The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of …

[Phys. Rev. E 94, 040401(R)] Published Mon Oct 24, 2016

]]>We use supersymmetry to calculate exact spectral densities for a class of complex random matrix models having the form $M=S+LXR$, where $X$ is a random noise part $X$, and $S,L,R$ are fixed structure parts. This is a certain version of the “external field” random matrix models. We find twofold integral form…

[Phys. Rev. E 94, 042130] Published Mon Oct 24, 2016

]]>We consider pinned diffusion paths that are explored by a particle moving via a conservative force while being in thermal equilibrium with its surroundings. To probe rare transitions, we use the Onsager-Machlup (OM) functional as a path probability distribution function for transition paths that are…

[Phys. Rev. E 94, 042131] Published Mon Oct 24, 2016

]]>We consider the survival probability $f\left(t\right)$ of a random walk with a constant hopping rate $w$ on a host lattice of fractal dimension $d$ and spectral dimension ${d}_{s}\le 2$, with spatially correlated traps. The traps form a sublattice with fractal dimension ${d}_{a}<d$ and are characterized by the absorption rate ${w}_{a}$ …

[Phys. Rev. E 94, 042132] Published Mon Oct 24, 2016

]]>Random search processes for targets that are inhomogeneously distributed in a search domain require spatially inhomogeneous search strategies to find the target as fast as possible. Here, we compare systematically the efficiency of homogeneous and inhomogeneous strategies for intermittent search, wh…

[Phys. Rev. E 94, 042133] Published Mon Oct 24, 2016

]]>We present experimental measurements concerning the response of an excitable micropillar laser with saturable absorber to incoherent as well as coherent perturbations. The excitable response is similar to the behavior of spiking neurons but with much faster time scales. It is accompanied by a subnan…

[Phys. Rev. E 94, 042219] Published Mon Oct 24, 2016

]]>We study the dynamical properties of human communication through different channels, i.e., short messages, phone calls, and emails, adopting techniques from neuronal spike train analysis in order to characterize the temporal fluctuations of successive interevent times. We first measure the so-called…

[Phys. Rev. E 94, 042313] Published Mon Oct 24, 2016

]]>A hybrid asymptotic-numerical method is presented for obtaining an asymptotic estimate for the full probability distribution of capture times of a random walker by multiple small traps located inside a bounded two-dimensional domain with a reflecting boundary. As motivation for this study, we calcul…

[Phys. Rev. E 94, 042418] Published Mon Oct 24, 2016

]]>The sporadic nature of gene expression at the single-cell level—long periods of inactivity punctuated by bursts of mRNA or protein production—plays a critical role in diverse cellular processes. To elucidate the cellular role of bursting in gene expression, synthetic biology approaches have been use…

[Phys. Rev. E 94, 042419] Published Mon Oct 24, 2016

]]>The phase-flip transition has been demonstrated in a host of coupled nonlinear oscillator models, many pertaining directly to understanding neural dynamics. However, there is little evidence that this phenomenon occurs in the brain. Using simultaneous microelectrode recordings in the nonhuman primat…

[Phys. Rev. E 94, 042420] Published Mon Oct 24, 2016

]]>We evaluate the effect of ions on the electric response of an insulting liquid by means of the total electric polarization induced in a cell by an external field. The limiting surfaces are assumed blocking and identical and the ions pointike nonpolarizable charged particles. The analysis is limited …

[Phys. Rev. E 94, 042608] Published Mon Oct 24, 2016

]]>In an attempt to quantify the role of polydispersity in colloidal suspensions, we present an efficient implementation of the renormalized jellium model for a mixture of spherical charged colloids. The different species may have different size, charge, and density. Advantage is taken from the fact th…

[Phys. Rev. E 94, 042609] Published Mon Oct 24, 2016

]]>Nanodrops on smooth or patterned rough surfaces are explored by many-body dissipative particle dynamics to demonstrate the influence of surface roughness on droplet wetting. On a smooth surface, nanodrops exhibit the random motion and contact angle hysteresis is absent. The diffusivity decays as the…

[Phys. Rev. E 94, 042807] Published Mon Oct 24, 2016

]]>We report on the results of extensive computer simulation of the effect of deformation on the morphology of a porous medium and its fluid flow properties. The porous medium is represented by packings of spherical particles. Both random and regular as well as dense and nondense packings are used. A q…

[Phys. Rev. E 94, 042903] Published Mon Oct 24, 2016

]]>Origami-based design holds promise for developing new mechanical metamaterials whose overall kinematic and mechanical properties can be programmed using purely geometric criteria. In this article, we demonstrate that the deformation of a generic degree-four vertex (4-vertex) origami cell is a combin…

[Phys. Rev. E 94, 043002] Published Mon Oct 24, 2016

]]>We study the problem of flow of a neutral gas past an infinite cylinder at right angle to its axis at low Reynolds number when the fluid is characterized by broken time-reversal invariance, and hence by odd viscosity in addition to the normal even one. We solve the Oseen approximation to Navier-Stok…

[Phys. Rev. E 94, 043111] Published Mon Oct 24, 2016

]]>We consider, both theoretically and experimentally, a thin sessile drop of conductive liquid that rests on the lower plate of a parallel-plate capacitor. We derive analytical expressions for both the initial deformation and the relaxation dynamics of the drop as the electric field is either abruptly…

[Phys. Rev. E 94, 043112] Published Mon Oct 24, 2016

]]>The existence of autoresonances for $m=2$ diocotron oscillations of non-neutral electron plasmas in a uniform magnetic field was predicted by particle-in-cell simulations and it was confirmed in experiments. The obtained results show clear deviations from the standard threshold amplitude dependence on…

[Phys. Rev. E 94, 043204] Published Mon Oct 24, 2016

]]>Effective classical dynamics provide a potentially powerful avenue for modeling large-scale dynamical quantum systems. We have examined the accuracy of a Hamiltonian-based approach that employs effective momentum-dependent potentials (MDPs) within a molecular-dynamics framework through studies of at…

[Phys. Rev. E 94, 043205] Published Mon Oct 24, 2016

]]>A decoupled scheme based on the Hermite expansion to construct lattice Boltzmann models for the compressible Navier-Stokes equations with arbitrary specific heat ratio is proposed. The local equilibrium distribution function including the rotational velocity of particle is decoupled into two parts, …

[Phys. Rev. E 94, 043314] Published Mon Oct 24, 2016

]]>Tight gas sandstones are low porosity media, with a very small permeability (i.e., below 1 mD). Their porosity is below 10%, and it is mainly composed of fine noncemented microcracks, which are present between neighboring quartz grains. While empirical models of permeability are available, their pre…

[Phys. Rev. E 94, 043316] Published Mon Oct 24, 2016

]]>We show that critical Casimir effects can be accessed through direct simulation of a model binary fluid passing through the demixing transition. We work in the semi-grand-canonical ensemble, in slab geometry, in which the Casimir force appears as the excess of the generalized pressure, ${P}_{\perp}-n\mu $. The ex…

[Phys. Rev. E 94, 040102(R)] Published Fri Oct 21, 2016

]]>A statistical model for a simple three-dimensional Mercedes-Benz model of water was used to study phase diagrams. This model on a simple level describes the thermal and volumetric properties of waterlike molecules. A molecule is presented as a soft sphere with four directions in which hydrogen bonds…

[Phys. Rev. E 94, 042126] Published Fri Oct 21, 2016

]]>Workhorse theories throughout all of physics derive effective Hamiltonians to describe slow time evolution, even though low-frequency modes are actually coupled to high-frequency modes. Such effective Hamiltonians are accurate because of *adiabatic decoupling*: the high-frequency modes “dress” the low…

[Phys. Rev. E 94, 042127] Published Fri Oct 21, 2016

]]>In this paper we study the fractional Brownian motion (FBM) time changed by the inverse Gaussian (IG) process and its inverse, called the inverse to the inverse Gaussian (IIG) process. Some properties of the time-changed processes are similar to those of the classical FBM, such as long-range depende…

[Phys. Rev. E 94, 042128] Published Fri Oct 21, 2016

]]>We analyze the stochastic dynamics of a large population of noninteracting particles driven by a common environmental input in the form of an Ornstein-Uhlenbeck (OU) process. The density of particles evolves according to a stochastic Fokker-Planck (FP) equation with respect to different realizations…

[Phys. Rev. E 94, 042129] Published Fri Oct 21, 2016

]]>Within the framework of the Maxwell-Cattaneo relaxation model extended to reaction-diffusion systems with nonlinear advection, travelling wave (TW) solutions are analytically investigated by studying a normalized reaction-telegraph equation in the case of the reaction and advection terms described b…

[Phys. Rev. E 94, 042218] Published Fri Oct 21, 2016

]]>We study the information loss of a class of inference strategies that is solely based on time averaging. For an array of independent binary sensors (e.g., receptors, single electron transistors) measuring a weak random signal (e.g., ligand concentration, gate voltage) this information loss is up to …

[Phys. Rev. E 94, 042416] Published Fri Oct 21, 2016

]]>A self-consistent field study is presented on the design of active and passive targeting block-copolymeric micelles. These micelles form in water by self-assembly of triblock copolymers with a hydrophilic middle block and two hydrophobic outer blocks. A minority amount of diblock copolymers with the…

[Phys. Rev. E 94, 042503] Published Fri Oct 21, 2016

]]>A theoretical analysis of the time-dependent electrohydrodynamics of a viscoelastic compressible capsule, characterized by the two-dimensional Young's modulus and surface viscosity, is studied in the small-deformation limit. A systematic ac electrohydrodynamics analysis is conducted, and time-indepe…

[Phys. Rev. E 94, 042607] Published Fri Oct 21, 2016

]]>The Bragg reflection band width and optical rotatory dispersion of liquid crystalline cholesteric blue phases (BPs) I and II are compared by numerical simulations. Attention is paid to the wavelength regions for which the reflection bands with lowest photon energies appear, i.e., the $\left[110\right]$ direction…

[Phys. Rev. E 94, 042703] Published Fri Oct 21, 2016

]]>We present studies of chiral nematic liquid crystals composed of flexible dimer molecules subject to large dc magnetic fields between 0 and 31 T. We observe that these fields lead to selective reflection of light depending on temperature and magnetic field. The band of reflected wavelengths can be t…

[Phys. Rev. E 94, 042705] Published Fri Oct 21, 2016

]]>We investigate the stability of thin liquid curtains with respect to two-dimensional perturbations. The dynamics of perturbations with wavelengths exceeding (or comparable to) the curtain's thickness are examined using the lubrication approximation (or a kind of geometric optics). It is shown that, …

[Phys. Rev. E 94, 043110] Published Fri Oct 21, 2016

]]>The dynamical scaling analysis for the Kosterlitz-Thouless transition in the nonequilibrium relaxation method is improved by the use of Bayesian statistics and the kernel method. This allows data to be fitted to a scaling function without using any parametric model function, which makes the results …

[Phys. Rev. E 94, 043312] Published Fri Oct 21, 2016

]]>In the lattice Boltzmann (LB) method, the forcing scheme, which is used to incorporate an external or internal force into the LB equation, plays an important role. It determines whether the force of the system is correctly implemented in an LB model and affects the numerical accuracy. In this paper …

[Phys. Rev. E 94, 043313] Published Fri Oct 21, 2016

]]>Crook's fluctuation theorem (CFT) and Jarzynski equality (JE) are effective tools for obtaining free-energy difference $\mathrm{\Delta}F({\lambda}_{A}\to {\lambda}_{B},{T}_{0})$ through a set of finite-time protocol driven nonequilibrium transitions between two equilibrium states $A$ and $B$ [parametrized by the time-varying protocol $\lambda \left(t\right)$] at the s…

[Phys. Rev. E 94, 040101(R)] Published Thu Oct 20, 2016

]]>Network reliability is the probability that a dynamical system composed of discrete elements interacting on a network will be found in a configuration that satisfies a particular property. We introduce a reliability property, Ising feasibility, for which the network reliability is the Ising model's …

[Phys. Rev. E 94, 042125] Published Thu Oct 20, 2016

]]>Earthquakes are quite hard to predict. One of the possible reasons can be the fact that the existing catalogs of past earthquakes are limited at most to the order of 100 years, while their characteristic time scale is sometimes greater than that time span. Here we rather use these limitations positi…

[Phys. Rev. E 94, 042217] Published Thu Oct 20, 2016

]]>The highly variable dynamics of neocortical circuits observed *in vivo* have been hypothesized to represent a signature of ongoing stochastic inference but stand in apparent contrast to the deterministic response of neurons measured *in vitro*. Based on a propagation of the membrane autocorrelation acro…

[Phys. Rev. E 94, 042312] Published Thu Oct 20, 2016

]]>We measure the vibrational modes and particle dynamics of quasi-two-dimensional colloidal glasses as a function of interparticle interaction strength. The interparticle attractions are controlled via a temperature-tunable depletion interaction. Specifically, the interparticle attraction energy is in…

[Phys. Rev. E 94, 042606] Published Thu Oct 20, 2016

]]>In this work, with focus on the energy-transport properties in quantum, low-dimensional, graded materials, we address the investigation of the energy (and spin) current in $XXZ$ open chains with graded inner structures and driven out of equilibrium by magnetization pumping applied at the ends. We stud…

[Phys. Rev. E 94, 042122] Published Wed Oct 19, 2016

]]>Recently it was stated that temporal disorder constitutes a relevant perturbation in absorbing phase transitions for all dimensions. However, its effect on systems other than the standard contact process (CP), its competition with other ingredients (e.g., particle diffusion), and other kinds of diso…

[Phys. Rev. E 94, 042123] Published Wed Oct 19, 2016

]]>Grand-canonical fluctuations of Bose-Einstein condensates of light are accessible to state-of-the-art experiments [J. Schmitt *et al.*, Phys. Rev. Lett. **112**, 030401 (2014).]. We phenomenologically describe these fluctuations by using the grand-canonical ensemble for a weakly interacting Bose gas at t…

[Phys. Rev. E 94, 042124] Published Wed Oct 19, 2016

]]>Under external mechanical loading, glassy materials, ranging from soft matter systems to metallic alloys, often respond via formation of inhomogeneous flow patterns, during yielding. These inhomogeneities can be precursors to catastrophic failure, implying that a better understanding of their underl…

[Phys. Rev. E 94, 042605] Published Wed Oct 19, 2016

]]>We study the behavior of high-energy positrons emitted from a radioactive source in a magnetospheric dipole field configuration. Because the conservation of the first and second adiabatic invariants is easily destroyed in a strongly inhomogeneous dipole field for high-energy charged particles, the p…

[Phys. Rev. E 94, 043203] Published Wed Oct 19, 2016

]]>We show that solutions to fermion sign problems that are found in the formulation where the path integral is expanded in powers of the interaction in continuous time can be extended to systems involving fermions interacting with dynamical quantum spins. While these sign problems seem unsolvable in t…

[Phys. Rev. E 94, 043311] Published Wed Oct 19, 2016

]]>Most self-sustained oscillations in biological systems and in technical applications are based on a feedback loop, and it is usually important to know how they will react when an external oscillatory force is applied. Here we investigate the effects that the introduction of a time delay in the feedb…

[Phys. Rev. E 94, 042212] Published Tue Oct 18, 2016

]]>The heterogeneity of coupled oscillators is important for the degree of their synchronization. According to the classical Kuramoto model, larger heterogeneity reduces synchronization. Here, we show that in a model for coupled pancreatic $\beta $-cells, higher diversity of the cells induces higher synchrony…

[Phys. Rev. E 94, 042213] Published Tue Oct 18, 2016

]]>State-space reconstruction is investigated for evaluating the randomness generated by an optically injected semiconductor laser in chaos. The reconstruction of the attractor requires only the emission intensity time series, allowing both experimental and numerical evaluations with good qualitative a…

[Phys. Rev. E 94, 042214] Published Tue Oct 18, 2016

]]>The motion of a self-propelled particle is affected by its surroundings, such as boundaries or external fields. In this paper, we investigated the bifurcation of the motion of a camphor grain, as a simple actual self-propelled system, confined in a one-dimensional finite region. A camphor grain exhi…

[Phys. Rev. E 94, 042215] Published Tue Oct 18, 2016

]]>Parametric excitation of autoresonant solutions of the nonlinear Schrodinger (NLS) equation by a chirped frequency traveling wave is discussed. Fully nonlinear theory of the process is developed based on Whitham's averaged variational principle and its predictions verified in numerical simulations. …

[Phys. Rev. E 94, 042216] Published Tue Oct 18, 2016

]]>Learning and memory are acquired through long-lasting changes in synapses. In the simplest models, such synaptic potentiation typically leads to runaway excitation, but in reality there must exist processes that robustly preserve overall stability of the neural system dynamics. How is this accomplis…

[Phys. Rev. E 94, 042310] Published Tue Oct 18, 2016

]]>In the traditional setup of the public goods game all players are involved in every available group and the mutual benefit is shared among competing cooperator and defector strategies. However, in real life situations the group formation of players could be more sophisticated because not all players…

[Phys. Rev. E 94, 042311] Published Tue Oct 18, 2016

]]>The diffusion of a reactant to a binding target plays a key role in many biological processes. The reaction radius at which the reactant and target may interact is often a small parameter relative to the diameter of the domain in which the reactant diffuses. We develop uniform in time asymptotic exp…

[Phys. Rev. E 94, 042414] Published Tue Oct 18, 2016

]]>Bending and Gaussian moduli of a homogenious single-component lipid bilayer are calculated analytically using microscopic model of the lipid hydrocarbon chains. The approach allows for thermodynamic averaging over different chains conformations. Each chain is modeled as a flexible string with finite…

[Phys. Rev. E 94, 042415] Published Tue Oct 18, 2016

]]>In contrast to thermotropic biaxial nematic phases, for which some long sought for experimental realizations have been obtained, no experimental realizations are yet known for their tetrahedratic and cubatic counterparts, involving orientational orders of ranks 3 and 4, respectively, also studied th…

[Phys. Rev. E 94, 042702] Published Tue Oct 18, 2016

]]>We study the clustering of inertial particles using a periodic kinematic simulation. Particle clustering is observed for different pairs of Stokes number and Froude number and different spectral power laws $\left(1.4\le p\le 2.1\right)$. The main focus is to identify and then quantify the effect of $p$ on the clustering…

[Phys. Rev. E 94, 043109] Published Tue Oct 18, 2016

]]>We present a numerical approach for the solution of the dissipative Gross-Pitaevskii equation coupled to the reservoir equation governing the exciton-polaritons Bose-Einstein condensation. It is based on the finite difference method applied to space variables and on the fourth order Range-Kutta algo…

[Phys. Rev. E 94, 043310] Published Tue Oct 18, 2016

]]>This paper introduces an analytical description of the probability density function of the dissipated and injected powers $p\left({j}_{\mathrm{dis}}\right)$ and $p\left({j}_{\mathrm{inj}}\right)$, respectively, in a paradigmatic nonequilibrium damped system in contact with a work reservoir that is analytically represented by telegraph noise and to whic…

[Phys. Rev. E 94, 042114] Published Mon Oct 17, 2016

]]>We investigate thermal transport along a one-dimensional lattice of classical inertial rotators, with attractive couplings that decrease with distance as ${r}^{-\alpha}\left(\alpha \ge 0\right)$, subject at its ends to Brownian heat reservoirs at different temperatures with average value $T$. By means of numerical integration of th…

[Phys. Rev. E 94, 042117] Published Mon Oct 17, 2016

]]>We present a resummed mean-field approximation for inferring the parameters of an Ising or a Potts model from empirical, noisy, one- and two-point correlation functions. Based on a resummation of a class of diagrams of the small correlation expansion of the log-likelihood, the method outperforms sta…

[Phys. Rev. E 94, 042118] Published Mon Oct 17, 2016

]]>We present a method to derive an analytical expression for the roughness of an eroded surface whose dynamics are ruled by cellular automaton. Starting from the automaton, we obtain the time evolution of the height average and height variance (roughness). We apply this method to the etching model in $\mathrm{\dots}$

[Phys. Rev. E 94, 042119] Published Mon Oct 17, 2016

]]>Recent theoretical and simulation work has predicted the existence of a so-called cluster crystal, where soft colloidal particles interacting through a repulsive potential are able to aggregate and form periodic crystals of particle clusters. The authors study this phenomenon using Brownian dynamics simulation and analytical theory based on the Dean-Kawasaki equation, and focus on the appearance and structure of patterns in one- and two-dimensional realizations.

[Phys. Rev. E 94, 042120] Published Mon Oct 17, 2016

]]>Motivated by uncertainty quantification in natural transport systems, we investigate an individual-based transport process involving particles undergoing a random walk along a line of point sinks whose strengths are themselves independent random variables. We assume particles are removed from the sy…

[Phys. Rev. E 94, 042121] Published Mon Oct 17, 2016

]]>We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain …

[Phys. Rev. E 94, 042603] Published Mon Oct 17, 2016

]]>Colloidal particles were sedimented onto patterned glass slides to grow three-dimensional bicrystals with a controlled structure. Three types of symmetric tilt grain boundaries between close-packed face-centered-cubic crystals were produced: $\mathrm{\Sigma}5\phantom{\rule{4pt}{0ex}}\left(100\right),\mathrm{\Sigma}17\phantom{\rule{4pt}{0ex}}\left(100\right)$, and $\mathrm{\Sigma}3\phantom{\rule{4pt}{0ex}}\left(110\right)$. The structure of the crysta…

[Phys. Rev. E 94, 042604] Published Mon Oct 17, 2016

]]>The crystallization process of Hertzian spheres is studied by means of molecular dynamics simulations in an *NPT* ensemble where the total number of particles *N*, the pressure *P*, and the temperature *T* are kept constant. It has been observed that the bond orientational ordering rather than the translati…

[Phys. Rev. E 94, 042805] Published Mon Oct 17, 2016

]]>A continuum elastic model, describing the wrinkling instability of graphene on substrate-supported silica nanoparticles [M. Yamamoto *et al.*, Phys. Rev. X **2**, 041018 (2012)], is analytically studied, and an exact analytical expression of the critical nanoparticle separation or the maximum wrinkle leng…

[Phys. Rev. E 94, 042806] Published Mon Oct 17, 2016

]]>The scaling theory of Grossmann and Lohse [J. Fluid Mech. **407**, 27 (2000)] for turbulent heat and momentum transfer is extended to the magnetoconvection case in the presence of a (strong) vertical magnetic field. A comparison with existing laboratory experiments and direct numerical simulations in th…

[Phys. Rev. E 94, 043108] Published Mon Oct 17, 2016

]]>Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with …

[Phys. Rev. E 94, 043308] Published Mon Oct 17, 2016

]]>A combination of finite difference (FD) and boundary integral (BI) methods is used to formulate an efficient solver for simulating unsteady Stokes flow around particles. The two-dimensional (2D) unsteady Stokes equation is being solved on a Cartesian grid using a second order FD method, while the 2D…

[Phys. Rev. E 94, 043309] Published Mon Oct 17, 2016

]]>Channel flow, the pressure driven flow between parallel plates, has exact coherent structures that show various degrees of localization. For states which are localized in streamwise direction but extended in spanwise direction, we show that they are exponentially localized, with decay constants that…

[Phys. Rev. E 94, 041101(R)] Published Fri Oct 14, 2016

]]>We study an asymmetric simple exclusion process in a strip in the presence of a solid impenetrable barrier. We focus on the effect of the barrier on the residence time of the particles, namely, the typical time needed by the particles to cross the whole strip. We explore the conditions for reduced j…

[Phys. Rev. E 94, 042115] Published Fri Oct 14, 2016

]]>We consider the setup of stationary zero range models and discuss the onset of condensation induced by a local blockage on the lattice. We show that the introduction of a local feedback on the hopping rates allows us to control the particle fraction in the condensed phase. This phenomenon results in…

[Phys. Rev. E 94, 042116] Published Fri Oct 14, 2016

]]>A major hurdle in the simulation of the steady state of epidemic processes is that the system will unavoidably visit an absorbing, disease-free state at sufficiently long times due to the finite size of the networks where epidemics evolves. In the present work, we compare different quasistationary (…

[Phys. Rev. E 94, 042308] Published Fri Oct 14, 2016

]]>We study the mean first passage time (MFPT) of true self-avoiding walks (TSAWs) on various networks as a measure of searching efficiency. From the numerical analysis, we find that the MFPT of TSAWs, ${\tau}^{\mathrm{TSAW}}$, approaches the theoretical minimum ${\tau}^{\mathrm{th}}/N=\frac{1}{2}$ on synthetic networks whose degree-degree correlat…

[Phys. Rev. E 94, 042309] Published Fri Oct 14, 2016

]]>Population dynamics is constrained by the environment, which needs to obey certain conditions to support population growth. We consider a standard model for the evolution of a single species population density, which includes reproduction, competition for resources, and spatial spreading, while subj…

[Phys. Rev. E 94, 042413] Published Fri Oct 14, 2016

]]>We analyze the shear strength and microstructure of binary granular mixtures consisting of disks and elongated particles by varying systematically both the mixture ratio and degree of homogeneity (from homogeneous to fully segregated). The contact dynamics method is used for numerical simulations wi…

[Phys. Rev. E 94, 042901] Published Fri Oct 14, 2016

]]>Accurate prediction of the time required to heat up granular materials to a target temperature is crucial for several processes. However, we do not have quantitative models to predict the average temperature or the temperature distribution of the particles. Here, we computationally investigate the s…

[Phys. Rev. E 94, 042902] Published Fri Oct 14, 2016

]]>Data assimilation (DA) is a fundamental computational technique that integrates numerical simulation models and observation data on the basis of Bayesian statistics. Originally developed for meteorology, especially weather forecasting, DA is now an accepted technique in various scientific fields. On…

[Phys. Rev. E 94, 043307] Published Fri Oct 14, 2016

]]>A spinning gas, heated adiabatically through axial compression, is known to exhibit a rotation-dependent heat capacity. However, as equilibrium is approached, an effect is identified here wherein the temperature does not grow homogeneously in the radial direction, but develops a temperature differen…

[Phys. Rev. E 94, 042113] Published Thu Oct 13, 2016

]]>The chaotic portion of phase space of the simplified Fermi-Ulam model is studied under the context of transport of trajectories in two scenarios: (i) the trajectories are originated from a region distant from the islands of regular motion and are transported to a region located at a high portion of …

[Phys. Rev. E 94, 042208] Published Thu Oct 13, 2016

]]>Periodic orbits for the classical ${\varphi}^{4}$ theory on the one-dimensional lattice are systematically constructed by extending the normal modes of the harmonic theory, for periodic, free and fixed boundary conditions. Through the process, we investigate which normal modes of the linear theory can or cannot …

[Phys. Rev. E 94, 042209] Published Thu Oct 13, 2016

]]>We explore identical Rössler systems organized into two equally sized groups, among which differing positive and negative in- and out-coupling strengths are allowed. With this asymmetric coupling, we analyze patterns in the phase dynamics that coexist with chaotic amplitudes. We specifically investi…

[Phys. Rev. E 94, 042210] Published Thu Oct 13, 2016

]]>We investigated experimentally the short- and long-range correlations in the fluctuations of the resonance frequencies of flat, rectangular microwave cavities that contained antennas acting as pointlike perturbations. We demonstrate that their spectral properties exhibit the features typical for sin…

[Phys. Rev. E 94, 042211] Published Thu Oct 13, 2016

]]>We investigate the synchronization properties between two excitatory coupled neurons in the presence of an inhibitory loop mediated by an interneuron. Dynamic inhibition together with noise independently applied to each neuron provide phase diversity in the dynamics of the neuronal motif. We show th…

[Phys. Rev. E 94, 042411] Published Thu Oct 13, 2016

]]>Protein receptor-ligand pairs are increasingly used as specific molecular handles in single-molecule protein-unfolding experiments. Further, known marker domains, also referred to as fingerprints, provide unique unfolding signatures to identify specific single-molecule interactions, when receptor-li…

[Phys. Rev. E 94, 042412] Published Thu Oct 13, 2016

]]>In this exposition we consider the wave dynamics of a one-dimensional periodic granular dimer (diatomic) chain mounted on a damped and an undamped linear elastic foundation (otherwise called the on-site potential). It is very well known that periodic granular dimers support solitary wave propagation…

[Phys. Rev. E 94, 043001] Published Thu Oct 13, 2016

]]>The spatial Markov model is a Lagrangian random walk model, widely and successfully used for upscaling transport in heterogeneous flows across a broad range of problems. It is particularly useful at early or pre-asymptotic times when many other conventional upscaling approaches may not be valid. How…

[Phys. Rev. E 94, 043107] Published Thu Oct 13, 2016

]]>The main objective of this work is to perform a detailed comparison of the lattice Boltzmann equation (LBE) and the recently developed discrete unified gas-kinetic scheme (DUGKS) methods for direct numerical simulation (DNS) of the decaying homogeneous isotropic turbulence and the Kida vortex flow i…

[Phys. Rev. E 94, 043304] Published Thu Oct 13, 2016

]]>Smoothed dissipative particle dynamics (SDPD) is a mesoscopic method that allows one to select the level of resolution at which a fluid is simulated. In this work, we study the consistency of the resulting thermodynamic properties as a function of the size of the mesoparticles, both at equilibrium a…

[Phys. Rev. E 94, 043305] Published Thu Oct 13, 2016

]]>The present work proposes a simple lattice Boltzmann model for incompressible axisymmetric thermal flows through porous media. By incorporating forces and source terms into the lattice Boltzmann equation, the incompressible Navier-Stokes equations are recovered through the Chapman-Enskog expansion. …

[Phys. Rev. E 94, 043306] Published Thu Oct 13, 2016

]]>Exact analytical expressions for the cross-section correlation functions of chaotic scattering systems have hitherto been derived only under special conditions. The objective of the present article is to provide expressions that are applicable beyond these restrictions. The derivation is based on a …

[Phys. Rev. E 94, 042207] Published Wed Oct 12, 2016

]]>We investigate the scaling of the cross-correlations calculated for two-variable time series containing vertex properties in the context of complex networks. Time series of such observables are obtained by means of stationary, unbiased random walks. We consider three vertex properties that provide, …

[Phys. Rev. E 94, 042307] Published Wed Oct 12, 2016

]]>The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties…

[Phys. Rev. E 94, 042409] Published Wed Oct 12, 2016

]]>Merging concepts of statistical mechanics, renormalization, topology, and graph theory, this paper aims to shed light on the problem of the three dimensional structure of RNA. The authors propose to include an additional term in the partition function, associated with a renormalized crossing number, that accounts for the observation that RNA unevenly populates the repertoire of pseudoknots with the same genus.

[Phys. Rev. E 94, 042410] Published Wed Oct 12, 2016

]]>The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates for further analysis, e.g., by force microscopy, or the pulli…

[Phys. Rev. E 94, 042502] Published Wed Oct 12, 2016

]]>The electrical conductivity of a monolayer produced by the random sequential adsorption (RSA) of linear $k$-mers (particles occupying $k$ adjacent adsorption sites) onto a square lattice was studied by means of computer simulation. Overlapping with predeposited $k$-mers and detachment from the surface wer…

[Phys. Rev. E 94, 042112] Published Tue Oct 11, 2016

]]>The flame or flow behavior of a turbulent reacting wake is known to be fundamentally different at high and low values of flame density ratio $\left({\rho}_{u}/{\rho}_{b}\right)$, as the flow transitions from globally stable to unstable. This paper analyzes the nonlinear dynamics present in a bluff-body stabilized flame, and ide…

[Phys. Rev. E 94, 042206] Published Tue Oct 11, 2016

]]>Networks with only central force interactions are floppy when their average connectivity is below an isostatic threshold. Although such networks are mechanically unstable, they can become rigid when strained. It was recently shown that the transition from floppy to rigid states as a function of simp…

[Phys. Rev. E 94, 042407] Published Tue Oct 11, 2016

]]>