We present experimental results of the jamming of noncohesive particles discharged from a flat bottomed silo subjected to vertical vibration. When the exit orifice is only a few grain diameters wide, the flow can be arrested due to the formation of blocking arches. Hence, an external excitation is needed to resume the flow. The use of a continuous gentle vibration is a usual technique to ease the flow in such situations. Even though jamming is less frequent, it is still an issue in vibrated silos. There are, in principle, two possible mechanisms through which vibrations may facilitate the flow: (i) a decrease in the probability of the formation of blocking arches and (ii) the breakage of blocking arches once they have been formed. By measuring the time intervals inside an avalanche during which no particles flow through the outlet, we are able to estimate the probability of breaking a blocking arch by vibrations. The result agrees with the prediction of a bivariate probabilistic model in which the formation of blocking arches is equally probable in vibrated and nonvibrated silos. This indicates that the second aforementioned mechanism is mainly responsible for improving the flowability in gently vibrated silos.

We present a nonequilibrium approach for the study of a two-dimensional phase-separating ternary mixture. When the component that promotes phase separation is dynamically exchanged with the medium, the separation process is halted and actively maintained finite-size segregation domains appear in the system. In addition to this effect, already reported in our earlier work [J. Gómez, F. Sagués, and R. Reigada, Phys. Rev. E 77, 021907 (2008)], the use of a generic Ginzburg-Landau formalism and the inclusion of thermal fluctuations provide a more dynamic description of the resulting domain organization. Its size, shape, and stability properties are studied. Larger and more circular and stable domains are formed when decreasing the recycling rate, increasing the mobility of the exchanged component, and the mixture is quenched deeper. We expect this outcome to be of applicability in raft phenomenology in plasmatic cell membranes.

Adhesions between neighboring cells or between cells and their surrounding tissue/matrix play a crucial role in a wide range of biological processes. In order to investigate the competitive mechanisms between cell-cell and cell-matrix adhesions, we here develop a theoretical framework for multiple interacting cells lying on a planar matrix coated with distributed ligands. This model allows us to study, from the viewpoints of energy and statistics, the effects of such physical mechanisms as binding energy of bonds, nonspecific interactions, elastic deformation of cell membranes, and mixing entropy. Our calculations show that cell-matrix adhesion cannot occur when the ligand density on the matrix is lower than a threshold value, and cell-cell adhesion does not happen for a high ligand density. Glycocalyx repulsion plays a more important role in cell-matrix adhesion than in cell-cell adhesion. In addition, it is found that the cell-cell adhesion density decreases as the number of cells increases.

We model the self-organization of the MinE ring that is observed during subcellular oscillations of the proteins MinD and MinE within the rod-shaped bacterium Escherichia coli. With a steady-state approximation, we can study the MinE ring generically—apart from the other details of the Min oscillation. Rebinding of MinE to depolymerizing MinD-filament tips controls MinE-ring formation through a scaled cell shape parameter $\tilde{r}$. We find two types of E-ring profiles near the filament tip: either a strong plateaulike E ring controlled by one-dimensional diffusion of MinE along the bacterial length or a weak cusplike E ring controlled by three-dimensional diffusion near the filament tip. While the width of a strong E ring depends on $\tilde{r}$, the occupation fraction of MinE at the MinD-filament tip is saturated and hence the depolymerization speed does not depend strongly on $\tilde{r}$. Conversely, for weak E rings both $\tilde{r}$ and the MinE to MinD stoichiometry strongly control the tip occupation and hence the depolymerization speed. MinE rings in vivo are close to the threshold between weak and strong, and so MinD-filament depolymerization speed should be sensitive to cell shape, stoichiometry, and MinE-rebinding rate. We also find that the transient to MinE-ring formation is quite long in the appropriate open geometry for assays of ATPase activity in vitro, explaining the long delays of ATPase activity observed for smaller MinE concentrations in those assays without the need to invoke cooperative MinE activity.

We remove the need for Laplace/inverse-Laplace transformations of experimental data, by presenting a direct and straightforward mathematical procedure for obtaining frequency-dependent storage and loss moduli [$G^{\prime }\left(\omega \right)$ and $G^{″}\left(\omega \right)$, respectively], from time-dependent experimental measurements. The procedure is applicable to ordinary rheological creep (stress-step) measurements, as well as all microrheological techniques, whether they access a Brownian mean-square displacement, or a forced compliance. Data can be substituted directly into our simple formula, thus eliminating traditional fitting and smoothing procedures that disguise relevant experimental noise.

We present results on the connection between the vorticity equation and the shape and evolution of the single-point vorticity probability density function. The statistical framework for these observations is based on the classical hierarchy of evolution equations for the probability density functions by Lundgren, Novikov, and Monin combined with conditional averaging of the unclosed terms. The numerical evaluation of these conditional averages provides insights into the intimate relation of dynamical effects such as vortex stretching and vorticity diffusion and non-Gaussian vorticity statistics.

An analytical method of electromagnetic wave interactions with a general radially anisotropic cloak is established. It is able to deal with arbitrary parameters [${\epsilon }_r\left(r\right)$, ${\mu }_r\left(r\right)$, ${\epsilon }_t\left(r\right)$, and ${\mu }_t\left(r\right)$] of a radially anisotropic inhomogeneous shell. The general cloaking condition is proposed from the wave relations, in contrast to the method of transformation optics. Spherical metamaterial cloaks with improved invisibility performance are achieved with optimal nonlinearity in transformation and core-shell ratio.

There exist some boundary-driven open systems with diffusive dynamics whose particle current fluctuations exhibit universal features that belong to the Edwards-Wilkinson universality class. We achieve this result by establishing a mapping, for the system fluctuations, to an equivalent open yet equilibrium-diffusive system. We discuss the possibility of observing dynamic phase transitions using the particle current as a control parameter.

Following our earlier work on the Ruppeiner geometry of an anyon gas [B. Mirza and H. Mohammadzadeh, Phys. Rev. E 78, 021127 (2008)], we will derive nonperturbative thermodynamic curvature of a two-dimensional ideal anyon gas. At different values of the thermodynamic parameter space, some unique and interesting behaviors of the anyon gas are explored. A complete picture of attractive and repulsive phases of the anyon gas is given.

We study the $q$-state clock models on heptagonal lattices assigned on a negatively curved surface. We show that the system exhibits three classes of equilibrium phases; in between ordered and disordered phases, an intermediate phase characterized by a diverging susceptibility with no magnetic order is observed at every $q\ge 2$. The persistence of the third phase for all $q$ is in contrast with the disappearance of the counterpart phase in a planar system for small $q$, which indicates the significance of nonvanishing surface-volume ratio that is peculiar in the heptagonal lattice. Analytic arguments based on Ginzburg-Landau theory and generalized Cayley trees make clear that the two-stage transition in the present system is attributed to an energy gap of spin-wave excitations and strong boundary-spin contributions. We further demonstrate that boundary effects break the mean-field character in the bulk region, which establishes the consistency with results of clock models on boundary-free hyperbolic lattices.

The naïve mode coupling theory (NMCT) for ideal kinetic arrest and the nonlinear Langevin equation theory of activated single-particle barrier hopping dynamics are generalized to treat the coupled center-of-mass (CM) translational and rotational motions of uniaxial hard objects in the glassy fluid regime. The key dynamical variables are the time-dependent displacements of the particle center-of-mass and orientational angle. The NMCT predicts a kinetic arrest diagram with three dynamical states: ergodic fluid, plastic glass, and fully nonergodic double glass, the boundaries of which meet at a “triple point” corresponding to a most difficult to vitrify diatomic of aspect ratio $\sim 1.43$. The relative roles of rotation and translation in determining ideal kinetic arrest are explored by examining three limits of the theory corresponding to nonrotating, pure rotation, and rotationally ergodic models. The ideal kinetic arrest boundaries represent a crossover to activated dynamics described by two coupled stochastic nonlinear Langevin equations for translational and rotational motions. The fundamental quantity is a dynamic free-energy surface, which for small aspect ratios in the high-volume fraction regime exhibits two saddle points reflecting a two-step activated dynamics where relatively rapid rotational dynamics coexists with slower CM translational motions. For large-enough aspect ratios, the dynamic free-energy surface has one saddle point which corresponds to a system-specific coordinated translation-rotation motion. The entropic barriers as a function of the relative amount of rotation versus translation are determined.

We study stress relaxation in bidisperse entangled polymer solutions. Shorter chains embedded in a majority of longer ones are known to be oriented by coupling to them. We analyze the mechanism for this both by computer simulation and theoretically. We show that the results can be understood in terms of stress fluctuations in a polymer melt and chain screening. Stress fluctuations are frozen on the relaxation time of the longer chains, and these will induce strong orientational couplings in the shorter chains.

In this paper we consider the anharmonic corrections to the anisotropic elastic rod model for DNA. Our model accounts for the difference between the bending energies of positive and negative rolls, which comes from the asymmetric structure of the DNA molecule. We will show that the model can explain the high flexibility of DNA at small length scales, as well as kink formation at high deformation limit.

The anisotropy of temperature is studied here in a strong two-dimensional shock wave, simulated with conventional molecular dynamics. Several forms of the kinetic temperature are considered, corresponding to different choices for the local instantaneous stream velocity. A local particle-based definition omitting any “self”-contribution to the stream velocity gives the best results. The configurational temperature is not useful for this shock-wave problem. The configurational temperature is subject to a shear instability and can give local negative temperatures in the vicinity of the shock front. The decay of sinusoidal shock-front perturbations shows that strong two-dimensional planar shock waves are stable to such perturbations.

We revise the problem of thermally activated crossing of a fluctuating potential barrier, laying stress on the asymmetry of the barrier. Considering as a working model a paradigmatic triangular dichotomously varying potential landscape we find an untypical dependence of the mean first-passage time on the correlation time $\tau$ of fluctuations. Namely, in the range of small $\tau$ an additional maximum appears. We propose a qualitative explanation of this feature emphasizing the relevance of dynamics in the vicinity of the barrier top, i.e., recrossing, which generally has not been recognized by this time in this particular context. Moreover, we observe that addition of fast barrier fluctuations of some finite intensity needs not to increase the relaxation rate, as has been indicated many times in extensive studies related to the resonant activation phenomenon. Our findings are confirmed numerically for some other systems.

The flow of immiscible particles ($A$, $B$) through a porous medium with a vertical slit is studied by an interacting lattice-gas computer simulation on a discrete lattice. The source of the particles is connected to the bottom and particles are driven upward by concentration gradient and a pressure bias against gravity. Distribution of flowing particles around the slit is examined as a function of the slit width and bias at high and low porosity at a steady state. At the low bias, a sharp change in the densities (high in slit to low in adjacent porous media) of both constituents occurs as expected. Onset of an undershooting in the density and mobility of particle profiles appears at the interface of slit and the porous medium on increasing the bias, an unexpected correlated response. The competition between the faster flow in the slit and slower motion of the particles in the surrounding porous medium induces stronger correlations at higher bias; as a result, a well-defined density profile emerges with higher density in the porous matrix away from the slit interface. The range of correlation and therefore the response increases on increasing the bias. Lowering the porosity to near the percolation threshold leads to the onset of oscillation in the density profile and broadening of the mobility profile, a distinct difference from the response at high porosity.

Recent experiments and simulations have shown that two-dimensional systems can form tetratic phases with fourfold rotational symmetry, even if they are composed of particles with only twofold symmetry. To understand this effect, we propose a model for the statistical mechanics of particles with almost fourfold symmetry, which is weakly broken down to twofold. We introduce a coefficient $\kappa$ to characterize the symmetry breaking, and find that the tetratic phase can still exist even up to a substantial value of $\kappa$. Through a Landau expansion of the free energy, we calculate the mean-field phase diagram, which is similar to the result of a previous hard-particle excluded-volume model. To verify our mean-field calculation, we develop a Monte Carlo simulation of spins on a triangular lattice. The results of the simulation agree very well with the Landau theory.

We experimentally observed synchronized calling behavior of male Japanese tree frogs Hyla japonica; namely, while isolated single frogs called nearly periodically, a pair of interacting frogs called synchronously almost in antiphase or inphase. In this study, we propose two types of phase-oscillator models on different degrees of approximations, which can quantitatively explain the phase and frequency properties in the experiment. Moreover, it should be noted that, although the second model is obtained by fitting to the experimental data of the two synchronized states, the model can also explain the transitory dynamics in the interactive calling behavior, namely, the shift from a transient inphase state to a stable antiphase state. We also discuss the biological relevance of the estimated parameter values to calling behavior of Japanese tree frogs and the possible biological meanings of the synchronized calling behavior.

Discrete element simulations are employed to study the influence of static friction on the mechanical response of assemblies of nonbonded semiflexible fibers during cycles of isostatic compressions and releases. Hysteresis is evidenced during the cycles and is related to the sensitivity of the frictional contacts on normal forces. Nonzero frictions are shown to decrease both the packing density and caging number but do not affect the critical exponents that characterize the pressure and bulk and shear moduli. Assemblies of frictionless fibers are found fragile in the sense that they resist isostatic compressions but have a zero shear modulus at all densities.

We study the collective dynamics of oscillator-network systems in the presence of noise. By focusing on the time-averaged fluctuation of dynamical variable of interest about the mean field, we discover a scaling law relating the average fluctuation to the node degree. The scaling law is quite robust as it holds for a variety of network topologies and node dynamics. Analyses and numerical support for different types of networks and node dynamics are provided. We also point out an immediate application of the scaling law: predicting complex networks based on time series only, and we articulate how this can be done.