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Preview: Recent Articles in Phys. Rev. E

Recent Articles in Phys. Rev. E

Recent articles in Physical Review E

Published: 2018-02-21T07:03:06+00:00


Metastable state en route to traveling-wave synchronization state


Author(s): Jinha Park and B. Kahng

The Kuramoto model with mixed signs of couplings is known to produce a traveling-wave synchronized state. Here, we consider an abrupt synchronization transition from the incoherent state to the traveling-wave state through a long-lasting metastable state with large fluctuations. Our explanation of t...

[Phys. Rev. E 97, 020203(R)] Published Tue Feb 20, 2018

Generalized thermodynamics of phase equilibria in scalar active matter


Author(s): Alexandre P. Solon, Joakim Stenhammar, Michael E. Cates, Yariv Kafri, and Julien Tailleur

Motility-induced phase separation (MIPS) arises generically in fluids of self-propelled particles when interactions lead to a kinetic slowdown at high densities. Starting from a continuum description of scalar active matter akin to a generalized Cahn-Hilliard equation, we give a general prescription...

[Phys. Rev. E 97, 020602(R)] Published Tue Feb 20, 2018

Entropic bounds between two thermal equilibrium states


Author(s): Julio A. López-Saldívar, Octavio Castaños, Margarita A. Man'ko, and Vladimir I. Man'ko

The positivity conditions of the relative entropy between two thermal equilibrium states ${\stackrel{̂}{ρ}}_{1}$ and ${\stackrel{̂}{ρ}}_{2}$ are used to obtain upper and lower bounds for the subtraction of their entropies, the Helmholtz potential and the Gibbs potential of the two systems. These lim...

[Phys. Rev. E 97, 022128] Published Tue Feb 20, 2018

Theory of transformation thermal convection for creeping flow in porous media: Cloaking, concentrating, and camouflage


Author(s): Gaole Dai, Jin Shang, and Jiping Huang

Heat can transfer via thermal conduction, thermal radiation, and thermal convection. All the existing theories of transformation thermotics and optics can treat thermal conduction and thermal radiation, respectively. Unfortunately, thermal convection has seldom been touched in transformation theorie...

[Phys. Rev. E 97, 022129] Published Tue Feb 20, 2018

Achieving the classical Carnot efficiency in a strongly coupled quantum heat engine


Author(s): Y. Y. Xu, B. Chen, and J. Liu

Generally, the efficiency of a heat engine strongly coupled with a heat bath is less than the classical Carnot efficiency. Through a model-independent method, we show that the classical Carnot efficiency is achieved in a strongly coupled quantum heat engine. First, we present the first law of quantu...

[Phys. Rev. E 97, 022130] Published Tue Feb 20, 2018

Heat leakage in overdamped harmonic systems


Author(s): Dominic Arold, Andreas Dechant, and Eric Lutz

We investigate the occurrence of heat leakages in overdamped nonequilibrium Brownian harmonic systems. We exactly compute the underdamped and overdamped stochastic heats exchanged with the bath for a sudden frequency or temperature switch. We show that the underdamped heat reduces to the correspondi...

[Phys. Rev. E 97, 022131] Published Tue Feb 20, 2018

Short-ranged memory model with preferential growth


Author(s): Ana L. Schaigorodsky, Juan I. Perotti, Nahuel Almeira, and Orlando V. Billoni

In this work we introduce a variant of the Yule-Simon model for preferential growth by incorporating a finite kernel to model the effects of bounded memory. We characterize the properties of the model combining analytical arguments with extensive numerical simulations. In particular, we analyze the ...

[Phys. Rev. E 97, 022132] Published Tue Feb 20, 2018

Orthogonality catastrophe and fractional exclusion statistics


Author(s): Filiberto Ares, Kumar S. Gupta, and Amilcar R. de Queiroz

We show that the $N$-particle Sutherland model with inverse-square and harmonic interactions exhibits orthogonality catastrophe. For a fixed value of the harmonic coupling, the overlap of the $N$-body ground state wave functions with two different values of the inverse-square interaction term goes t...

[Phys. Rev. E 97, 022133] Published Tue Feb 20, 2018

Mechanism of Kuznetsov-Ma breathers


Author(s): Li-Chen Zhao, Liming Ling, and Zhan-Ying Yang

We discuss how to understand the dynamical process of Kuznetsov-Ma breather, based on some basic physical mechanisms. It is shown that the dynamical process of Kuznetsov-Ma breather involves at least two distinctive mechanisms: modulational instability and the interference effects between a bright s...

[Phys. Rev. E 97, 022218] Published Tue Feb 20, 2018

Rapid decay in the relative efficiency of quarantine to halt epidemics in networks


Author(s): Giovanni Strona and Claudio Castellano

Several recent studies have tackled the issue of optimal network immunization by providing efficient criteria to identify key nodes to be removed in order to break apart a network, thus preventing the occurrence of extensive epidemic outbreaks. Yet, although the efficiency of those criteria has been...

[Phys. Rev. E 97, 022308] Published Tue Feb 20, 2018

Burst of virus infection and a possibly largest epidemic threshold of non-Markovian susceptible-infected-susceptible processes on networks


Author(s): Qiang Liu and Piet Van Mieghem

Since a real epidemic process is not necessarily Markovian, the epidemic threshold obtained under the Markovian assumption may be not realistic. To understand general non-Markovian epidemic processes on networks, we study the Weibullian susceptible-infected-susceptible (SIS) process in which the inf...

[Phys. Rev. E 97, 022309] Published Tue Feb 20, 2018

Phase diagram of restricted Boltzmann machines and generalized Hopfield networks with arbitrary priors


Author(s): Adriano Barra, Giuseppe Genovese, Peter Sollich, and Daniele Tantari

This paper studies the connection between Hopfield networks and restricted Boltzmann machines, two common tools in the developing area of machine learning. The work focuses on the behavior of models whose variables are either discrete and binary or take on a range of continuous values. The authors find a large degree of robustness in the retrieval capabilities of the models, especially when the number of stored patterns is small.

[Phys. Rev. E 97, 022310] Published Tue Feb 20, 2018

Diffuse correlation tomography in the transport regime: A theoretical study of the sensitivity to Brownian motion


Author(s): Ugo Tricoli, Callum M. Macdonald, Turgut Durduran, Anabela Da Silva, and Vadim A. Markel

Diffuse correlation tomography (DCT) uses the electric-field temporal autocorrelation function to measure the mean-square displacement of light-scattering particles in a turbid medium over a given exposure time. The movement of blood particles is here estimated through a Brownian-motion-like model i...

[Phys. Rev. E 97, 022408] Published Tue Feb 20, 2018

Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times


Author(s): Ajeet K. Sharma, Nabeel Ahmed, and Edward P. O’Brien

Ribosome profiling experiments have found greater than 100-fold variation in ribosome density along mRNA transcripts, indicating that individual codon elongation rates can vary to a similar degree. This wide range of elongation times, coupled with differences in codon usage between transcripts, sugg...

[Phys. Rev. E 97, 022409] Published Tue Feb 20, 2018

Social forces for team coordination in ball possession game


Author(s): Keiko Yokoyama, Hiroyuki Shima, Keisuke Fujii, Noriyuki Tabuchi, and Yuji Yamamoto

Team coordination is a basic human behavioral trait observed in many real-life communities. To promote teamwork, it is important to cultivate social skills that elicit team coordination. In the present work, we consider which social skills are indispensable for individuals performing a ball possessi...

[Phys. Rev. E 97, 022410] Published Tue Feb 20, 2018

Microbial mutualism at a distance: The role of geometry in diffusive exchanges


Author(s): François J. Peaudecerf, Freddy Bunbury, Vaibhav Bhardwaj, Martin A. Bees, Alison G. Smith, Raymond E. Goldstein, and Ottavio A. Croze

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or...

[Phys. Rev. E 97, 022411] Published Tue Feb 20, 2018

Kinetic theory of pattern formation in mixtures of microtubules and molecular motors


Author(s): Ivan Maryshev, Davide Marenduzzo, Andrew B. Goryachev, and Alexander Morozov

In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E 74, 031915 (2006)] we model the m...

[Phys. Rev. E 97, 022412] Published Tue Feb 20, 2018

Hill functions for stochastic gene regulatory networks from master equations with split nodes and time-scale separation


Author(s): Ovidiu Lipan and Cameron Ferwerda

The deterministic Hill function depends only on the average values of molecule numbers. To account for the fluctuations in the molecule numbers, the argument of the Hill function needs to contain the means, the standard deviations, and the correlations. Here we present a method that allows for stoch...

[Phys. Rev. E 97, 022413] Published Tue Feb 20, 2018

Effect of crosslink torsional stiffness on elastic behavior of semiflexible polymer networks


Author(s): H. Hatami-Marbini

Networks of semiflexible filaments are building blocks of different biological and structural materials such as cytoskeleton and extracellular matrix. The mechanical response of these systems when subjected to an applied strain at zero temperature is often investigated numerically using networks com...

[Phys. Rev. E 97, 022504] Published Tue Feb 20, 2018

Nematic liquid crystal in a cylindrical sample: Theoretical analysis of the electrical response


Author(s): O. A. Gomes, C. A. R. Yednak, B. V. H. V. da Silva, and R. T. Teixeira-Souza

The electrical responses of a nematic liquid crystal sample confined between two cylindrical surfaces are investigated in the framework of elastic continuum theory. The responses are the result of the molecular reorientation induced by both the applied electric field and the cylindrical geometry of ...

[Phys. Rev. E 97, 022703] Published Tue Feb 20, 2018

Pair creation, motion, and annihilation of topological defects in two-dimensional nematic liquid crystals


Author(s): Dario Cortese, Jens Eggers, and Tanniemola B. Liverpool

We present a framework for the study of disclinations in two-dimensional active nematic liquid crystals and topological defects in general. The order tensor formalism is used to calculate exact multiparticle solutions of the linearized static equations inside a planar uniformly aligned state so that...

[Phys. Rev. E 97, 022704] Published Tue Feb 20, 2018

Distributions of pore sizes and atomic densities in binary mixtures revealed by molecular dynamics simulations


Author(s): Maxim A. Makeev and Nikolai V. Priezjev

We report on the results of a molecular dynamics simulation study of porous glassy media, formed in the process of isochoric rapid quenching from a high-temperature liquid state. The transition to a porous solid occurs due to the concurrent processes of phase separation and material solidification. ...

[Phys. Rev. E 97, 023002] Published Tue Feb 20, 2018

Detecting singular weak-dissipation limit for flutter onset in reversible systems


Author(s): Davide Bigoni, Diego Misseroni, Mirko Tommasini, Oleg N. Kirillov, and Giovanni Noselli

A “flutter machine” is introduced for the investigation of a singular interface between the classical and reversible Hopf bifurcations that is theoretically predicted to be generic in nonconservative reversible systems with vanishing dissipation. In particular, such a singular interface exists for t...

[Phys. Rev. E 97, 023003] Published Tue Feb 20, 2018

Electroconvection in a dielectric liquid between two concentric half-cylinders with rigid walls: Linear and nonlinear analysis


Author(s): Pedro A. Vázquez, Alberto T. Pérez, Philippe Traoré, and Jian Wu

We study the linear stability and nonlinear behavior of the electroconvection between two concentric half-cylinders with no-slip conditions on all boundaries. The no-slip condition makes impossible to apply the standard modal approach. Hence, we apply a finite element technique similar to the one we...

[Phys. Rev. E 97, 023106] Published Tue Feb 20, 2018

Energy transfer in compressible magnetohydrodynamic turbulence for isothermal self-gravitating fluids


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

Three-dimensional, compressible, magnetohydrodynamic turbulence of an isothermal, self-gravitating fluid is analyzed using two-point statistics in the asymptotic limit of large Reynolds numbers (both kinetic and magnetic). Following an alternative formulation proposed by Banerjee and Galtier [Phys. ...

[Phys. Rev. E 97, 023107] Published Tue Feb 20, 2018

Fluid-structure interaction with the entropic lattice Boltzmann method


Author(s): B. Dorschner, S. S. Chikatamarla, and I. V. Karlin

We propose a fluid-structure interaction (FSI) scheme using the entropic multi-relaxation time lattice Boltzmann (KBC) model for the fluid domain in combination with a nonlinear finite element solver for the structural part. We show the validity of the proposed scheme for various challenging setups ...

[Phys. Rev. E 97, 023305] Published Tue Feb 20, 2018

Third-order discrete unified gas kinetic scheme for continuum and rarefied flows: Low-speed isothermal case


Author(s): Chen Wu, Baochang Shi, Chang Shu, and Zhen Chen

An efficient third-order discrete unified gas kinetic scheme (DUGKS) is presented in this paper for simulating continuum and rarefied flows. By employing a two-stage time-stepping scheme and the high-order DUGKS flux reconstruction strategy, third order of accuracy in both time and space can be achi...

[Phys. Rev. E 97, 023306] Published Tue Feb 20, 2018

Accurate modeling and evaluation of microstructures in complex materials


Author(s): Pejman Tahmasebi

Accurate characterization of heterogeneous materials is of great importance for different fields of science and engineering. Such a goal can be achieved through imaging. Acquiring three- or two-dimensional images under different conditions is not, however, always plausible. On the other hand, accura...

[Phys. Rev. E 97, 023307] Published Tue Feb 20, 2018

Generalized network modeling of capillary-dominated two-phase flow


Author(s): Ali Q. Raeini, Branko Bijeljic, and Martin J. Blunt

We present a generalized network model for simulating capillary-dominated two-phase flow through porous media at the pore scale. Three-dimensional images of the pore space are discretized using a generalized network—described in a companion paper [A. Q. Raeini, B. Bijeljic, and M. J. Blunt, Phys. Re...

[Phys. Rev. E 97, 023308] Published Tue Feb 20, 2018

Corner-transport-upwind lattice Boltzmann model for bubble cavitation


Author(s): V. Sofonea, T. Biciuşcă, S. Busuioc, Victor E. Ambruş, G. Gonnella, and A. Lamura

Aiming to study the bubble cavitation problem in quiescent and sheared liquids, a third-order isothermal lattice Boltzmann model that describes a two-dimensional (2D) fluid obeying the van der Waals equation of state, is introduced. The evolution equations for the distribution functions in this off-...

[Phys. Rev. E 97, 023309] Published Tue Feb 20, 2018

Roughening of $k$-mer–growing interfaces in stationary regimes


Author(s): M. D. Grynberg and F. I. Schaposnik Massolo

We discuss the steady-state dynamics of interfaces with periodic boundary conditions arising from body-centered solid-on-solid growth models in $1+1$ dimensions involving random aggregation of extended particles (dimers, trimers, $...,k$-mers). Roughening exponents as well as width and maximal heigh...

[Phys. Rev. E 97, 022125] Published Fri Feb 16, 2018

Exact combinatorial approach to finite coagulating systems


Author(s): Agata Fronczak, Anna Chmiel, and Piotr Fronczak

This paper outlines an exact combinatorial approach to finite coagulating systems. In this approach, cluster sizes and time are discrete and the binary aggregation alone governs the time evolution of the systems. By considering the growth histories of all possible clusters, an exact expression is de...

[Phys. Rev. E 97, 022126] Published Fri Feb 16, 2018

Semiclassical theory of strong localization for quantum thermalization


Author(s): Christine Khripkov, Amichay Vardi, and Doron Cohen

We introduce a semiclassical theory for strong localization that may arise in the context of many-body thermalization. As a minimal model for thermalization we consider a few-site Bose-Hubbard model consisting of two weakly interacting subsystems that can exchange particles. The occupation of a subs...

[Phys. Rev. E 97, 022127] Published Fri Feb 16, 2018

Discrete breathers assist energy transfer to ac-driven nonlinear chains


Author(s): Danial Saadatmand, Daxing Xiong, Vitaly A. Kuzkin, Anton M. Krivtsov, Alexander V. Savin, and Sergey V. Dmitriev

A one-dimensional chain of pointwise particles harmonically coupled with nearest neighbors and placed in sixth-order polynomial on-site potentials is considered. The power of the energy source in the form of single ac driven particle is calculated numerically for different amplitudes $A$ and frequen...

[Phys. Rev. E 97, 022217] Published Fri Feb 16, 2018

Effects of electrostatic interactions on ligand dissociation kinetics


Author(s): Aykut Erbaş, Monica Olvera de la Cruz, and John F. Marko

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning...

[Phys. Rev. E 97, 022405] Published Fri Feb 16, 2018

Survival behavior in the cyclic Lotka-Volterra model with a randomly switching reaction rate


Author(s): Robert West, Mauro Mobilia, and Alastair M. Rucklidge

We study the influence of a randomly switching reproduction-predation rate on the survival behavior of the nonspatial cyclic Lotka-Volterra model, also known as the zero-sum rock-paper-scissors game, used to metaphorically describe the cyclic competition between three species. In large and finite po...

[Phys. Rev. E 97, 022406] Published Fri Feb 16, 2018

Statistics of optimal information flow in ensembles of regulatory motifs


Author(s): Andrea Crisanti, Andrea De Martino, and Jonathan Fiorentino

Genetic regulatory circuits universally cope with different sources of noise that limit their ability to coordinate input and output signals. In many cases, optimal regulatory performance can be thought to correspond to configurations of variables and parameters that maximize the mutual information ...

[Phys. Rev. E 97, 022407] Published Fri Feb 16, 2018

Universality of crossover scaling for the adsorption transition of lattice polymers


Author(s): C. J. Bradly, A. L. Owczarek, and T. Prellberg

Recently, it has been proposed that the adsorption transition for a single polymer in dilute solution, modeled by lattice walks in three dimensions, is not universal with respect to intermonomer interactions. Moreover, it has been conjectured that key critical exponents $ϕ$, measuring the growth of ...

[Phys. Rev. E 97, 022503] Published Fri Feb 16, 2018

Nematic liquid crystal director structures in rectangular regions


Author(s): J. Walton, N. J. Mottram, and G. McKay

We consider a shallow rectangular well of nematic liquid crystal subject to weak anchoring on the sides of the well. By considering weak anchoring instead of infinitely strong anchoring, we are able to analyze nematic equilibria in the well without the need to exclude point defects at the corners, a...

[Phys. Rev. E 97, 022702] Published Fri Feb 16, 2018

Publisher's Note: Killing (absorption) versus survival in random motion [Phys. Rev. E 96, 032104 (2017)]


Author(s): Piotr Garbaczewski

[Phys. Rev. E 97, 029902] Published Fri Feb 16, 2018

Thermodynamics of quasideterministic digital computers


Author(s): Dominique Chu

A central result of stochastic thermodynamics is that irreversible state transitions of Markovian systems entail a cost in terms of an infinite entropy production. A corollary of this is that strictly deterministic computation is not possible. Using a thermodynamically consistent model, we show that...

[Phys. Rev. E 97, 022121] Published Thu Feb 15, 2018

Hyperbolic heat conduction, effective temperature, and third law for nonequilibrium systems with heat flux


Author(s): S. L. Sobolev

Some analogies between different nonequilibrium heat conduction models, particularly random walk, the discrete variable model, and the Boltzmann transport equation with the single relaxation time approximation, have been discussed. We show that, under an assumption of a finite value of the heat carr...

[Phys. Rev. E 97, 022122] Published Thu Feb 15, 2018

Influence of turbulent mixing on critical behavior of directed percolation process: Effect of compressibility


Author(s): J. Honkonen, T. Lučivjanský, and V. Škultéty

Universal behavior is a typical emergent feature of critical systems. A paramount model of the nonequilibrium critical behavior is the directed bond percolation process that exhibits an active-to-absorbing state phase transition in the vicinity of a percolation threshold. Fluctuations of the ambient...

[Phys. Rev. E 97, 022123] Published Thu Feb 15, 2018

Frustrated spin-$\frac{1}{2}$ Ising antiferromagnet on a square lattice in a transverse field


Author(s): A. Bobák, E. Jurčišinová, M. Jurčišin, and M. Žukovič

We investigate the phase transitions and tricritical behaviors of the frustrated Ising antiferromagnet with first- (${J}_{1}<0$) and second- (${J}_{2}<0$) nearest-neighbor interactions in a transverse field $\mathrm{Ω}$ on the square lattice using an effective-field theory with correlations ba...

[Phys. Rev. E 97, 022124] Published Thu Feb 15, 2018

Dynamics of coupled mode solitons in bursting neural networks


Author(s): N. Oma Nfor, P. Guemkam Ghomsi, and F. M. Moukam Kakmeni

Using an electrically coupled chain of Hindmarsh-Rose neural models, we analytically derived the nonlinearly coupled complex Ginzburg-Landau equations. This is realized by superimposing the lower and upper cutoff modes of wave propagation and by employing the multiple scale expansions in the semidis...

[Phys. Rev. E 97, 022214] Published Thu Feb 15, 2018

Global and local diffusion in the standard map


Author(s): Mirella Harsoula and George Contopoulos

We study the global and the local transport and diffusion in the case of the standard map, by calculating the diffusion exponent $μ$. In the global case, we find that the mean diffusion exponent for the whole phase space is either $μ=1$, denoting normal diffusion, or $μ=2$ denoting anomalous diffusi...

[Phys. Rev. E 97, 022215] Published Thu Feb 15, 2018

Exact relations between homoclinic and periodic orbit actions in chaotic systems


Author(s): Jizhou Li and Steven Tomsovic

Homoclinic and unstable periodic orbits in chaotic systems play central roles in various semiclassical sum rules. The interferences between terms are governed by the action functions and Maslov indices. In this article, we identify geometric relations between homoclinic and unstable periodic orbits,...

[Phys. Rev. E 97, 022216] Published Thu Feb 15, 2018

Topology determines force distributions in one-dimensional random spring networks


Author(s): Knut M. Heidemann, Andrew O. Sageman-Furnas, Abhinav Sharma, Florian Rehfeldt, Christoph F. Schmidt, and Max Wardetzky

Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber-reinforced materials are also common in technology. An important characteristic of such materials is their resistance to failure under load. Rupture occurs when fibers b...

[Phys. Rev. E 97, 022306] Published Thu Feb 15, 2018

Cascading failures in interdependent systems under a flow redistribution model


Author(s): Yingrui Zhang, Alex Arenas, and Osman Yağan

Robustness and cascading failures in interdependent systems has been an active research field in the past decade. However, most existing works use percolation-based models where only the largest component of each network remains functional throughout the cascade. Although suitable for communication ...

[Phys. Rev. E 97, 022307] Published Thu Feb 15, 2018

Thermal transport in binary colloidal glasses: Composition dependence and percolation assessment


Author(s): Pia Ruckdeschel, Alexandra Philipp, Bernd A. F. Kopera, Flora Bitterlich, Martin Dulle, Nelson W. Pech-May, and Markus Retsch

The combination of various types of materials is often used to create superior composites that outperform the pure phase components. For any rational design, the thermal conductivity of the composite as a function of the volume fraction of the filler component needs to be known. When approaching the...

[Phys. Rev. E 97, 022612] Published Thu Feb 15, 2018

Statistics of the relative velocity of particles in turbulent flows: Monodisperse particles


Author(s): Akshay Bhatnagar, K. Gustavsson, and Dhrubaditya Mitra

We use direct numerical simulations to calculate the joint probability density function of the relative distance $R$ and relative radial velocity component ${V}_{R}$ for a pair of heavy inertial particles suspended in homogeneous and isotropic turbulent flows. At small scales the distribution is sca...

[Phys. Rev. E 97, 023105] Published Thu Feb 15, 2018

Induction of subterahertz surface waves on a metal wire by intense laser interaction with a foil


Author(s): Kensuke Teramoto, Shunsuke Inoue, Shigeki Tokita, Ryo Yasuhara, Yoshihide Nakamiya, Takeshi Nagashima, Kazuaki Mori, Masaki Hashida, and Shuji Sakabe

We have demonstrated that a pulsed electromagnetic wave (Sommerfeld wave) of subterahertz frequency and 11-MV/m field strength can be induced on a metal wire by the interaction of an intense femtosecond laser pule with an adjacent metal foil at a laser intensity of $8.5×{10}^{18}\phantom{\rule{0.16e...

[Phys. Rev. E 97, 023204] Published Thu Feb 15, 2018

Effect of the image resolution on the statistical descriptors of heterogeneous media


Author(s): René Ledesma-Alonso, Romeli Barbosa, and Jaime Ortegón

The characterization and reconstruction of heterogeneous materials, such as porous media and electrode materials, involve the application of image processing methods to data acquired by scanning electron microscopy or other microscopy techniques. Among them, binarization and decimation are critical ...

[Phys. Rev. E 97, 023304] Published Thu Feb 15, 2018

From the nonlinear Fokker-Planck equation to the Vlasov description and back: Confined interacting particles with drag


Author(s): A. R. Plastino, E. M. F. Curado, F. D. Nobre, and C. Tsallis

Nonlinear Fokker-Planck equations endowed with power-law diffusion terms have proven to be valuable tools for the study of diverse complex systems in physics, biology, and other fields. The nonlinearity appearing in these evolution equations can be interpreted as providing an effective description o...

[Phys. Rev. E 97, 022120] Published Wed Feb 14, 2018

Double-layer force suppression between charged microspheres


Author(s): D. S. Ether, F. S. S. Rosa, D. M. Tibaduiza, L. B. Pires, R. S. Decca, and P. A. Maia Neto

In this paper we propose a protocol to suppress double-layer forces between two microspheres immersed in a dielectric medium, being one microsphere metallic at a controlled potential ${ψ}_{\mathrm{M}}$ and the other a charged one either metallic or dielectric. The approach is valid for a wide range ...

[Phys. Rev. E 97, 022611] Published Wed Feb 14, 2018

Early-stage aggregation in three-dimensional charged granular gas


Author(s): Chamkor Singh and Marco G. Mazza

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely cooling granular gas of viscoelastic particles that exchange charges during co...

[Phys. Rev. E 97, 022904] Published Wed Feb 14, 2018

Fast Laplace solver approach to pore-scale permeability


Author(s): C. H. Arns and P. M. Adler

We introduce a powerful and easily implemented method to calculate the permeability of porous media at the pore scale using an approximation based on the Poiseulle equation to calculate permeability to fluid flow with a Laplace solver. The method consists of calculating the Euclidean distance map of...

[Phys. Rev. E 97, 023303] Published Wed Feb 14, 2018

Liquid-vapor rectilinear diameter revisited


Author(s): Y. Garrabos, C. Lecoutre, S. Marre, D. Beysens, and I. Hahn

In the modern theory of critical phenomena, the liquid-vapor density diameter in simple fluids is generally expected to deviate from a rectilinear law approaching the critical point. However, by performing precise scannerlike optical measurements of the position of the ${\mathrm{SF}}_{6}$ liquid-vap...

[Phys. Rev. E 97, 020101(R)] Published Tue Feb 13, 2018

Fractional Brownian motion with a reflecting wall


Author(s): Alexander H. O. Wada and Thomas Vojta

Fractional Brownian motion, a stochastic process with long-time correlations between its increments, is a prototypical model for anomalous diffusion. We analyze fractional Brownian motion in the presence of a reflecting wall by means of Monte Carlo simulations. Whereas the mean-square displacement o...

[Phys. Rev. E 97, 020102(R)] Published Tue Feb 13, 2018

Observing golden-mean universality class in the scaling of thermal transport


Author(s): Daxing Xiong

We address the issue of whether the golden-mean $[ψ=(\sqrt{5}+1)/2≃1.618]$ universality class, as predicted by several theoretical models, can be observed in the dynamical scaling of thermal transport. Remarkably, we show strong evidence that $ψ$ appears to be the scaling exponent of heat mode corre...

[Phys. Rev. E 97, 022116] Published Tue Feb 13, 2018

Log-correlated random-energy models with extensive free-energy fluctuations: Pathologies caused by rare events as signatures of phase transitions


Author(s): Xiangyu Cao, Yan V. Fyodorov, and Pierre Le Doussal

We address systematically an apparent nonphysical behavior of the free-energy moment generating function for several instances of the logarithmically correlated models: the fractional Brownian motion with Hurst index $H=0$ (fBm0) (and its bridge version), a one-dimensional model appearing in decayin...

[Phys. Rev. E 97, 022117] Published Tue Feb 13, 2018

Localization of soft modes at the depinning transition


Author(s): Xiangyu Cao, Sebastian Bouzat, Alejandro B. Kolton, and Alberto Rosso

We characterize the soft modes of the dynamical matrix at the depinning transition, and compare the matrix with the properties of the Anderson model (and long-range generalizations). The density of states at the edge of the spectrum displays a universal linear tail, different from the Lifshitz tails...

[Phys. Rev. E 97, 022118] Published Tue Feb 13, 2018

Thermodynamic curvature of soft-sphere fluids and solids


Author(s): A. C. Brańka, S. Pieprzyk, and D. M. Heyes

The influence of the strength of repulsion between particles on the thermodynamic curvature scalar $R$ for the fluid and solid states is investigated for particles interacting with the inverse power (${r}^{−n}$) potential, where $r$ is the pair separation and $1/n$ is the softness. Exact results are...

[Phys. Rev. E 97, 022119] Published Tue Feb 13, 2018

Nonequilibrium transition and pattern formation in a linear reaction-diffusion system with self-regulated kinetics


Author(s): Shibashis Paul, Shyamolina Ghosh, and Deb Shankar Ray

We consider a reaction-diffusion system with linear, stochastic activator-inhibitor kinetics where the time evolution of concentration of a species at any spatial location depends on the relative average concentration of its neighbors. This self-regulating nature of kinetics brings in spatial correl...

[Phys. Rev. E 97, 022213] Published Tue Feb 13, 2018

Spontaneous membrane formation and self-encapsulation of active rods in an inhomogeneous motility field


Author(s): Jens Grauer, Hartmut Löwen, and Liesbeth M. C. Janssen

We study the collective dynamics of self-propelled rods in an inhomogeneous motility field. At the interface between two regions of constant but different motility, a smectic rod layer is spontaneously created through aligning interactions between the active rods, reminiscent of an artificial, semip...

[Phys. Rev. E 97, 022608] Published Tue Feb 13, 2018

Anomalous vibrational properties in the continuum limit of glasses


Author(s): Masanari Shimada, Hideyuki Mizuno, and Atsushi Ikeda

The low-temperature thermal properties of glasses are anomalous with respect to those of crystals. These thermal anomalies indicate that the low-frequency vibrational properties of glasses differ from those of crystals. Recent studies revealed that, in the simplest model of glasses, i.e., the harmon...

[Phys. Rev. E 97, 022609] Published Tue Feb 13, 2018

Wall accumulation of bacteria with different motility patterns


Author(s): Paolo Sartori, Enrico Chiarello, Gaurav Jayaswal, Matteo Pierno, Giampaolo Mistura, Paola Brun, Adriano Tiribocchi, and Enzo Orlandini

We systematically investigate the role of different swimming patterns on the concentration distribution of bacterial suspensions confined between two flat walls, by considering wild-type motility Escherichia coli and Pseudomonas aeruginosa, which perform Run and Tumble and Run and Reverse patterns, ...

[Phys. Rev. E 97, 022610] Published Tue Feb 13, 2018

Is the kinetic equation for turbulent gas-particle flows ill posed?


Author(s): M. Reeks, D. C. Swailes, and A. D. Bragg

This paper is about the kinetic equation for gas-particle flows, in particular its well-posedness and realizability and its relationship to the generalized Langevin model (GLM) probability density function (PDF) equation. Previous analyses, e.g. [J.-P. Minier and C. Profeta, Phys. Rev. E 92, 053020 ...

[Phys. Rev. E 97, 023104] Published Tue Feb 13, 2018

Stopping power of dense plasmas: The collisional method and limitations of the dielectric formalism


Author(s): C. F. Clauser and N. R. Arista

We present a study of the stopping power of plasmas using two main approaches: the collisional (scattering theory) and the dielectric formalisms. In the former case, we use a semiclassical method based on quantum scattering theory. In the latter case, we use the full description given by the extensi...

[Phys. Rev. E 97, 023202] Published Tue Feb 13, 2018

Hydrodynamic evolution of plasma waveguides for soft-x-ray amplifiers


Author(s): Eduardo Oliva, Adrien Depresseux, Manuel Cotelo, Agustín Lifschitz, Fabien Tissandier, Julien Gautier, Gilles Maynard, Pedro Velarde, and Stéphane Sebban

High-density, collisionally pumped plasma-based soft-x-ray lasers have recently delivered hundreds of femtosecond pulses, breaking the longstanding barrier of one picosecond. To pump these amplifiers an intense infrared pulse must propagate focused throughout all the length of the amplifier, which s...

[Phys. Rev. E 97, 023203] Published Tue Feb 13, 2018

Boltzmann-distribution-equivalent for Lévy noise and how it leads to thermodynamically consistent epicatalysis


Author(s): Martin Bier

Nonequilibrium systems commonly exhibit Lévy noise. This means that the distribution for the size of the Brownian fluctuations has a “fat” power-law tail. Large Brownian kicks are then more common as compared to the ordinary Gaussian distribution. We consider a two-state system, i.e., two wells and ...

[Phys. Rev. E 97, 022113] Published Mon Feb 12, 2018

Helical thermoelectrics and refrigeration


Author(s): Arjun Mani and Colin Benjamin

The thermoelectric properties of a three-terminal quantum spin Hall (QSH) sample are examined. The inherent helicity of the QSH sample helps to generate a large charge power efficiently. Along with charge the system can be designed to work as a highly efficient spin heat engine too. The advantage of...

[Phys. Rev. E 97, 022114] Published Mon Feb 12, 2018

Heat, work, and energy currents in the boundary-driven $XXZ$ spin chain


Author(s): Emmanuel Pereira

We address the detailed study of the energy current and its components, heat and work, in the boundary-driven one-dimensional $XXZ$ quantum model. We carry out the investigation by considering two different approaches present in the literature. First, we take the repeated interaction scheme and deri...

[Phys. Rev. E 97, 022115] Published Mon Feb 12, 2018

Phase reduction approach to elastohydrodynamic synchronization of beating flagella


Author(s): Yoji Kawamura and Remi Tsubaki

We formulate a theory for the phase reduction of a beating flagellum. The theory enables us to describe the dynamics of a beating flagellum in a systematic manner using a single variable called the phase. The theory can also be considered as a phase reduction method for the limit-cycle solutions in ...

[Phys. Rev. E 97, 022212] Published Mon Feb 12, 2018

Phase transition of the susceptible-infected-susceptible dynamics on time-varying configuration model networks


Author(s): Guillaume St-Onge, Jean-Gabriel Young, Edward Laurence, Charles Murphy, and Louis J. Dubé

We present a degree-based theoretical framework to study the susceptible-infected-susceptible (SIS) dynamics on time-varying (rewired) configuration model networks. Using this framework on a given degree distribution, we provide a detailed analysis of the stationary state using the rewiring rate to ...

[Phys. Rev. E 97, 022305] Published Mon Feb 12, 2018

Theory of invasion extinction dynamics in minimal food webs


Author(s): Jan O. Haerter, Namiko Mitarai, and Kim Sneppen

When food webs are exposed to species invasion, secondary extinction cascades may be set off. Although much work has gone into characterizing the structure of food webs, systematic predictions on their evolutionary dynamics are still scarce. Here we present a theoretical framework that predicts exti...

[Phys. Rev. E 97, 022404] Published Mon Feb 12, 2018

Effective equilibrium picture in the $xy$ model with exponentially correlated noise


Author(s): Matteo Paoluzzi, Umberto Marini Bettolo Marconi, and Claudio Maggi

We study the effect of exponentially correlated noise on the $xy$ model in the limit of small correlation time, discussing the order-disorder transition in the mean field and the topological transition in two dimensions. We map the steady states of the nonequilibrium dynamics into an effective equil...

[Phys. Rev. E 97, 022605] Published Mon Feb 12, 2018

Dynamically generated patterns in dense suspensions of active filaments


Author(s): K. R. Prathyusha, Silke Henkes, and Rastko Sknepnek

In this work, the authors simulated the dynamics of a dense suspension of self-propelled semiflexible filaments. One intriguing finding is a crossover from a state of coherently flowing bundles of filaments to one without global flow, formed by individual filaments coiled into rotating spirals. The model has the potential to inspire further experimental studies on motility assays and also on swimming bacteria.

[Phys. Rev. E 97, 022606] Published Mon Feb 12, 2018

Theory of anomalous collective diffusion in colloidal monolayers on a spherical interface


Author(s): Alvaro Domínguez

A planar colloidal monolayer exhibits anomalous collective diffusion due to the hydrodynamic interactions. We investigate how this behavior is affected by the curvature of the monolayer when it resides on the interface of a spherical droplet. It is found that the characteristic times of the dynamics...

[Phys. Rev. E 97, 022607] Published Mon Feb 12, 2018

Triple-line kinetics for solid films


Author(s): Ashwani K. Tripathi and Olivier Pierre-Louis

We present a derivation of the triple-line kinetic boundary conditions for a solid film in contact with a solid substrate for both nonconserved (evaporation-condensation) and conserved (surface diffusion) dynamics. The result is obtained via a matched asymptotic expansion from a mesoscopic model wit...

[Phys. Rev. E 97, 022801] Published Mon Feb 12, 2018

Optimally frugal foraging


Author(s): O. Bénichou, U. Bhat, P. L. Krapivsky, and S. Redner

We introduce the frugal foraging model in which a forager performs a discrete-time random walk on a lattice in which each site initially contains $\mathcal{S}$ food units. The forager metabolizes one unit of food at each step and starves to death when it last ate $\mathcal{S}$ steps in the past. Whe...

[Phys. Rev. E 97, 022110] Published Fri Feb 09, 2018

Effect of coherence of nonthermal reservoirs on heat transport in a microscopic collision model


Author(s): Lei Li, Jian Zou, Hai Li, Bao-Ming Xu, Yuan-Mei Wang, and Bin Shao

We investigate the heat transport between two nonthermal reservoirs based on a microscopic collision model. We consider a bipartite system consisting of two identical subsystems, and each subsystem interacts with its own local reservoir, which consists of a large collection of initially uncorrelated...

[Phys. Rev. E 97, 022111] Published Fri Feb 09, 2018

Extinction and survival in two-species annihilation


Author(s): J. G. Amar, E. Ben-Naim, S. M. Davis, and P. L. Krapivsky

We study diffusion-controlled two-species annihilation with a finite number of particles. In this stochastic process, particles move diffusively, and when two particles of opposite type come into contact, the two annihilate. We focus on the behavior in three spatial dimensions and for initial condit...

[Phys. Rev. E 97, 022112] Published Fri Feb 09, 2018

Adaptive control of dynamical synchronization on evolving networks with noise disturbances


Author(s): Wu-Jie Yuan, Jian-Fang Zhou, Irene Sendiña-Nadal, Stefano Boccaletti, and Zhen Wang

In real-world networked systems, the underlying structure is often affected by external and internal unforeseen factors, making its evolution typically inaccessible. An adaptive strategy was introduced for maintaining synchronization on unpredictably evolving networks [Sorrentino and Ott, Phys. Rev....

[Phys. Rev. E 97, 022211] Published Fri Feb 09, 2018

Nascent RNA kinetics: Transient and steady state behavior of models of transcription


Author(s): Sandeep Choubey

Regulation of transcription is a vital process in cells, but mechanistic details of this regulation still remain elusive. The dominant approach to unravel the dynamics of transcriptional regulation is to first develop mathematical models of transcription and then experimentally test the predictions ...

[Phys. Rev. E 97, 022402] Published Fri Feb 09, 2018

Design principles and optimal performance for molecular motors under realistic constraints


Author(s): Yuhai Tu and Yuansheng Cao

The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations show that a gating mechanism that restricts forwa...

[Phys. Rev. E 97, 022403] Published Fri Feb 09, 2018

Waterlike anomalies in a two-dimensional core-softened potential


Author(s): José Rafael Bordin and Marcia C. Barbosa

We investigate the structural, thermodynamic, and dynamic behavior of a two-dimensional (2D) core-corona system using Langevin dynamics simulations. The particles are modeled by employing a core-softened potential which exhibits waterlike anomalies in three dimensions. In previous studies in a quasi...

[Phys. Rev. E 97, 022604] Published Fri Feb 09, 2018

Interfacial behavior of confined mesogens at smectic-C*–water boundary


Author(s): Achu Chandran, P. K. Khanna, D. Haranath, and Ashok M. Biradar

In this paper, we have investigated the behavior of mesogens at smectic-C*–water interface confined in a liquid crystal (LC) cell with interfacial geometry. Polarized optical microscopy was used to probe the appearance of various smectic-C* domain patterns at water interface owing to the reorientati...

[Phys. Rev. E 97, 022701] Published Fri Feb 09, 2018

Evidence of reverse and intermediate size segregation in dry granular flows down a rough incline


Author(s): Nathalie Thomas and Umberto D'Ortona

In a dry granular flow, size segregation had been shown to behave differently for a mixture containing a few large particles with a size ratio above 5 [N. Thomas, Phys. Rev. E 62, 961 (2000)]. For moderately large size ratios, large particles migrate to an intermediate depth in the bed: this is call...

[Phys. Rev. E 97, 022903] Published Fri Feb 09, 2018

Modeling evolution of crosstalk in noisy signal transduction networks


Author(s): Ammar Tareen, Ned S. Wingreen, and Ranjan Mukhopadhyay

Signal transduction networks can form highly interconnected systems within cells due to crosstalk between constituent pathways. To better understand the evolutionary design principles underlying such networks, we study the evolution of crosstalk for two parallel signaling pathways that arise via gen...

[Phys. Rev. E 97, 020402(R)] Published Thu Feb 08, 2018

Shape control of surface-stabilized disclination loops in nematic liquid crystals


Author(s): Kanta Sunami, Koki Imamura, Tomohiro Ouchi, Hiroyuki Yoshida, and Masanori Ozaki

Recent studies on topological defects in conventional and active nematic liquid crystals have revealed their potential as sources of advanced functionality whereby the collective behavior of the constituent molecules or cells is controlled. On the other hand, the fact that they have high energies an...

[Phys. Rev. E 97, 020701(R)] Published Thu Feb 08, 2018

Vapor-liquid phase behavior of a size-asymmetric model of ionic fluids confined in a disordered matrix: The collective-variables-based approach


Author(s): O. V. Patsahan, T. M. Patsahan, and M. F. Holovko

We develop a theory based on the method of collective variables to study the vapor-liquid equilibrium of asymmetric ionic fluids confined in a disordered porous matrix. The approach allows us to formulate the perturbation theory using an extension of the scaled particle theory for a description of a...

[Phys. Rev. E 97, 022109] Published Thu Feb 08, 2018

Metastable modular metastructures for on-demand reconfiguration of band structures and nonreciprocal wave propagation


Author(s): Z. Wu, Y. Zheng, and K. W. Wang

We present an approach to achieve adaptable band structures and nonreciprocal wave propagation by exploring and exploiting the concept of metastable modular metastructures. Through studying the dynamics of wave propagation in a chain composed of finite metastable modules, we provide experimental and...

[Phys. Rev. E 97, 022209] Published Thu Feb 08, 2018

Solitons in a nonlinear model of spin transport in helical molecules


Author(s): P. Albares, E. Díaz, Jose M. Cerveró, F. Domínguez-Adame, E. Diez, and P. G. Estévez

We study an effective integrable nonlinear model describing an electron moving along the axis of a deformable helical molecule. The helical conformation of dipoles in the molecular backbone induces an unconventional Rashba-like interaction that couples the electron spin with its linear momentum. In ...

[Phys. Rev. E 97, 022210] Published Thu Feb 08, 2018

Continuous-time quantum walk on an extended star graph: Trapping and superradiance transition


Author(s): Saad Yalouz and Vincent Pouthier

A tight-binding model is introduced for describing the dynamics of an exciton on an extended star graph whose central node is occupied by a trap. On this graph, the exciton dynamics is governed by two kinds of eigenstates: many eigenstates are associated with degenerate real eigenvalues insensitive ...

[Phys. Rev. E 97, 022304] Published Thu Feb 08, 2018

Multidimensional biochemical information processing of dynamical patterns


Author(s): Yoshihiko Hasegawa

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We ...

[Phys. Rev. E 97, 022401] Published Thu Feb 08, 2018

Evidence for the extended de Gennes regime of a semiflexible polymer in slit confinement


Author(s): Guo Kang Cheong, Xiaolan Li, and Kevin D. Dorfman

We use off-lattice, pruned-enriched Rosenbluth method simulations to compute the confinement free energy of a real wormlike chain of effective width $w$ and persistence length ${l}_{\mathrm{p}}$ in a slit of height $H$. For slit heights much larger than the persistence length of the polymer and much...

[Phys. Rev. E 97, 022502] Published Thu Feb 08, 2018

Forceless Sadowsky strips are spherical


Author(s): E. L. Starostin and G. H. M. van der Heijden

We show that thin rectangular ribbons, defined as energy-minimizing configurations of the Sadowsky functional for narrow developable elastic strips, have a propensity to form spherical shapes in the sense that forceless solutions lie on a sphere. This has implications for ribbonlike objects in (bio)...

[Phys. Rev. E 97, 023001] Published Thu Feb 08, 2018

Self-similar regimes of turbulence in weakly coupled plasmas under compression


Author(s): Giovanni Viciconte, Benoît-Joseph Gréa, and Fabien S. Godeferd

Turbulence in weakly coupled plasmas under compression can experience a sudden dissipation of kinetic energy due to the abrupt growth of the viscosity coefficient governed by the temperature increase. We investigate in detail this phenomenon by considering a turbulent velocity field obeying the inco...

[Phys. Rev. E 97, 023201] Published Thu Feb 08, 2018

Consistent second-order boundary implementations for convection-diffusion lattice Boltzmann method


Author(s): Liangqi Zhang, Shiliang Yang, Zhong Zeng, and Jia Wei Chew

In this study, an alternative second-order boundary scheme is proposed under the framework of the convection-diffusion lattice Boltzmann (LB) method for both straight and curved geometries. With the proposed scheme, boundary implementations are developed for the Dirichlet, Neumann and linear Robin c...

[Phys. Rev. E 97, 023302] Published Thu Feb 08, 2018