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Preview: Recent Articles in Phys. Rev. E

Recent Articles in Phys. Rev. E

Recent articles in Physical Review E

Published: 2018-03-16T23:04:44+00:00


Cooperativity in plastic crystals


Author(s): Marco Pieruccini and Elpidio Tombari

A statistical mechanical model previously adopted for the analysis of the $α$-relaxation in structural glass formers is rederived within a general theoretical framework originally developed for systems approaching the ideal glassy state. The interplay between nonexponentiality and cooperativity is r...

[Phys. Rev. E 97, 032116] Published Fri Mar 16, 2018

Emergence of nonwhite noise in Langevin dynamics with magnetic Lorentz force


Author(s): Hyun-Myung Chun, Xavier Durang, and Jae Dong Noh

We investigate the low mass limit of Langevin dynamics for a charged Brownian particle driven by a magnetic Lorentz force. In the low mass limit, velocity variables relaxing quickly are coarse-grained out to yield effective dynamics for position variables. Without the Lorentz force, the low mass lim...

[Phys. Rev. E 97, 032117] Published Fri Mar 16, 2018

Statistical physics of medical diagnostics: Study of a probabilistic model


Author(s): Alireza Mashaghi and Abolfazl Ramezanpour

We study a diagnostic strategy which is based on the anticipation of the diagnostic process by simulation of the dynamical process starting from the initial findings. We show that such a strategy could result in more accurate diagnoses compared to a strategy that is solely based on the direct implic...

[Phys. Rev. E 97, 032118] Published Fri Mar 16, 2018

Deep neural networks for direct, featureless learning through observation: The case of two-dimensional spin models


Author(s): Kyle Mills and Isaac Tamblyn

We demonstrate the capability of a convolutional deep neural network in predicting the nearest-neighbor energy of the $4×4$ Ising model. Using its success at this task, we motivate the study of the larger $8×8$ Ising model, showing that the deep neural network can learn the nearest-neighbor Ising Ha...

[Phys. Rev. E 97, 032119] Published Fri Mar 16, 2018

Jamming and condensation in one-dimensional driven flow


Author(s): Hyungjoon Soh, Meesoon Ha, and Hawoong Jeong

We revisit the slow-bond (SB) problem of the one-dimensional (1D) totally asymmetric simple exclusion process (TASEP) with modified hopping rates. In the original SB problem, it turns out that a local defect is always relevant to the system as jamming, so that phase separation occurs in the 1D TASEP...

[Phys. Rev. E 97, 032120] Published Fri Mar 16, 2018

Limits of the memory coefficient in measuring correlated bursts


Author(s): Hang-Hyun Jo and Takayuki Hiraoka

Temporal inhomogeneities in event sequences of natural and social phenomena have been characterized in terms of interevent times and correlations between interevent times. The inhomogeneities of interevent times have been extensively studied, while the correlations between interevent times, often ca...

[Phys. Rev. E 97, 032121] Published Fri Mar 16, 2018

Information-theoretic model selection for optimal prediction of stochastic dynamical systems from data


Author(s): David Darmon

In the absence of mechanistic or phenomenological models of real-world systems, data-driven models become necessary. The discovery of various embedding theorems in the 1980s and 1990s motivated a powerful set of tools for analyzing deterministic dynamical systems via delay-coordinate embeddings of o...

[Phys. Rev. E 97, 032206] Published Fri Mar 16, 2018

Group percolation in interdependent networks


Author(s): Zexun Wang, Dong Zhou, and Yanqing Hu

In many real network systems, nodes usually cooperate with each other and form groups to enhance their robustness to risks. This motivates us to study an alternative type of percolation, group percolation, in interdependent networks under attack. In this model, nodes belonging to the same group surv...

[Phys. Rev. E 97, 032306] Published Fri Mar 16, 2018

Actin filaments growing against an elastic membrane: Effect of membrane tension


Author(s): Raj Kumar Sadhu and Sakuntala Chatterjee

We study the force generation by a set of parallel actin filaments growing against an elastic membrane. The elastic membrane tries to stay flat and any deformation from this flat state, either caused by thermal fluctuations or due to protrusive polymerization force exerted by the filaments, costs en...

[Phys. Rev. E 97, 032408] Published Fri Mar 16, 2018

Least-rattling feedback from strong time-scale separation


Author(s): Pavel Chvykov and Jeremy England

In most interacting many-body systems associated with some “emergent phenomena,” we can identify subgroups of degrees of freedom that relax on dramatically different time scales. Time-scale separation of this kind is particularly helpful in nonequilibrium systems where only the fast variables are su...

[Phys. Rev. E 97, 032115] Published Thu Mar 15, 2018

Derivation of Markov processes that violate detailed balance


Author(s): Julian Lee

Time-reversal symmetry of the microscopic laws dictates that the equilibrium distribution of a stochastic process must obey the condition of detailed balance. However, cyclic Markov processes that do not admit equilibrium distributions with detailed balance are often used to model systems driven out...

[Phys. Rev. E 97, 032110] Published Wed Mar 14, 2018

Effect of multiplicative noise on stationary stochastic process


Author(s): A. V. Kargovsky, A. Yu. Chikishev, and O. A. Chichigina

An open system that can be analyzed using the Langevin equation with multiplicative noise is considered. The stationary state of the system results from a balance of deterministic damping and random pumping simulated as noise with controlled periodicity. The dependence of statistical moments of the ...

[Phys. Rev. E 97, 032112] Published Wed Mar 14, 2018

Unifying model for random matrix theory in arbitrary space dimensions


Author(s): Giovanni M. Cicuta, Johannes Krausser, Rico Milkus, and Alessio Zaccone

A sparse random block matrix model suggested by the Hessian matrix used in the study of elastic vibrational modes of amorphous solids is presented and analyzed. By evaluating some moments, benchmarked against numerics, differences in the eigenvalue spectrum of this model in different limits of space...

[Phys. Rev. E 97, 032113] Published Wed Mar 14, 2018

Zero-crossing statistics for non-Markovian time series


Author(s): Markus Nyberg, Ludvig Lizana, and Tobias Ambjörnsson

In applications spanning from image analysis and speech recognition to energy dissipation in turbulence and time-to failure of fatigued materials, researchers and engineers want to calculate how often a stochastic observable crosses a specific level, such as zero. At first glance this problem looks ...

[Phys. Rev. E 97, 032114] Published Wed Mar 14, 2018

Slowdown of surface diffusion during early stages of bacterial colonization


Author(s): T. Vourc'h, H. Peerhossaini, J. Léopoldès, A. Méjean, F. Chauvat, and C. Cassier-Chauvat

We study the surface diffusion of the model cyanobacterium Synechocystis sp. PCC6803 during the incipient stages of cell contact with a glass surface in the dilute regime. We observe a twitching motility with alternating immobile tumble and mobile run periods, resulting in a normal diffusion describ...

[Phys. Rev. E 97, 032407] Published Wed Mar 14, 2018

Engineering single-polymer micelle shape using nonuniform spontaneous surface curvature


Author(s): Brian Moths and T. A. Witten

Conventional micelles, composed of simple amphiphiles, exhibit only a few standard morphologies, each characterized by its mean surface curvature set by the amphiphiles. Here we demonstrate a rational design scheme to construct micelles of more general shape from polymeric amphiphiles. We replace th...

[Phys. Rev. E 97, 032505] Published Wed Mar 14, 2018

Self-driven particles in linear flows and trapped in a harmonic potential


Author(s): Mario Sandoval, Julio C. Hidalgo-Gonzalez, and Jose I. Jimenez-Aquino

We present analytical expressions for the mean-square displacement of self-driven particles in general linear flows and trapped in a harmonic potential. The general expressions are applied to three types of linear flows, namely, shear flow, solid-body rotation flow, and extensional flow. By using Br...

[Phys. Rev. E 97, 032603] Published Wed Mar 14, 2018

Active processes in one dimension


Author(s): Thibaut Demaerel and Christian Maes

We consider the thermal and athermal overdamped motion of particles in one-dimensional geometries where discrete internal degrees of freedom (spin) are coupled with the translational motion. Adding a driving velocity that depends on the time-dependent spin constitutes the simplest model of active pa...

[Phys. Rev. E 97, 032604] Published Wed Mar 14, 2018

Probing a dusty magnetized plasma with self-excited dust-density waves


Author(s): Benjamin Tadsen, Franko Greiner, and Alexander Piel

A cloud of nanodust particles is created in a reactive argon-acetylene plasma. It is then transformed into a dusty magnetized argon plasma. Plasma parameters are obtained with the dust-density wave diagnostic introduced by Tadsen et al. [Phys. Plasmas 22, 113701 (2015)]. A change from an open to a c...

[Phys. Rev. E 97, 033203] Published Wed Mar 14, 2018

Entropic lattice Boltzmann model for charged leaky dielectric multiphase fluids in electrified jets


Author(s): Marco Lauricella, Simone Melchionna, Andrea Montessori, Dario Pisignano, Giuseppe Pontrelli, and Sauro Succi

We present a lattice Boltzmann model for charged leaky dielectric multiphase fluids in the context of electrified jet simulations, which are of interest for a number of production technologies including electrospinning. The role of nonlinear rheology on the dynamics of electrified jets is considered...

[Phys. Rev. E 97, 033308] Published Wed Mar 14, 2018

Local box-counting dimensions of discrete quantum eigenvalue spectra: Analytical connection to quantum spectral statistics


Author(s): Jamal Sakhr and John M. Nieminen

Two decades ago, Wang and Ong, [Phys. Rev. A 55, 1522 (1997)] hypothesized that the local box-counting dimension of a discrete quantum spectrum should depend exclusively on the nearest-neighbor spacing distribution (NNSD) of the spectrum. In this Rapid Communication, we validate their hypothesis by ...

[Phys. Rev. E 97, 030202(R)] Published Tue Mar 13, 2018

Mapping of uncertainty relations between continuous and discrete time


Author(s): Davide Chiuchiù and Simone Pigolotti

Lower bounds on fluctuations of thermodynamic currents depend on the nature of time, discrete or continuous. To understand the physical reason, we compare current fluctuations in discrete-time Markov chains and continuous-time master equations. We prove that current fluctuations in the master equati...

[Phys. Rev. E 97, 032109] Published Tue Mar 13, 2018

Optimal stabilization of Boolean networks through collective influence


Author(s): Jiannan Wang, Sen Pei, Wei Wei, Xiangnan Feng, and Zhiming Zheng

Boolean networks have attracted much attention due to their wide applications in describing dynamics of biological systems. During past decades, much effort has been invested in unveiling how network structure and update rules affect the stability of Boolean networks. In this paper, we aim to identi...

[Phys. Rev. E 97, 032305] Published Tue Mar 13, 2018

Early-warning signals of critical transition: Effect of extrinsic noise


Author(s): Shanshan Qin and Chao Tang

Complex dynamical systems often have tipping points and exhibit catastrophic regime shift. Despite the notorious difficulty of predicting such transitions, accumulating studies have suggested the existence of generic early-warning signals (EWSs) preceding upcoming transitions. However, previous theo...

[Phys. Rev. E 97, 032406] Published Tue Mar 13, 2018

Polyelectrolyte brush bilayers in weak interpenetration regime: Scaling theory and molecular dynamics simulations


Author(s): Parth Rakesh Desai, Shayandev Sinha, and Siddhartha Das

We employ molecular dynamics (MD) simulations and develop scaling theories to quantify the equilibrium behavior of polyelectrolyte (PE) brush bilayers (BBLs) in the weakly interpenetrated regime, which is characterized by ${d}_{0}<{d}_{g}<2{d}_{0}$, where ${d}_{g}$ is the gap between the oppos...

[Phys. Rev. E 97, 032503] Published Tue Mar 13, 2018

Star polymers as unit cells for coarse-graining cross-linked networks


Author(s): Taras Y. Molotilin, Salim R. Maduar, and Olga I. Vinogradova

Reducing the complexity of cross-linked polymer networks by preserving their main macroscale properties is key to understanding them, and a crucial issue is to relate individual properties of the polymer constituents to those of the reduced network. Here we study polymer networks in a good solvent, ...

[Phys. Rev. E 97, 032504] Published Tue Mar 13, 2018

$N\text{−}\mathrm{Sm}A\text{−}\mathrm{Sm}C$ phase transitions probed by a pair of elastically bound colloids


Author(s): Muhammed Rasi M, K. P. Zuhail, Arun Roy, and Surajit Dhara

The competing effect of surface anchoring of dispersed microparticles and elasticity of nematic and cholesteric liquid crystals has been shown to stabilize a variety of topological defects. Here we study a pair of colloidal microparticles with homeotropic and planar surface anchoring across $N\text{...

[Phys. Rev. E 97, 032702] Published Tue Mar 13, 2018

Tunable hybrid optical modes in a bounded cholesteric liquid crystal with a twist defect


Author(s): Maxim V. Pyatnov, Stepan Ya. Vetrov, and Ivan V. Timofeev

Coupling between the defect mode of a cholesteric liquid crystal and the localized mode of a cholesteric liquid crystal–phase plate–metal structure is theoretically demonstrated. It is shown that the transmittance spectrum can be tuned by changing the twist-defect angle and helix pitch, which are go...

[Phys. Rev. E 97, 032703] Published Tue Mar 13, 2018

Regularized lattice Boltzmann model for immiscible two-phase flows with power-law rheology


Author(s): Yan Ba, Ningning Wang, Haihu Liu, Qiang Li, and Guoqiang He

In this work, a regularized lattice Boltzmann color-gradient model is developed for the simulation of immiscible two-phase flows with power-law rheology. This model is as simple as the Bhatnagar-Gross-Krook (BGK) color-gradient model except that an additional regularization step is introduced prior ...

[Phys. Rev. E 97, 033307] Published Tue Mar 13, 2018

Thermal decay of a metastable state: Influence of rescattering on the quasistationary dynamical rate


Author(s): M. V. Chushnyakova and I. I. Gontchar

We study the effect of backscattering of the Brownian particles as they escape out of a metastable state overcoming the potential barrier. For this aim, we model this process numerically using the Langevin equations. This modeling is performed for the wide range of the friction constant covering bot...

[Phys. Rev. E 97, 032107] Published Mon Mar 12, 2018

Statistical investigation of avalanches of three-dimensional small-world networks and their boundary and bulk cross-sections


Author(s): M. N. Najafi and H. Dashti-Naserabadi

In many situations we are interested in the propagation of energy in some portions of a three-dimensional system with dilute long-range links. In this paper, a sandpile model is defined on the three-dimensional small-world network with real dissipative boundaries and the energy propagation is studie...

[Phys. Rev. E 97, 032108] Published Mon Mar 12, 2018

Collective conflict resolution in groups on the move


Author(s): Itai Pinkoviezky, Iain D. Couzin, and Nir S. Gov

Collective decision-making regarding direction of travel is observed during natural motion of animal and cellular groups. This phenomenon is exemplified, in the simplest case, by a group that contains two informed subgroups that hold conflicting preferred directions of motion. Under such circumstanc...

[Phys. Rev. E 97, 032304] Published Mon Mar 12, 2018

Effect of ac electric field on the dynamics of a vesicle under shear flow in the small deformation regime


Author(s): Kumari Priti Sinha and Rochish M. Thaokar

Vesicles or biological cells under simultaneous shear and electric field can be encountered in dielectrophoretic devices or designs used for continuous flow electrofusion or electroporation. In this work, the dynamics of a vesicle subjected to simultaneous shear and uniform alternating current (ac) ...

[Phys. Rev. E 97, 032404] Published Mon Mar 12, 2018

Optimal entrainment of circadian clocks in the presence of noise


Author(s): Michele Monti, David K. Lubensky, and Pieter Rein ten Wolde

Circadian clocks are biochemical oscillators that allow organisms to estimate the time of the day. These oscillators are inherently noisy due to the discrete nature of the reactants and the stochastic character of their interactions. To keep these oscillators in sync with the daily day-night rhythm ...

[Phys. Rev. E 97, 032405] Published Mon Mar 12, 2018

Relation between boundary slip mechanisms and waterlike fluid behavior


Author(s): Patricia Ternes, Evy Salcedo, and Marcia C. Barbosa

The slip of a fluid layer in contact with a solid confining surface is investigated for different temperatures and densities using molecular dynamic simulations. We show that for an anomalous waterlike fluid the slip goes as follows: for low levels of shear, defect slip appears and is related to the...

[Phys. Rev. E 97, 033104] Published Mon Mar 12, 2018

Modeling thermal inkjet and cell printing process using modified pseudopotential and thermal lattice Boltzmann methods


Author(s): Salman Sohrabi and Yaling Liu

Pseudopotential lattice Boltzmann methods (LBMs) can simulate a phase transition in high-density ratio multiphase flow systems. If coupled with thermal LBMs through equation of state, they can be used to study instantaneous phase transition phenomena with a high-temperature gradient where only one s...

[Phys. Rev. E 97, 033105] Published Mon Mar 12, 2018

Solvation suppression of ion recombination in gas discharge afterglow


Author(s): R. Kh. Amirov, A. V. Lankin, and G. E. Norman

An effect which suppresses recombination in ion plasmas is considered both theoretically and experimentally. Experimental results are presented for the ion recombination rate in fluorine plasma, which are obtained from data for the gas discharge afterglow. To interpret them, a suppression factor is ...

[Phys. Rev. E 97, 033202] Published Mon Mar 12, 2018

Sensitivity of electrospray molecular dynamics simulations to long-range Coulomb interaction models


Author(s): Neil A. Mehta and Deborah A. Levin

Molecular dynamics (MD) electrospray simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-${\mathrm{BF}}_{4}$) ion liquid were performed with the goal of evaluating the influence of long-range Coulomb models on ion emission characteristics. The direct Coulomb (DC), shifted force Coulom...

[Phys. Rev. E 97, 033306] Published Mon Mar 12, 2018

Publisher's Note: Negative pressure in shear thickening band of a dilatant fluid [Phys. Rev. E 94, 062614 (2016)]


Author(s): Shin-ichiro Nagahiro and Hiizu Nakanishi

[Phys. Rev. E 97, 039901] Published Mon Mar 12, 2018

Periodic sequence of stabilized wave segments in an excitable medium


Author(s): V. S. Zykov and E. Bodenschatz

Numerical computations show that a stabilization of a periodic sequence of wave segments propagating through an excitable medium is possible only in a restricted domain within the parameter space. By application of a free-boundary approach, we demonstrate that at the boundary of this domain the para...

[Phys. Rev. E 97, 030201(R)] Published Fri Mar 09, 2018

Inhibition delay increases neural network capacity through Stirling transform


Author(s): Alain Nogaret and Alastair King

Inhibitory neural networks are found to encode high volumes of information through delayed inhibition. We show that inhibition delay increases storage capacity through a Stirling transform of the minimum capacity which stabilizes locally coherent oscillations. We obtain both the exact and asymptotic...

[Phys. Rev. E 97, 030301(R)] Published Fri Mar 09, 2018

Spatial solitons and stability in the one-dimensional and the two-dimensional generalized nonlinear Schrödinger equation with fourth-order diffraction and parity-time-symmetric potentials


Author(s): C. G. L. Tiofack, F. II Ndzana, A. Mohamadou, and T. C. Kofane

We investigate the existence and stability of solitons in parity-time ($\mathcal{PT}$)-symmetric optical media characterized by a generic complex hyperbolic refractive index distribution and fourth-order diffraction (FOD). For the linear case, we demonstrate numerically that the FOD parameter can al...

[Phys. Rev. E 97, 032204] Published Fri Mar 09, 2018

Transition from normal to ballistic diffusion in a one-dimensional impact system


Author(s): André L. P. Livorati, Tiago Kroetz, Carl P. Dettmann, Iberê L. Caldas, and Edson D. Leonel

We characterize a transition from normal to ballistic diffusion in a bouncing ball dynamics. The system is composed of a particle, or an ensemble of noninteracting particles, experiencing elastic collisions with a heavy and periodically moving wall under the influence of a constant gravitational fie...

[Phys. Rev. E 97, 032205] Published Fri Mar 09, 2018

Tuning the overlap and the cross-layer correlations in two-layer networks: Application to a susceptible-infectious-recovered model with awareness dissemination


Author(s): David Juher and Joan Saldaña

We study the properties of the potential overlap between two networks $A,B$ sharing the same set of $N$ nodes (a two-layer network) whose respective degree distributions ${p}_{A}(k),{p}_{B}(k)$ are given. Defining the overlap coefficient $α$ as the Jaccard index, we prove that $α$ is very close to 0...

[Phys. Rev. E 97, 032303] Published Fri Mar 09, 2018

Revised model for the radiation force exerted by standing surface acoustic waves on a rigid cylinder


Author(s): Shen Liang and Wang Chaohui

In this paper, a model for the radiation force exerted by standing surface acoustic waves (SSAWs) on a rigid cylinder in inviscid fluids is extended to account for the dependence on the Rayleigh angle. The conventional model for the radiation force used in the SSAW-based applications is developed in...

[Phys. Rev. E 97, 033103] Published Fri Mar 09, 2018

Modeling flow and transport in fracture networks using graphs


Author(s): S. Karra, D. O'Malley, J. D. Hyman, H. S. Viswanathan, and G. Srinivasan

Fractures form the main pathways for flow in the subsurface within low-permeability rock. For this reason, accurately predicting flow and transport in fractured systems is vital for improving the performance of subsurface applications. Fracture sizes in these systems can range from millimeters to ki...

[Phys. Rev. E 97, 033304] Published Fri Mar 09, 2018

Applicability of Kerker preconditioning scheme to the self-consistent density functional theory calculations of inhomogeneous systems


Author(s): Yuzhi Zhou, Han Wang, Yu Liu, Xingyu Gao, and Haifeng Song

The Kerker preconditioner, based on the dielectric function of homogeneous electron gas, is designed to accelerate the self-consistent field (SCF) iteration in the density functional theory calculations. However, a question still remains regarding its applicability to the inhomogeneous systems. We d...

[Phys. Rev. E 97, 033305] Published Fri Mar 09, 2018

Efficient thermal diode with ballistic spacer


Author(s): Shunda Chen, Davide Donadio, Giuliano Benenti, and Giulio Casati

Thermal rectification is of importance not only for fundamental physics, but also for potential applications in thermal manipulations and thermal management. However, thermal rectification effect usually decays rapidly with system size. Here, we show that a mass-graded system, with two diffusive lea...

[Phys. Rev. E 97, 030101(R)] Published Thu Mar 08, 2018

Glassy phase in quenched disordered crystalline membranes


Author(s): O. Coquand, K. Essafi, J.-P. Kownacki, and D. Mouhanna

We investigate the flat phase of $D$-dimensional crystalline membranes embedded in a $d$-dimensional space and submitted to both metric and curvature quenched disorders using a nonperturbative renormalization group approach. We identify a second-order phase transition controlled by a finite-temperat...

[Phys. Rev. E 97, 030102(R)] Published Thu Mar 08, 2018

Absorbing phase transitions in deterministic fixed-energy sandpile models


Author(s): Su-Chan Park (박수찬)

We investigate the origin of the difference, which was noticed by Fey et al. [Phys. Rev. Lett. 104, 145703 (2010)], between the steady state density of an Abelian sandpile model (ASM) and the transition point of its corresponding deterministic fixed-energy sandpile model (DFES). Being deterministic,...

[Phys. Rev. E 97, 032105] Published Thu Mar 08, 2018

Ferromagnetic Potts models with multisite interaction


Author(s): Nir Schreiber, Reuven Cohen, and Simi Haber

We study the $q$-state Potts model with four-site interaction on a square lattice. Based on the asymptotic behavior of lattice animals, it is argued that when $q≤4$ the system exhibits a second-order phase transition and when $q>4$ the transition is first order. The $q=4$ model is borderline. We ...

[Phys. Rev. E 97, 032106] Published Thu Mar 08, 2018

Investigation of a chaotic thermostat


Author(s): G. J. Morales

A numerical study is presented of a free particle interacting with a deterministic thermostat in which the usual friction force is supplemented with a fluctuating force that depends on the self-consistent damping coefficient associated with coupling to the heat bath. It is found that this addition r...

[Phys. Rev. E 97, 032203] Published Thu Mar 08, 2018

Multifrequency Raman amplifiers


Author(s): Ido Barth and Nathaniel J. Fisch

In its usual implementation, the Raman amplifier features only one pump carrier frequency. However, pulses with well-separated frequencies can also be Raman amplified while compressed in time. Amplification with frequency-separated pumps is shown to hold even in the highly nonlinear, pump-depletion ...

[Phys. Rev. E 97, 033201] Published Thu Mar 08, 2018

Tensor network method for reversible classical computation


Author(s): Zhi-Cheng Yang, Stefanos Kourtis, Claudio Chamon, Eduardo R. Mucciolo, and Andrei E. Ruckenstein

We develop a tensor network technique that can solve universal reversible classical computational problems, formulated as vertex models on a square lattice [Nat. Commun. 8, 15303 (2017)]. By encoding the truth table of each vertex constraint in a tensor, the total number of solutions compatible with...

[Phys. Rev. E 97, 033303] Published Thu Mar 08, 2018

Fractal dimension of interfaces in Edwards-Anderson spin glasses for up to six space dimensions


Author(s): Wenlong Wang, M. A. Moore, and Helmut G. Katzgraber

The fractal dimension of domain walls produced by changing the boundary conditions from periodic to antiperiodic in one spatial direction is studied using both the strong-disorder renormalization group algorithm and the greedy algorithm for the Edwards-Anderson Ising spin-glass model for up to six s...

[Phys. Rev. E 97, 032104] Published Wed Mar 07, 2018

Simple and universal model for electron-impact ionization of complex biomolecules


Author(s): Hong Qi Tan, Zhaohong Mi, and Andrew A. Bettiol

We present a simple and universal approach to calculate the total ionization cross section (TICS) for electron impact ionization in DNA bases and other biomaterials in the condensed phase. Evaluating the electron impact TICS plays a vital role in ion-beam radiobiology simulation at the cellular leve...

[Phys. Rev. E 97, 032403] Published Wed Mar 07, 2018

Size effects in finite systems with long-range interactions


Author(s): E. S. Loscar and C. M. Horowitz

Small systems consisting of particles interacting with long-range potentials exhibit enormous size effects. The Tsallis conjecture [Tsallis, Fractals 3, 541 (1995)], valid for translationally invariant systems with long-range interactions, states a well-known scaling relating different sizes. Here w...

[Phys. Rev. E 97, 032103] Published Tue Mar 06, 2018

Transition between inverse and direct energy cascades in multiscale optical turbulence


Author(s): V. M. Malkin and N. J. Fisch

Multiscale turbulence naturally develops and plays an important role in many fluid, gas, and plasma phenomena. Statistical models of multiscale turbulence usually employ Kolmogorov hypotheses of spectral locality of interactions (meaning that interactions primarily occur between pulsations of compar...

[Phys. Rev. E 97, 032202] Published Tue Mar 06, 2018

Heat transport in oscillator chains with long-range interactions coupled to thermal reservoirs


Author(s): Stefano Iubini, Pierfrancesco Di Cintio, Stefano Lepri, Roberto Livi, and Lapo Casetti

The authors investigate heat propagation in one-dimensional chains of long-range interacting oscillators connected to thermal baths. They study two different models and find that for nonadditive interactions, heat transport shows a mean-field-like behavior irrespective of the particular details of the interactions.

[Phys. Rev. E 97, 032102] Published Mon Mar 05, 2018

Impact of hydrodynamic interactions on protein folding rates depends on temperature


Author(s): Fabio C. Zegarra, Dirar Homouz, Yossi Eliaz, Andrei G. Gasic, and Margaret S. Cheung

This paper examines the influence of hydrodynamic interactions on protein folding. The authors take two model proteins and perform Brownian dynamics simulations with a coarse-grained approach. Their results suggest that the long-range hydrodynamic interactions favor protein folding below the folding temperature, but retard it above that temperature

[Phys. Rev. E 97, 032402] Published Mon Mar 05, 2018

Universal size properties of a star-ring polymer structure in disordered environments


Author(s): K. Haydukivska and V. Blavatska

We consider the complex polymer system, consisting of a ring polymer connected to the ${f}_{1}$-branched starlike structure, in a good solvent in the presence of structural inhomogeneities. In particular cases ${f}_{1}=1$ and ${f}_{1}=2$, such a system restores the synthesized tadpole-shaped polysty...

[Phys. Rev. E 97, 032502] Published Mon Mar 05, 2018

Local yield stress statistics in model amorphous solids


Author(s): Armand Barbot, Matthias Lerbinger, Anier Hernandez-Garcia, Reinaldo García-García, Michael L. Falk, Damien Vandembroucq, and Sylvain Patinet

We develop and extend a method presented by Patinet, Vandembroucq, and Falk [Phys. Rev. Lett. 117, 045501 (2016)] to compute the local yield stresses at the atomic scale in model two-dimensional Lennard-Jones glasses produced via differing quench protocols. This technique allows us to sample the pla...

[Phys. Rev. E 97, 033001] Published Mon Mar 05, 2018

Shielding property for thermal equilibrium states in the quantum Ising model


Author(s): N. S. Móller, A. L. de Paula, Jr., and R. C. Drumond

We show that Gibbs states of nonhomogeneous transverse Ising chains satisfy a shielding property. Namely, whatever the fields on each spin and exchange couplings between neighboring spins are, if the field in one particular site is null, then the reduced states of the subchains to the right and to t...

[Phys. Rev. E 97, 032101] Published Fri Mar 02, 2018

Attractor hopping between polarization dynamical states in a vertical-cavity surface-emitting laser subject to parallel optical injection


Author(s): Florian Denis-le Coarer, Ana Quirce, Angel Valle, Luis Pesquera, Miguel A. Rodríguez, Krassimir Panajotov, and Marc Sciamanna

We present experimental and theoretical results of noise-induced attractor hopping between dynamical states found in a single transverse mode vertical-cavity surface-emitting laser (VCSEL) subject to parallel optical injection. These transitions involve dynamical states with different polarizations ...

[Phys. Rev. E 97, 032201] Published Fri Mar 02, 2018

Algorithmic detectability threshold of the stochastic block model


Author(s): Tatsuro Kawamoto

The assumption that the values of model parameters are known or correctly learned, i.e., the Nishimori condition, is one of the requirements for the detectability analysis of the stochastic block model in statistical inference. In practice, however, there is no example demonstrating that we can know...

[Phys. Rev. E 97, 032301] Published Fri Mar 02, 2018

Exact analytical solution of irreversible binary dynamics on networks


Author(s): Edward Laurence, Jean-Gabriel Young, Sergey Melnik, and Louis J. Dubé

In binary cascade dynamics, the nodes of a graph are in one of two possible states (inactive, active), and nodes in the inactive state make an irreversible transition to the active state, as soon as their precursors satisfy a predetermined condition. We introduce a set of recursive equations to comp...

[Phys. Rev. E 97, 032302] Published Fri Mar 02, 2018

Post-transcriptional bursting in genes regulated by small RNA molecules


Author(s): Guillermo Rodrigo

Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to het...

[Phys. Rev. E 97, 032401] Published Fri Mar 02, 2018

Electrostatic stiffening and induced persistence length for coassembled molecular bottlebrushes


Author(s): Ingeborg M. Storm, Martien A. Cohen Stuart, Renko de Vries, and Frans A. M. Leermakers

A self-consistent field analysis for tunable contributions to the persistence length of isolated semiflexible polymer chains including electrostatically driven coassembled deoxyribonucleic acid (DNA) bottlebrushes is presented. When a chain is charged, i.e., for polyelectrolytes, there is, in additi...

[Phys. Rev. E 97, 032501] Published Fri Mar 02, 2018

Paramagnetic colloids: Chaotic routes to clusters and molecules


Author(s): Hamed Abdi, Rasam Soheilian, Randall M. Erb, and Craig E. Maloney

We present computer simulations and experiments on dilute suspensions of superparamagnetic particles subject to rotating magnetic fields. We focus on chains of four particles and their decay routes to stable structures. At low rates, the chains track the external field. At intermediate rates, the ch...

[Phys. Rev. E 97, 032601] Published Fri Mar 02, 2018

Soft inclusion in a confined fluctuating active gel


Author(s): Amit Singh Vishen, J.-F. Rupprecht, G. V. Shivashankar, J. Prost, and Madan Rao

We study stochastic dynamics of a point and extended inclusion within a one-dimensional confined active viscoelastic gel. We show that the dynamics of a point inclusion can be described by a Langevin equation with a confining potential and multiplicative noise. Using a systematic adiabatic eliminati...

[Phys. Rev. E 97, 032602] Published Fri Mar 02, 2018

Modeling deformation and chaining of flexible shells in a nematic solvent with finite elements on an adaptive moving mesh


Author(s): Andrew DeBenedictis, Timothy J. Atherton, Andrea L. Rodarte, and Linda S. Hirst

A micrometer-scale elastic shell immersed in a nematic liquid crystal may be deformed by the host if the cost of deformation is comparable to the cost of elastic deformation of the nematic. Moreover, such inclusions interact and form chains due to quadrupolar distortions induced in the host. A conti...

[Phys. Rev. E 97, 032701] Published Fri Mar 02, 2018

Heavy inertial particles in turbulent flows gain energy slowly but lose it rapidly


Author(s): Akshay Bhatnagar, Anupam Gupta, Dhrubaditya Mitra, and Rahul Pandit

We present an extensive numerical study of the time irreversibility of the dynamics of heavy inertial particles in three-dimensional, statistically homogeneous, and isotropic turbulent flows. We show that the probability density function (PDF) of the increment, $W(τ)$, of a particle's energy over a ...

[Phys. Rev. E 97, 033102] Published Fri Mar 02, 2018

Analysis and optimization of population annealing


Author(s): Christopher Amey and Jonathan Machta

Population annealing is an easily parallelizable sequential Monte Carlo algorithm that is well suited for simulating the equilibrium properties of systems with rough free-energy landscapes. In this work we seek to understand and improve the performance of population annealing. We derive several usef...

[Phys. Rev. E 97, 033301] Published Fri Mar 02, 2018

Accelerating simulation for the multiple-point statistics algorithm using vector quantization


Author(s): Chen Zuo, Zhibin Pan, and Hao Liang

Multiple-point statistics (MPS) is a prominent algorithm to simulate categorical variables based on a sequential simulation procedure. Assuming training images (TIs) as prior conceptual models, MPS extracts patterns from TIs using a template and records their occurrences in a database. However, comp...

[Phys. Rev. E 97, 033302] Published Fri Mar 02, 2018

Announcement: The Irwin Oppenheim Award


Author(s): Eli Ben-Naim
[Phys. Rev. E 97, 030001] Published Thu Mar 01, 2018

Statistical symmetry restoration in fully developed turbulence: Renormalization group analysis of two models


Author(s): N. V. Antonov, N. M. Gulitskiy, M. M. Kostenko, and A. V. Malyshev

In this paper we consider the model of incompressible fluid described by the stochastic Navier-Stokes equation with finite correlation time of a random force. Inertial-range asymptotic behavior of fully developed turbulence is studied by means of the field theoretic renormalization group within the ...

[Phys. Rev. E 97, 033101] Published Thu Mar 01, 2018

Two-dimensional Ising model on random lattices with constant coordination number


Author(s): Manuel Schrauth, Julian A. J. Richter, and Jefferson S. E. Portela

We study the two-dimensional Ising model on networks with quenched topological (connectivity) disorder. In particular, we construct random lattices of constant coordination number and perform large-scale Monte Carlo simulations in order to obtain critical exponents using finite-size scaling relation...

[Phys. Rev. E 97, 022144] Published Wed Feb 28, 2018

Diffusion with finite-helicity field tensor: A mechanism of generating heterogeneity


Author(s): N. Sato and Z. Yoshida

Topological constraints on a dynamical system often manifest themselves as breaking of the Hamiltonian structure; well-known examples are nonholonomic constraints on Lagrangian mechanics. The statistical mechanics under such topological constraints is the subject of this study. Conventional argument...

[Phys. Rev. E 97, 022145] Published Wed Feb 28, 2018

Possible ergodic-nonergodic regions in the quantum Sherrington-Kirkpatrick spin glass model and quantum annealing


Author(s): Sudip Mukherjee, Atanu Rajak, and Bikas K. Chakrabarti

We explore the behavior of the order parameter distribution of the quantum Sherrington-Kirkpatrick model in the spin glass phase using Monte Carlo technique for the effective Suzuki-Trotter Hamiltonian at finite temperatures and that at zero temperature obtained using the exact diagonalization metho...

[Phys. Rev. E 97, 022146] Published Wed Feb 28, 2018

Universality in chaos: Lyapunov spectrum and random matrix theory


Author(s): Masanori Hanada, Hidehiko Shimada, and Masaki Tezuka

We propose the existence of a new universality in classical chaotic systems when the number of degrees of freedom is large: the statistical property of the Lyapunov spectrum is described by random matrix theory. We demonstrate it by studying the finite-time Lyapunov exponents of the matrix model of ...

[Phys. Rev. E 97, 022224] Published Wed Feb 28, 2018

Discrete breathers in an electric lattice with an impurity: Birth, interaction, and death


Author(s): A. Gómez-Rojas and P. Halevi

We have simulated aspects of intrinsic localized modes or discrete breathers in a modulated lumped transmission line with nonlinear varactors and a defect unit cell. As the inductance or capacitance of this cell is increased, a transition from instability to stability takes place. Namely, there exis...

[Phys. Rev. E 97, 022225] Published Wed Feb 28, 2018

Multiple mechanisms for stochastic resonance are inherent to sinusoidally driven noisy Hopf oscillators


Author(s): Dáibhid Ó Maoiléidigh

To ensure their sensitivity to weak periodic signals, some physical systems likely operate near a Hopf bifurcation. Many systems operating near such a bifurcation exhibit stochastic resonance, but it is unclear which mechanisms for resonance are inherent to the bifurcation. To address this question,...

[Phys. Rev. E 97, 022226] Published Wed Feb 28, 2018

Comparative analysis on the selection of number of clusters in community detection


Author(s): Tatsuro Kawamoto and Yoshiyuki Kabashima

We conduct a comparative analysis on various estimates of the number of clusters in community detection. An exhaustive comparison requires testing of all possible combinations of frameworks, algorithms, and assessment criteria. In this paper we focus on the framework based on a stochastic block mode...

[Phys. Rev. E 97, 022315] Published Wed Feb 28, 2018

Decoding communities in networks


Author(s): Filippo Radicchi

According to a recent information-theoretical proposal, the problem of defining and identifying communities in networks can be interpreted as a classical communication task over a noisy channel: memberships of nodes are information bits erased by the channel, edges and nonedges in the network are pa...

[Phys. Rev. E 97, 022316] Published Wed Feb 28, 2018

Mutual information identifies spurious Hurst phenomena in resting state EEG and fMRI data


Author(s): Frederic von Wegner, Helmut Laufs, and Enzo Tagliazucchi

Long-range memory in time series is often quantified by the Hurst exponent $H$, a measure of the signal's variance across several time scales. We analyze neurophysiological time series from electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) resting state experiments with t...

[Phys. Rev. E 97, 022415] Published Wed Feb 28, 2018

Defect-facilitated buckling in supercoiled double-helix DNA


Author(s): Sumitabha Brahmachari, Andrew Dittmore, Yasuharu Takagi, Keir C. Neuman, and John F. Marko

We present a statistical-mechanical model for stretched twisted double-helix DNA, where thermal fluctuations are treated explicitly from a Hamiltonian without using any scaling hypotheses. Our model applied to defect-free supercoiled DNA describes the coexistence of multiple plectoneme domains in lo...

[Phys. Rev. E 97, 022416] Published Wed Feb 28, 2018

Thermodynamics and dynamics of two-dimensional systems with dipolelike repulsive interactions


Author(s): Sergey A. Khrapak, Nikita P. Kryuchkov, and Stanislav O. Yurchenko

Thermodynamics and dynamics of a classical two-dimensional system with dipolelike isotropic repulsive interactions are studied systematically using extensive molecular dynamics (MD) simulations supplemented by appropriate theoretical approximations. This interaction potential, which decays as an inv...

[Phys. Rev. E 97, 022616] Published Wed Feb 28, 2018

Mechanical trapping of particles in granular media


Author(s): Abdulla Kerimov, Gary Mavko, Tapan Mukerji, and Mustafa A. Al Ibrahim

Mechanical trapping of fine particles in the pores of granular materials is an essential mechanism in a wide variety of natural and industrial filtration processes. The progress of invading particles is primarily limited by the network of pore throats and connected pathways encountered by the partic...

[Phys. Rev. E 97, 022907] Published Wed Feb 28, 2018

Density effects on electronic configurations in dense plasmas


Author(s): Gérald Faussurier and Christophe Blancard

We present a quantum mechanical model to describe the density effects on electronic configurations inside a plasma environment. Two different approaches are given by starting from a quantum average-atom model. Illustrations are shown for an aluminum plasma in local thermodynamic equilibrium at solid...

[Phys. Rev. E 97, 023206] Published Wed Feb 28, 2018

Transition point prediction in a multicomponent lattice Boltzmann model: Forcing scheme dependencies


Author(s): Knut Küllmer, Andreas Krämer, Wolfgang Joppich, Dirk Reith, and Holger Foysi

Pseudopotential-based lattice Boltzmann models are widely used for numerical simulations of multiphase flows. In the special case of multicomponent systems, the overall dynamics are characterized by the conservation equations for mass and momentum as well as an additional advection diffusion equatio...

[Phys. Rev. E 97, 023313] Published Wed Feb 28, 2018

Quantum thermodynamics with local control


Author(s): J. Lekscha, H. Wilming, J. Eisert, and R. Gallego

We investigate the limitations that emerge in thermodynamic tasks as a result of having local control only over the components of a thermal machine. These limitations are particularly relevant for devices composed of interacting many-body systems. Specifically, we study protocols of work extraction ...

[Phys. Rev. E 97, 022142] Published Tue Feb 27, 2018

Large deviation function for a driven underdamped particle in a periodic potential


Author(s): Lukas P. Fischer, Patrick Pietzonka, and Udo Seifert

Employing large deviation theory, we explore current fluctuations of underdamped Brownian motion for the paradigmatic example of a single particle in a one-dimensional periodic potential. Two different approaches to the large deviation function of the particle current are presented. First, we derive...

[Phys. Rev. E 97, 022143] Published Tue Feb 27, 2018

Characterization and detection of thermoacoustic combustion oscillations based on statistical complexity and complex-network theory


Author(s): Shogo Murayama, Hikaru Kinugawa, Isao T. Tokuda, and Hiroshi Gotoda

We present an experimental study on the characterization of dynamic behavior of flow velocity field during thermoacoustic combustion oscillations in a turbulent confined combustor from the viewpoints of statistical complexity and complex-network theory, involving detection of a precursor of thermoac...

[Phys. Rev. E 97, 022223] Published Tue Feb 27, 2018

Curvature instability of membranes near rigid inclusions


Author(s): S. Alex Rautu

In multicomponent membranes, internal scalar fields may couple to membrane curvature, thus renormalizing the membrane elastic constants and destabilizing the flat membranes. Here, a general elasticity theory of membranes is considered that employs a quartic curvature expansion. The shape of the memb...

[Phys. Rev. E 97, 022414] Published Tue Feb 27, 2018

Rational design of stealthy hyperuniform two-phase media with tunable order


Author(s): Robert A. DiStasio, Jr., Ge Zhang, Frank H. Stillinger, and Salvatore Torquato

Disordered stealthy hyperuniform materials are exotic amorphous states of matter that have attracted recent attention because of their novel structural characteristics (hidden order at large length scales) and physical properties, including desirable photonic and transport properties. It is therefor...

[Phys. Rev. E 97, 023311] Published Tue Feb 27, 2018

Lattice Boltzmann model for three-phase viscoelastic fluid flow


Author(s): Chiyu Xie, Wenhai Lei, and Moran Wang

A lattice Boltzmann (LB) framework is developed for simulation of three-phase viscoelastic fluid flows in complex geometries. This model is based on a Rothman-Keller type model for immiscible multiphase flows which ensures mass conservation of each component in porous media even for a high density r...

[Phys. Rev. E 97, 023312] Published Tue Feb 27, 2018

Reducing the extinction risk of stochastic populations via nondemographic noise


Author(s): Shay Be'er and Michael Assaf

We consider nondemographic noise in the form of uncertainty in the reaction step size and reveal a dramatic effect this noise may have on the stability of self-regulating populations. Employing the reaction scheme $mA→kA$ but allowing, e.g., the product number $k$ to be a priori unknown and sampled ...

[Phys. Rev. E 97, 020302(R)] Published Mon Feb 26, 2018

Entropy generation and unified optimization of Carnot-like and low-dissipation refrigerators


Author(s): Julian Gonzalez-Ayala, A. Medina, J. M. M. Roco, and A. Calvo Hernández

The connection between Carnot-like and low-dissipation refrigerators is proposed by means of their entropy generation and the optimization of two unified, compromise-based figures of merit. Their optimization shows that only a limited set of heat transfer laws in the Carnot-like model are compatible...

[Phys. Rev. E 97, 022139] Published Mon Feb 26, 2018

Path-integral Monte Carlo simulation of time-reversal noninvariant bulk systems with a case study of rotating Yukawa gases


Author(s): Tamás Haidekker Galambos and Csaba Tőke

We elaborate on the methodology to simulate bulk systems in the absence of time-reversal symmetry by the phase-fixed path-integral Monte Carlo method under (possibly twisted) periodic boundary conditions. Such systems include two-dimensional electrons in the quantum Hall regime and rotating ultracol...

[Phys. Rev. E 97, 022140] Published Mon Feb 26, 2018

Enhanced diffusion on oscillating surfaces through synchronization


Author(s): Jin Wang, Wei Cao, Ming Ma, and Quanshui Zheng

The diffusion of molecules and clusters under nanoscale confinement or absorbed on surfaces is the key controlling factor in dynamical processes such as transport, chemical reaction, or filtration. Enhancing diffusion could benefit these processes by increasing their transport efficiency. Using a no...

[Phys. Rev. E 97, 022141] Published Mon Feb 26, 2018