We present a semiclassical prediction of regular-to-chaotic tunneling in systems with a mixed phase space, including the effect of a nonlinear resonance chain. We identify complex paths for direct and resonance-assisted tunneling in the phase space of an integrable approximation with one nonlinear r…

[Phys. Rev. E 95, 020202(R)] Published Mon Feb 27, 2017

]]>We investigate the effect of nonlinear interaction on the geometric structure of a nonequilibrium process. Specifically, by considering a driven-dissipative system where a stochastic variable $x$ is damped either linearly ($\propto x$) or nonlinearly ($\propto {x}^{3}$) while driven by a white noise, we compute the time-dep…

[Phys. Rev. E 95, 022137] Published Mon Feb 27, 2017

]]>An alternative analytical solution is presented, based on irreversible thermodynamics, that describes the equilibrium distribution of the components of a nonideal fluid mixture in a one-dimensional hydrostatic and isothermal system. In such a system, the vertical compositional profile of the fluid a…

[Phys. Rev. E 95, 022138] Published Mon Feb 27, 2017

]]>The continuous packing of a flexible rod in two-dimensional cavities yields a countable set of interacting domains that resembles nonequilibrium cellular systems and belongs to a new class of lightweight material. However, the link between the length of the rod and the number of domains requires inv…

[Phys. Rev. E 95, 022312] Published Mon Feb 27, 2017

]]>While the statistical and resilience properties of the Internet are no longer changing significantly across time, the Darknet, a network devoted to keep anonymous its traffic, still experiences rapid changes to improve the security of its users. Here we study the structure of the Darknet and find th…

[Phys. Rev. E 95, 022313] Published Mon Feb 27, 2017

]]>We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test-charge theory [S. Buyukdagli *et al.*, Phys. Rev. E **94**, 042502 (2016)] to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loo…

[Phys. Rev. E 95, 022502] Published Mon Feb 27, 2017

]]>A theory for phase coarsening in multicomponent systems is developed in which both the multicomponent thermodynamic effect and kinetic effect from a nonzero volume fraction are considered. In contrast to previous theory, a diffusion screening zone for a coarsening particle due to nonzero volume frac…

[Phys. Rev. E 95, 022609] Published Mon Feb 27, 2017

]]>The fracture toughness of colloidal films is measured by characterizing cracks which form during directional drying. Images from a confocal microscope are processed to measure the crack width as a function of distance from the crack tip. Applying theory for thin elastic films the fracture toughness …

[Phys. Rev. E 95, 022610] Published Mon Feb 27, 2017

]]>Fluid flow of suspended liquid films induced by non-uniform alternating electric fields has been reported. The electric fields were generated by two rod-like electrodes perpendicular to the fluid surface. The observed fluid flow was explained qualitatively by considering a *charge induction mechanism*…

[Phys. Rev. E 95, 022806] Published Mon Feb 27, 2017

]]>We construct an ensemble distribution to describe steady immiscible two-phase flow of two incompressible fluids in a porous medium. The system is found to be ergodic. The distribution is used to compute macroscopic flow parameters. In particular, we find an expression for the overall mobility of the…

[Phys. Rev. E 95, 023116] Published Mon Feb 27, 2017

]]>The growth rates of seeded QED cascades in counterpropagating lasers are calculated with first-principles two- and three-dimensional QED-PIC (particle-in-cell) simulations. The dependence of the growth rate on the laser polarization and intensity is compared with analytical models that support the f…

[Phys. Rev. E 95, 023210] Published Mon Feb 27, 2017

]]>We consider a model of semiflexible interacting self-avoiding trails (sISATs) on a lattice, where the walks are constrained to visit each lattice edge at most once. Such models have been studied as an alternative to the self-attracting self-avoiding walks (SASAWs) to investigate the collapse transit…

[Phys. Rev. E 95, 022132] Published Fri Feb 24, 2017

]]>Mutual diffusion in multicomponent liquids is studied. It is taken into consideration that the influence of complex formation on the diffusion process may be substantial. The theory is applied to analyze mass transfer in an acetone-chloroform solution. The molecular complex concentration was obtaine…

[Phys. Rev. E 95, 022133] Published Fri Feb 24, 2017

]]>We develop a method to calculate left-right eigenvector correlations of the product of $m$ independent $N\times N$ complex Ginibre matrices. For illustration, we present explicit analytical results for the vector overlap for a couple of examples for small $m$ and $N$. We conjecture that the integrated overlap bet…

[Phys. Rev. E 95, 022134] Published Fri Feb 24, 2017

]]>We propose a quantum thermal machine composed of two nanomechanical resonators (two membranes suspended over a trench in a substrate) placed a few $\mu \mathrm{m}$ from each other. The quantum thermodynamical cycle is powered by the Casimir interaction between the resonators and the working fluid is the polariton…

[Phys. Rev. E 95, 022135] Published Fri Feb 24, 2017

]]>Onsager reciprocity relations derive from the fundamental time reversibility of the underlying microscopic equations of motion. This gives rise to a large set of symmetric cross-coupling phenomena. We here demonstrate that different reciprocity relations may arise from the notion of mesoscopic time …

[Phys. Rev. E 95, 022136] Published Fri Feb 24, 2017

]]>We investigate experimentally and numerically the synchronization of two-dimensional spiral wave patterns in the Belousov-Zhabotinsky reaction due to point-to-point coupling of two separate domains. Different synchronization modalities appear depending on the coupling strength and the initial patter…

[Phys. Rev. E 95, 022215] Published Fri Feb 24, 2017

]]>Reconstructing network connection topology and interaction strengths solely from measurement of the dynamics of the nodes is a challenging inverse problem of broad applicability in various areas of science and engineering. For a discrete-time step network under noises whose noise-free dynamics is st…

[Phys. Rev. E 95, 022311] Published Fri Feb 24, 2017

]]>While it is widely accepted that information is encoded in neurons via action potentials or spikes, it is far less understood what specific features of spiking contain encoded information. Experimental evidence has suggested that the timing of the first spike may be an energy-efficient coding mechan…

[Phys. Rev. E 95, 022414] Published Fri Feb 24, 2017

]]>We propose a surface model of spin dephasing in lung tissue that includes both susceptibility and diffusion effects to provide a closed-form solution of the Bloch-Torrey equation on the alveolar surface. The nonlocal susceptibility effects of the model are validated against numerical simulations of …

[Phys. Rev. E 95, 022415] Published Fri Feb 24, 2017

]]>Direct numerical simulations of homogeneous decaying turbulence with background rotation show the existence of a systematic and significant imbalance between the non-linear energy cascade to small scales and its dissipation. By starting the decay from a statistically stationary and weakly rotating t…

[Phys. Rev. E 95, 023114] Published Fri Feb 24, 2017

]]>Time evolution of the fully resolved incompressible homogeneous turbulent shear flow in noninteger Fourier dimensions is numerically investigated. The Fourier dimension of the flow field is extended from the integer value 3 to the noninteger values by projecting the Navier-Stokes equation on the fra…

[Phys. Rev. E 95, 023115] Published Fri Feb 24, 2017

]]>Scaling properties of a two-dimensional (2d) plasma physical current-sheet simulation model involving a full set of magnetohydrodynamic (MHD) equations with current-dependent resistivity are investigated. The current sheet supports a spatial magnetic field reversal that is forced through loading of …

[Phys. Rev. E 95, 023209] Published Fri Feb 24, 2017

]]>In this work, a high-order weighted essentially nonoscillatory (WENO) finite-difference lattice Boltzmann method (WENOLBM) is developed and assessed for an accurate simulation of incompressible flows. To handle curved geometries with nonuniform grids, the incompressible form of the discrete Boltzman…

[Phys. Rev. E 95, 023314] Published Fri Feb 24, 2017

]]>Spatially extended systems can support local transient excitations in which just a part of the system is excited. The mechanisms reported so far are local excitability and excitation of a localized structure. Here we introduce an alternative mechanism based on the coexistence of two homogeneous stab…

[Phys. Rev. E 95, 020201(R)] Published Thu Feb 23, 2017

]]>For a low-dissipation heat engine model we present the role of the partial contact times and the total operational time as control parameters to switch from maximum power state to maximum $\mathrm{\Omega}$ trade-off state. The symmetry of the dissipation coefficients may be used in the design of the heat engine to …

[Phys. Rev. E 95, 022131] Published Thu Feb 23, 2017

]]>For quite some time nonmonotonic flow curve was thought to be a requirement for shear banded flows in complex fluids. Thus, in simple yield stress fluids shear banding was considered to be absent. Recent spatially resolved rheological experiments have found simple yield stress fluids to exhibit shea…

[Phys. Rev. E 95, 022608] Published Thu Feb 23, 2017

]]>The application of an electric field to microspheres suspended in a liquid crystal causes particle translation in a plane perpendicular to the applied field direction. Depending on applied electric field amplitude and frequency, a wealth of different motion modes may be observed above a threshold, w…

[Phys. Rev. E 95, 022703] Published Thu Feb 23, 2017

]]>The impact of water drops onto a solid surface at subfreezing temperatures has been experimentally studied. Drop nucleation has been observed using a high-speed video system. The statistics of nucleation allows the estimation of the average number of nucleation sites per unit area of the wetted part…

[Phys. Rev. E 95, 022805] Published Thu Feb 23, 2017

]]>We investigate numerically and theoretically the internal structures of a driven granular gas in cuboidal cell geometries. Clustering is reported and particles are classified as gaseous or clustered via a local packing fraction criterion based on a Voronoi tessellation. We observe that small cluster…

[Phys. Rev. E 95, 022905] Published Thu Feb 23, 2017

]]>The nonequilibrium gas flow in a two-dimensional microchannel with a ratchet surface and a moving wall is investigated numerically with a kinetic method [Guo *et al.*, Phys. Rev. E **91**, 033313 (2015)]. The presence of periodic asymmetrical ratchet structures on the bottom wall of the channel and the t…

[Phys. Rev. E 95, 023113] Published Thu Feb 23, 2017

]]>The generalized Crank-Nicolson method is employed to obtain numerical solutions of the two-dimensional time-dependent Schrödinger equation. An adapted alternating-direction implicit method is used, along with a high-order finite-difference scheme in space. Extra care has to be taken for the needed p…

[Phys. Rev. E 95, 023310] Published Thu Feb 23, 2017

]]>Within the framework of the central-moment-based lattice Boltzmann method, we propose a strategy to account for external forces in two and three dimensions. Its numerical properties are evaluated against consolidated benchmark problems, highlighting very high accuracy and optimal convergence. Moreov…

[Phys. Rev. E 95, 023311] Published Thu Feb 23, 2017

]]>The apparent ubiquity of binary random processes in physics and many other fields has attracted considerable attention from the modeling community. However, generation of binary sequences with prescribed autocorrelation is a challenging task owing to the discrete nature of the marginal distributions…

[Phys. Rev. E 95, 023312] Published Thu Feb 23, 2017

]]>In this paper, a higher order Chapmann-Enskog expansion technique is applied to pseudopotential lattice Boltzmann equation (LBE), and the contribution of third order error terms to pressure tensor is analyzed in detail. To be consistent with the thermodynamic theory, a force term is introduced to mo…

[Phys. Rev. E 95, 023313] Published Thu Feb 23, 2017

]]>[Phys. Rev. E 95, 029902] Published Thu Feb 23, 2017

]]>Aging can be observed for numerous physical systems. In such systems statistical properties [like probability distribution, mean square displacement (MSD), first-passage time] depend on a time span ${t}_{a}$ between the initialization and the beginning of observations. In this paper we study aging properti…

[Phys. Rev. E 95, 022126] Published Wed Feb 22, 2017

]]>We investigate the excitation dynamics at a first-order quantum phase transition (QPT). More specifically, we consider the quench-induced QPT in the quantum search algorithm, which aims at finding out a marked element in an unstructured list. We begin by deriving the exact dynamics of the model, whi…

[Phys. Rev. E 95, 022127] Published Wed Feb 22, 2017

]]>We demonstrate that two interacting spinlike systems characterized by different excitation frequencies and coupled to a thermal bath each, can be used as a quantum thermal diode capable of efficiently rectifying the heat current. This is done by deriving analytical expressions for both the heat curr…

[Phys. Rev. E 95, 022128] Published Wed Feb 22, 2017

]]>Entanglement prethermalization (EP) refers to a quasi-stationary nonequilibrium state of a composite system in which each individual subsystem looks thermal but the entire system remains nonthermal due to quantum entanglement between subsystems. We theoretically study the dynamics of EP following a …

[Phys. Rev. E 95, 022129] Published Wed Feb 22, 2017

]]>Networks of particles connected by springs model many condensed-matter systems, from colloids interacting with a short-range potential and complex fluids near jamming, to self-assembled lattices and various metamaterials. Under small thermal fluctuations the vibrational entropy of a ground state is …

[Phys. Rev. E 95, 022130] Published Wed Feb 22, 2017

]]>It is widely accepted that neuronal firing rates contain a significant amount of information about the stimulus intensity. Nevertheless, theoretical studies on the coding accuracy inferred from the exact spike counting distributions are rare. We present an analysis based on the number of observed sp…

[Phys. Rev. E 95, 022310] Published Wed Feb 22, 2017

]]>Radical-ion-pair reactions, central for understanding the avian magnetic compass and spin transport in photosynthetic reaction centers, were recently shown to be a fruitful paradigm of the new synthesis of quantum information science with biological processes. We show here that the master equation s…

[Phys. Rev. E 95, 022413] Published Wed Feb 22, 2017

]]>Thin fluid membranes embedded in a bulk fluid of different viscosity are of fundamental interest as experimental realizations of quasi-two-dimensional fluids and as models of biological membranes. We have probed the hydrodynamics of thin fluid membranes by active microrheology using small tracer par…

[Phys. Rev. E 95, 022702] Published Wed Feb 22, 2017

]]>Hydrodynamic fields, macroscopic boundary conditions, and non-Newtonian rheology of the acceleration-driven Poiseuille flow of a dilute granular gas are probed using “direct simulation Monte Carlo” method for a range of Knudsen numbers ($\text{Kn}$, the ratio between the mean free path and the macroscopic le…

[Phys. Rev. E 95, 022903] Published Wed Feb 22, 2017

]]>We report on the existence of discrete breathers in a one-dimensional, mass-in-mass chain with linear intersite coupling and nonlinear, precompressed Hertzian local resonators, which is motivated by recent studies of the dynamics of microspheres adhered to elastic substrates. After predicting theore…

[Phys. Rev. E 95, 022904] Published Wed Feb 22, 2017

]]>Electrokinetic (EK) turbulence or electrohydrodynamic (EHD) turbulence has been recently achieved in different fluids under both ac [G. Wang *et al.*, Lab Chip **14**, 1452 (2014); Phys. Rev. E **93**, 013106 (2016)] and dc electric fields [A. Varshney *et al.*, Soft Matter **12**, 1759 (2016)]. Here, through dim…

[Phys. Rev. E 95, 023111] Published Wed Feb 22, 2017

]]>Magnetic Archimedes Coriolis (MAC) waves are omnipresent in several geophysical and astrophysical flows such as the solar tachocline. In the present study, we use linear spectral theory (LST) and investigate the energy partition, scale by scale, in MAC weak wave turbulence for a Boussinesq fluid. At…

[Phys. Rev. E 95, 023112] Published Wed Feb 22, 2017

]]>We study quantum enhancement of transport in open systems in the presence of disorder and dephasing. Quantum coherence effects may significantly enhance transport in open systems even in the semiclassical regime (where the decoherence rate is greater than the intersite hopping amplitude), as long as…

[Phys. Rev. E 95, 022122] Published Tue Feb 21, 2017

]]>This paper is the second in a series devoted to the study of Langevin systems subjected to a continuous time-delayed feedback control. The goal of our previous paper [Phys. Rev. E **91**, 042114 (2015)] was to derive second-law-like inequalities that provide bounds to the average extracted work. Here we…

[Phys. Rev. E 95, 022123] Published Tue Feb 21, 2017

]]>This paper presents an approximation for the density-dependent diffusion coefficient that describes the behavior of kinetically constrained lattice-gas models. The authors show that non-negligible correlations appear in these models when the system is driven out of equilibrium. Such correlations also appear to be the reason for small discrepancies between approximations and numerical results for a broader group of models.

[Phys. Rev. E 95, 022124] Published Tue Feb 21, 2017

]]>Thermodynamic fluxes (diffusion fluxes, heat flux, etc.) are often proportional to thermodynamic forces (gradients of chemical potentials, temperature, etc.) via the matrix of phenomenological coefficients. Onsager's relations imply that the matrix is symmetric, which reduces the number of unknown c…

[Phys. Rev. E 95, 022125] Published Tue Feb 21, 2017

]]>This paper tackles the problem of mixing in materials that, in addition to smooth flows, can also exhibit discontinuous rearrangements of the components. The authors go beyond traditional measures of mixing to study the dynamical properties of these mixings and specifically focus on the rate of mixing.

[Phys. Rev. E 95, 022213] Published Tue Feb 21, 2017

]]>The trajectory equations for classical periodic orbits in the equilateral-triangular and circular billiards are systematically extracted from quantum stationary coherent states. The relationship between the phase factors of quantum stationary coherent states and the initial positions of classical pe…

[Phys. Rev. E 95, 022214] Published Tue Feb 21, 2017

]]>Memory has a great impact on the evolution of every process related to human societies. Among them, the evolution of an epidemic is directly related to the individuals' experiences. Indeed, any real epidemic process is clearly sustained by a non-Markovian dynamics: memory effects play an essential r…

[Phys. Rev. E 95, 022409] Published Tue Feb 21, 2017

]]>Some types of bacteria possess a propulsion mechanism that uses a helical flagellum that rotates and allows for swimming. The authors perform numerical simulations to study the hydrodynamics of this flagellum and show an array of different dynamical behaviors, further differentiated by the presence or absence of a flexible link to the motor.

[Phys. Rev. E 95, 022410] Published Tue Feb 21, 2017

]]>Our study considers the mechanism of the spontaneous oscillations of molecular motors that are driven by the power stroke principle by applying linear stability analysis around the stationary solution. By representing the coupling equation of microscopic molecular motor dynamics and mesoscopic sarco…

[Phys. Rev. E 95, 022411] Published Tue Feb 21, 2017

]]>The response of bursting neurons to fluctuating inputs is usually hard to predict, due to their strong nonlinearity. For the same reason, decoding the injected stimulus from the activity of a bursting neuron is generally difficult. In this paper we propose a method describing (for neuron models) a m…

[Phys. Rev. E 95, 022412] Published Tue Feb 21, 2017

]]>The Green-Kubo method is a commonly used approach for predicting transport properties in a system from equilibrium molecular dynamics simulations. The approach is founded on the fluctuation dissipation theorem and relates the property of interest to the lifetime of fluctuations in its thermodynamic …

[Phys. Rev. E 95, 023308] Published Tue Feb 21, 2017

]]>We have developed a method to calculate the weak localization and antilocalization corrections based on the real-space simulation, where we provide 147 885 predetermined return orbitals of quasi-two-dimensional electrons with up to 5000 scattering events that are repeatedly used. Our model subsumes …

[Phys. Rev. E 95, 023309] Published Tue Feb 21, 2017

]]>We demonstrate that the time evolution of a first-order phase transition may be described quite generally in terms of the statistics of point processes, thereby providing an intuitive framework for visualizing transition kinetics. A number of attractive and repulsive nucleation scenarios is examined…

[Phys. Rev. E 95, 022121] Published Fri Feb 17, 2017

]]>Biochemical systems with switch-like interactions, such as gene regulatory networks, are well modeled by autonomous Boolean networks. Specifically, the topology and logic of gene interactions can be described by systems of continuous piecewise-linear differential equations, enabling analytical predi…

[Phys. Rev. E 95, 022211] Published Fri Feb 17, 2017

]]>We present an analytical description of the large-amplitude stationary oscillations of the finite discrete system of harmonically coupled pendulums without any restrictions on their amplitudes (excluding a vicinity of $\pi )$. Although this model has numerous applications in different fields of physics, …

[Phys. Rev. E 95, 022212] Published Fri Feb 17, 2017

]]>Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We investigate the dynamics of two identical synthetic genetic…

[Phys. Rev. E 95, 022408] Published Fri Feb 17, 2017

]]>We study the dynamics of a Brownian circle swimmer with a time-dependent self-propulsion velocity in an external temporally varying harmonic potential. For several situations, the noise-free swimming paths, the noise-averaged mean trajectories, and the mean-square displacements are calculated analyt…

[Phys. Rev. E 95, 022606] Published Fri Feb 17, 2017

]]>The elusive connection between dynamics and local structure in supercooled liquids is an important piece of the puzzle in the unsolved problem of the glass transition. The Johari-Goldstein $\beta $ relaxation, ubiquitous in glass-forming liquids, exhibits mean properties that are strongly correlated to the…

[Phys. Rev. E 95, 022607] Published Fri Feb 17, 2017

]]>We study the small scale clustering of gyrotactic swimmers transported by a turbulent flow, when the intrinsic variability of the swimming parameters within the population is considered. By means of extensive numerical simulations, we find that the variety of the population introduces a characterist…

[Phys. Rev. E 95, 023108] Published Fri Feb 17, 2017

]]>The Rayleigh-Taylor (RT) mixing induced by random interface disturbances between two incompressible viscous fluids is simulated numerically. The ensemble averaged spike velocity is found to be remarkably retarded when the random interface disturbances are superimposed with an optimized additional mo…

[Phys. Rev. E 95, 023109] Published Fri Feb 17, 2017

]]>Based on the central limit theorem, we discuss the problem of evaluation of the statistical error of Monte Carlo calculations using a time-discretized diffusion process. We present a robust and practical method to determine the effective variance of general observables and show how to verify the equ…

[Phys. Rev. E 95, 023307] Published Fri Feb 17, 2017

]]>The neutron-spin-echo method (NSE) is a powerful technique for studying internal dynamics of macromolecules in solutions because it can simultaneously probe length and time scales comparable to intramolecular density fluctuations of macromolecules. Recently, there has been increased, strong interest…

[Phys. Rev. E 95, 020501(R)] Published Thu Feb 16, 2017

]]>We investigate energy transfer by the radiation from a cavity quantum electrodynamics system in the context of quantum thermodynamics. We propose a method of decomposing it into work and heat within the framework of quantum master equations. We find that the work and heat correspond, respectively, t…

[Phys. Rev. E 95, 022119] Published Thu Feb 16, 2017

]]>The deposition of one-dimensional objects (such as polymers) on a one-dimensional lattice with the presence of impurities is studied in order to find saturation conditions in what is known as jamming. Over a critical concentration of $k$-mers (polymers of length $k$), no further depositions are possible…

[Phys. Rev. E 95, 022120] Published Thu Feb 16, 2017

]]>In this work, we show that under specific anomalous diffusion conditions, chemical systems can produce well-ordered self-similar concentration patterns through diffusion-driven instability. We also find spiral patterns and patterns with mixtures of rotational symmetries. The type of anomalous diffus…

[Phys. Rev. E 95, 022210] Published Thu Feb 16, 2017

]]>Investigating the relation between various structural patterns found in real-world networks and the stability of underlying systems is crucial to understand the importance and evolutionary origin of such patterns. We evolve multiplex networks, comprising antisymmetric couplings in one layer depictin…

[Phys. Rev. E 95, 022309] Published Thu Feb 16, 2017

]]>Turbulence is a ubiquitous phenomenon in natural and industrial flows. Since the celebrated work of Kolmogorov in 1941, understanding the statistical properties of fully developed turbulence has remained a major quest. In particular, deriving the properties of turbulent flows from a mesoscopic descr…

[Phys. Rev. E 95, 023107] Published Thu Feb 16, 2017

]]>A Monte Carlo approach to proton stopping in warm dense matter is implemented into an existing particle-in-cell code. This approach is based on multiple electron-electron, electron-ion, and ion-ion binary collision and accounts for both the free and the bound electrons in the plasmas. This approach …

[Phys. Rev. E 95, 023207] Published Thu Feb 16, 2017

]]>A physical model based on a Monte Carlo approach is proposed to calculate the ionization dynamics of hot-solid-density plasmas within particle-in-cell (PIC) simulations, and where the impact (collision) ionization (CI), electron-ion recombination (RE), and ionization potential depression (IPD) by su…

[Phys. Rev. E 95, 023208] Published Thu Feb 16, 2017

]]>Shadowgraphy is a technique widely used to diagnose objects or systems in various fields in physics and engineering. In shadowgraphy, an optical beam is deflected by the object and then the intensity modulation is captured on a screen placed some distance away. However, retrieving quantitative infor…

[Phys. Rev. E 95, 023306] Published Thu Feb 16, 2017

]]>Many coordination phenomena are based on a synchronization process, whose global behavior emerges from the interactions among the individual parts. Often in nature, such self-organized mechanism allows the system to behave as a whole and thus grounding its very first existence, or expected functioni…

[Phys. Rev. E 95, 022209] Published Wed Feb 15, 2017

]]>Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well-defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte…

[Phys. Rev. E 95, 022501] Published Wed Feb 15, 2017

]]>A lattice version of the driven inelastic Maxwell gas is studied in one dimension with periodic boundary conditions. Each site $i$ of the lattice is assigned with a scalar “velocity,” ${v}_{i}$. Nearest neighbors on the lattice interact, with a rate ${\tau}_{c}^{-1}$, according to an inelastic collision rule. External dr…

[Phys. Rev. E 95, 022115] Published Tue Feb 14, 2017

]]>We study the thermodynamic properties of a one-dimensional gas with one-dimensional gravitational interactions. Periodic boundary conditions are implemented as a modification of the potential consisting of a sum over mirror images (Ewald sum), regularized with an exponential cutoff. As a consequence…

[Phys. Rev. E 95, 022116] Published Tue Feb 14, 2017

]]>Motivated by recent progress in using restricted Boltzmann machines as preprocessing algorithms for deep neural network, we revisit the mean-field equations [belief-propagation and Thouless-Anderson Palmer (TAP) equations] in the best understood of such machines, namely the Hopfield model of neural …

[Phys. Rev. E 95, 022117] Published Tue Feb 14, 2017

]]>The dynamics of driven-dissipative systems is shown to be well-fitted for achieving efficient combinatorial optimization. The proposed method can be applied to solve any combinatorial optimization problem that is equivalent to minimizing an Ising Hamiltonian. Moreover, the dynamics considered can be…

[Phys. Rev. E 95, 022118] Published Tue Feb 14, 2017

]]>Given a network, the statistical ensemble of its graph-Voronoi diagrams with randomly chosen cell centers exhibits properties convertible into information on the network's large scale structures. We define a node-pair level measure called Voronoi cohesion which describes the probability for sharing …

[Phys. Rev. E 95, 022306] Published Tue Feb 14, 2017

]]>We investigate the presence of triangles in a class of correlated random graphs in which hidden variables determine the pairwise connections between vertices. The class rules out self-loops and multiple edges. We focus on the regime where the hidden variables follow a power law with exponent $\tau \in (2,3)$…

[Phys. Rev. E 95, 022307] Published Tue Feb 14, 2017

]]>In this paper we derive alternative continuous time limits of the utterance selection model (USM) for language change [G. J. Baxter *et al.*, Phys. Rev. E **73**, 046118 (2006)]. This is motivated by the fact that the Fokker-Planck continuous time limit derived in the original version of the USM is only …

[Phys. Rev. E 95, 022308] Published Tue Feb 14, 2017

]]>Electrons can be efficiently injected into a plasma wave by colliding two counterpropagating laser pulses in a laser wakefield acceleration. However, the generation of a high-quality electron beam with a large charge is difficult in the traditional on-axis colliding scheme due to the growth of the e…

[Phys. Rev. E 95, 023206] Published Tue Feb 14, 2017

]]>Understanding fundamental growth processes is key to the control of nonequilibrium structure formation for a wide range of materials on all length scales, from atomic to molecular and even colloidal systems. While atomic systems are relatively well studied, molecular and colloidal growth are current…

[Phys. Rev. E 95, 020801(R)] Published Mon Feb 13, 2017

]]>We study a one-dimensional Coulomb system, where two charged colloids are neutralized by a collection of point counterions, with global neutrality. With temperature being given, two situations are addressed: Either the colloids are kept at fixed positions (canonical ensemble) or the force acting on …

[Phys. Rev. E 95, 022112] Published Mon Feb 13, 2017

]]>Anomalous diffusion processes, in particular superdiffusive ones, are known to be efficient strategies for searching and navigation in animals and also in human mobility. One way to create such regimes are Lévy flights, where the walkers are allowed to perform jumps, the “flights,” that can eventual…

[Phys. Rev. E 95, 022113] Published Mon Feb 13, 2017

]]>The properties of the random sequential adsorption of objects of various shapes on a two-dimensional triangular lattice are studied numerically by means of Monte Carlo simulations. The depositing objects are formed by self-avoiding lattice steps, whereby the size of the objects is gradually increase…

[Phys. Rev. E 95, 022114] Published Mon Feb 13, 2017

]]>Honeybees (*Apis mellifera*) exhibit complex coordination and interaction across multiple behaviors such as swarming. This coordination among honeybees in the same colony is remarkably similar to the concept of informational cascades. The multifractal geometry of cascades suggests that multifractal me…

[Phys. Rev. E 95, 022402] Published Mon Feb 13, 2017

]]>The cable equation describes the voltage in a straight cylindrical cable, and this model has been employed to model electrical potential in dendrites and axons. However, sometimes this equation might give incorrect predictions for some realistic geometries, in particular when the radius of the cable…

[Phys. Rev. E 95, 022403] Published Mon Feb 13, 2017

]]>Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of spin-bearing particles. Examples of such pores comprise cells in biol…

[Phys. Rev. E 95, 022404] Published Mon Feb 13, 2017

]]>We present systematic numerical studies of the possible effects of the coupling of human endocardial and Purkinje cells at cellular and two-dimensional tissue levels. We find that the autorhythmic-activity frequency of the Purkinje cell in a composite decreases with an increase in the coupling stren…

[Phys. Rev. E 95, 022405] Published Mon Feb 13, 2017

]]>The authors study a model of cytoskeletal filaments and molecular motors and explore the conditions under which the maximum forces are additive: the force of the group is the sum of the individual contributions of each motor. They conclude that as long as the system is in a detailed-balance condition, equivalent to thermodynamic reversibility, the maximum forces are additive.

[Phys. Rev. E 95, 022406] Published Mon Feb 13, 2017

]]>Evolutionary games on graphs describe how strategic interactions and population structure determine evolutionary success, quantified by the probability that a single mutant takes over a population. Graph structures, compared to the well-mixed case, can act as amplifiers or suppressors of selection b…

[Phys. Rev. E 95, 022407] Published Mon Feb 13, 2017

]]>To date investigations of the dynamics of driven colloidal systems have focused on hydrodynamic interactions and often employ optical (laser) tweezers for manipulation. However, the optical fields that provide confinement and drive also result in electrodynamic interactions that are generally neglec…

[Phys. Rev. E 95, 022604] Published Mon Feb 13, 2017

]]>We study, using Langevin dynamics simulations, the change in composition of a binary colloidal mixture confined in a finite-length channel, induced by an external field. The field-induced transition from a near-bulk composition to an inverted population is studied as a function of time, for differen…

[Phys. Rev. E 95, 022605] Published Mon Feb 13, 2017

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