We derive from first principles a one-way radiative transfer equation for the wave intensity resolved over directions (Wigner transform of the wave field) in random media. It is an initial value problem with excitation from a source which emits waves in a preferred, forward direction. The equation i…

[Phys. Rev. E 93, 022115] Published Tue Feb 09, 2016

]]>In this paper we establish a connection between particle trajectories subject to a nonholonomic constraint and light ray trajectories in a variable index of refraction. In particular, we extend the analysis of systems with linear nonholonomic constraints to the dynamics of particles in a potential s…

[Phys. Rev. E 93, 023005] Published Tue Feb 09, 2016

]]>We investigate nonequilibrium fluctuations of a solid surface governed by the stochastic Mullins-Herring equation with conserved noise. This equation describes surface diffusion of adatoms accompanied by their exchange between the surface and the bulk of the solid, when desorption of adatoms is negl…

[Phys. Rev. E 93, 020102(R)] Published Mon Feb 08, 2016

]]>Granular self-assembly of confined non-Brownian spheres under gravity is studied by molecular dynamics simulations. Starting from a disordered phase, dry or cohesive spheres organize, by vibrational annealing, into body-centered-tetragonal or face-centered-cubic structures, respectively. During the …

[Phys. Rev. E 93, 020902(R)] Published Mon Feb 08, 2016

]]>Mechanical instability takes different forms in various ordered and disordered systems and little is known about how thermal fluctuations affect different classes of mechanical instabilities. We develop an analytic theory involving renormalization of rigidity and coherent potential approximation tha…

[Phys. Rev. E 93, 022110] Published Mon Feb 08, 2016

]]>We revisit the universal behavior of crystalline membranes at and below the crumpling transition, which pertains to the mechanical properties of important soft and hard matter materials, such as the cytoskeleton of red blood cells or graphene. Specifically, we perform large-scale Monte Carlo simulat…

[Phys. Rev. E 93, 022111] Published Mon Feb 08, 2016

]]>Bento *et al.* [Phys. Rev. E **91**, 022105 (2015)] recently stated that the Tsallis entropy violates the third law of thermodynamics for $0<q<1$ in the subadditive regime. We first show that the division between the regimes $q<1$ and $q>1$ is already inherent in the fundamental incomplete structure…

[Phys. Rev. E 93, 022112] Published Mon Feb 08, 2016

]]>Critical dynamics in two-dimension Ising lattices up to $2048\times 2048$ is simulated on field-programmable-gate-array- based computing devices. Linear relaxation times are measured from extremely long Monte Carlo simulations. The longest simulation has $7.1\times {10}^{16}$ spin updates, which would take over 37 years…

[Phys. Rev. E 93, 022113] Published Mon Feb 08, 2016

]]>From the Horowitz-Esposito stochastic thermodynamical description of information flows in dynamical systems [J. M. Horowitz and M. Esposito, Phys. Rev. X **4**, 031015 (2014)], it is known that while the second law of thermodynamics is satisfied by a joint system, the entropic balance for the subsystems…

[Phys. Rev. E 93, 022114] Published Mon Feb 08, 2016

]]>Chaos synchronization may arise in networks of nonlinear units with delayed couplings. We study complete and sublattice synchronization generated by resonance of two large time delays with a specific ratio. As it is known for single-delay networks, the number of synchronized sublattices is determine…

[Phys. Rev. E 93, 022206] Published Mon Feb 08, 2016

]]>We introduce new quantities for exploratory causal inference between bivariate time series. The quantities, called penchants and leanings, are computationally straightforward to apply, follow directly from assumptions of probabilistic causality, do not depend on any assumed models for the time serie…

[Phys. Rev. E 93, 022207] Published Mon Feb 08, 2016

]]>In many adult tissues, stem cells and differentiated cells are not homogeneously distributed: stem cells are arranged in periodic “niches,” and differentiated cells are constantly produced and migrate out of these niches. In this article, we provide a general theoretical framework to study mixtures …

[Phys. Rev. E 93, 022405] Published Mon Feb 08, 2016

]]>We discuss the plastic behavior of an amorphous matrix reinforced by hard particles. A mesoscopic depinning-like model accounting for Eshelby elastic interactions is implemented. Only the effect of a plastic disorder is considered. Numerical results show a complex size dependence of the effective fl…

[Phys. Rev. E 93, 023004] Published Mon Feb 08, 2016

]]>We consider viscous fluids in spherical geometry, a lighter fluid supporting a heavier one. Chandrasekhar [Q. J. Mech. Appl. Math. **8**, 1 (1955)] analyzed this unstable configuration providing the equations needed to find, numerically, the exact growth rates for the ensuing Rayleigh-Taylor instability…

[Phys. Rev. E 93, 023104] Published Mon Feb 08, 2016

]]>Equal size air bubbles that are entrapped by a Taylor vortex of the secondary flow in a Couette device, thereby defying buoyancy, slowly form a stable ordered ring with equal separation distances between all neighbors. We present two models of the process dynamics based on force balance on a bubble …

[Phys. Rev. E 93, 023105] Published Mon Feb 08, 2016

]]>We analyze the migration characteristics of a droplet in an oscillatory flow field in a parallel plate microconfinement. Using phase field formalism, we capture the dynamical evolution of the droplet over a wide range of the frequency of the imposed oscillation in the flow field, drop size relative …

[Phys. Rev. E 93, 023106] Published Mon Feb 08, 2016

]]>The Fisher information matrix (FIM) is a widely used measure for applications including statistical inference, information geometry, experiment design, and the study of criticality in biological systems. The FIM is defined for a parametric family of probability distributions and its estimation from …

[Phys. Rev. E 93, 023301] Published Mon Feb 08, 2016

]]>The growth of snow crystals is dependent on the temperature and saturation of the environment. In the case of dendrites, Reiter's local two-dimensional model provides a realistic approach to the study of dendrite growth. In this paper we obtain a new geometric rule that incorporates interface contro…

[Phys. Rev. E 93, 023302] Published Mon Feb 08, 2016

]]>We experimentally demonstrate self-excited oscillation and shedding of millimeter-sized water drops, acoustically levitated in a single-node standing waves cavity, by decreasing the steady acoustic wave intensity below a threshold. The perturbation of the acoustic field by drop motion is a possible …

[Phys. Rev. E 93, 021101(R)] Published Fri Feb 05, 2016

]]>The formation of a stable protein aggregate is regarded as the rate limiting step in the establishment of prion diseases. In these systems, once aggregates reach a critical size the growth process accelerates and thus the waiting time until the appearance of the first critically sized aggregate is a…

[Phys. Rev. E 93, 022109] Published Fri Feb 05, 2016

]]>Equilibrium solutions are believed to structure the pathways for ergodic trajectories in a dynamical system. However, equilibria are atypical for systems with continuous symmetries, i.e., for systems with homogeneous spatial dimensions, whereas *relative* equilibria (traveling waves) are generic. In o…

[Phys. Rev. E 93, 022204] Published Fri Feb 05, 2016

]]>We study the influence of dual-cavity optical feedback on the emission dynamics and timing stability of a passively mode-locked semiconductor laser using a delay differential equation model and verify the timing stability results by an initial experiment. By bifurcation analysis in dependence of the…

[Phys. Rev. E 93, 022205] Published Fri Feb 05, 2016

]]>Using a generalized random recurrent neural network model, and by extending our recently developed mean-field approach [J. Aljadeff, M. Stern, and T. Sharpee, Phys. Rev. Lett. **114**, 088101 (2015)], we study the relationship between the network connectivity structure and its low-dimensional dynamics. …

[Phys. Rev. E 93, 022302] Published Fri Feb 05, 2016

]]>Notable recent works have focused on the multilayer properties of coevolving diseases. We point out that very similar systems play an important role in population ecology. Specifically we study a meta-food-web model that was recently proposed by Pillai *et al.* [Theor. Ecol. **3**, 223 (2009)]. This model…

[Phys. Rev. E 93, 022303] Published Fri Feb 05, 2016

]]>The interaction of oppositely and asymmetrically charged rods in salt—a simple model of (bio)macromolecular assembly—is observed via simulation to exhibit two free energy minima, separated by a repulsive barrier. In contrast to similar minima in the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, th…

[Phys. Rev. E 93, 022602] Published Fri Feb 05, 2016

]]>Recently, frequency-resolved iron opacity measurements at electron temperatures of 170–200 eV and electron densities of $(0.7\u20134.0)\times {10}^{22}\phantom{\rule{4pt}{0ex}}{\mathrm{cm}}^{-3}$ revealed a $30\u2013400\phantom{\rule{0.16em}{0ex}}\%$ disagreement with the calculated opacities [J. E. Bailey *et al.*, Nature (London) **517**, 56 (2015)]. The discrepancies have a high impact on astr…

[Phys. Rev. E 93, 023202] Published Fri Feb 05, 2016

]]>The behaviors of large, dynamic assemblies of macroscopic particles are of direct relevance to geophysical and industrial processes and may also be used as easily studied analogs to micro- or nano-scale systems, or model systems for microbiological, zoological, and even anthropological phenomena. We…

[Phys. Rev. E 93, 020901(R)] Published Thu Feb 04, 2016

]]>Systems with long-range interactions display a short-time relaxation towards quasistationary states (QSSs) whose lifetime increases with the system size. In the paradigmatic Hamiltonian mean-field model (HMF) out-of-equilibrium phase transitions are predicted and numerically detected which separate …

[Phys. Rev. E 93, 022107] Published Thu Feb 04, 2016

]]>We examine the conditions of validity for the Lifshitz-Matsubara sum formula for the Casimir pressure between magnetic metallic plane mirrors. As in the previously studied case of nonmagnetic materials [Guérout *et al.*, Phys. Rev. E **90**, 042125 (2014)], we recover the usual expression for the lossy m…

[Phys. Rev. E 93, 022108] Published Thu Feb 04, 2016

]]>Dissipative patterns in excitable reaction-diffusion systems can be strongly affected by spatial heterogeneities. Using the photosensitive Belousov-Zhabotinsky reaction, we show a hysteresis effect in the transition between free and pinned spiral rotation. The latter state involves the rotation arou…

[Phys. Rev. E 93, 022203] Published Thu Feb 04, 2016

]]>A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precisio…

[Phys. Rev. E 93, 022404] Published Thu Feb 04, 2016

]]>The interfacial free energy is a central quantity in crystallization from the metastable melt. In suspensions of charged colloidal spheres, nucleation and growth kinetics can be accurately measured from optical experiments. In previous work, from these data effective nonequilibrium values for the in…

[Phys. Rev. E 93, 022601] Published Wed Feb 03, 2016

]]>A liquid-immersed granular medium is shaken vertically under a wide range of accelerations ($\mathrm{\Gamma}$ in dimensionless form) and frequencies $\left(f\right)$ and its fluidization process is studied. The granular medium is formed by settling and consists of two size-graded layers (particle diameter $d$) such that the upper…

[Phys. Rev. E 93, 022901] Published Wed Feb 03, 2016

]]>Four rigid panels connected by hinges that meet at a point form a four-vertex, the fundamental building block of origami metamaterials. Most materials designed so far are based on the same four-vertex geometry, and little is known regarding how different geometries affect folding behavior. Here we s…

[Phys. Rev. E 93, 023003] Published Wed Feb 03, 2016

]]>An improved system of Boltzmann model equations is developed for binary gas mixture. This system of model equations has a complete asymptotic preserving property that can strictly recover the Navier-Stokes equations in the continuum limit with the correct constitutive relations and the correct visco…

[Phys. Rev. E 93, 023102] Published Wed Feb 03, 2016

]]>A fingering instability can develop at the interface between two fluids when the more mobile fluid is injected into the less-mobile one. For example, viscous fingering appears when a less viscous (i.e., more mobile) fluid displaces a more viscous (and hence less mobile) one in a porous medium. Finge…

[Phys. Rev. E 93, 023103] Published Wed Feb 03, 2016

]]>The authors study the equilibration dynamics of ultracold plasmas, where a rapid increase in temperature after plasma creation is followed by temperature oscillations. They verify that this behavior exhibits universal scaling, so that plasmas with a range of densities and temperatures show identical dynamics in scaled units.

[Phys. Rev. E 93, 023201] Published Wed Feb 03, 2016

]]>The pretransitional behavior of dodecylcyanobiphenyl (12CB) (isotropic–smectic-$A$–solid mesomorphism) with $d=50\phantom{\rule{0.16em}{0ex}}\mathrm{nm}\mathrm{BaTi}{\mathrm{O}}_{3}$ nanoparticles (NPs) linked to the cubic phase was monitored via temperature studies of dielectric constant. Tests were carried out in the isotropic, liquid crystal mesomorphic, and …

[Phys. Rev. E 93, 020701(R)] Published Tue Feb 02, 2016

]]>The ding-a-ling model is a kind of half lattice and half hard-point-gas (HPG) model. The original ding-a-ling model proposed by Casati *et al.* does not conserve total momentum and has been found to exhibit normal heat conduction behavior. Recently, a modified ding-a-ling model which conserves total m…

[Phys. Rev. E 93, 022102] Published Tue Feb 02, 2016

]]>Among Markovian processes, the hallmark of Lévy flights is superdiffusion, or faster-than-Brownian dynamics. Here we show that Lévy laws, as well as Gaussian distributions, can also be the limit distributions of processes with long-range memory that exhibit very slow diffusion, logarithmic in time. …

[Phys. Rev. E 93, 022103] Published Tue Feb 02, 2016

]]>Incoherent neutron scattering by water confined in carbon nanohorns was measured with the backscattering spectrometer SPHERES and analyzed in exemplary breadth and depth. Quasielastic spectra admit $\delta $-plus-Kohlrausch fits over a wide $q$ and $T$ range. From the $q$ and $T$ dependence of fitted amplitudes and…

[Phys. Rev. E 93, 022104] Published Tue Feb 02, 2016

]]>In this paper, we present an estimation of the conductivity of composites constituted of identical spheres embedded in a host material. A family of polarization integral equations for the localization problem is constructed and the operator is then minimized to yield an optimal integral equation. As…

[Phys. Rev. E 93, 022105] Published Tue Feb 02, 2016

]]>It is known that introducing a stochastic resetting in a random-walk process can lead to the emergence of a stationary state. Here we study this point from a general perspective through the derivation and analysis of mesoscopic (continuous-time random walk) equations for both jump and velocity model…

[Phys. Rev. E 93, 022106] Published Tue Feb 02, 2016

]]>We examine immunostaining experimental data for the formation of stripe 2 of even-skipped (*eve*) transcripts on *D. melanogaster* embryos. An estimate of the factor converting immunofluorescence intensity units into molecular numbers is given. The analysis of the eve dynamics at the region of stripe 2 …

[Phys. Rev. E 93, 022403] Published Tue Feb 02, 2016

]]>This paper aims to understand the physics behind the observation that there seems to exist a critical wind speed at which trees are damaged by trunk failure. The authors do so by modeling the trees as fragile rods and by using Hooke’s law and Griffith’s theory of fracture. Interestingly, the critical speed hardly depends on tree characteristics, in agreement with field data collected after storms.

[Phys. Rev. E 93, 023001] Published Tue Feb 02, 2016

]]>A theory of acoustic vector solitons of self-induced transparency of the Rayleigh wave is constructed. A thin resonance transition layer on an elastic surface is considered using a model of a two-dimensional gas of impurity paramagnetic atoms or quantum dots. Explicit analytical expressions for the …

[Phys. Rev. E 93, 023002] Published Tue Feb 02, 2016

]]>We derive the single integrodifferential wave equation for the probability density function of the position of a classical one-dimensional Lévy walk with continuous sample paths. This equation involves a classical wave operator together with memory integrals describing the spatiotemporal coupling of…

[Phys. Rev. E 93, 020101(R)] Published Mon Feb 01, 2016

]]>For discrete-state stochastic systems obeying Markovian dynamics, we establish the counterpart of the *conditional reversibility theorem* obtained by Gallavotti for deterministic systems [Ann. de l'Institut Henri Poincaré (A) **70**, 429 (1999)]. Our result states that stochastic trajectories conditioned …

[Phys. Rev. E 93, 022101] Published Mon Feb 01, 2016

]]>A multimode optical fiber with a truncated transverse cross section acts as a powerful versatile support to investigate the wave features of complex ray dynamics. In this paper, we concentrate on the case of a geometry inducing mixed dynamics. We highlight that regular modes associated with stable p…

[Phys. Rev. E 93, 022201] Published Mon Feb 01, 2016

]]>The reduced dynamics for dark and bright soliton chains in the one-dimensional nonlinear Schrödinger equation is used to study the behavior of collective compression waves corresponding to Toda lattice solitons. We coin the term hypersoliton to describe such solitary waves riding on a chain of solit…

[Phys. Rev. E 93, 022202] Published Mon Feb 01, 2016

]]>A simple but efficient spectral approach for analyzing the community structure of complex networks is introduced. It works the same way for all types of networks, by spectrally splitting the adjacency matrix into a “unipartite” and a “multipartite” component. These two matrices reveal the structure …

[Phys. Rev. E 93, 022301] Published Mon Feb 01, 2016

]]>Solid-state nanopores are single-molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage, and salt dependence of the frequency of double-stranded DNA translocations through conical quartz n…

[Phys. Rev. E 93, 022401] Published Mon Feb 01, 2016

]]>Mean-field models of the brain approximate spiking dynamics by assuming that each neuron responds to its neighbors via a naive spatial average that neglects local fluctuations and correlations in firing activity. In this paper we address this issue by introducing a rigorous formalism to enable spati…

[Phys. Rev. E 93, 022402] Published Mon Feb 01, 2016

]]>Electroclinic measurements are reported for two chiral liquid crystals above their bulk chiral isotropic–nematic phase transition temperatures. It is found that an applied electric field $E$ induces a rotation *θ* $[\propto {\rm E}]$ of the director in the very thin paranematic layers that are induced by the cell's tw…

[Phys. Rev. E 93, 022701] Published Mon Feb 01, 2016

]]>Equilibrium and nonequilibrium molecular dynamics simulations were conducted in order to evaluate the hypothesis that the hydrodynamic slip length is a surface property. The system under investigation was water confined between two graphite layers to form nanochannels of different sizes (3–8 nm). Th…

[Phys. Rev. E 93, 023101] Published Mon Feb 01, 2016

]]>We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu $ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis loop, ${A}_{\mathrm{loop}}$, scales with the same exponents as observed in a rece…

[Phys. Rev. E 93, 010402(R)] Published Fri Jan 29, 2016

]]>The direct bond percolation process (Gribov process) is studied in the presence of random velocity fluctuations generated by the Gaussian self-similar ensemble with finite correlation time. We employ the renormalization group in order to analyze a combined effect of the compressibility and finite co…

[Phys. Rev. E 93, 012151] Published Fri Jan 29, 2016

]]>We examine the existence and properties of certain discrete breathers for a discrete nonlinear Schrödinger model where all but one site are placed in a ring and coupled to the additional central site. The discrete breathers we focus on are stationary solutions mainly localized on one or a few of the…

[Phys. Rev. E 93, 012219] Published Fri Jan 29, 2016

]]>Strong-coupling phenomena, such as like-charge macroion attraction, opposite-charged macroion repulsion, charge renormalization, and charge inversion, are known to be mediated by multivalent counterions. Most theories treat the counterions as point charges and describe the system by a single couplin…

[Phys. Rev. E 93, 012504] Published Fri Jan 29, 2016

]]>Using a probabilistic approximation of a mean-field mechanistic model of sheared systems, we analytically calculate the statistical properties of large failures under slow shear loading. For general shear $F\left(t\right)$, the distribution of waiting times between large system-spanning failures is a generalized…

[Phys. Rev. E 93, 013003] Published Fri Jan 29, 2016

]]>We propose a theoretical framework within which a robust micromechanical definition of precursors to plastic instabilities, often termed soft spots, naturally emerges. They are shown to be collective displacements (modes) $\widehat{z}$ that correspond to local minima of a barrier function $b\left(\widehat{z}\right)$, which depends …

[Phys. Rev. E 93, 011001(R)] Published Thu Jan 28, 2016

]]>We report the results of an experimental investigation of the spatiotemporal dynamics of stable imbibition fronts in a disordered medium, in the regime of capillary disorder, for a wide range of experimental conditions. We have used silicone oils of various viscosities $\mu $ and nearly identical oil-air…

[Phys. Rev. E 93, 012149] Published Thu Jan 28, 2016

]]>We report the results of an experimental investigation of the spatiotemporal dynamics of stable imbibition fronts in a disordered medium, in the regime of capillary disorder, for a wide range of experimental conditions. We have used silicone oils of various viscosities $\mu $ and nearly identical oil-air…

[Phys. Rev. E 93, 012150] Published Thu Jan 28, 2016

]]>Chimera states are dynamical patterns in networks of coupled oscillators in which regions of synchronous and asynchronous oscillation coexist. Although these states are typically observed in large ensembles of oscillators and analyzed in the continuum limit, chimeras may also occur in systems with f…

[Phys. Rev. E 93, 012218] Published Thu Jan 28, 2016

]]>Many experimental and theoretical methods have been developed to calculate the coarse-grained continuum elastic properties of macromolecules. However, all of those methods assume uniform elastic properties. Following the continuum mechanics framework, we present a systematic way of calculating the n…

[Phys. Rev. E 93, 012417] Published Thu Jan 28, 2016

]]>We investigate scaling of work and efficiency of a photonic Carnot engine with a number of quantum coherent resources. Specifically, we consider a generalization of the “phaseonium fuel” for the photonic Carnot engine, which was first introduced as a three-level atom with two lower states in a quant…

[Phys. Rev. E 93, 012145] Published Wed Jan 27, 2016

]]>The interplay between geometrical frustration (GF) and inverse freezing (IF) is studied within a cluster approach. The model considers first-neighbor $\left({J}_{1}\right)$ and second-neighbor $\left({J}_{2}\right)$ intracluster antiferromagnetic interactions between Ising spins on a checkerboard lattice and long-range disordered coup…

[Phys. Rev. E 93, 012147] Published Wed Jan 27, 2016

]]>Casimir forces have been shown to arise from fluctuations in a variety of systems, both classical and quantum. In this paper, the authors present two mechanisms for the appearance of Casimir forces in non-equilibrium fluids, namely the coupling of hydrodynamic modes and the existence of inhomogeneous thermal noise. They identify the former as the leading contribution, and show that its effect is much larger than that of other Casimir forces.

[Phys. Rev. E 93, 012148] Published Wed Jan 27, 2016

]]>We analyze the controllability of a two-layer network, where driver nodes can be chosen randomly only from one layer. Each layer contains a scale-free network with directed links and the node dynamics depends on the incoming links from other nodes. We combine the in-degree and out-degree values to a…

[Phys. Rev. E 93, 012309] Published Wed Jan 27, 2016

]]>We study the interacting self-avoiding trail (ISAT) model on a Bethe lattice of general coordination $q$ and on a Husimi lattice built with squares and coordination $q=4$. The exact grand-canonical solutions of the model are obtained, considering that up to $K$ monomers can be placed on a site and associa…

[Phys. Rev. E 93, 012502] Published Wed Jan 27, 2016

]]>Inspired by recent experiments and simulations on pattern formation in biomolecules by optical tweezers, a theoretical description based on the reference interaction site model (RISM) is developed to calculate the equilibrium density profiles of small polyelectrolytes in an external potential. The f…

[Phys. Rev. E 93, 012503] Published Wed Jan 27, 2016

]]>It is well known that the polymer glass transition temperature ${T}_{g}$ is dependent on molecular weight, but the role of molecular-weight polydispersity on ${T}_{g}$ is unclear. Using molecular-dynamics simulations, we clarify that for polymers with the same number-average molecular weight, the molecular-weight…

[Phys. Rev. E 93, 012613] Published Wed Jan 27, 2016

]]>A multiple-relaxation-time lattice Boltzmann model of Couette flow is developed to investigate the rarified gas flow through microchannels with roughness characterized by fractal geometry, especially to elucidate the coupled effects of roughness and rarefaction on microscale gas flow in the transiti…

[Phys. Rev. E 93, 013128] Published Wed Jan 27, 2016

]]>We investigate a quasi-two-dimensional system composed of an initially circular ferrofluid droplet surrounded by a nonmagnetic fluid of higher density. These immiscible fluids flow in a rotating Hele-Shaw cell, under the influence of an in-plane radial magnetic field. We focus on the situation in wh…

[Phys. Rev. E 93, 013129] Published Wed Jan 27, 2016

]]>Rogue waves (RWs) are unexpectedly strong excitations emerging from an otherwise tranquil background. The nonlinear Schrödinger equation (NLSE), a ubiquitous model with wide applications to fluid mechanics, optics, plasmas, etc., exhibits RWs only in the regime of modulation instability (MI) of the …

[Phys. Rev. E 93, 012217] Published Tue Jan 26, 2016

]]>Cell physiology is orchestrated, on a molecular level, through complex networks of biochemical reactions. The propagation of random fluctuations through these networks can significantly impact cell behavior, raising challenging questions about how network design shapes the cell's ability to suppress…

[Phys. Rev. E 93, 012415] Published Tue Jan 26, 2016

]]>Optogenetics provides a method of neuron stimulation that has high spatial, temporal, and cell-type specificity. Here we present a model of optogenetic feedback control that targets the inhibitory population, which expresses light-sensitive channelrhodopsin-2 channels, in a mean-field model of undif…

[Phys. Rev. E 93, 012416] Published Tue Jan 26, 2016

]]>The physical approach of a small particle (virus, medical drug) to the cell membrane represents the crucial first step before active internalization and is governed by thermal diffusion. Using a fully analytical theory we show that the stretching and bending of the elastic membrane by the approachin…

[Phys. Rev. E 93, 012612] Published Tue Jan 26, 2016

]]>We demonstrate both theoretically and experimentally propagation dynamics of surface gravity water-wave pulses, having Hermite-Gauss envelopes. We show that these waves propagate self-similarly along an 18-m wave tank, preserving their general Hermite-Gauss envelopes in both the linear and the nonli…

[Phys. Rev. E 93, 013127] Published Tue Jan 26, 2016

]]>Because of the coupling between local lipid composition and the thickness of the membrane, microphase separation in two-component lipid membranes can take place; such effects may underlie the formation of equilibrium nanoscale rafts. Using a kinetic description, this phenomenon is analytically and n…

[Phys. Rev. E 93, 010401(R)] Published Mon Jan 25, 2016

]]>A symmetry-based theory is developed for the description of (streamwise) kinetic energy $K$ in turbulent pipes at extremely high Reynolds numbers (Re's). The theory assumes a mesolayer with continual deformation of wall-attached eddies which introduce an anomalous dissipation, breaking the exact balan…

[Phys. Rev. E 93, 011102(R)] Published Mon Jan 25, 2016

]]>We study a generic model of coupled oscillators. In the model there is competition between phase synchronization and diffusive effects. For a model with a finite number of states we derive how a phase transition occurs when the coupling parameter is varied. The phase transition is characterized by a…

[Phys. Rev. E 93, 012143] Published Mon Jan 25, 2016

]]>Using the Wilson renormalization group, we show that if no integrated vector operator of scaling dimension $-1$ exists, then scale invariance implies conformal invariance. By using the Lebowitz inequalities, we prove that this necessary condition is fulfilled in all dimensions for the Ising universali…

[Phys. Rev. E 93, 012144] Published Mon Jan 25, 2016

]]>Scroll waves in a three-dimensional media may develop into turbulence due to negative tension of the filament. Such negative tension-induced instability of scroll waves has been observed in the Belousov-Zhabotinsky reaction systems. Here we propose a method to restabilize scroll wave turbulence caus…

[Phys. Rev. E 93, 012216] Published Mon Jan 25, 2016

]]>Rippling patterns of myxobacteria appear in starving colonies before they aggregate to form fruiting bodies. These periodic traveling cell density waves arise from the coordination of individual cell reversals, resulting from an internal clock regulating them and from contact signaling during bacter…

[Phys. Rev. E 93, 012412] Published Mon Jan 25, 2016

]]>We report on the formation of tubular membrane protrusions from giant unilamellar vesicles in alternating electric fields. The construction of the experimental chamber permitted the application of external AC fields with strength of dozens of V/mm and kHz frequency during relatively long time period…

[Phys. Rev. E 93, 012413] Published Mon Jan 25, 2016

]]>We show systematic electrical impedance measurements of single motile cells on microelectrodes. Wild-type cells and mutant strains were studied that differ in their cell-substrate adhesion strength. We recorded the projected cell area by time-lapse microscopy and observed irregular oscillations of t…

[Phys. Rev. E 93, 012414] Published Mon Jan 25, 2016

]]>Particle rheology is used to extract the linear viscoelastic properties of an entangled polymer melt from molecular dynamics simulations. The motion of a stiff, approximately spherical particle is tracked in both passive and active modes. We demonstrate that the dynamic modulus of the melt can be ex…

[Phys. Rev. E 93, 012501] Published Mon Jan 25, 2016

]]>We investigated the effects of varying the volume fraction of large particles $\left(r\right)$ on the linear rheology and microstructure of mixtures of polymers and bidisperse colloids, in which the ratio of the small and large particle diameters was $\alpha =0.31$ or $\alpha =0.45$. Suspensions formulated at a total volume fra…

[Phys. Rev. E 93, 012610] Published Mon Jan 25, 2016

]]>Enzymatic “machines,” such as catalytic rods or colloids, can self-propel and interact by generating gradients of their substrates. We theoretically investigate the behaviors of such machines in a chemically active environment where their catalytic substrates are continuously synthesized and destroy…

[Phys. Rev. E 93, 012611] Published Mon Jan 25, 2016

]]>The Brownian diffusion of micron-scale inclusions in freely suspended smectic-$A$ liquid crystal films a few nanometers thick and several millimeters in diameter depends strongly on the air surrounding the film. Near atmospheric pressure, the three-dimensionally coupled film-gas system is well describ…

[Phys. Rev. E 93, 012706] Published Mon Jan 25, 2016

]]>We present a numerical calculation of the total number of disordered jammed configurations $\mathrm{\Omega}$ of $N$ repulsive, three-dimensional spheres in a fixed volume $V$. To make these calculations tractable, we increase the computational efficiency of the approach of Xu *et al.* [Phys. Rev. Lett. **106**, 245502 (2011)…

[Phys. Rev. E 93, 012906] Published Mon Jan 25, 2016

]]>We study head-on impacts of equal-speed but unequal-width incompressible jets in two dimensions with a focus on dense granular jets. We use discrete particle simulations to show that head-on impact of granular jets produces a quasi-steady-state where a fraction of the excess incident momentum from t…

[Phys. Rev. E 93, 012907] Published Mon Jan 25, 2016

]]>Mechanical impulse propagation in granular media depends strongly on the imposed confinement conditions. In this work, the propagation of sound in a granular packing contained by flexible walls that enable confinement under hydrostatic pressure conditions is investigated. This configuration also all…

[Phys. Rev. E 93, 012908] Published Mon Jan 25, 2016

]]>Linear and nonlinear mechanisms for conical wave propagation in two-dimensional lattices are explored in the realm of phononic crystals. As a prototypical example, a statically compressed granular lattice of spherical particles arranged in a hexagonal packing configuration is analyzed. Upon identify…

[Phys. Rev. E 93, 012909] Published Mon Jan 25, 2016

]]>In this paper, a generalization of the Cahn-Hilliard theory of binary liquids is presented for multicomponent incompressible liquid mixtures. First, a thermodynamically consistent convection-diffusion-type dynamics is derived on the basis of the Lagrange multiplier formalism. Next, a generalization …

[Phys. Rev. E 93, 013126] Published Mon Jan 25, 2016

]]>This paper presents a study of the nonequilibrium relaxation process of chemically reactive systems using steepest-entropy-ascent quantum thermodynamics (SEAQT). The trajectory of the chemical reaction, i.e., the accessible intermediate states, is predicted and discussed. The prediction is made usin…

[Phys. Rev. E 93, 012137] Published Fri Jan 22, 2016

]]>We compare two calculations of the particle density in the superfluid phase of the O(2) model with a chemical potential $\mu $ in 1+1 dimensions. The first relies on exact blocking formulas from the Tensor Renormalization Group (TRG) formulation of the transfer matrix. The second is a worm algorithm. We …

[Phys. Rev. E 93, 012138] Published Fri Jan 22, 2016

]]>Three-dimensional (3D) structures are useful for studying the spatial structures and physical properties of porous media. A 3D structure can be reconstructed from a single two-dimensional (2D) training image (TI) by using mathematical modeling methods. Among many reconstruction algorithms, an optima…

[Phys. Rev. E 93, 012140] Published Fri Jan 22, 2016

]]>The phase transition of the Ising model is investigated on a planar lattice that has a fractal structure. On the lattice, the number of bonds that cross the border of a finite area is doubled when the linear size of the area is extended by a factor of 4. The free energy and the spontaneous magnetiza…

[Phys. Rev. E 93, 012141] Published Fri Jan 22, 2016

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