A statistical model for the fragmentation of a conserved quantity is analyzed, using the principle of maximum entropy and the theory of partitions. Upper and lower bounds for the restricted partitioning problem are derived and applied to the distribution of fragments. The resulting power law directl…

[Phys. Rev. E 91, 062138] Published Mon Jun 29, 2015

]]>We present the exact closed-form expression for the partition function of a dimer model on a generalized finite checkerboard rectangular lattice under periodic boundary conditions. We investigate three different sets of dimer weights, each with different critical behaviors. We then consider differen…

[Phys. Rev. E 91, 062139] Published Mon Jun 29, 2015

]]>We present a comprehensive study of the two-dimensional one-component plasma in the cell model with charged boundaries. Starting from weak couplings through a convenient approximation of the interacting potential we were able to obtain an analytic formulation to the problem deriving the partition fu…

[Phys. Rev. E 91, 062140] Published Mon Jun 29, 2015

]]>We have studied the dynamic phase transition (DPT) of the kinetic Ising model in systems with surfaces within the mean-field approximation. Varying the surface exchange coupling strength ${J}_{s}$, the amplitude of the externally applied oscillating field ${h}_{0}$, and its period $P$, we explore the dynamic behavi…

[Phys. Rev. E 91, 062141] Published Mon Jun 29, 2015

]]>It is common knowledge that the microcanonical, canonical, and grand-canonical ensembles are equivalent in thermodynamically large systems. Here, we study finite-size effects in the latter two ensembles. We show that contrary to naive expectations, finite-size errors are exponentially small in grand…

[Phys. Rev. E 91, 062142] Published Mon Jun 29, 2015

]]>In studying fundamental physical limits and properties of computational processes, one is faced with the challenges of interpreting primitive information-processing functions through well-defined information-theoretic as well as thermodynamic quantities. In particular, transfer entropy, characterizi…

[Phys. Rev. E 91, 062143] Published Mon Jun 29, 2015

]]>Two-dimensional (2D) nuclear magnetic resonance (NMR) experiments involve a sequence of longitudinal (${T}_{1}$) and transverse (${T}_{2}$) measurements. In a previous paper we showed that if each of these 1D measurements can be represented by two exponential decays then there can be an accurate analytic solution…

[Phys. Rev. E 91, 062406] Published Mon Jun 29, 2015

]]>The curvature elasticity of a polyelectrolyte brush monolayer attached to curved surface is investigated theoretically. An analytical method based on the strong-stretching theory for a Gaussian chain is developed to calculate the elastic modulus induced by a polyelectrolyte brush. In particular, the…

[Phys. Rev. E 91, 062602] Published Mon Jun 29, 2015

]]>The mean-squared displacement (MSD) and velocity autocorrelation (VAC) of tracked single particles or molecules are ubiquitous metrics for extracting parameters that describe the object's motion, but they are both corrupted by experimental errors that hinder the quantitative extraction of underlying…

[Phys. Rev. E 91, 062716] Published Mon Jun 29, 2015

]]>The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with unfolded coil and folded globule conformations. Microscopic observa…

[Phys. Rev. E 91, 062717] Published Mon Jun 29, 2015

]]>In spite of the extensive previous efforts on traffic dynamics and epidemic spreading in complex networks, the problem of traffic-driven epidemic spreading on *correlated* networks has not been addressed. Interestingly, we find that the epidemic threshold, a fundamental quantity underlying the spreadi…

[Phys. Rev. E 91, 062817] Published Mon Jun 29, 2015

]]>In a forked road, the provision of inappropriate information to car drivers sometimes leads to undesirable situations such as one-sided congestion, which is called the hunting phenomenon in real traffic. To address such problems, we propose a forked exclusion model and investigate the behavior of tr…

[Phys. Rev. E 91, 062818] Published Mon Jun 29, 2015

]]>We study a hyperbolic version of the FitzHugh-Nagumo (also known as the Bonhoeffer-van der Pol) reaction-diffusion system. To be able to obtain analytical results, we employ a piecewise linear approximation of the nonlinear kinetic term. The hyperbolic version is compared with the standard parabolic…

[Phys. Rev. E 91, 062917] Published Mon Jun 29, 2015

]]>We investigate the scaling behavior of the maximal Lyapunov exponent in chaotic systems with time delay. In the large-delay limit, it is known that one can distinguish between strong and weak chaos depending on the delay scaling, analogously to strong and weak instabilities for steady states and per…

[Phys. Rev. E 91, 062918] Published Mon Jun 29, 2015

]]>We show that the addition of pairwise repulsive inhibition to excitatory networks of bursting neurons induces synchrony, in contrast to one's expectations. Through stability analysis, we reveal the mechanism underlying this purely synergistic phenomenon and demonstrate that it originates from the tr…

[Phys. Rev. E 91, 062919] Published Mon Jun 29, 2015

]]>We present results for the equilibrium statistics and dynamic evolution of moderately large $[n=O({10}^{2}-{10}^{3})]$ numbers of interacting point vortices on the sphere under the constraint of zero mean angular momentum. For systems with equal numbers of positive and negative identical circulations, the densi…

[Phys. Rev. E 91, 063014] Published Mon Jun 29, 2015

]]>Flow structure of a dust medium electrostatically suspended and confined in a plasma presents a unique setup where the spatial scale of a volumetric drive by the plasma flow might exceed that of the boundaries confining the dust. By means of a formal implementation of a two-dimensional hydrodynamic …

[Phys. Rev. E 91, 063110] Published Mon Jun 29, 2015

]]>In this work, minimal kinetic theories based on unconventional entropy functions, $H\sim \text{ln}f$ (Burg entropy) for 2D and $H\sim {f}^{1-\frac{2}{n}}$ (Tsallis entropy) for $n\text{D}$ with $n\ge 3$, are studied. These entropy functions were originally derived by Boghosian *et al.* [Phys. Rev. E **68**, 025103 (2003)] as a basis for discrete-veloc…

[Phys. Rev. E 91, 063311] Published Mon Jun 29, 2015

]]>[Phys. Rev. E 91, 069903] Published Mon Jun 29, 2015

]]>We study the distribution of the mean radial displacement of charges of a two-dimensional (2D) one-component plasma in the thermodynamic limit $N\to \infty $ at finite temperature $\beta >0$. We compute explicitly the large deviation functions showing the emergence of a fourth-order phase transition as a consequen…

[Phys. Rev. E 91, 060105(R)] Published Fri Jun 26, 2015

]]>When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this “melting” transition have been intensively investigated. Recently there has been a surge of interest in this questi…

[Phys. Rev. E 91, 060702(R)] Published Fri Jun 26, 2015

]]>In many complex systems, states and interaction structure coevolve towards a dynamic equilibrium. For the adaptive contact process, we obtain approximate expressions for the degree distributions that characterize the interaction network in such active steady states. These distributions are shown to …

[Phys. Rev. E 91, 060801(R)] Published Fri Jun 26, 2015

]]>A granular gas in gravity heated from below develops a certain stationary density profile. When the heating is switched off, the granular gas collapses. We investigate the process of sedimentation using computational hydrodynamics, based on the Jenkins-Richman theory, and find that the process is si…

[Phys. Rev. E 91, 062214] Published Fri Jun 26, 2015

]]>In recent years there has been a growing interest in the study of shape formation using modern responsive materials that can be preprogrammed to undergo spatially inhomogeneous local deformations. In particular, nematic liquid crystalline solids offer exciting possibilities in this context. Consider…

[Phys. Rev. E 91, 062405] Published Fri Jun 26, 2015

]]>When common factors strongly influence two power-law cross-correlated time series recorded in complex natural or social systems, using detrended cross-correlation analysis (DCCA) without considering these common factors will bias the results. We use detrended partial cross-correlation analysis (DPXA…

[Phys. Rev. E 91, 062816] Published Fri Jun 26, 2015

]]>The dynamics of two-dimensional bubbles ascending under the influence of buoyant forces is numerically studied with a one-fluid model coupled with the front-tracking technique. The bubble dynamics are described by recording the position, shape, and orientation of the bubbles as functions of time. Th…

[Phys. Rev. E 91, 063013] Published Fri Jun 26, 2015

]]>We ask what happens when two nonequilibrium systems in steady state are kept in contact and allowed to exchange a quantity, say mass, which is conserved in the combined system. Will the systems eventually evolve to a new stationary state where a certain intensive thermodynamic variable, like equilib…

[Phys. Rev. E 91, 062136] Published Thu Jun 25, 2015

]]>The performance of a quantum Otto refrigerator coupled to a squeezed cold reservoir has been evaluated using the $\chi $ figure of merit. We have shown that squeezing can enhance the coefficient of performance (COP) dramatically, surpassing the Carnot COP defined by the initial temperatures of the heat ba…

[Phys. Rev. E 91, 062137] Published Thu Jun 25, 2015

]]>We consider the transition of a horizontally vibrated monodisperse granular monolayer between its condensed state and its three-dimensional gaseous state as a function of the vibration parameters, amplitude, and frequency as well as particle number density. The transition is characterized by an abru…

[Phys. Rev. E 91, 062213] Published Thu Jun 25, 2015

]]>The low-energy physics of (quasi)degenerate one-dimensional systems is typically understood as the particle-like dynamics of kinks between stable, ordered structures. Such dynamics, we show, becomes highly nontrivial when the ground states are topologically constrained: a dynamics *of the domains* rat…

[Phys. Rev. E 91, 062601] Published Thu Jun 25, 2015

]]>The motion of self-propelled particles is modeled as a persistent random walk. An analytical framework is developed that allows the derivation of exact expressions for the time evolution of arbitrary moments of the persistent walk's displacement. It is shown that the interplay of step length and tur…

[Phys. Rev. E 91, 062715] Published Thu Jun 25, 2015

]]>The evolution in time of the score in professional sports games can be described by a random walk. Based on this picture, the authors present a model showing that, surprisingly, the time of the last lead change and the time of the largest lead size are both governed by the arcsine law, a distribution that diverges at the start and at the end of the game.

[Phys. Rev. E 91, 062815] Published Thu Jun 25, 2015

]]>We show that coexisting domains of coherent and incoherent oscillations can be induced in an ensemble of any identical nonlinear dynamical systems using nonlocal rotational matrix coupling with an asymmetry parameter. Further, a chimera is shown to emerge in a wide range of the asymmetry parameter i…

[Phys. Rev. E 91, 062916] Published Thu Jun 25, 2015

]]>The propagation of axisymmetric waves on the surface of a liquid jet under the action of a radial electric field is considered. The jet is assumed to be inviscid and perfectly conducting, and a field is set up by placing the jet concentrically inside a perfectly cylindrical tube whose wall is mainta…

[Phys. Rev. E 91, 063012] Published Thu Jun 25, 2015

]]>A theory of wave modes in shear-deformed two-dimensional plasma crystals is presented. Modification of the dispersion relations upon the pure and simple shear, and the resulting effect on the onset of the mode-coupling instability, are studied. In particular, it is explained why the velocity fluctua…

[Phys. Rev. E 91, 063108] Published Thu Jun 25, 2015

]]>The ion-ion dynamic structure factor of warm dense matter is determined using the recently developed pseudoatom molecular dynamics method [Starrett *et al.*, Phys. Rev. E **91**, 013104 (2015)]. The method uses density functional theory to determine ion-ion pair interaction potentials that have no free pa…

[Phys. Rev. E 91, 063109] Published Thu Jun 25, 2015

]]>A density-functional microscopic model for soft tissues (STmod) is presented. The model was based on a prototype molecular structure from experimentally resolved type I collagen peptide residues and water clusters treated in periodic boundary conditions. We obtained the optimized geometry, binding a…

[Phys. Rev. E 91, 063310] Published Thu Jun 25, 2015

]]>We investigate the effect of preferentially connecting oscillators with similar frequency to each other in networks of coupled phase oscillators (i.e., frequency assortativity). Using the network Kuramoto model as an example, we find that frequency assortativity can induce chaos in the macroscopic d…

[Phys. Rev. E 91, 060902(R)] Published Wed Jun 24, 2015

]]>The Verhulst model is probably the best known macroscopic rate equation in population ecology. It depends on two parameters, the intrinsic growth rate and the carrying capacity. These parameters can be estimated for different populations and are related to the reproductive fitness and the competitio…

[Phys. Rev. E 91, 062133] Published Wed Jun 24, 2015

]]>We propose and theoretically investigate a system of two coupled harmonic oscillators as a heat engine. We show how these two coupled oscillators within undamped regime can be controlled to realize an Otto cycle that consists of two adiabatic and two isochoric processes. During the two isochores the…

[Phys. Rev. E 91, 062134] Published Wed Jun 24, 2015

]]>We illustrate a complex-network approach to study the phase spaces of spin glasses. By mapping the whole ground-state phase spaces of two-dimensional Edwards-Anderson bimodal $(\pm J)$ spin glasses exactly into networks for analysis, we discovered various phase-space properties. The Gaussian connectivity…

[Phys. Rev. E 91, 062135] Published Wed Jun 24, 2015

]]>We report a combined experimental and simulation study of deformation-induced diffusion in compacted quasi-two-dimensional amorphous granular pillars, in which thermal fluctuations play a negligible role. The pillars, consisting of bidisperse cylindrical acetal plastic particles standing upright on …

[Phys. Rev. E 91, 062212] Published Wed Jun 24, 2015

]]>A model of a banking network predicts the balance of high- and low-priority debts that ensures financial stability.

[Phys. Rev. E 91, 062813] Published Wed Jun 24, 2015

]]>Hierarchical network clustering is an approach to find tightly and internally connected clusters (groups or communities) of nodes in a network based on its structure. Instead of nodes, it is possible to cluster links of the network. The sets of nodes belonging to clusters of links can overlap. While…

[Phys. Rev. E 91, 062814] Published Wed Jun 24, 2015

]]>We study analytically the dynamics of modulated waves in a dissipative modified Noguchi nonlinear electrical network. In the continuum limit, we use the reductive perturbation method in the semidiscrete limit to establish that the propagation of modulated waves in the network is governed by a dissip…

[Phys. Rev. E 91, 062915] Published Wed Jun 24, 2015

]]>We recast the atomic processes in a warm, dense plasma using Fermi-Dirac statistics and compare them to the rates of the usual Maxwell-Boltzmann approach of many collisional-radiative models. Population calculations show insignificant differences to calculations assuming nondegenerate free electrons…

[Phys. Rev. E 91, 063106] Published Wed Jun 24, 2015

]]>Concepts underlying the Enskog kinetic theory of hard-spheres are applied to include short-range correlation effects in a model for transport coefficients of strongly coupled plasmas. The approach is based on an extension of the effective potential transport theory [S. D. Baalrud and J. Daligault, P…

[Phys. Rev. E 91, 063107] Published Wed Jun 24, 2015

]]>We consider a power system with $N$ transmission lines whose initial loads (i.e., power flows) ${L}_{1},...,{L}_{N}$ are independent and identically distributed with ${P}_{L}\left(x\right)=\mathbb{P}\left[L\le x\right]$. The *capacity* ${C}_{i}$ defines the maximum flow allowed on line $i$ and is assumed to be given by ${C}_{i}=(1+\alpha ){L}_{i}$, with $\alpha >0$. We study the robustnes…

[Phys. Rev. E 91, 062811] Published Tue Jun 23, 2015

]]>This paper studies the spread of perturbations through networks composed of Boolean functions with special canalyzing properties. Canalyzing functions have the property that at least for one value of one of the inputs the output is fixed, irrespective of the values of the other inputs. In this paper…

[Phys. Rev. E 91, 062812] Published Tue Jun 23, 2015

]]>A detailed study of non-Bragg-gap solitons in one-dimensional Kerr-metamaterial quasiperiodic Fibonacci heterostructures is performed. The transmission coefficient is numerically obtained by combining the transfer-matrix formalism in the metamaterial layers with a numerical solution of the nonlinear…

[Phys. Rev. E 91, 063205] Published Tue Jun 23, 2015

]]>The quantum evolution maps of closed chaotic quantum graphs are unitary and known to have universal spectral correlations matching predictions of random matrix theory. In chaotic graphs with absorption the quantum maps become nonunitary. We show that their spectral statistics exhibit universality at…

[Phys. Rev. E 91, 060901(R)] Published Mon Jun 22, 2015

]]>Heat diffusion processes in various one-dimensional total-momentum-conserving nonlinear lattices with symmetric interaction and asymmetric interaction are systematically studied. It is revealed that the asymmetry of interaction largely enhances the heat diffusion; while according to our existing stu…

[Phys. Rev. E 91, 062130] Published Mon Jun 22, 2015

]]>We study the high-temperature behavior of an intermediate-statistics fermionic gas model whose quantum statistical properties enable us to effectively deduce the details about both the interaction among deformed (quasi)particles and their anyonic behavior. Starting with a deformed fermionic grand pa…

[Phys. Rev. E 91, 062131] Published Mon Jun 22, 2015

]]>We present theoretical expressions for the density, strain rate, and shear pressure profiles in strongly inhomogeneous fluids undergoing steady shear flow with periodic boundary conditions. The expressions that we obtain take the form of truncated functional expansions. In these functional expansion…

[Phys. Rev. E 91, 062132] Published Mon Jun 22, 2015

]]>We experimentally study rearranging regions in slow athermal flow by observing the flow of a concentrated oil-in-water emulsion in a thin chamber with a constricting hopper shape. The gap of the chamber is smaller than the droplet diameters, so that the droplets are compressed into quasi-two-dimensi…

[Phys. Rev. E 91, 062306] Published Mon Jun 22, 2015

]]>We study the evolution of heterogeneous networks of oscillators subject to a state-dependent interconnection rule. We find that heterogeneity in the node dynamics is key in organizing the architecture of the functional emerging networks. We demonstrate that increasing heterogeneity among the nodes i…

[Phys. Rev. E 91, 062913] Published Mon Jun 22, 2015

]]>The aim of this paper is to show how to extract dynamical behavior and ergodic properties from deterministic chaos with the assistance of exact invariant measures. On the one hand, we provide an approach to deal with the inverse problem of finding nonlinear interval maps from a given invariant measu…

[Phys. Rev. E 91, 062914] Published Mon Jun 22, 2015

]]>Construction, in the framework of a nonequilibrium statistical ensemble formalism, of a higher-order generalized hydrodynamics, also referred to as mesoscopic hydrothermodynamics, that is, covering phenomena involving motion of fluids displaying variations short in space and fast in time—unrestricte…

[Phys. Rev. E 91, 063011] Published Mon Jun 22, 2015

]]>The dust particles contained in a complex plasma can form two-dimensional crystals, and the authors experimentally study cavities formed in these crystals. They show that cavities that are produced by positively and negatively charged probes, and those that are naturally occurring, are due to three different mechanisms.

[Phys. Rev. E 91, 063105] Published Mon Jun 22, 2015

]]>We introduce an enhanced sampling simulation technique based on continuous tempering, i.e., on continuously varying the temperature of the system under investigation. Our approach is mathematically straightforward, being based on an extended Hamiltonian formulation in which an auxiliary degree of fr…

[Phys. Rev. E 91, 061301(R)] Published Fri Jun 19, 2015

]]>We study the dynamics of colonization of a territory by a stochastic population at low immigration pressure. We assume a sufficiently strong Allee effect that introduces, in deterministic theory, a large critical population size for colonization. At low immigration rates, the average precolonization…

[Phys. Rev. E 91, 062126] Published Fri Jun 19, 2015

]]>The Cahn-Hilliard equation with an externally prescribed chaotic shear flow is studied in two and three dimensions. The main goal is to compare and contrast the phase separation in two and three dimensions, using high-resolution numerical simulation as the basis for the study. The model flow is para…

[Phys. Rev. E 91, 062127] Published Fri Jun 19, 2015

]]>We explore the dynamics of the entanglement entropy near equilibrium in highly entangled pure states of two quantum-chaotic spin chains undergoing unitary time evolution. We examine the relaxation to equilibrium from initial states with either less or more entanglement entropy than the equilibrium v…

[Phys. Rev. E 91, 062128] Published Fri Jun 19, 2015

]]>We study occupation time statistics in ergodic continuous-time random walks. Under thermal detailed balance conditions, the average occupation time is given by the Boltzmann-Gibbs canonical law. But close to the nonergodic phase, the finite-time fluctuations around this mean are large and nontrivial…

[Phys. Rev. E 91, 062129] Published Fri Jun 19, 2015

]]>We use Monte Carlo simulations of a Lennard-Jones fluid adsorbed on a short-range planar wall substrate to study the fluctuations in the thickness of the wetting layer, and we get a quantitative and consistent characterization of their mesoscopic Hamiltonian, $\mathcal{H}\left[\xi \right]$. We have observed important finite-…

[Phys. Rev. E 91, 062404] Published Fri Jun 19, 2015

]]>Irreversible thermodynamics of single-molecule experiments subject to external constraining forces of a mechanical nature is presented. Extending Onsager's formalism to the nonlinear case of systems under nonequilibrium external constraints, we are able to calculate the entropy production and the ge…

[Phys. Rev. E 91, 062714] Published Fri Jun 19, 2015

]]>The recent availability of electronic data sets containing large volumes of communication data has made it possible to study human behavior on a larger scale than ever before. From this, it has been discovered that across a diverse range of data sets, the interevent times between consecutive communi…

[Phys. Rev. E 91, 062809] Published Fri Jun 19, 2015

]]>We study the dependence on crowd density of the spatial size, configuration, and velocity of pedestrian social groups. We find that, in the investigated density range, the extension of pedestrian groups in the direction orthogonal to that of motion decreases linearly with the pedestrian density arou…

[Phys. Rev. E 91, 062810] Published Fri Jun 19, 2015

]]>The field-theoretic renormalization group and the operator product expansion are used to investigate the influence of spatial parity violation of the conductive turbulent environment on the anomalous scaling behavior of correlation functions of a weak magnetic field in the framework of the Kazantsev…

[Phys. Rev. E 91, 063009] Published Fri Jun 19, 2015

]]>The lattice-Boltzmann (LB) method is commonly used for the simulation of fluid flows at the hydrodynamic level of description. Due to its kinetic theory origins, the standard LB schemes carry more degrees of freedom than strictly needed, e.g., for the approximation of solutions to the Navier-stokes …

[Phys. Rev. E 91, 063010] Published Fri Jun 19, 2015

]]>We study numerically the coarsening dynamics of the Ising model on a regular lattice with random bonds and on deterministic fractal substrates. We propose a unifying interpretation of the phase-ordering processes based on two classes of dynamical behaviors characterized by different growth laws of t…

[Phys. Rev. E 91, 062122] Published Thu Jun 18, 2015

]]>We present a study that addresses both the stationary properties of the energy current and quantum correlations in a three-mode chain subjected to Ohmic and super-Ohmic dissipations. An extensive numerical analysis shows that the mean value and the fluctuations of the energy current remain insensiti…

[Phys. Rev. E 91, 062123] Published Thu Jun 18, 2015

]]>We study the dynamical properties of a two-dimensional ensemble of self-propelled dumbbells with only repulsive interactions. This model undergoes a phase transition between a homogeneous and a segregated phase and we focus on the former. We analyze the translational and rotational mean-square displ…

[Phys. Rev. E 91, 062124] Published Thu Jun 18, 2015

]]>We analyze the random Euclidean bipartite matching problem on the hypertorus in $d$ dimensions with quadratic cost and we derive the two-point correlation function for the optimal matching, using a proper ansatz introduced by Caracciolo *et al.* [Phys. Rev. E **90**, 012118 (2014)] to evaluate the average …

[Phys. Rev. E 91, 062125] Published Thu Jun 18, 2015

]]>Nanochannels made in solid-state materials are used for various applications such as nanoparticle separation or DNA manipulation. In this work we examine the effects of the electric and dielectrophoretic forces on a charged nanoparticle confined in a nanochannel. To this end, we solve the Poisson eq…

[Phys. Rev. E 91, 062713] Published Thu Jun 18, 2015

]]>Irregular sampling of data sets is one of the challenges often encountered in time-series analysis, since traditional methods cannot be applied and the frequently used interpolation approach can corrupt the data and bias the subsequence analysis. Here we present the TrAnsformation-Cost Time-Series (…

[Phys. Rev. E 91, 062911] Published Thu Jun 18, 2015

]]>Observability is a very useful concept for determining whether the dynamics of complicated systems can be correctly reconstructed from a single (univariate or multivariate) time series. When the governing equations of dynamical systems are high-dimensional and/or rational, analytical computations of…

[Phys. Rev. E 91, 062912] Published Thu Jun 18, 2015

]]>Mechanical avalanches during compression of martensitic porous Ti-Ni have been characterized by high-frequency acoustic emission (AE). Two sequences of AE signals were found in the same sample. The first sequence is mainly generated by detwinning at the early stages of compression while fracture dom…

[Phys. Rev. E 91, 060401(R)] Published Wed Jun 17, 2015

]]>Geometric frustration effects were studied systematically with the Ising antiferromagnet on the 11 Archimedean lattices using the Monte Carlo methods. The Wang-Landau algorithm for static properties (specific heat and residual entropy) and the Metropolis algorithm for a freezing order parameter were…

[Phys. Rev. E 91, 062121] Published Wed Jun 17, 2015

]]>Attenuation of short, strongly nonlinear stress pulses in chains of spheres and cylinders was investigated experimentally and numerically for two ratios of their masses keeping their contacts identical. The chain with mass ratio 0.98 supports solitary waves and another one (with mass ratio 0.55) sup…

[Phys. Rev. E 91, 062211] Published Wed Jun 17, 2015

]]>Hierarchical networks are attracting a renewal interest for modeling the organization of a number of biological systems and for tackling the complexity of statistical mechanical models beyond mean-field limitations. Here we consider the Dyson hierarchical construction for ferromagnets, neural networ…

[Phys. Rev. E 91, 062807] Published Wed Jun 17, 2015

]]>The eigenvalues of the transition matrix for random walks on a network play a significant role in the structural and dynamical aspects of the network. Nevertheless, it is still not well understood how the eigenvalues behave in small-world and scale-free networks, which describe a large variety of re…

[Phys. Rev. E 91, 062808] Published Wed Jun 17, 2015

]]>In a rarefied gas in an infinitely long channel between two parallel plates, an array of infinitely many plates, arranged longitudinally with uniform interval, is placed along the channel. The array is assumed to be freely movable along the channel. If one side of each plate is heated, the radiometr…

[Phys. Rev. E 91, 063007] Published Wed Jun 17, 2015

]]>The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the so-called hydrodynamic interactions (HIs). In this paper, an eff…

[Phys. Rev. E 91, 063008] Published Wed Jun 17, 2015

]]>Based on the phase-field theory, we propose a conservative lattice Boltzmann method to track the interface between two different fluids. The presented model recovers the conservative phase-field equation and conserves mass locally and globally. Two entirely different approaches are used to calculate…

[Phys. Rev. E 91, 063309] Published Wed Jun 17, 2015

]]>We revisit the problem of the overdamped (large-friction) limit of the Brownian dynamics in an inhomogeneous medium characterized by a position-dependent friction coefficient and a multiplicative noise (local temperature) in one-dimensional space. Starting from the Kramers equation and analyzing it …

[Phys. Rev. E 91, 062118] Published Tue Jun 16, 2015

]]>Exact analytical solutions of the master equation are limited to special cases and exact numerical methods are inefficient. Even the generic one-dimensional, one-step master equation has evaded exact solution, aside from the steady-state case. This type of master equation describes the dynamics of a…

[Phys. Rev. E 91, 062119] Published Tue Jun 16, 2015

]]>Recently Mazenko and Das and Mazenko [Phys. Rev. E **81**, 061102 (2010); J. Stat. Phys. **149**, 643 (2012); J. Stat. Phys. **152**, 159 (2013); Phys. Rev. E **83**, 041125 (2011)] introduced a nonequilibrium field-theoretical approach to describe the statistical properties of a classical particle ensemble startin…

[Phys. Rev. E 91, 062120] Published Tue Jun 16, 2015

]]>The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe…

[Phys. Rev. E 91, 062403] Published Tue Jun 16, 2015

]]>We study two intertwined globally coupled networks of noisy Kuramoto phase oscillators that have the same natural frequency but differ in their perception of the mean field and their contribution to it. Such a give-and-take mechanism is given by asymmetric in- and out-coupling strengths which can be…

[Phys. Rev. E 91, 062910] Published Tue Jun 16, 2015

]]>The time-independent lattice Boltzmann algorithm (TILBA) is developed to calculate the hydrodynamic interactions between two particles in a Stokes flow. The TILBA is distinguished from the traditional lattice Boltzmann method in that a background matrix (BGM) is generated prior to the calculation. T…

[Phys. Rev. E 91, 063308] Published Tue Jun 16, 2015

]]>Out-of-equilibrium systems exhibit domain walls between different states. These walls, depending on the type of connected states, can display rich spatiotemporal dynamics. In this Rapid Communication, we investigate the asymmetrical counterpropagation of fronts in an in-plane-switching cell filled w…

[Phys. Rev. E 91, 060501(R)] Published Mon Jun 15, 2015

]]>Motivated by the recent proposed models of the information engine [Proc. Natl. Acad. Sci. USA **109**, 11641 (2012)] and the information refrigerator [Phys. Rev. Lett. **111**, 030602 (2013)], we propose a minimal model of the information pump and the information eraser based on enzyme kinetics. This device…

[Phys. Rev. E 91, 062117] Published Mon Jun 15, 2015

]]>We study the jamming transition in a model of elastic particles under shear at zero temperature. The key quantity is the relaxation time $\tau $ which is obtained by stopping the shearing and letting energy and pressure decay to zero. At many different densities and initial shear rates we do several such …

[Phys. Rev. E 91, 062209] Published Mon Jun 15, 2015

]]>Swelling clay minerals play a key role in the control of water and pollutant migration in natural media such as soils. Moreover, swelling clay particles’ orientational properties in porous media have significant implications for the directional dependence of fluid transfer. Herein we investigate the…

[Phys. Rev. E 91, 062210] Published Mon Jun 15, 2015

]]>In this paper, we investigate how changes in the system entropy influence the characteristic time scale of the system molecular dynamics near the glass transition. Independently of any model of thermodynamic evolution of the time scale, against some previous suppositions, we show that the system ent…

[Phys. Rev. E 91, 062305] Published Mon Jun 15, 2015

]]>The authors construct a spatial-stochastic model of gene regulation and analyze the effect of spatial coupling on the ability of a genetic network to specify positional information. They find conditions in which diffusive coupling can markedly improve information transmission in spatially coupled stochastic gene expression models.

[Phys. Rev. E 91, 062710] Published Mon Jun 15, 2015

]]>Unicellular organisms exhibit elaborate collective behaviors in response to environmental cues. These behaviors are controlled by complex biochemical networks within individual cells and coordinated through cell-to-cell communication. Describing these behaviors requires new mathematical models that …

[Phys. Rev. E 91, 062711] Published Mon Jun 15, 2015

]]>X-ray free-electron lasers (XFELs) may allow us to employ the single-particle imaging (SPI) method to determine the structure of macromolecules that do not form stable crystals. Ultrashort pulses of 10 fs and less allow us to outrun complete disintegration by Coulomb explosion and minimize radiation…

[Phys. Rev. E 91, 062712] Published Mon Jun 15, 2015

]]>We propose a generalized stochastic block model to explore the mesoscopic structures in signed networks by grouping vertices that exhibit similar positive and negative connection profiles into the same cluster. In this model, the group memberships are viewed as hidden or unobserved quantities, and t…

[Phys. Rev. E 91, 062805] Published Mon Jun 15, 2015

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