The dynamical evolution of dislocations in plastically deformed metals is controlled by both deterministic factors arising out of applied loads and stochastic effects appearing due to fluctuations of internal stress. Such types of stochastic dislocation processes and the associated spatially inhomog…

[Phys. Rev. E 94, 022139] Published Fri Aug 26, 2016

]]>We demonstrate a nonlinear, nonequilibrium field-driven ion flux phenomenon, which unlike Teorell's nonlinear multiple field theory, requires only the application of one field: robust autonomous current-mass flux oscillations across a porous monolith coupled to a capillary with a long air bubble, wh…

[Phys. Rev. E 94, 022613] Published Fri Aug 26, 2016

]]>Determining the correct matching boundary condition is fundamental to our understanding of several everyday problems. Despite over a century of scientific work, existing velocity boundary conditions are unable to consistently explain and capture the complete physics associated with certain common bu…

[Phys. Rev. E 94, 023113] Published Fri Aug 26, 2016

]]>We apply the matrix-product ansatz to study the totally asymmetric simple exclusion process on a ring with a generalized discrete-time dynamics depending on two hopping probabilities, $p$ and $\stackrel{\u0303}{p}$. The model contains as special cases the TASEP with parallel update, when $\stackrel{\u0303}{p}=0$, and with sequential backwar…

[Phys. Rev. E 94, 022138] Published Thu Aug 25, 2016

]]>It is known that amplitude death can occur in networks of coupled identical oscillators if they interact via diffusive time-delayed coupling links. Here we consider networks of oscillators that interact via direct time-delayed coupling links. It is shown analytically that amplitude death is impossib…

[Phys. Rev. E 94, 022215] Published Thu Aug 25, 2016

]]>We introduce an intuitive model that describes both the emergence of community structure and the evolution of the internal structure of communities in growing social networks. The model comprises two complementary mechanisms: One mechanism accounts for the evolution of the internal link structure of…

[Phys. Rev. E 94, 022317] Published Thu Aug 25, 2016

]]>We investigate the driven polymer translocation through a nanometer-scale pore in the presence and absence of hydrodynamics both in good and bad solvent. We present our results on tension propagating along the polymer segment on the *cis* side that is measured for the first time using our method that …

[Phys. Rev. E 94, 022501] Published Thu Aug 25, 2016

]]>The impact of the volumetric charged density of the dielectric rigid core on the electrophoresis of a soft particle is analyzed numerically. The volume charge density of the inner core of a soft particle can arise for a dendrimer structure or bacteriophage MS2. We consider the electrokinetic model b…

[Phys. Rev. E 94, 022611] Published Thu Aug 25, 2016

]]>Large collections of autonomously moving agents, such as animals or micro-organisms, are able to flock coherently in space even in the absence of a central control mechanism. While the direction of the flock resulting from this critical behavior is random, this can be controlled by a small subset of…

[Phys. Rev. E 94, 022612] Published Thu Aug 25, 2016

]]>We present a numerical implementation of an active inclusion in a granular material submitted to a biaxial test. We discuss the dependence of the response to this perturbation on two parameters: the intragranular friction coefficient on one hand, and the degree of the loading on the other hand. We c…

[Phys. Rev. E 94, 022907] Published Thu Aug 25, 2016

]]>In this work, a generalized form of the BGK-Boltzmann equation is proposed, where the velocity, position, and time can be represented by real or complex variables. The real representation leads to the conventional BGK-Boltzmann equation, which can recover the continuity and Navier-Stokes equations. …

[Phys. Rev. E 94, 023316] Published Thu Aug 25, 2016

]]>We use small-angle neutron scattering (SANS) to study labeled short chains with and without the influence of an entangled and highly stretched surrounding environment of longer chains. We find unequivocal evidence of nematic effects as the blend chains in steady state flow are stretched a factor $\sim \mathrm{1.\dots}$

[Phys. Rev. E 94, 020502(R)] Published Wed Aug 24, 2016

]]>Recent developments have cemented the realization that many concepts and quantities in thermodynamics and information theory are shared. In this paper, we consider a highly relevant quantity in information theory and complex systems, the transfer entropy, and explore its thermodynamic role by consid…

[Phys. Rev. E 94, 022135] Published Wed Aug 24, 2016

]]>We examine energy and particle exchange between finite-sized quantum systems and find a new form of nonequilibrium state. The exchange rate undergoes stepwise evolution in time, and its magnitude and sign dramatically change according to system size differences. The origin lies in interference effec…

[Phys. Rev. E 94, 022136] Published Wed Aug 24, 2016

]]>We study the dynamics of the paradigmatic Kuramoto-Sakaguchi model of identical coupled phase oscillators with various kinds of time-dependent connectivity using Eulerian discretization. We explore the parameter spaces for various types of collective states using the phase plots of the two statistic…

[Phys. Rev. E 94, 022213] Published Wed Aug 24, 2016

]]>In nonautonomous dynamical systems, like in climate dynamics, an ensemble of trajectories initiated in the remote past defines a unique probability distribution, the natural measure of a snapshot attractor, for any instant of time, but this distribution typically changes in time. In cases with an ap…

[Phys. Rev. E 94, 022214] Published Wed Aug 24, 2016

]]>We present an exhaustive mathematical analysis of the recently proposed Non-Poissonian Activity Driven (NoPAD) model [Moinet *et al.*, Phys. Rev. Lett. **114**, 108701 (2015)], a temporal network model incorporating the empirically observed bursty nature of social interactions. We focus on the aging effe…

[Phys. Rev. E 94, 022316] Published Wed Aug 24, 2016

]]>Two overall neutral surfaces with positively and negatively charged domains (“patches”) have been shown in recent experiments to exhibit long-range attraction when immersed in an ionic solution. Motivated by the experiments, we calculate analytically the osmotic pressure between such surfaces within…

[Phys. Rev. E 94, 022803] Published Wed Aug 24, 2016

]]>The properties of the nonlinear frequency shift (NFS), especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas, have been researched by Vlasov simulation. Pictures of the nonlinear frequency shift from harmonic generation and particle trappin…

[Phys. Rev. E 94, 023205] Published Wed Aug 24, 2016

]]>[Phys. Rev. E 94, 029904] Published Wed Aug 24, 2016

]]>Using an event-driven molecular dynamics simulation, we show that simple monodisperse granular beads confined in coupled columns may oscillate as a different type of granular clock. To trigger this oscillation, the system needs to be driven against gravity into a density-inverted state, with a high-…

[Phys. Rev. E 94, 020901(R)] Published Tue Aug 23, 2016

]]>The multistate Potts models on two-dimensional hyperbolic lattices are studied with respect to various boundary effects. The free energy is numerically calculated using the corner transfer matrix renormalization group method. We analyze phase transitions of the Potts models in the thermodynamic limi…

[Phys. Rev. E 94, 022133] Published Tue Aug 23, 2016

]]>Phase diagram of a discrete counterpart of the classical Heisenberg model, the truncated tetrahedral model, is analyzed on the square lattice, when the interaction is ferromagnetic. Each spin is represented by a unit vector that can point to one of the 12 vertices of the truncated tetrahedron, which…

[Phys. Rev. E 94, 022134] Published Tue Aug 23, 2016

]]>Turbulence in integrable systems exhibits a noticeable scientific advantage: it can be expressed in terms of the nonlinear modes of these systems. Whether the majority of the excitations in the system are breathers or solitons defines the properties of the turbulent state. In the two extreme cases w…

[Phys. Rev. E 94, 022212] Published Tue Aug 23, 2016

]]>We investigate the replicator dynamics with “sparse” symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction $u$, we conduct a perturbative expansion which manifests that the nature of the interactions has a direct im…

[Phys. Rev. E 94, 022312] Published Tue Aug 23, 2016

]]>Mathematical models of pedestrian evacuation and the associated simulation software have become essential tools for the assessment of the safety of public facilities and buildings. While a variety of models is now available, their calibration and test against empirical data are generally restricted …

[Phys. Rev. E 94, 022313] Published Tue Aug 23, 2016

]]>This paper examines the occurrence and modeling of aftershocks in systems exhibiting avalanche-like behavior, particularly focusing on the case of earthquakes. The authors propose a self-similar description of the spatiotemporal correlation of events and find agreement with high-precision seismic data. This suggests that self-similarity is a general principle in seismicity, and it may have consequences for probabilistic earthquake forecasting.

[Phys. Rev. E 94, 022314] Published Tue Aug 23, 2016

]]>We consider the problem of finding optimal strategies that maximize the average growth rate of multiplicative stochastic processes. For a geometric Brownian motion, the problem is solved through the so-called Kelly criterion, according to which the optimal growth rate is achieved by investing a cons…

[Phys. Rev. E 94, 022315] Published Tue Aug 23, 2016

]]>Chain formation in diatoms is relevant because of several aspects of their adaptation to the ecosystem. However, the tools to quantify the regulation of their assemblage and infer specific mechanisms in a laboratory setting are scarce. To address this problem, we define an approach based on a statis…

[Phys. Rev. E 94, 022418] Published Tue Aug 23, 2016

]]>Many problems in science and engineering require the ability to grow tubular or polymeric structures up to large volume fractions within a bounded region of three-dimensional space. Examples range from the construction of fibrous materials and biological cells such as neurons, to the creation of ini…

[Phys. Rev. E 94, 023315] Published Tue Aug 23, 2016

]]>Recurrence quantification analysis (RQA) is used to characterize a dynamical transition that takes place in the diffusive sandpile. The transition happens when a combination of the drive strength, diffusivity, and overturning size exceeds a critical value. Above the transition, the self-similar tran…

[Phys. Rev. E 94, 022128] Published Mon Aug 22, 2016

]]>In this paper we revisited the Ziff-Gulari-Barshad model to study its phase transitions and critical exponents through time-dependent Monte Carlo simulations. We use a method proposed recently to locate the nonequilibrium second-order phase transitions and that has been successfully used in systems …

[Phys. Rev. E 94, 022129] Published Mon Aug 22, 2016

]]>Lévy walks have proved to be useful models of stochastic dynamics with a number of applications in the modeling of real-life phenomena. In this paper we derive explicit formulas for densities of the two- (2D) and three-dimensional (3D) ballistic Lévy walks, which are most important in applications. …

[Phys. Rev. E 94, 022130] Published Mon Aug 22, 2016

]]>We study the linear response in systems driven away from thermal equilibrium into a nonequilibrium steady state with nonvanishing entropy production rate. A simple derivation of a general response formula is presented under the condition that the generating function describes a transformation that (…

[Phys. Rev. E 94, 022131] Published Mon Aug 22, 2016

]]>We consider the continuous-time random walk (CTRW) model of tracer motion in porous medium flows based on the experimentally determined distributions of pore velocity and pore size reported by Holzner *et al.* [M. Holzner *et al.*, Phys. Rev. E **92**, 013015 (2015)]. The particle's passing through one cha…

[Phys. Rev. E 94, 022132] Published Mon Aug 22, 2016

]]>A concept of bypass rewiring is introduced, and random bypass rewiring is analytically and numerically investigated with simulations. Our results show that bypass rewiring makes networks robust against removal of nodes including random failures and attacks. In particular, random bypass rewiring conn…

[Phys. Rev. E 94, 022310] Published Mon Aug 22, 2016

]]>The gain-loss asymmetry, observed in the inverse statistics of stock indices is present for logarithmic return levels that are over $2\%$, and it is the result of the non-Pearson-type autocorrelations in the index. These non-Pearson-type correlations can be viewed also as functionally dependent daily v…

[Phys. Rev. E 94, 022311] Published Mon Aug 22, 2016

]]>Lipid bilayers forming biological membranes are known to behave as viscous two-dimensional fluids on submicrometer scales; usually they contain a large number of active protein inclusions. Recently, it was shown [A. S. Mikhailov and R. Kapral, Proc. Natl. Acad. Sci. USA **112**, E3639 (2015)] that such …

[Phys. Rev. E 94, 022416] Published Mon Aug 22, 2016

]]>The flow-induced aggregation of dilute colloidal polystyrene nanoparticles suspended in Newtonian and viscoelastic solutions is reported. A rheo-optical method has been used to detect real-time aggregation processes via measuring optical absorption or scattering in a quartz Couette cell. The observe…

[Phys. Rev. E 94, 022610] Published Mon Aug 22, 2016

]]>The effects of friction mobilization on the stress profile within a two-dimensional silo are investigated via simulations of discrete elements. Friction mobilization is driven by cyclic vertical displacement of the sidewalls. Two regimes have been observed for small filling height, with stress profi…

[Phys. Rev. E 94, 022906] Published Mon Aug 22, 2016

]]>This work presents a detailed study of the dispersion of capillary waves with small amplitude in viscous fluids using an analytically derived solution to the initial value problem of a small-amplitude capillary wave as well as direct numerical simulation. A rational parametrization for the dispersio…

[Phys. Rev. E 94, 023110] Published Mon Aug 22, 2016

]]>To understand the mechanism of the self-sustenance of subcritical turbulence in spectrally stable (constant) shear flows, we performed direct numerical simulations of homogeneous shear turbulence for different aspect ratios of the flow domain with subsequent analysis of the dynamical processes in sp…

[Phys. Rev. E 94, 023111] Published Mon Aug 22, 2016

]]>Hydrodynamic interactions between air bubbles and particles have wide applications in multiphase separation and reaction processes. In the present work, we explore the fundamental mechanism of such complex processes by studying the collision of a single bubble with a fixed solid particle inside a He…

[Phys. Rev. E 94, 023112] Published Mon Aug 22, 2016

]]>The unified gas kinetic scheme (UGKS) is an asymptotic preserving (AP) scheme for kinetic equations. It is superior for transition flow simulation and has been validated in the past years. However, compared to the well-known discrete ordinate method (DOM), which is a classical numerical method solvi…

[Phys. Rev. E 94, 023313] Published Mon Aug 22, 2016

]]>An accurate method for time propagation of the coupled Maxwell and time-dependent Kohn-Sham (TDKS) equation is presented. The new approach uses a simultaneous fourth-order Runge-Kutta–based propagation of the vector potential and the Kohn-Sham orbitals. The approach is compared to the conventional f…

[Phys. Rev. E 94, 023314] Published Mon Aug 22, 2016

]]>A laminar flow control technique based on spanwise mean velocity gradients (SVGs) has recently proven successful in delaying transition in boundary layers. Here we take advantage of a well-known nonlinear effect, namely, the interaction of two oblique waves at high amplitude, to produce spanwise mea…

[Phys. Rev. E 94, 021103(R)] Published Fri Aug 19, 2016

]]>Data of the numerical solution of the time-dependent Schrödinger equation of a system containing one spin-$\frac{1}{2}$ particle interacting with a bath of up to 32 spin-$\frac{1}{2}$ particles is used to construct a Markovian quantum master equation describing the dynamics of the system spin. The procedure of obtaining …

[Phys. Rev. E 94, 022126] Published Fri Aug 19, 2016

]]>Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are …

[Phys. Rev. E 94, 022127] Published Fri Aug 19, 2016

]]>Colloidal particles of two types, driven in opposite directions, can segregate into lanes [Vissers *et al.*, Soft Matter **7**, 2352 (2011)]. This phenomenon can be reproduced by two-dimensional Brownian dynamics simulations of model particles [Dzubiella *et al.*, Phys. Rev. E **65**, 021402 (2002)]. Here we …

[Phys. Rev. E 94, 022608] Published Fri Aug 19, 2016

]]>The standard theory of induced-charge electro-osmosis (ICEO) often overpredicts experimental values of ICEO velocities. Using a nonsteady direct multiphysics simulation technique based on the coupled Poisson-Nernst-Planck and Stokes equations for an electrolyte around a conductive cylinder subject t…

[Phys. Rev. E 94, 022609] Published Fri Aug 19, 2016

]]>We report an experimental study of bubble dynamics in a non-Newtonian fluid subjected to a pressure decrease. The fluid is a hydrogel, composed of water and a synthetic clay, prepared and sandwiched between two glass plates in a Hele-Shaw geometry. The rheological properties of the material can be t…

[Phys. Rev. E 94, 023109] Published Fri Aug 19, 2016

]]>We discuss the energy distribution of free-electron Fermi-gas, a problem with a textbook solution of Gaussian energy fluctuations in the limit of a large system. We find that for a small system, characterized solely by its heat capacity $C$, the distribution can be solved analytically, and it is both …

[Phys. Rev. E 94, 022123] Published Thu Aug 18, 2016

]]>We develop a translational-rotational cage model that describes the behavior of dense two-dimensional (2D) Brownian systems of hard annular sector particles (ASPs), resembling C shapes. At high particle densities, pairs of ASPs can form mutually interdigitating lock-and-key dimers. This cage model c…

[Phys. Rev. E 94, 022124] Published Thu Aug 18, 2016

]]>As an indicator of cooperative motion in a system of Brownian particles that models two-dimensional colloidal liquids, a displacement correlation tensor is calculated analytically and compared with numerical results. The key idea for the analytical calculation is to relate the displacement correlati…

[Phys. Rev. E 94, 022125] Published Thu Aug 18, 2016

]]>Uncertain recognition success, unfavorable scaling of connection complexity, or dependence on complex external input impair the usefulness of current oscillatory neural networks for pattern recognition or restrict technical realizations to small networks. We propose a network architecture of coupled…

[Phys. Rev. E 94, 022309] Published Thu Aug 18, 2016

]]>We consider a class of adaptive network models where links can only be created or deleted between nodes in different states. These models provide an approximate description of a set of systems where nodes represent agents moving in physical or abstract space, the state of each node represents the ag…

[Phys. Rev. E 94, 022415] Published Thu Aug 18, 2016

]]>A complete lattice Boltzmann model (LBM) is proposed for the steady radiative transfer equation (RTE). The RTE can be regarded as a pure convection equation with a source term. To derive the expressions for the equilibrium distribution function and the relaxation time, an artificial isotropic diffus…

[Phys. Rev. E 94, 023312] Published Thu Aug 18, 2016

]]>We consider continuous-time quantum walks (CTQWs) on multilayer dendrimer networks (MDs) and their application to quantum transport. A detailed study of properties of CTQWs is presented and transport efficiency is determined in terms of the exact and average return probabilities. The latter depends …

[Phys. Rev. E 94, 022307] Published Wed Aug 17, 2016

]]>We present an exact analysis of the physical properties of bimodal networks specified by the two peak degree distribution fully incorporating the degree-degree correlation between node connections. The structure of the correlated bimodal network is uniquely determined by the Pearson coefficient of t…

[Phys. Rev. E 94, 022308] Published Wed Aug 17, 2016

]]>Microswimmers such as bacteria perform random walks known as run-and-tumbles to move up chemoattractant gradients and as a result aggregate with others. It is also known that such micro-swimmers can self-organize into macroscopic patterns due to interactions with neighboring cells through the fluidi…

[Phys. Rev. E 94, 022414] Published Wed Aug 17, 2016

]]>We present a data-driven framework to study the relationship between fluid flow at the macroscale and the internal pore structure, across the micro- and mesoscales, in porous, granular media. Sphere packings with varying particle size distribution and confining pressure are generated using the discr…

[Phys. Rev. E 94, 022904] Published Wed Aug 17, 2016

]]>Velocity distributions in normal shock waves obtained in dilute granular flows are studied. These distributions cannot be described by a simple functional shape and are believed to be bimodal. Our results show that these distributions are not strictly bimodal but a trimodal distribution is shown to …

[Phys. Rev. E 94, 022905] Published Wed Aug 17, 2016

]]>The primary and key task of binary fluid flow modeling is to track the interface with good accuracy, which is usually challenging due to the sharp-interface limit and numerical dispersion. This article concentrates on further development of the conservative Allen-Cahn equation (ACE) [Geier *et al.*, …

[Phys. Rev. E 94, 023311] Published Wed Aug 17, 2016

]]>When a droplet of water impacts a heated surface, the drop may be observed to bounce. Recently is has been found that small quantities ($\sim 100$ ppm) of polymer additives such as polyethylene oxide can significantly increase the maximum bouncing height of drops. This effect has been explained in terms o…

[Phys. Rev. E 94, 021102(R)] Published Tue Aug 16, 2016

]]>We outline a basic strategy of how self-propulsion can be used to improve the yield of a typical colloidal self-assembly process. The success of this approach is predicated on the thoughtful design of the colloidal building block as well as how self-propulsion is endowed to the particle. As long as …

[Phys. Rev. E 94, 022607] Published Tue Aug 16, 2016

]]>The shock dissemination of granular rings or shells is characterized by the formation of coherent particle jets that have different dimensions from those associated with the constituent grains. In order to identify the mechanisms governing the formation of particle jets, we carry out the simulations…

[Phys. Rev. E 94, 022903] Published Tue Aug 16, 2016

]]>We extend the (1+1)-dimensional fluid solid-on-solid (SOS) model to include a confining flat surface opposite to the SOS surface subject to a constant load. This load is balanced by a repulsive surface-surface interaction given by an ansatz which agrees with known analytical solutions in the limit o…

[Phys. Rev. E 94, 023005] Published Tue Aug 16, 2016

]]>This paper studies the equation of state of an ablator material used for inertial confinement fusion. The authors simulate the material in the warm dense matter regime using quantum molecular dynamics and show that atomic bond dissociation affects the compressibility. Their findings are confirmed by performing shock wave experiments in the LULI2000 laser facility.

[Phys. Rev. E 94, 023204] Published Tue Aug 16, 2016

]]>An accurate understanding of burn dynamics in implosions of cryogenically layered deuterium (D) and tritium (T) filled capsules, obtained partly through precision diagnosis of these experiments, is essential for assessing the impediments to achieving ignition at the National Ignition Facility. We pr…

[Phys. Rev. E 94, 021202(R)] Published Mon Aug 15, 2016

]]>Particle simulations confined by sharp walls usually develop an oscillatory density profile. For some applications, most notably soft matter liquids, this behavior is often unrealistic and one expects a monotonic density climb instead. To reconcile simulations with experiments, we propose mirror-and…

[Phys. Rev. E 94, 021302(R)] Published Mon Aug 15, 2016

]]>A recent proposal of an effective temperature $\theta $, conjugated to a generalized entropy ${s}_{q}$, typical of nonextensive statistical mechanics, has led to a consistent thermodynamic framework in the case $q=2$. The proposal was explored for repulsively interacting vortices, currently used for modeling type-II…

[Phys. Rev. E 94, 022120] Published Mon Aug 15, 2016

]]>The purpose of this paper is to provide a formula for the effective diffusion operator obtained by projecting the three-dimensional diffusion equation onto a two-dimensional plane, assuming reflective boundary conditions at two surfaces in three-dimensional space and a finite transversal stabilizati…

[Phys. Rev. E 94, 022121] Published Mon Aug 15, 2016

]]>Disordered many-particle hyperuniform systems are exotic amorphous states of matter that lie between crystal and liquid: They are like perfect crystals in the way they suppress large-scale density fluctuations and yet are like liquids or glasses in that they are statistically isotropic with no Bragg…

[Phys. Rev. E 94, 022122] Published Mon Aug 15, 2016

]]>We investigate disease spreading on eight empirical data sets of human contacts (mostly proximity networks recording who is close to whom, at what time). We compare three levels of representations of these data sets: temporal networks, static networks, and a fully connected topology. We notice that …

[Phys. Rev. E 94, 022305] Published Mon Aug 15, 2016

]]>The position of the coherent and incoherent domain of a chimera state in a ring of nonlocally coupled oscillators is strongly influenced by the initial conditions, making nontrivial the problem of confining them in a specific region of the structure. In this paper we propose the use of spatial pinni…

[Phys. Rev. E 94, 022306] Published Mon Aug 15, 2016

]]>We investigate protein evolution using an off-lattice polymer model evolved to imitate the behavior of small enzymes. Model proteins evolve through mutations to nucleotide sequences (including insertions and deletions) and are selected to fold and maintain a specific binding site compatible with a m…

[Phys. Rev. E 94, 022410] Published Mon Aug 15, 2016

]]>As local signals, calcium puffs arise from the concerted opening of a few nearby inositol 1,4,5-trisphospate receptor channels to release $\mathrm{C}{\mathrm{a}}^{2+}$ ions from the endoplasmic reticulum. Although $\mathrm{C}{\mathrm{a}}^{2+}$ puffs have been well studied, little is known about the modulation of cytosolic basal $\mathrm{C}{\mathrm{a}}^{2+}$ concentration (${\dots}_{}$

[Phys. Rev. E 94, 022411] Published Mon Aug 15, 2016

]]>A recent physiologically based model of the ascending arousal system is used to analyze the dynamics near the transition from wake to sleep, which corresponds to a saddle-node bifurcation at a critical point. A normal form is derived by approximating the dynamics by those of a particle in a paraboli…

[Phys. Rev. E 94, 022412] Published Mon Aug 15, 2016

]]>Dynamic light scattering (DLS) is widely used to characterize diffusive motion to obtain precise information on colloidal suspensions by calculating the autocorrelation function of the signal from a heterodyne optical system. DLS can also be used to determine the flow velocity field in systems that …

[Phys. Rev. E 94, 022604] Published Mon Aug 15, 2016

]]>We simulate the influence of a reversible isomerization reaction on the phase segregation process occurring after spinodal decomposition of a deeply quenched regular binary mixture, restricting attention to systems wherein material transport occurs solely by diffusion. Our theoretical approach follo…

[Phys. Rev. E 94, 022605] Published Mon Aug 15, 2016

]]>We demonstrate that irreversible structural reorganization is not necessary for the observation of yield behavior in an amorphous solid. While the majority of solids strained to their yield point do indeed undergo an irreversible reorganization, we find that a significant fraction of solids exhibits…

[Phys. Rev. E 94, 022606] Published Mon Aug 15, 2016

]]>The concept of symmetry breaking has been a propelling force in understanding phases of matter. While rotational-symmetry breaking is one of the most prevalent examples, the rich landscape of orientational orders breaking the rotational symmetries of isotropic space, i.e., O(3), to a three-dimension…

[Phys. Rev. E 94, 022701] Published Mon Aug 15, 2016

]]>We deploy linear stability analysis to find the threshold wavelength ($\lambda $) and surface tension ($\gamma $) of Rayleigh-Plateau type “peristaltic” instabilities in incompressible neo-Hookean solids in a range of cylindrical geometries with radius ${R}_{0}$. First we consider a solid cylinder, and recover the well-kno…

[Phys. Rev. E 94, 023107] Published Mon Aug 15, 2016

]]>The behavior of a droplet impinging onto a solid substrate can be influenced significantly by the horizontal motion of the substrate. The coupled interactions between the moving wall and the impacting droplet may result in various outcomes, which may be different from the usual normal droplet impact…

[Phys. Rev. E 94, 023108] Published Mon Aug 15, 2016

]]>In this paper we propose a color-gradient lattice Boltzmann (LB) model for simulating two-phase flows with high density ratio and high Reynolds number. The model applies a multirelaxation-time (MRT) collision operator to enhance the stability of the simulation. A source term, which is derived by the…

[Phys. Rev. E 94, 023310] Published Mon Aug 15, 2016

]]>We develop a consistent stochastic thermodynamics for environments composed of thermodynamic reservoirs in an external conservative force field, that is, environments described by the generalized or Gibbs canonical ensemble. We demonstrate that small systems weakly coupled to such reservoirs exchang…

[Phys. Rev. E 94, 020102(R)] Published Fri Aug 12, 2016

]]>This study focuses on fluctuating classical systems in contact with a thermal bath, and whose configurational energetics undergoes cyclic transformations due to interaction with external perturbing agents. Under the assumptions that the configurational dynamics is a stochastic Markov process in the …

[Phys. Rev. E 94, 022117] Published Fri Aug 12, 2016

]]>Permutation entropy (PE) is commonly used to discriminate complex structure from white noise in a time series. While the PE of white noise is well understood in the long time-series limit, analysis in the general case is currently lacking. Here the expectation value and variance of white-noise PE ar…

[Phys. Rev. E 94, 022118] Published Fri Aug 12, 2016

]]>The long-time collective behavior of globally coupled Langevin equations in a dichotomous fluctuating potential driven by a periodic source is investigated. By describing the collective behavior using the moments of the mean field and single-particle displacements, we study stochastic resonance and …

[Phys. Rev. E 94, 022119] Published Fri Aug 12, 2016

]]>In this paper we show the interaction of a composite of a periodic or aperiodic signal and intrinsic electrochemical noise with the nonlinear dynamics of an electrochemical cell configured to study the corrosion of iron in an acidic media. The anodic voltage setpoint $\left({V}_{0}\right)$ in the cell is chosen such …

[Phys. Rev. E 94, 022210] Published Fri Aug 12, 2016

]]>We report results of an analysis of the spontaneous symmetry breaking (SSB) in a basic (actually, simplest) model that is capable of producing the SSB phenomenology in a one-dimensional setting. It is based on the Gross-Pitaevskii–nonlinear Schrödinger equation with the cubic self-attractive term an…

[Phys. Rev. E 94, 022211] Published Fri Aug 12, 2016

]]>The flux of visitors through popular places undoubtedly influences viral spreading—from H1N1 and Zika viruses spreading through physical spaces such as airports, to rumors and ideas spreading through online spaces such as chat rooms and social media. However, there is a lack of understanding of the …

[Phys. Rev. E 94, 022304] Published Fri Aug 12, 2016

]]>We study experimentally the dynamics of granular media in a discharging hopper. In such flows, there often appears to be a critical outlet size ${D}_{c}$ such that the flow never clogs for $D>{D}_{c}$. We report on the time-averaged velocity distributions, as well as temporal intermittency in the ensemble-aver…

[Phys. Rev. E 94, 022901] Published Fri Aug 12, 2016

]]>We study Brownian motion of a single millimeter size bead confined in a quasi-two-dimensional horizontal channel with built-in anisotropy and asymmetry. Channel asymmetry is implemented by ratchet walls while anisotropy is introduced using a channel base that is grooved along the channel axis so tha…

[Phys. Rev. E 94, 022902] Published Fri Aug 12, 2016

]]>The influence of periodic shear deformation on nonaffine atomic displacements in an amorphous solid is examined via molecular dynamics simulations. We study the three-dimensional Kob-Andersen binary mixture model at a finite temperature. It is found that when the material is periodically strained, m…

[Phys. Rev. E 94, 023004] Published Fri Aug 12, 2016

]]>The effects of compressibility on Rayleigh-Taylor instability (RTI) are investigated by inspecting the interplay between thermodynamic and hydrodynamic nonequilibrium phenomena (TNE, HNE, respectively) via a discrete Boltzmann model. Two effective approaches are presented, one tracking the evolution…

[Phys. Rev. E 94, 023106] Published Fri Aug 12, 2016

]]>We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustnes…

[Phys. Rev. E 94, 023309] Published Fri Aug 12, 2016

]]>We comment on the main result given by Ourabah *et al.* [Phys. Rev. E **92**, 032114 (2015)], noting that it can be derived as a special case of the more general study that we have provided in [Quantum Inf Process **15**, 3393 (2016)]. Our proof of the nondecreasing character under projective measurements of …

[Phys. Rev. E 94, 026103] Published Fri Aug 12, 2016

]]>We rely on our proof of the nondecreasing character of quantum Kaniadakis entropy under projective measurement [Phys. Rev. E **92**, 032114 (2015)], and we put it into perspective with the results of Bosyk *et al.* [Quantum Inf Process **15**, 3393 (2016)]. Our method, adopted for the proof that Kaniadakis en…

[Phys. Rev. E 94, 026104] Published Fri Aug 12, 2016

]]>The existence of a zealot who stays a cooperator irrespective of the result of an interaction has been reported to add “social viscosity” to a population and thereby helps increase the cooperation level in prisoner's dilemma games, which premises the so-called well-mixed situation of a population. W…

[Phys. Rev. E 94, 022114] Published Thu Aug 11, 2016

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