Multistable systems exhibit a rich front dynamics between equilibria. In one-dimensional scalar gradient systems, the spread of the fronts is proportional to the energy difference between equilibria. Fronts spreading proportionally to the energetic difference between equilibria is a characteristic o…

[Phys. Rev. E 95, 010202(R)] Published Tue Jan 17, 2017

]]>This work investigates the influence of geometrical features of the Apollonian packing (AP) on the behavior of magnetic models. The proposed model differs from previous investigations on the Apollonian network (AN), where the magnetic coupling constants depend only on the properties of the network s…

[Phys. Rev. E 95, 012123] Published Tue Jan 17, 2017

]]>We analyze the stochastic dynamics of a large population of noninteracting particles driven by a global environmental input in the form of a dichotomous Markov noise process (DMNP). The population density of particle states evolves according to a stochastic Liouville equation with respect to differe…

[Phys. Rev. E 95, 012124] Published Tue Jan 17, 2017

]]>Negative absolute temperatures were introduced into experimental physics by Purcell and Pound, who successfully applied this concept to nuclear spins; nevertheless, the concept has proved controversial: a recent article aroused considerable interest by its claim, based on a classical entropy formula…

[Phys. Rev. E 95, 012125] Published Tue Jan 17, 2017

]]>We study the radiative heat transfer between two semi-infinite half-spaces, bounded by conductive surfaces in contact with vacuum. This setup is interpreted as a four-terminal mesoscopic transport problem. The slabs and interfaces are viewed as bosonic reservoirs, coupled perfectly to a scattering c…

[Phys. Rev. E 95, 012126] Published Tue Jan 17, 2017

]]>We consider the optical fiber channel modeled by the nonlinear Schrödinger equation with zero dispersion and additive Gaussian noise. Using the Feynman path-integral approach for the model, we find corrections to conditional probability density function, output signal distribution, conditional and o…

[Phys. Rev. E 95, 012127] Published Tue Jan 17, 2017

]]>Noise-induced escape from the domain of attraction of a nonhyperbolic chaotic attractor in a periodically excited nonlinear oscillator is further investigated. Deviations are found to be amplified at the primary homoclinic tangency from which the optimal force begins to fluctuate dramatically. Escap…

[Phys. Rev. E 95, 012208] Published Tue Jan 17, 2017

]]>We explore the classical dynamics of two interacting rotating dipoles that are fixed in the space and exposed to an external homogeneous electric field. Kinetic energy transfer mechanisms between the dipoles are investigated by varying both the amount of initial excess kinetic energy of one of them …

[Phys. Rev. E 95, 012209] Published Tue Jan 17, 2017

]]>We present the mathematical analysis of generalized complex contagions in a class of clustered multiplex networks. The model is intended to understand spread of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. …

[Phys. Rev. E 95, 012312] Published Tue Jan 17, 2017

]]>We show that the recently introduced logarithmic metrics used to predict disease arrival times on complex networks are approximations of more general network-based measures derived from random walks theory. Using the daily air-traffic transportation data we perform numerical experiments to compare t…

[Phys. Rev. E 95, 012313] Published Tue Jan 17, 2017

]]>The giant $k$-core—maximal connected subgraph of a network where each node has at least $k$ neighbors—is important in the study of phase transitions and in applications of network theory. Unlike Erdős-Rényi graphs and other random networks where $k$-cores emerge discontinuously for $k\ge 3$, we show that trans…

[Phys. Rev. E 95, 012314] Published Tue Jan 17, 2017

]]>The dynamical tolerance of coupled oscillator networks against local failures is studied. As the fraction of failed oscillator nodes gradually increases, the mean oscillation amplitude in the entire network decreases and then suddenly vanishes at a critical fraction as a phase transition. This criti…

[Phys. Rev. E 95, 012315] Published Tue Jan 17, 2017

]]>We study the structure of loops in networks using the notion of modulus of loop families. We introduce an alternate measure of network clustering by quantifying the richness of families of (simple) loops. Modulus tries to minimize the expected overlap among loops by spreading the expected link usage…

[Phys. Rev. E 95, 012316] Published Tue Jan 17, 2017

]]>A principled approach to characterize the hidden modular structure of networks is to formulate generative models and then infer their parameters from data. When the desired structure is composed of modules or “communities,” a suitable choice for this task is the stochastic block model (SBM), where n…

[Phys. Rev. E 95, 012317] Published Tue Jan 17, 2017

]]>In neurons, several intracellular cargoes are transported by motor proteins (kinesins) which walk on microtubules (MTs). However, kinesins can possibly unbind from the MTs before they reach their destinations. The unbound kinesins randomly diffuse in neurons until they bind to MTs. Then, they walk a…

[Phys. Rev. E 95, 012405] Published Tue Jan 17, 2017

]]>We examine numerically the transport of an assembly of active run-and-tumble disks interacting with a traveling-wave substrate. We show that as a function of substrate strength, wave speed, disk activity, and disk density, a variety of dynamical phases arise that are correlated with the structure an…

[Phys. Rev. E 95, 012607] Published Tue Jan 17, 2017

]]>The confinement of liquid crystals inside curved geometries leads to exotic structures, with applications ranging from biosensors to optical switches and privacy windows. Here we study how curvature affects the alignment of a cholesteric liquid crystal. We model the system on the mesoscale using the…

[Phys. Rev. E 95, 012702] Published Tue Jan 17, 2017

]]>We investigate the mechanical behavior of particle-stabilized droplets using micropipette aspiration. We observe that droplets stabilized with amphiphilic dumbbell-shaped particles exhibit a two-stage response to increasing suction pressure. Droplets first drip, then wrinkle and buckle like an elast…

[Phys. Rev. E 95, 012805] Published Tue Jan 17, 2017

]]>Buoyant material clustering in a stochastic flow, which is homogeneous and isotropic in space and stationary in time, is addressed. The dynamics of buoyant material in three-dimensional hydrodynamic flows can be considered as the motion of passive tracers in a compressible two-dimensional velocity f…

[Phys. Rev. E 95, 013109] Published Tue Jan 17, 2017

]]>Magnetic fields in rotating and radiating astrophysical plasma can be produced due to a radiative interaction between plasma layers moving relative to each other. The efficiency of current drive, and with it the associated dynamo effect, is considered in a number of limits. It is shown here, however…

[Phys. Rev. E 95, 013205] Published Tue Jan 17, 2017

]]>Self-diffusion and interdiffusion coefficients of binary ionic mixtures are evaluated using the effective potential theory (EPT), and the predictions are compared with the results of molecular dynamics simulations. We find that EPT agrees with molecular dynamics from weak coupling well into the stro…

[Phys. Rev. E 95, 013206] Published Tue Jan 17, 2017

]]>The work investigates the coupling between ion-acoustic waves and neutrino flavor oscillations in a nonrelativistic electron-ion plasma under the influence of a mixed neutrino beam. Neutrino oscillations are mediated by the flavor polarization vector dynamics in a material medium. The linear dispers…

[Phys. Rev. E 95, 013207] Published Tue Jan 17, 2017

]]>Interaction of a high-intensity short laser pulse with near-critical plasmas allows us to achieve extremely high coupling efficiency and transfer laser energy to energetic ions. One-dimensional particle-in-cell simulations are considered to detail the processes involved in the energy transfer. A con…

[Phys. Rev. E 95, 013208] Published Tue Jan 17, 2017

]]>We derive alternative Markov approximations for the projected (stochastic) force and memory function in the coarse-grained (CG) generalized Langevin equation, which describes the time evolution of the center-of-mass coordinates of clusters of particles in the microscopic ensemble. This is done with …

[Phys. Rev. E 95, 013303] Published Tue Jan 17, 2017

]]>The effect of the heterogeneity in the soil structure or the nonuniformity of the velocity field on the modeled resident time distribution (RTD) and breakthrough curves is quantified by their moments. While the first moment provides the effective velocity, the second moment is related to the longitu…

[Phys. Rev. E 95, 013304] Published Tue Jan 17, 2017

]]>Impact of the unphysical tangential advective-diffusion constraint of the bounce-back (BB) reflection on the impermeable solid surface is examined for the first four moments of concentration. Despite the number of recent improvements for the Neumann condition in the lattice Boltzmann method–advectio…

[Phys. Rev. E 95, 013305] Published Tue Jan 17, 2017

]]>For systems of classical spins interacting with the bath via damping and thermal noise, an approach is suggested to replace the white noise by a pulse noise acting at regular time intervals $\mathrm{\Delta}t$, within which the system evolves conservatively. The method is working well in the typical case of a small …

[Phys. Rev. E 95, 013306] Published Tue Jan 17, 2017

]]>We present results from a new variant of a diffusion hopping model, the convective diffusive lattice model, to describe the behavior of a particulate flux around bluff obstacles. Particle interactions are constrained to an underlying square lattice where particles are subject to excluded volume cond…

[Phys. Rev. E 95, 013307] Published Tue Jan 17, 2017

]]>We present average performance results for dynamical inference problems in large networks, where a set of nodes is hidden while the time trajectories of the others are observed. Examples of this scenario can occur in signal transduction and gene regulation networks. We focus on the linear stochastic…

[Phys. Rev. E 95, 012122] Published Fri Jan 13, 2017

]]>The effect of derivative nonlinearity and parity-time-symmetric ($\mathcal{PT}$-symmetric) potentials on the wave propagation dynamics is explored in the derivative nonlinear Schrödinger equation, where the physically interesting Scarf-II and harmonic-Hermite-Gaussian potentials are chosen. We study numerically…

[Phys. Rev. E 95, 012205] Published Fri Jan 13, 2017

]]>We study the path toward equilibrium of pairs of solitary wave envelopes (*bubbles*) that modulate a regular zigzag pattern in an annular channel. We evidence that bubble pairs are metastable states, which spontaneously evolve toward a stable single bubble. We exhibit the concept of *topological frustr…*

[Phys. Rev. E 95, 012206] Published Fri Jan 13, 2017

]]>Maintaining the stability of synchronization state is crucial for the functioning of many natural and artificial systems. In this study, we develop methods to optimize the synchronization stability of the Kuramoto model by minimizing the dominant Lyapunov exponent. Using the recently proposed cut-se…

[Phys. Rev. E 95, 012207] Published Fri Jan 13, 2017

]]>We apply a persistent homology analysis to investigate the behavior of nanovoids during the crazing process of glassy polymers. We carry out a coarse-grained molecular dynamics simulation of the uniaxial deformation of an amorphous polymer and analyze the results with persistent homology. Persistent…

[Phys. Rev. E 95, 012504] Published Fri Jan 13, 2017

]]>We present a detailed analysis of oscillatory modes during three-dimensional cellular growth in a diffusive transport regime. We ground our analysis primarily on *in situ* observations of directional solidification experiments of a transparent succinonitrile $0.24\phantom{\rule{0.16em}{0ex}}\mathrm{wt}\phantom{\rule{0.16em}{0ex}}\%$ camphor alloy performed in microgra…

[Phys. Rev. E 95, 012803] Published Fri Jan 13, 2017

]]>Atomically thin cylindrical nanopores can change shape in response to physically adsorbed gas inside. Coupled to a gas reservoir, an initially collapsed pore can expand to allow the adsorbed gas to form concentric shells on the inner part of the pore, driven by adsorption energetics, not gas pressur…

[Phys. Rev. E 95, 012804] Published Fri Jan 13, 2017

]]>The authors establish a framework for calculating distribution functions for quantities characterizing conformation and connectivity of randomly branched and interacting lattice trees or polymers. The work expands the analysis of Flory theory, which is widely used to calculate average values of such quantities.

[Phys. Rev. E 95, 012117] Published Thu Jan 12, 2017

]]>The dispersion and connectivity of particles with a high degree of polydispersity is relevant to problems involving composite material properties and reaction decomposition prediction and has been the subject of much study in the literature. This work utilizes Monte Carlo models to predict percolati…

[Phys. Rev. E 95, 012118] Published Thu Jan 12, 2017

]]>Decay of the metastable state is analyzed within the quantum Kramers model in the weak-to-intermediate dissipation regime. The decay kinetics in this regime is determined by energy exchange between the unstable mode and the stable modes of thermal bath. In our previous paper [Phys. Rev. A **42**, 4427 (…

[Phys. Rev. E 95, 012119] Published Thu Jan 12, 2017

]]>We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM…

[Phys. Rev. E 95, 012120] Published Thu Jan 12, 2017

]]>We use a kinetic mode-coupling theory (MCT) combining with generalized Langevin equation (GLE) to study the diffusion and conformational dynamics of a bead-spring Rouse chain (RC) dissolved in porous media. The media contains fluid particles and immobile matrix ones wherein the latter leads to the l…

[Phys. Rev. E 95, 012121] Published Thu Jan 12, 2017

]]>We study the stability of patterns in Hopfield networks in which a part of memorized patterns are similar. The similarity between patterns impacts the stability of these patterns, but the stability of other independent patterns is only changed slightly. We show that the stability of patterns is affe…

[Phys. Rev. E 95, 012309] Published Thu Jan 12, 2017

]]>In this work, we use the approximate-master-equation approach to study the dynamics of the Kinouchi-Copelli neural model on various networks. By categorizing each neuron in terms of its state and also the states of its neighbors, we are able to uncover how the coupled system evolves with respective …

[Phys. Rev. E 95, 012310] Published Thu Jan 12, 2017

]]>We study the Nagel-Schreckenberg cellular automata model for traffic flow by both simulations and analytical techniques. To better understand the nature of the jamming transition, we analyze the fraction of stopped cars $P(v=0)$ as a function of the mean car density. We present a simple argument that …

[Phys. Rev. E 95, 012311] Published Thu Jan 12, 2017

]]>The Landau–de Gennes free energy is used to study theoretically the effective interaction of spherical “key” and anisotropic “lock” colloidal particles. We assume identical anchoring properties of the surfaces of the key and of the lock particles, and we consider planar degenerate and perpendicular …

[Phys. Rev. E 95, 012606] Published Thu Jan 12, 2017

]]>By means of a finite elements technique we solve numerically the dynamics of an amorphous solid under deformation in the quasistatic driving limit. We study the noise statistics of the stress-strain signal in the steady-state plastic flow, focusing on systems with low internal dissipation. We analyz…

[Phys. Rev. E 95, 013003] Published Thu Jan 12, 2017

]]>We investigate the behavior of a model neuron that receives a biophysically realistic noisy postsynaptic current based on uncorrelated spiking activity from a large number of afferents. We show that, with static synapses, such noise can give rise to inverse stochastic resonance (ISR) as a function o…

[Phys. Rev. E 95, 012404] Published Wed Jan 11, 2017

]]>This analytical and experimental study should be useful in designing deployable origami bellows for a variety of applications. The authors present a unified geometrical description of several classes of origami bellows and identify parameters that control their properties. In addition, they describe construction of physical models and measurements of their mechanical responses.

[Phys. Rev. E 95, 013002] Published Wed Jan 11, 2017

]]>The Richtmyer-Meshkov (RM) instability of a nominally flat interface (${\mathrm{N}}_{2}/{\mathrm{SF}}_{6}$) subjected to a rippled shock, as the counterpart of a corrugated interface interacting with a planar shock, is studied experimentally in a vertical shock tube using both schlieren photography and fog visualization diagnost…

[Phys. Rev. E 95, 013107] Published Wed Jan 11, 2017

]]>We use the image solution technique to compute the leading order frequency-dependent self-mobility function of a small solid particle moving perpendicular to the surface of a spherical capsule whose membrane possesses shearing and bending rigidities. Comparing our results with those obtained earlier…

[Phys. Rev. E 95, 013108] Published Wed Jan 11, 2017

]]>Ising spin-glass models with bimodal, Gaussian, uniform, and Laplacian interaction distributions in dimension five are studied through detailed numerical simulations. The data are analyzed in both the finite-size scaling regime and the thermodynamic limit regime. It is shown that the values of criti…

[Phys. Rev. E 95, 012112] Published Tue Jan 10, 2017

]]>The escape rate of a Brownian particle over a potential barrier is accurately described by the Kramers theory. A quantitative theory explicitly taking the activity of Brownian particles into account has been lacking due to the inherently out-of-equilibrium nature of these particles. Using an effecti…

[Phys. Rev. E 95, 012115] Published Tue Jan 10, 2017

]]>Directed transport of self-propelled particles is numerically investigated in a three-dimensional asymmetric potential. Beside the steric repulsive forces, hydrodynamic interactions between particles have been taken into account in an approximate way. From numerical simulations, we find that hydrody…

[Phys. Rev. E 95, 012116] Published Tue Jan 10, 2017

]]>Range expansion of species is driven by the interactions among individual- and population-level processes and the spatial pattern of habitats. In this work we study how cooperatively growing populations spread on networks representing the skeleton of complex landscapes. By separating the slow and fa…

[Phys. Rev. E 95, 012306] Published Tue Jan 10, 2017

]]>We investigate the $q$-voter model with stochastic noise arising from independence on complex networks. Using the pair approximation, we provide a comprehensive, mathematical description of its behavior and derive a formula for the critical point. The analytical results are validated by carrying out M…

[Phys. Rev. E 95, 012307] Published Tue Jan 10, 2017

]]>We investigate the dynamical role of inhibitory and highly connected nodes (hub) in synchronization and input processing of leaky-integrate-and-fire neural networks with short term synaptic plasticity. We take advantage of a heterogeneous mean-field approximation to encode the role of network struct…

[Phys. Rev. E 95, 012308] Published Tue Jan 10, 2017

]]>The interactions between T-cell receptor (TCR) and peptide-major-histocompatibility complex (pMHC), which enable T-cell development and initiate adaptive immune responses, have been intensively studied. However, a central issue of how lipid rafts affect the TCR-pMHC interactions remains unclear. Her…

[Phys. Rev. E 95, 012403] Published Tue Jan 10, 2017

]]>We have performed Monte Carlo (MC) simulations on two-dimensional systems of quadrupole particles confined to a triangular lattice in order to determine the conditions that permit the formation of a limit-periodic phase. We have found that limit-periodic structures form only when the rotations of th…

[Phys. Rev. E 95, 012604] Published Tue Jan 10, 2017

]]>We use numerical simulations to study the effect of particle friction on suspension flows of non-Brownian hard particles. By systematically varying the microscopic friction coefficient ${\mu}_{p}$ and the viscous number $J$, we build a phase diagram that identifies three regimes of flow: frictionless, friction…

[Phys. Rev. E 95, 012605] Published Tue Jan 10, 2017

]]>The influence of line tension on the thermostability of a droplet nucleated from an oversaturated vapor at the interface of the vapor and another immiscible liquid is investigated. Along with the condition of mechanical equilibrium, the notion of extremization of the reversible work of formation is …

[Phys. Rev. E 95, 012802] Published Tue Jan 10, 2017

]]>Periodical patterns (bands) developing at the interface of two immiscible fluids under vibration parallel to interface are observed under zero-gravity conditions. Fluids are slightly below their liquid-vapor critical point where they behave in a scaled, universal manner. In addition, liquid and vapo…

[Phys. Rev. E 95, 013105] Published Tue Jan 10, 2017

]]>We present findings from an experimental study of the impact of liquid marbles onto solid surfaces. Using dual-view high-speed imaging, we reveal details of the impact dynamics previously not reported. During the spreading stage it is observed that particles at the surface flow rapidly to the periph…

[Phys. Rev. E 95, 013106] Published Tue Jan 10, 2017

]]>We identify the temperature being measured by a thermometer in a nonequilibrium scenario by studying heat conduction in a three-dimensional Lennard-Jones (LJ) system whose two ends are kept at different temperatures. It is accomplished by modeling the thermometer particles also with the LJ potential…

[Phys. Rev. E 95, 013302] Published Tue Jan 10, 2017

]]>The spanning cluster properties of a percolation model with nucleation and preferential growth exhibit first-order transitions depending on the values of the growth parameter ${g}_{0}$ and the initial seed concentration $\rho $. Except for the preferential growth of smaller clusters with a size-dependent growth …

[Phys. Rev. E 95, 010101(R)] Published Mon Jan 09, 2017

]]>The ground state of a two-level system (associated with probabilities $p$ and $1-p$, respectively) defined by a general Hamiltonian $\widehat{H}={\widehat{H}}_{0}+\lambda \widehat{V}$ is studied. The simple case characterized by $\lambda =0$, whose Hamiltonian ${\widehat{H}}_{0}$ is represented by a diagonal matrix, is well established and solvable within Boltzmann-Gi…

[Phys. Rev. E 95, 012111] Published Mon Jan 09, 2017

]]>We study the totally asymmetric exclusion process (TASEP) on a nonuniform one-dimensional ring consisting of two segments having unequal hopping rates, or *defects*. We allow weak particle nonconservation via Langmuir kinetics (LK), which are parametrized by generic unequal attachment and detachment r…

[Phys. Rev. E 95, 012113] Published Mon Jan 09, 2017

]]>First-passage-time problems are ubiquitous across many fields of study, including transport processes in semiconductors and biological synapses, evolutionary game theory and percolation. Despite their prominence, first-passage-time calculations have proven to be particularly challenging. Analytical …

[Phys. Rev. E 95, 012114] Published Mon Jan 09, 2017

]]>We investigate the detectability thresholds of various modular structures in the stochastic block model. Our analysis reveals how the detectability threshold is related to the details of the modular pattern, including the hierarchy of the clusters. We show that certain planted structures are impossi…

[Phys. Rev. E 95, 012304] Published Mon Jan 09, 2017

]]>The development of neuromorphic systems based on memristive elements—resistors with memory—requires a fundamental understanding of their collective dynamics when organized in networks. Here, we study an experimentally inspired model of two-dimensional disordered memristive networks subject to a slow…

[Phys. Rev. E 95, 012305] Published Mon Jan 09, 2017

]]>We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a nonequilibrium steady state. We apply this method to study the globule-stretch transition of a single tethered model polymer in shear flow. The folding and unfoldin…

[Phys. Rev. E 95, 012503] Published Mon Jan 09, 2017

]]>Unlike dry granular materials, a dense granular suspension like cornstarch in water can strongly resist extensional flows. At low extension rates, such a suspension behaves like a viscous fluid, but rapid extension results in a response where stresses far exceed the predictions of lubrication hydrod…

[Phys. Rev. E 95, 012603] Published Mon Jan 09, 2017

]]>The Reynolds number effects on the nonlinear growth rates of the Richtmyer-Meshkov instability are investigated using two-dimensional numerical simulations. A decrease in Reynolds number gives an increased time to reach nonlinear saturation, with Reynolds number effects only significant in the range…

[Phys. Rev. E 95, 013104] Published Mon Jan 09, 2017

]]>The liquid-crystal type of phase transition in complex plasmas has been observed repeatedly. However, more studies need to be done on the liquid-vapor transition in complex plasmas. In this paper, the phenomenon of coupling (condensation) of particles into self-confined particle pairs in an anisotro…

[Phys. Rev. E 95, 013202] Published Mon Jan 09, 2017

]]>Approximate one-dimensional (1D) as well as 2D and 3D simulations are playing an important supporting role in the design and analysis of future experiments at National Ignition Facility. This paper is mainly concerned with 1D simulations, used extensively in design and optimization. We couple a 1D b…

[Phys. Rev. E 95, 013203] Published Mon Jan 09, 2017

]]>We use large-scale classical molecular dynamics to determine microfield properties for several dense plasma mixtures. By employing quantum statistical potentials (QSPs) to regularize the Coulomb interaction, our simulations follow motions of electrons as well as ions for times long enough to track r…

[Phys. Rev. E 95, 013204] Published Mon Jan 09, 2017

]]>We consider the time-dependent dispersion properties of overdamped tracer particles diffusing in a one-dimensional periodic potential under the influence of an additional constant tilting force $F$. The system is studied in the region where the force is close to the critical value ${F}_{c}$ at which the barr…

[Phys. Rev. E 95, 012109] Published Fri Jan 06, 2017

]]>Steady-state properties of a driven tracer moving in a narrow two-dimensional (2D) channel of quiescent medium are studied. The tracer drives the system out of equilibrium, perturbs the density and pressure fields, and gives the bath particles a nonzero average velocity, creating a current in the ch…

[Phys. Rev. E 95, 012110] Published Fri Jan 06, 2017

]]>We study the effect of time delay on the dynamics of a system of repulsively coupled nonlinear oscillators that are configured as a geometrically frustrated network. In the absence of time delay, frustrated systems are known to possess a high degree of multistability among a large number of coexisti…

[Phys. Rev. E 95, 012204] Published Fri Jan 06, 2017

]]>The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual-based model of Wright and Fisher, we compute the amplitude of *neutral* aggregation in the genome sp…

[Phys. Rev. E 95, 012402] Published Fri Jan 06, 2017

]]>We investigate the simulation of stiff (extensible) and rigid (inextensible) semiflexible polymers in solution. In particular, we focus on polymers represented as chains of beads, interconnected by bonds with a low to zero extensibility, and significant persistence in the bond orientations along the…

[Phys. Rev. E 95, 012502] Published Fri Jan 06, 2017

]]>The nucleation of islands in a supersaturated solution of surface adatoms is considered taking into account the possibility of diffusion profile formation in the island vicinity. It is shown that the treatment of diffusion-controlled cluster growth in terms of the Fokker-Planck equation is justified…

[Phys. Rev. E 95, 012801] Published Fri Jan 06, 2017

]]>We address the long-standing challenge of how to reconstruct links in directed networks from measurements, and present a general method that makes use of a noise-induced relation between network structure and both the time-lagged covariance of measurements taken at two different times and the covari…

[Phys. Rev. E 95, 010301(R)] Published Thu Jan 05, 2017

]]>Work is one of the most basic notions in statistical mechanics, with work fluctuation theorems being one central topic in nanoscale thermodynamics. With Hamiltonian chaos commonly thought to provide a foundation for classical statistical mechanics, here we present general salient results regarding h…

[Phys. Rev. E 95, 012106] Published Thu Jan 05, 2017

]]>We derive the necessary conditions for implementing a regulator that depends on both momentum and frequency in the nonperturbative renormalization-group flow equations of out-of-equilibrium statistical systems. We consider model A as a benchmark and compute its dynamical critical exponent $z$. This al…

[Phys. Rev. E 95, 012107] Published Thu Jan 05, 2017

]]>Extending a preceding study of the velocity autocorrelation function (VAF) in a simulated Lennard-Jones fluid [Phys. Rev. E **92**, 042166 (2015)] to cover higher-density and lower-temperature states, we show that the recently demonstrated multiexponential expansion method allows for a full account and …

[Phys. Rev. E 95, 012108] Published Thu Jan 05, 2017

]]>This paper presents a model to describe the crawling of cells based on the cell shape, which is determined by the force balance in the membrane, and its internal chemical dynamics which controls the steering mechanism. The interplay of these two factors gives rise to a phase diagram where a transition from straight to circular trajectories is observed.

[Phys. Rev. E 95, 012401] Published Thu Jan 05, 2017

]]>Active Brownian particles (ABPs) represent a minimal model of active matter consisting of self-propelled spheres with purely repulsive interactions and rotational noise. Here we examine the pressure of ABPs in two dimensions in both closed boxes and systems with periodic boundary conditions and show…

[Phys. Rev. E 95, 012601] Published Thu Jan 05, 2017

]]>This work presents a numerical and theoretical investigation of the collective dynamics of colloids in an unbounded solution but trapped in a harmonic potential. Under strict two-dimensional confinement (infinitely stiff trap) the collective colloidal diffusion is enhanced and diverges at zero wave …

[Phys. Rev. E 95, 012602] Published Thu Jan 05, 2017

]]>We consider a mathematical model that consists of a nematic liquid crystal layer sandwiched between two parallel bounding plates, across which an external field is applied. We investigate how the number and type of solutions for the director orientation within the layer change as the field strength,…

[Phys. Rev. E 95, 012701] Published Thu Jan 05, 2017

]]>Generation of intense coherent THz radiation by obliquely incidenting an intense laser pulse on a wire target is studied using particle-in-cell simulation. The laser-accelerated fast electrons are confined and guided along the surface of the wire, which then acts like a current-carrying line antenna…

[Phys. Rev. E 95, 013201] Published Thu Jan 05, 2017

]]>[Phys. Rev. E 95, 019901] Published Thu Jan 05, 2017

]]>An array of excitable Josephson junctions under a global mean-field interaction and a common periodic forcing shows the emergence of two important classes of coherent dynamics, librational and rotational motion, in the weaker and stronger coupling limits, respectively, with transitions to chimeralik…

[Phys. Rev. E 95, 010201(R)] Published Wed Jan 04, 2017

]]>The phase diagram and the critical behavior of the spin-1 and the spin-3/2 two-dimensional Baxter-Wu model in a crystal field are studied by conventional finite-size scaling and conformal invariance theory. The phase diagram of this model, for the spin-1 case, is qualitatively the same as those of t…

[Phys. Rev. E 95, 012103] Published Wed Jan 04, 2017

]]>We study the dynamics of the out-of-equilibrium nonlinear $q$-voter model with two types of susceptible voters and zealots, introduced in Mellor *et al.* [Europhys. Lett. **113**, 48001 (2016)]. In this model, each individual supports one of two parties and is either a susceptible voter of type ${q}_{1}$ or ${q}_{2}$, or…

[Phys. Rev. E 95, 012104] Published Wed Jan 04, 2017

]]>The entanglement entropy $\mathcal{S}$ is an indicator of quantum correlations in the ground state of a many-body quantum system. At a second-order quantum phase-transition point in one dimension $\mathcal{S}$ generally has a logarithmic singularity. Here we consider quantum spin chains with a first-order quantum phase tra…

[Phys. Rev. E 95, 012105] Published Wed Jan 04, 2017

]]>We study waves with exponentially decaying oscillatory tails in a reaction-diffusion system with linear cross diffusion. To be specific, we consider a piecewise linear approximation of the FitzHugh-Nagumo model, also known as the Bonhoeffer-van der Pol model. We focus on two types of traveling waves…

[Phys. Rev. E 95, 012203] Published Wed Jan 04, 2017

]]>Multistrategy evolutionary games are studied on a square lattice when the pair interactions are composed of coordinations between strategy pairs and an additional term with self-dependent payoff. We describe a method for determining the strength of each elementary coordination component in $n$-strateg…

[Phys. Rev. E 95, 012303] Published Wed Jan 04, 2017

]]>This paper examines the behavior of the dimensionless dissipation rate ${C}_{\varepsilon}$ for stationary and nonstationary magnetohydrodynamic (MHD) turbulence in the presence of external forces. By combining with previous studies for freely decaying MHD turbulence, we obtain here both the most general model equati…

[Phys. Rev. E 95, 013102] Published Wed Jan 04, 2017

]]>We develop an approach for computing the hydrodynamic friction tensor and scalar friction coefficient for an aerosol fractal aggregate in the transition regime. Our approach involves solving the Bhatnagar-Gross-Krook equation for the velocity field around a sphere and using the velocity field to cal…

[Phys. Rev. E 95, 013103] Published Wed Jan 04, 2017

]]>The majority-vote model with noise was studied on the 11 Archimedean lattices by the Monte Carlo method and finite-size scaling. The critical noises and critical exponents were obtained with precision. Contrary to some previous reports, we confirmed that the majority-vote model on the Archimedean la…

[Phys. Rev. E 95, 012101] Published Tue Jan 03, 2017

]]>The Giardinà-Kurchan-Peliti algorithm is a numerical procedure that uses population dynamics in order to calculate large deviation functions associated to the distribution of time-averaged observables. To study the numerical errors of this algorithm, we explicitly devise a stochastic birth-death pro…

[Phys. Rev. E 95, 012102] Published Tue Jan 03, 2017

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