We investigate the small-scale properties of a stochastic cubic-autocatalytic reaction-diffusion (CARD) model using renormalization techniques. We renormalize noise-induced ultraviolet divergences and obtain $\beta $ functions for the decay rate and coupling at one loop. Assuming colored (power-law) noise,…

[Phys. Rev. E 92, 042114] Published Wed Oct 07, 2015

]]>We study the effects of next-nearest-neighbor (NNN) interactions on the dynamics of the one-dimensional spin-$1/2$ transverse Ising model in the high-temperature limit. We use exact diagonalization to obtain the time-dependent transverse correlation function and the corresponding spectral density for …

[Phys. Rev. E 92, 042115] Published Wed Oct 07, 2015

]]>As a generation of the classical percolation, clique percolation focuses on the connection of cliques in a graph, where the connection of two $k$ cliques means that they share at least $l<k$ vertices. In this paper we develop a theoretical approach to study clique percolation in Erdős-Rényi graphs, w…

[Phys. Rev. E 92, 042116] Published Wed Oct 07, 2015

]]>We study distributed-order time fractional diffusion equations characterized by multifractal memory kernels, in contrast to the simple power-law kernel of common time fractional diffusion equations. Based on the physical approach to anomalous diffusion provided by the seminal Scher-Montroll-Weiss co…

[Phys. Rev. E 92, 042117] Published Wed Oct 07, 2015

]]>The authors report on the oscillation patterns of rounded structures formed at the solid-liquid interface in directional solidification, by performing experiments in gravity-reduced conditions aboard the International Space Station. They complement their observations with a phase-field theoretical approach that successfully reproduces the main feature of their observations, namely the onset of a so-called breathing mode that, for large samples, does not exhibit long-ranged coherence.

[Phys. Rev. E 92, 042401] Published Wed Oct 07, 2015

]]>Polymer nanocomposites have been an issue of both academic and industrial interest due to promising electrical, mechanical, optical, and magnetic properties. The dynamics of nanoparticles in polymer nanocomposites is a key to understanding those properties of polymer nanocomposites and is important …

[Phys. Rev. E 92, 042601] Published Wed Oct 07, 2015

]]>Detecting communities in a network, based only on the adjacency matrix, is a problem of interest to several scientific disciplines. Recently, Zhang and Moore have introduced an algorithm [Proc. Natl. Acad. Sci. USA **111**, 18144 (2014)], called mod-bp, that avoids overfitting the data by optimizing a w…

[Phys. Rev. E 92, 042804] Published Wed Oct 07, 2015

]]>The role of committed minorities in shaping public opinion has been recently addressed with the help of multiagent models. However, previous studies focused on homogeneous populations where zealots stand out only for their stubbornness. Here we consider the more general case in which individuals are…

[Phys. Rev. E 92, 042805] Published Wed Oct 07, 2015

]]>Extreme events occur in many spatially extended dynamical systems, often devastatingly affecting human life, which makes their reliable prediction and efficient prevention highly desirable. We study the prediction and prevention of extreme events in a spatially extended system, a system of coupled F…

[Phys. Rev. E 92, 042910] Published Wed Oct 07, 2015

]]>The lack of a first-principles derivation has made the hydrodynamic boundary condition a classical issue for the past century. The fact that the fluid can have interfacial structures adds additional complications and ambiguities to the problem. Here we report the use of molecular dynamics to identif…

[Phys. Rev. E 92, 043007] Published Wed Oct 07, 2015

]]>Mixing at low Reynolds numbers, especially in the framework of confined flows occurring in Hele-Shaw cells, porous media, and microfluidic devices, has attracted considerable attention lately. Under such circumstances, enhanced mixing is limited due to the lack of turbulence, and absence of sizable …

[Phys. Rev. E 92, 043008] Published Wed Oct 07, 2015

]]>The microscopic quantum theory of plasma nonlinear interaction with the coherent shortwave electromagnetic radiation of arbitrary intensity is developed. The Liouville–von Neumann equation for the density matrix is solved analytically considering a wave field exactly and a scattering potential of pl…

[Phys. Rev. E 92, 043103] Published Wed Oct 07, 2015

]]>We investigate site percolation on a weighted planar stochastic lattice (WPSL), which is a multifractal and whose dual is a scale-free network. Percolation is typically characterized by a threshold value ${p}_{c}$ at which a transition occurs and by a set of critical exponents $\beta ,\gamma ,\nu $ which describe the cr…

[Phys. Rev. E 92, 040101(R)] Published Tue Oct 06, 2015

]]>Connectivity and conductivity of two-dimensional fracture networks (FNs), as an important type of continuous random networks, are examined systematically through Monte Carlo simulations under a variety of conditions, including different power law distributions of the fracture lengths and domain size…

[Phys. Rev. E 92, 041001(R)] Published Tue Oct 06, 2015

]]>We consider linear arrays of cells of volume ${V}_{\mathrm{c}}$ populated by monodisperse rods of size $\sigma {V}_{\mathrm{c}},\sigma =1,2,...$, subject to hardcore exclusion interaction. Each rod experiences a position-dependent external potential. In one application we also examine effects of contact forces between rods. We employ two dist…

[Phys. Rev. E 92, 042112] Published Tue Oct 06, 2015

]]>We extend the exchange fluctuation theorem for energy exchange between thermal quantum systems beyond the assumption of molecular chaos, and describe the nonequilibrium exchange dynamics of correlated quantum states. The relation quantifies how the tendency for systems to equilibrate is modified in …

[Phys. Rev. E 92, 042113] Published Tue Oct 06, 2015

]]>Equilibrium behavior of a single chain of dipolar spheres is investigated by the method of molecular dynamics in a wide range of the dipolar coupling constant $\lambda $. Two cases are considered: rodlike and flexible chains. In the first case, particle centers are immovably fixed on one axis, but their magn…

[Phys. Rev. E 92, 042303] Published Tue Oct 06, 2015

]]>We provide a comprehensive physical description of the vaporization, self-assembly, agglomeration, and buckling kinetics of sessile nanofluid droplets pinned on a hydrophobic substrate. We have deciphered five distinct regimes of the droplet life cycle. Regimes I–III consists of evaporation-induced …

[Phys. Rev. E 92, 042304] Published Tue Oct 06, 2015

]]>Liquid crystalline elastomers combine the ordering properties of liquid crystals with elasticity of crosslinked polymer networks. In monodomain (permanently aligned) elastomers, altering the orientational (nematic) order causes changes in the equilibrium sample length, which is the basis of the famo…

[Phys. Rev. E 92, 042502] Published Tue Oct 06, 2015

]]>Integrin receptors mediate interaction between the cellular actin-cytoskeleton and extracellular matrix. Based on their activation properties, we propose a reaction-diffusion model where the kinetics of the two-state receptors is modulated by their lipidic environment. This environment serves as an …

[Phys. Rev. E 92, 042704] Published Tue Oct 06, 2015

]]>The impact of connectivity and individual dynamics on the basin stability of the burst synchronization regime in small-world networks consisting of chaotic slow-fast oscillators is studied. It is shown that there are rewiring probabilities corresponding to the largest basin stabilities, which uncove…

[Phys. Rev. E 92, 042803] Published Tue Oct 06, 2015

]]>We experimentally investigated the noise-induced dynamics of a prototypical thermoacoustic system undergoing a subcritical Hopf bifurcation to limit cycle oscillations. The study was performed prior to the bistable regime. Analysis of the characteristics of pressure oscillations in the combustor and…

[Phys. Rev. E 92, 042909] Published Tue Oct 06, 2015

]]>Ultrasonic melt processing significantly improves the properties of metallic materials. However, this promising technology has not been successfully transferred to the industry because of difficulties in treating large volumes of melt. To circumvent these difficulties, a fundamental understanding of…

[Phys. Rev. E 92, 043004] Published Tue Oct 06, 2015

]]>We present fluid velocity measurements in a modified Taylor-Couette device operated in the quasi-Keplerian regime, where it is observed that nearly ideal flows exhibit self-similarity under scaling of the Reynolds number. In contrast, nonideal flows show progressive departure from ideal Couette as t…

[Phys. Rev. E 92, 043005] Published Tue Oct 06, 2015

]]>The dynamics in the thin boundary layers of temperature and velocity is the key to a deeper understanding of turbulent transport of heat and momentum in thermal convection. The velocity gradient at the hot and cold plates of a Rayleigh-Bénard convection cell forms the two-dimensional skin friction f…

[Phys. Rev. E 92, 043006] Published Tue Oct 06, 2015

]]>We investigated ion acceleration by an electrostatic shock in an exploded target irradiated by an ultrashort, circularly polarized laser pulse by means of one- and three-dimensional particle-in-cell simulations. We discovered that the laser field penetrating via relativistic transparency (RT) rapidl…

[Phys. Rev. E 92, 043102] Published Tue Oct 06, 2015

]]>An alternative application of duality relations of stochastic processes is demonstrated. Although conventional usages of the duality relations need analytical solutions for the dual processes, here I employ numerical solutions of the dual processes and investigate the usefulness. As a demonstration,…

[Phys. Rev. E 92, 043302] Published Tue Oct 06, 2015

]]>An interconnected network features a structural transition between two regimes [F. Radicchi and A. Arenas, Nat. Phys. **9**, 717 (2013)]: one where the network components are structurally distinguishable and one where the interconnected network functions as a whole. Our exact solution for the coupling t…

[Phys. Rev. E 92, 040801(R)] Published Mon Oct 05, 2015

]]>Networks of fast nonlinear elements may display slow fluctuations if interactions are strong. We find a transition in the long-term variability of a sparse recurrent network of perfect integrate-and-fire neurons at which the Fano factor switches from zero to infinity and the correlation time is mini…

[Phys. Rev. E 92, 040901(R)] Published Mon Oct 05, 2015

]]>We study the non-Hermitian Hofstadter dynamics of a quantum particle with biased motion on a square lattice in the background of a magnetic field. We show that in quasimomentum space, the energy spectrum is an overlap of infinitely many inequivalent fractals. The energy levels in each fractal are sp…

[Phys. Rev. E 92, 042102] Published Mon Oct 05, 2015

]]>Selective energy transport throughout a quantum network connected to more than one reaction center can play an important role in many natural and technological considerations in photosystems. In this work, we propose a method in which an excitation can be transported from the original site of the ne…

[Phys. Rev. E 92, 042103] Published Mon Oct 05, 2015

]]>In analogy to Brownian computers we explicitly show how to construct stochastic models which mimic the behavior of a general-purpose computer (a Turing machine). Our models are discrete state systems obeying a Markovian master equation, which are logically reversible and have a well-defined and cons…

[Phys. Rev. E 92, 042104] Published Mon Oct 05, 2015

]]>We develop a generating functional description of the dynamics of non-Markovian individual-based systems in which delay reactions can be terminated before completion. This generalizes previous work in which a path-integral approach was applied to dynamics in which delay reactions complete with certa…

[Phys. Rev. E 92, 042105] Published Mon Oct 05, 2015

]]>Models of three-dimensional space filling based on growth of two-dimensional sheets are proposed. Beginning from planar Eden-style growth of sheets, additional growth modes are introduced. These enable the sheets to form layered or disordered structures. The growth modes can also be combined. An off…

[Phys. Rev. E 92, 042106] Published Mon Oct 05, 2015

]]>We study the critical behavior of the Sherrington-Kirkpatrick model in transverse field (at finite temperature) using Monte Carlo simulation and exact diagonalization (at zero temperature). We determine the phase diagram of the model by estimating the Binder cumulant. We also determine the correlati…

[Phys. Rev. E 92, 042107] Published Mon Oct 05, 2015

]]>We compute statistical properties of the stochastic entropy production associated with the nonstationary transport of heat through a system coupled to a time dependent nonisothermal heat bath. We study the one-dimensional stochastic evolution of a bound particle in such an environment by solving the…

[Phys. Rev. E 92, 042108] Published Mon Oct 05, 2015

]]>We study the bidimensional voter model on a square lattice with numerical simulations. We demonstrate that the evolution takes place in two distinct dynamic regimes; a first approach towards critical site percolation and a further approach towards full consensus. We calculate the time dependence of …

[Phys. Rev. E 92, 042109] Published Mon Oct 05, 2015

]]>We study the active to absorbing phase transition (AAPT) in a simple two-component model system for a species and its mutant. We uncover the nontrivial critical scaling behavior and weak dynamic scaling near the AAPT that shows the significance of mutation and highlights the connection of this model…

[Phys. Rev. E 92, 042110] Published Mon Oct 05, 2015

]]>When playing games in groups, it is an advantage for individuals to have accurate statistical information on the strategies of their opponents. Such information may be obtained by remembering previous interactions. We consider a rock-paper-scissors game in which agents are able to recall their last $\dots $

[Phys. Rev. E 92, 042111] Published Mon Oct 05, 2015

]]>The viscosity of fluids is generally understood in terms of kinetic mechanisms, i.e., particle collisions, or thermodynamic ones as imposed through structural distortions upon, e.g., applying shear. Often the latter are more relevant, which allows a simpler theoretical description, and, e.g., (dampe…

[Phys. Rev. E 92, 042301] Published Mon Oct 05, 2015

]]>We present a sharp-interface model of two-dimensional ramified growth during quasisteady electrodeposition. Our model differs from previous modeling methods in that it includes the important effects of extended space-charge regions and nonlinear electrode reactions. The electrokinetics is described …

[Phys. Rev. E 92, 042302] Published Mon Oct 05, 2015

]]>Due to elastic anisotropy, two-dimensional patterning of substrates can promote weak azimuthal alignment of adjacent nematic liquid crystals. Here we consider how such alignment can be achieved using a periodic square lattice of circular or elliptical motifs. In particular, we examine ways in which …

[Phys. Rev. E 92, 042501] Published Mon Oct 05, 2015

]]>The activity of pancreatic $\beta $ cells can be described by biological networks of coupled nonlinear oscillators that, via electrochemical synchronization, release insulin in response to augmented glucose levels. In this work, we analyze the emergent behavior of regular and percolated $\beta $-cells clusters th…

[Phys. Rev. E 92, 042702] Published Mon Oct 05, 2015

]]>We perform a comprehensive analysis of the spectral statistics of the molecular resonances in ${}^{166}\mathrm{Er}$ and ${}^{168}\mathrm{Er}$ observed in recent ultracold collision experiments [Frisch *et al.*, Nature (London) **507**, 475 (2014)] with the aim of determining the chaoticity of this system. We calculate different indepen…

[Phys. Rev. E 92, 042906] Published Mon Oct 05, 2015

]]>We consider an Ehrenfest approximation for a particle in a double-well potential in the presence of an external environment schematized as a finite resource heat bath. This allows us to explore how the limitations in the applicability of Ehrenfest dynamics to nonlinear systems are modified in an ope…

[Phys. Rev. E 92, 042907] Published Mon Oct 05, 2015

]]>We study a stochastic dynamics of systems with hard excitement of auto-oscillations possessing a bistability mode with coexistence of the stable equilibrium and limit cycle. A principal difference in the results of the impact of additive and parametric random disturbances is shown. For the stochasti…

[Phys. Rev. E 92, 042908] Published Mon Oct 05, 2015

]]>A theoretical model is developed that describes nonlinear spherical pulsations and translational motions of two interacting bubbles at arbitrary separation distances between the bubbles. The derivation of the model is based on the multipole expansion of the bubble velocity potentials and the use of …

[Phys. Rev. E 92, 043001] Published Mon Oct 05, 2015

]]>We conduct numerical experiments on spreading of viscoelastic droplets on a flat surface. Our work considers a Giesekus fluid characterized by a shear-thinning viscosity and an Oldroyd-B fluid, which is close to a Boger fluid with constant viscosity. Our results qualitatively agree with experimental…

[Phys. Rev. E 92, 043002] Published Mon Oct 05, 2015

]]>This paper is concerned with the evaluation of two Lagrangian measures which arise in oscillatory or fluctuating shear flows when the fluctuating field is rotational and the spectrum of wave numbers which comprise it is continuous. The measures are the drift and pseudomomentum. Phillips [J. Fluid Me…

[Phys. Rev. E 92, 043003] Published Mon Oct 05, 2015

]]>Diffusive transport is a universal phenomenon, throughout both biological and physical sciences, and models of diffusion are routinely used to interrogate diffusion-driven processes. However, most models neglect to take into account the role of volume exclusion, which can significantly alter diffusi…

[Phys. Rev. E 92, 040701(R)] Published Fri Oct 02, 2015

]]>Non-Markovian processes are widespread in natural and human-made systems, yet explicit modeling and analysis of such systems is underdeveloped. We consider a non-Markovian dynamic network with random link activation and deletion (RLAD) and heavy-tailed Mittag-Leffler distribution for the interevent …

[Phys. Rev. E 92, 042801] Published Fri Oct 02, 2015

]]>We identify a universal mathematical structure in microscopic deterministic traffic models (with identical drivers), and thus we show that all such existing models in the literature, including both the two-phase and three-phase models, can be understood as special cases of a master model by expansio…

[Phys. Rev. E 92, 042802] Published Fri Oct 02, 2015

]]>We articulate an adaptive and reference-free framework based on the principle of random switching to *detect and control* unstable steady states in high-dimensional nonlinear dynamical systems, without requiring any *a priori* information about the system or about the target steady state. Starting from …

[Phys. Rev. E 92, 042902] Published Fri Oct 02, 2015

]]>Dynamical systems with multiple, hierarchically long-delayed feedback are introduced and studied extending our previous work [Yanchuk and Giacomelli, Phys. Rev. Lett. **112**, 174103 (2014)]. Focusing on the phenomenological model of a Stuart-Landau oscillator with two feedbacks, we show the multiscale …

[Phys. Rev. E 92, 042903] Published Fri Oct 02, 2015

]]>Two types of random evolution processes are studied for ensembles of the standard map with driving parameter $K$ that determines its degree of stochasticity. For one type of process the parameter $K$ is chosen at random from a Gaussian distribution and is then kept fixed, while for the other type it var…

[Phys. Rev. E 92, 042904] Published Fri Oct 02, 2015

]]>We explore the long-time dynamics of a system of identical charged particles trapped on a closed helix. This system has recently been found to exhibit an unconventional deformation of the linear spectrum when tuning the helix radius. Here we show that the same geometrical parameter can affect signif…

[Phys. Rev. E 92, 042905] Published Fri Oct 02, 2015

]]>Previous papers by the authors report that they obtained compact, arbitrarily accurate expressions for two-center, one- and two-electron relativistic molecular integrals expressed over Slater-type orbitals. In the present study, accuracy limits of expressions given are examined for three-center nucl…

[Phys. Rev. E 92, 043301] Published Fri Oct 02, 2015

]]>The momentum or velocity autocorrelation function $C\left(t\right)$ for a tagged oscillator in a finite harmonic system decays like that of an infinite system for short times, but exhibits erratic behavior at longer time scales. We introduce the autocorrelation function of the long-time noisy tail of $C\left(t\right)$ (“a co…

[Phys. Rev. E 92, 042101] Published Thu Oct 01, 2015

]]>Synchronized neural bursts are one of the most noticeable dynamic features of neural networks, being essential for various phenomena in neuroscience, yet their complex dynamics are not well understood. With extrinsic electrical and optical manipulations on cultured neural networks, we demonstrate th…

[Phys. Rev. E 92, 042701] Published Thu Oct 01, 2015

]]>In the present work, we combine the notion of parity-time ($\mathcal{PT}$) symmetry with that of supersymmetry (SUSY) for a prototypical case example with a complex potential that is related by SUSY to the so-called Pöschl-Teller potential which is real. Not only are we able to identify and numerically confirm …

[Phys. Rev. E 92, 042901] Published Thu Oct 01, 2015

]]>A master equation was formulated to study intrinsic charge fluctuations of a grain in a plasma as ions and primary electrons are attached to the grain through collisional collection, and secondary electrons are emitted from the grain. Two different plasmas with Maxwellian and non-Maxwellian distribu…

[Phys. Rev. E 92, 043101] Published Thu Oct 01, 2015

]]>We consider percolation and jamming transitions for particulate systems exposed to compression. For the systems built of particles interacting by purely repulsive forces in addition to friction and viscous damping, it is found that these transitions are influenced by a number of effects, and in part…

[Phys. Rev. E 92, 032204] Published Wed Sep 30, 2015

]]>The electric Freedericksz transition is a second-order quadratic effect, which, in a planarly aligned nematic liquid crystal layer, manifests above a threshold field as a homogeneous symmetric distortion with maximum director-tilt in the midplane. We find that, upon excitation by a low frequency $(\&l\dots $

[Phys. Rev. E 92, 032504] Published Wed Sep 30, 2015

]]>A model of filaments of the twist-grain-boundary smectic-$A$ phase (TGBA) arising from the homeotropic smectic-$A$ phase and nucleating on the sample surface is proposed. The model is based on the concept of finite blocks of parallel smectic layers forming a helical structure. The blocks are surrounded …

[Phys. Rev. E 92, 032505] Published Wed Sep 30, 2015

]]>Changes in cell size often accompany multicellular motion in tissue, and cell number density is known to strongly influence collective migration in monolayers. Density fluctuations in other forms of active matter have been explored extensively, but not the potential role of density fluctuations in c…

[Phys. Rev. E 92, 032729] Published Wed Sep 30, 2015

]]>The results presented in this study are aimed at the theoretical estimate of the interactions between a spherical microbial cell and the colloidal cell imprints in terms of the Derjaguin, Landau, Vervey, and Overbeek (DLVO) surface forces. We adapted the Derjaguin approximation to take into account …

[Phys. Rev. E 92, 032730] Published Wed Sep 30, 2015

]]>For a symmetric ion permselective system, in terms of geometry and bulk concentrations, the system response is also symmetric under opposite electric field polarity. In this work we derive an analytical solution for the concentration distribution, electric potential, and current-voltage response for…

[Phys. Rev. E 92, 033018] Published Wed Sep 30, 2015

]]>The isentropic expansion of an instantaneously and homogeneously heated foil is calculated using a 1D fluid model. The initial temperature and density are assumed to be in the vicinity of the critical temperature and solid density, respectively. The fluid is assumed to satisfy the van der Waals equa…

[Phys. Rev. E 92, 033019] Published Wed Sep 30, 2015

]]>Dynamics of low-temperature water in nanostructured materials is important to a variety of phenomena, ranging from transport in cement and asphaltene, to conformational dynamics of proteins in “crowded” cellular environments, survival of microorganisms at very low temperatures, and diffusion in nano…

[Phys. Rev. E 92, 030301(R)] Published Tue Sep 29, 2015

]]>We investigate poly($N$-isopropylacrylamide) (pNIPAM) microgels randomly copolymerized with large mol % of protonated acrylic acid (AAc), finding that above the lower critical solution temperature the presence of the acid strongly disrupts pNIPAM's collapse, leading to unexpected new behavior at high …

[Phys. Rev. E 92, 030302(R)] Published Tue Sep 29, 2015

]]>A method for computing the thermopower in interacting systems is proposed. This approach, which relies on Monte Carlo simulations, is illustrated first for a diatomic chain of hard-point elastically colliding particles and then in the case of a one-dimensional gas with (screened) Coulomb interpartic…

[Phys. Rev. E 92, 032139] Published Tue Sep 29, 2015

]]>The mean-square displacement (MSD) is widely utilized to study the dynamical properties of stochastic processes. The time-averaged MSD (TAMSD) provides some information on the dynamics which cannot be extracted from the ensemble-averaged MSD. In particular, the relative standard deviation (RSD) of t…

[Phys. Rev. E 92, 032140] Published Tue Sep 29, 2015

]]>We investigate stochastic models of particles entering a channel with a random time distribution. When the number of particles present in the channel exceeds a critical value $N$, a blockage occurs and the particle flux is definitively interrupted. By introducing an integral representation of the $n$-pa…

[Phys. Rev. E 92, 032141] Published Tue Sep 29, 2015

]]>We derive exact analytic expressions for the average work done and work fluctuations in instantaneous quenches of the ground and thermal states of a one-dimensional anisotropic *XY* model. The average work and a quantum fluctuation relation is used to determine the amount of irreversible entropy produ…

[Phys. Rev. E 92, 032142] Published Tue Sep 29, 2015

]]>We consider stochastic energy balance and entropy production (EP) in a generalized Langevin dynamics of macrospins, allowing for both amplitude and direction fluctuations, under external magnetic field. EP is calculated using a Fokker-Planck equation, distinguishing between reversible and irreversib…

[Phys. Rev. E 92, 032143] Published Tue Sep 29, 2015

]]>We examine the ordering properties of rectangular hard rods with length $L$ and diameter $D$ at a single planar wall and between two parallel hard walls using the second virial density-functional theory. The theory is implemented in the three-state Zwanzig approximation, where only three mutually perpen…

[Phys. Rev. E 92, 032503] Published Tue Sep 29, 2015

]]>Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the absence of hydrodynamic interactions. The dsDNA is modeled with o…

[Phys. Rev. E 92, 032603] Published Tue Sep 29, 2015

]]>We present a model of biopolymer gels that includes two types of elastic nonlinearities, stiffening under extension and softening (due to buckling) under compression, to predict the elastic anisotropy induced by both external as well as internal (e.g., due to cell contractility) stresses in biopolym…

[Phys. Rev. E 92, 032728] Published Tue Sep 29, 2015

]]>In this work, we analyze the hyperbolicity of real-world networks, a geometric quantity that measures if a space is negatively curved. We provide two improvements in our understanding of this quantity: first of all, in our interpretation, a hyperbolic network is “aristocratic”, since few elements “c…

[Phys. Rev. E 92, 032812] Published Tue Sep 29, 2015

]]>We present an experimental study on the statistical properties of the injected power needed to maintain an inelastic ball bouncing constantly on a randomly accelerating piston in the presence of gravity. We compute the injected power at each collision of the ball with the moving piston by measuring …

[Phys. Rev. E 92, 032915] Published Tue Sep 29, 2015

]]>The signals emanating from complex systems are usually composed of a mixture of different oscillations which, for a reliable analysis, should be separated from each other and from the inevitable background of noise. Here we introduce an adaptive decomposition tool—*nonlinear mode decomposition* (NMD)—…

[Phys. Rev. E 92, 032916] Published Tue Sep 29, 2015

]]>Using high-resolution particle tracking velocimetry and filter-space techniques, we study the links between the scale-to-scale transfer of energy and enstrophy and instantaneously rotational and straining regions as determined by the classic Okubo-Weiss parameter in a quasi-two-dimensional laborator…

[Phys. Rev. E 92, 033017] Published Tue Sep 29, 2015

]]>We describe the impact of heating and ionization on emission from the target of $K\alpha $ and $K\beta $ radiation induced by the propagation of hot electrons generated by laser-matter interaction. We consider copper as a test case and, starting from basic principles, we calculate the changes in emission wavelengt…

[Phys. Rev. E 92, 033108] Published Tue Sep 29, 2015

]]>The emission of x rays from warm dense matter is of great interest for both spectroscopic diagnostics and development of intense x-ray sources. We report the results from the collisional-radiative steady-state (CRSS) modeling of atomic and optical properties of copper plasmas at near-solid and solid…

[Phys. Rev. E 92, 033109] Published Tue Sep 29, 2015

]]>Evaluating the concentration dependence of static and dynamic properties of macromolecules in semidilute polymer solutions requires accurate calculation of long-range hydrodynamic interactions (HI) and short range excluded volume (EV) forces. In conventional Brownian dynamics simulations (BDS), comp…

[Phys. Rev. E 92, 033307] Published Tue Sep 29, 2015

]]>[Phys. Rev. E 92, 039905] Published Tue Sep 29, 2015

]]>We solve the Navier-Stokes equations with two simultaneous forcings. One forcing is applied at a given large scale and it injects energy. The other forcing is applied at all scales belonging to the inertial range and it injects helicity. In this way we can vary the degree of turbulence helicity from…

[Phys. Rev. E 92, 031004(R)] Published Mon Sep 28, 2015

]]>The direction of the steady-state heat currents across a generic quantum system connected to multiple baths may be engineered to realize virtually any thermodynamic cycle. In spite of their versatility, such continuous energy-conversion systems are generally unable to operate at maximum efficiency d…

[Phys. Rev. E 92, 032136] Published Mon Sep 28, 2015

]]>The quantum Jarzynski equality is an important theorem of modern quantum thermodynamics. We show that the Jarzynski equality readily generalizes to relativistic quantum mechanics described by the Dirac equation. After establishing the conceptual framework we solve a pedagogical, yet experimentally r…

[Phys. Rev. E 92, 032137] Published Mon Sep 28, 2015

]]>We study effects of interaction symmetry in one-dimensional, momentum-conserving disordered lattices. It is found that asymmetric and symmetric interparticle interactions may result in significant difference: localized modes can be delocalized by very weak asymmetric interactions but survive much st…

[Phys. Rev. E 92, 032138] Published Mon Sep 28, 2015

]]>Experiments on confined two-phase flow systems, involving air and a dense suspension, have revealed a diverse set of flow morphologies. As the air displaces the suspension, the beads that make up the suspension can accumulate along the interface. The dynamics can generate “frictional fingers” of air…

[Phys. Rev. E 92, 032203] Published Mon Sep 28, 2015

]]>A fundamental process of surface energy minimization is the decay of a wire into separate droplets initiated by the Rayleigh-Plateau instability. Here we study the linear stability of a wire deposited on a unidirectionally patterned substrate with the wire being aligned with the pattern. We show tha…

[Phys. Rev. E 92, 032408] Published Mon Sep 28, 2015

]]>We present the frequency- and temperature-dependent dielectric properties of lysozyme solutions in a broad concentration regime, measured at subzero temperatures, and compare the results with measurements above the freezing point of water and on hydrated lysozyme powder. Our experiments allow examin…

[Phys. Rev. E 92, 032727] Published Mon Sep 28, 2015

]]>In an excitable thin-layer Belousov-Zhabotinsky (BZ) medium a localized perturbation leads to the formation of omnidirectional target or spiral waves of excitation. A subexcitable BZ medium responds to asymmetric local perturbation by producing traveling localized excitation wave-fragments, distant …

[Phys. Rev. E 92, 032811] Published Mon Sep 28, 2015

]]>We present a comprehensive study of the destruction of quantum multifractality in the presence of perturbations. We study diverse representative models displaying multifractality, including a pseudointegrable system, the Anderson model, and a random matrix model. We apply several types of natural pe…

[Phys. Rev. E 92, 032914] Published Mon Sep 28, 2015

]]>We study theoretically and experimentally coherent imaging of surface plasmon polaritons using either leakage radiation microscopy through a thin metal film or interference microscopy through a thick metal film. Using a rigorous modal formalism based on scalar Whittaker potentials, we develop a syst…

[Phys. Rev. E 92, 033202] Published Mon Sep 28, 2015

]]>We study the thermal boundary conduction in one-dimensional harmonic and ${\varphi}^{4}$ lattices, both of which consist of two segments coupled by a harmonic interaction. For the ballistic interfacial heat transport through the harmonic lattice, we use both theoretical calculation and molecular dynamics simulat…

[Phys. Rev. E 92, 032135] Published Fri Sep 25, 2015

]]>Neurons in many brain areas can develop a pronounced depolarized state of membrane potential (up state) in addition to the normal hyperpolarized state near the resting potential. The influence of the up state on signal encoding, however, is not well investigated. Here we construct a one-dimensional …

[Phys. Rev. E 92, 032726] Published Fri Sep 25, 2015

]]>In this paper, we present a method for characterizing the evolution of time-varying complex networks by adopting a thermodynamic representation of network structure computed from a polynomial (or algebraic) characterization of graph structure. Commencing from a representation of graph structure base…

[Phys. Rev. E 92, 032810] Published Fri Sep 25, 2015

]]>Penitentes are thin pinnacles of snow or ice that appear at high altitudes, naturally arranged in closely spaced formations and oriented in the general direction of the sun. The authors focus on the initial stages of their growth by performing a linear stability analysis and show, in their detailed analysis, that as sunlight sublimates the ice, the mixing of vapor above the ice surface controls the typical size of the penitentes.

[Phys. Rev. E 92, 033015] Published Fri Sep 25, 2015

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