor instability is a gravitational instability in two fluids where the heavier fluid is set over the lighter fluid. The instability occurs both in classical fluids and quantum fluids. We numerically study the Rayleigh-Taylor instability using coupled Gross-Pitaevskii equations for tw...

[Phys. Rev. E 96, 052222] Published Tue Nov 28, 2017

Nonlinear dynamics of a buoyancy-induced turbulent fire


Author(s): Kazushi Takagi, Hiroshi Gotoda, Isao T. Tokuda, and Takaya Miyano

We conduct a numerical study on the dynamic behavior of a buoyancy-induced turbulent fire from the viewpoints of symbolic dynamics, complex networks, and statistical complexity. Here, we consider two classes of entropies: the permutation entropy and network entropy in $ε$-recurrence networks, both o...

[Phys. Rev. E 96, 052223] Published Tue Nov 28, 2017

Pathways to equilibrium orientation fluctuations in finite stripe-forming systems


Author(s): Christian Riesch, Günter Radons, and Robert Magerle

Small-angle orientation fluctuations in ordered stripe-forming systems free of topological defects can exhibit aging and anisotropic growth of two length scales. In infinitely extended systems, the stripe orientation field develops a dominant modulation length ${λ}_{∥}^{*}(t)$ in the direction paral...

[Phys. Rev. E 96, 052224] Published Tue Nov 28, 2017

Zealotry effects on opinion dynamics in the adaptive voter model


Author(s): Pascal P. Klamser, Marc Wiedermann, Jonathan F. Donges, and Reik V. Donner

The adaptive voter model has been widely studied as a conceptual model for opinion formation processes on time-evolving social networks. Past studies on the effect of zealots, i.e., nodes aiming to spread their fixed opinion throughout the system, only considered the voter model on a static network....

[Phys. Rev. E 96, 052315] Published Tue Nov 28, 2017

Physics behind the mechanical nucleosome positioning code


Author(s): Martijn Zuiddam, Ralf Everaers, and Helmut Schiessel

The positions along DNA molecules of nucleosomes, the most abundant DNA-protein complexes in cells, are influenced by the sequence-dependent DNA mechanics and geometry. This leads to the “nucleosome positioning code”, a preference of nucleosomes for certain sequence motives. Here we introduce a simp...

[Phys. Rev. E 96, 052412] Published Tue Nov 28, 2017

Orientation-shape coupling between liquid crystal and membrane through the anchoring effect


Author(s): Shun Okushima and Toshihiro Kawakatsu

We perform a series of Monte Carlo simulations on an interface between a liquid crystal (LC) material in isotropic phase in its bulk and a surfactant membrane. These two objects are simulated using coarse-grained molecular models. We estimate physical properties of the membrane such as the interfaci...

[Phys. Rev. E 96, 052704] Published Tue Nov 28, 2017

Plasma $q$-plate for generation and manipulation of intense optical vortices


Author(s): Kenan Qu, Qing Jia, and Nathaniel J. Fisch

An optical vortex is a light wave with a twisting wavefront around its propagation axis and null intensity in the beam center. Its unique spatial structure of field lends itself to a broad range of applications, including optical communication, quantum information, superresolution microscopy, and mu...

[Phys. Rev. E 96, 053207] Published Tue Nov 28, 2017

Viscosity of two-dimensional strongly coupled dusty plasma modified by a perpendicular magnetic field


Author(s): Yan Feng, Wei Lin, and M. S. Murillo

Transport properties of two-dimensional (2D) strongly coupled dusty plasmas have been investigated in detail, but never for viscosity with a strong perpendicular magnetic field; here, we examine this scenario using Langevin dynamics simulations of 2D liquids with a binary Yukawa interparticle intera...

[Phys. Rev. E 96, 053208] Published Tue Nov 28, 2017

Effects of group velocity and multiplasmon resonances on the modulation of Langmuir waves in a degenerate plasma


Author(s): Amar P. Misra, Debjani Chatterjee, and Gert Brodin

We study the nonlinear wave modulation of Langmuir waves (LWs) in a fully degenerate plasma. Using the Wigner–Moyal equation coupled to the Poisson equation and the multiple scale expansion technique, a modified nonlocal nonlinear Schrödinger (NLS) equation is derived which governs the evolution of ...

[Phys. Rev. E 96, 053209] Published Tue Nov 28, 2017

Ideal radiation source for plasma spectroscopy generated by laser ablation


Author(s): Jörg Hermann, David Grojo, Emanuel Axente, Christoph Gerhard, Miloš Burger, and Valentin Craciun

Laboratory plasmas inherently exhibit temperature and density gradients leading to complex investigations. We show that plasmas generated by laser ablation can constitute a robust exception to this. Supported by emission features not observed with other sources, we achieve plasmas of various composi...

[Phys. Rev. E 96, 053210] Published Tue Nov 28, 2017

Stochastic thermodynamics for a periodically driven single-particle pump


Author(s): Alexandre Rosas, Christian Van den Broeck, and Katja Lindenberg

We present the stochastic thermodynamic analysis of a time-periodic single-particle pump, including explicit results for flux, thermodynamic force, entropy production, work, heat, and efficiency. These results are valid far from equilibrium. The deviations from the linear (Onsager) regime are discus...

[Phys. Rev. E 96, 052135] Published Mon Nov 27, 2017

Universal Gaussian behavior of driven lattice gases at short times


Author(s): Valerio Volpati, Urna Basu, Sergio Caracciolo, and Andrea Gambassi

In this work, the authors study the behavior of equilibrium and nonequilibrium lattice gas models. They find that, although the models belong to different universality classes and exhibit different critical properties, they display very similar behavior at short times after a critical quench. The short-time dynamics can be described with an effective Gaussian theory.

[Phys. Rev. E 96, 052136] Published Mon Nov 27, 2017

Stationary uphill currents in locally perturbed zero-range processes


Author(s): Emilio N. M. Cirillo and Matteo Colangeli

Uphill currents are observed when mass diffuses in the direction of the density gradient. We study this phenomenon in stationary conditions in the framework of locally perturbed one-dimensional zero range processes (ZRPs). We show that the onset of currents flowing from the reservoir with smaller de...

[Phys. Rev. E 96, 052137] Published Mon Nov 27, 2017

Directionality indices: Testing information transfer with surrogate correction


Author(s): Beth Jelfs and Rosa H. M. Chan

Directionality indices can be used as an indicator of the asymmetry in coupling between systems and have found particular application in relation to neurological systems. The directionality index between two systems is a function of measures of information transfer in both directions. Here we illust...

[Phys. Rev. E 96, 052220] Published Mon Nov 27, 2017

Correlations in eigenfunctions of quantum chaotic systems with sparse Hamiltonian matrices


Author(s): Jiaozi Wang and Wen-ge Wang

In most realistic models for quantum chaotic systems, the Hamiltonian matrices in unperturbed bases have a sparse structure. We study correlations in eigenfunctions of such systems and derive explicit expressions for some of the correlation functions with respect to energy. The analytical results ar...

[Phys. Rev. E 96, 052221] Published Mon Nov 27, 2017

Unified mean-field framework for susceptible-infected-susceptible epidemics on networks, based on graph partitioning and the isoperimetric inequality


Author(s): K. Devriendt and P. Van Mieghem

We propose an approximation framework that unifies and generalizes a number of existing mean-field approximation methods for the susceptible-infected-susceptible (SIS) epidemic model on complex networks. We derive the framework, which we call the unified mean-field framework (UMFF), as a set of appr...

[Phys. Rev. E 96, 052314] Published Mon Nov 27, 2017

Crystallization of finite-extensible nonlinear elastic Lennard-Jones coarse-grained polymers


Author(s): Julien Morthomas, Claudio Fusco, Zengqiang Zhai, Olivier Lame, and Michel Perez

The ability of a simple coarse-grained finite-extensible nonlinear elastic (FENE) Lennard-Jones (LJ) polymer model to be crystallized is investigated by molecular dynamics simulations. The optimal FENE Lennard-Jones parameter combinations (ratio between FENE and LJ equilibrium distances) and the opt...

[Phys. Rev. E 96, 052502] Published Mon Nov 27, 2017

Flow properties and hydrodynamic interactions of rigid spherical microswimmers


Author(s): Tapan Chandra Adhyapak and Sara Jabbari-Farouji

We analyze a minimal model for a rigid spherical microswimmer and explore the consequences of its extended surface on the interplay between its self-propulsion and flow properties. The model is the first order representation of microswimmers, such as bacteria and algae, with rigid bodies and flexibl...

[Phys. Rev. E 96, 052608] Published Mon Nov 27, 2017

Modified mean-field theory of the magnetic properties of concentrated, high-susceptibility, polydisperse ferrofluids


Author(s): Anna Yu. Solovyova, Ekaterina A. Elfimova, Alexey O. Ivanov, and Philip J. Camp

The effects of particle-size polydispersity on the magnetostatic properties of concentrated ferrofluids are studied using theory and computer simulation. The second-order modified mean-field (MMF2) theory of Ivanov and Kuznetsova [Phys. Rev. E 64, 041405 (2001)] has been extended by calculating addi...

[Phys. Rev. E 96, 052609] Published Mon Nov 27, 2017

Effective viscosity of a suspension of flagellar-beating microswimmers: Three-dimensional modeling


Author(s): Levan Jibuti, Walter Zimmermann, Salima Rafaï, and Philippe Peyla

Micro-organisms usually can swim in their liquid environment by flagellar or ciliary beating. In this numerical work, we analyze the influence of flagellar beating on the orbits of a swimming cell in a shear flow. We also calculate the effect of the flagellar beating on the rheology of a dilute susp...

[Phys. Rev. E 96, 052610] Published Mon Nov 27, 2017

Analytical mesoscale modeling of aeolian sand transport


Author(s): Marc Lämmel and Klaus Kroy

The mesoscale structure of aeolian sand transport determines a variety of natural phenomena studied in planetary and Earth science. We analyze it theoretically beyond the mean-field level, based on the grain-scale transport kinetics and splash statistics. A coarse-grained analytical model is propose...

[Phys. Rev. E 96, 052906] Published Mon Nov 27, 2017

Deceleration of one-dimensional mixing by discontinuous mappings


Author(s): Hannah Kreczak, Rob Sturman, and Mark C. T. Wilson

We present a computational study of a simple one-dimensional map with dynamics composed of stretching, permutations of equally sized cells, and diffusion. We observe that the combination of the aforementioned dynamics results in eigenmodes with long-time exponential decay rates. The decay rate of th...

[Phys. Rev. E 96, 053112] Published Mon Nov 27, 2017

Kinetic-contact-driven gigantic energy transfer in a two-dimensional Lennard-Jones fluid confined to a rotating pore


Author(s): Paweł Karbowniczek and Agnieszka Chrzanowska

A two-dimensional Lennard-Jones system in a circular and rotating container has been studied by means of molecular dynamics technique. A nonequilibrium transition to the rotating stage has been detected in a delayed time since an instant switching of the frame rotation. This transition is attributed...

[Phys. Rev. E 96, 053113] Published Mon Nov 27, 2017

Role of red cells and plasma composition on blood sessile droplet evaporation


Author(s): Luca Lanotte, Didier Laux, Benoît Charlot, and Manouk Abkarian

The morphology of dried blood droplets derives from the deposition of red cells, the main components of their solute phase. Up to now, evaporation-induced convective flows were supposed to be at the base of red cell distribution in blood samples. Here, we present a direct visualization by videomicro...

[Phys. Rev. E 96, 053114] Published Mon Nov 27, 2017

Nonlinear and subharmonic stability analysis in film-driven morphological patterns


Author(s): Matteo Bernard Bertagni and Carlo Camporeale

The interaction of a gravity-driven water film with an evolving solid substrate (calcite or ice) results in the formation of fascinating wavy patterns similar both in caves and in ice-falls. Due to their remarkable similarity, we adopt a unified approach in the study of pattern formation of longitud...

[Phys. Rev. E 96, 053115] Published Mon Nov 27, 2017

Isochoric, isobaric, and ultrafast conductivities of aluminum, lithium, and carbon in the warm dense matter regime


Author(s): M. W. C. Dharma-wardana, D. D. Klug, L. Harbour, and Laurent J. Lewis

We study the conductivities $σ$ of (i) the equilibrium isochoric state ${σ}_{\mathrm{is}}$, (ii) the equilibrium isobaric state ${σ}_{\mathrm{ib}}$, and also the (iii) nonequilibrium ultrafast matter state ${σ}_{\mathrm{uf}}$ with the ion temperature ${T}_{i}$ less than the electron temperature ${T}...

[Phys. Rev. E 96, 053206] Published Mon Nov 27, 2017

Corrected simulations for one-dimensional diffusion processes with naturally occurring boundaries


Author(s): Hassan Shafiey, Xinjun Gan, and David Waxman

To simulate a diffusion process, a usual approach is to discretize the time in the associated stochastic differential equation. This is the approach used in the Euler method. In the present work we consider a one-dimensional diffusion process where the terms occurring, within the stochastic differen...

[Phys. Rev. E 96, 053310] Published Mon Nov 27, 2017