We continue studying long-ranged quantum correlations of surface charge densities on the interface between two media of distinct dielectric functions which are in thermal equilibrium with the radiated electromagnetic field. Two regimes are considered: the nonretarded one with the speed of light $c$ taken to be infinitely large and the retarded one with a finite value of $c$. The analysis is based on our results obtained by using fluctuational electrodynamics [L. Šamaj and B. Jancovici, Phys. Rev. E 78, 051119 (2008)]. Using an integration method in the complex plane and the general analytical properties of dielectric functions in the frequency upper half plane, we derive explicit forms of prefactors to the long-range decay of the surface charge correlation functions for all possible media (conductor, dielectric, and vacuum) configurations. The main result is that the time-dependent quantum prefactor in the retarded regime takes its static classical form for any temperature.

Spatial heterogeneity in the elastic properties of soft random solids is examined via vulcanization theory. The spatial heterogeneity in the structure of soft random solids is a result of the fluctuations locked-in at their synthesis, which also brings heterogeneity in their elastic properties. Vulcanization theory studies semimicroscopic models of random-solid-forming systems and applies replica field theory to deal with their quenched disorder and thermal fluctuations. The elastic deformations of soft random solids are argued to be described by the Goldstone sector of fluctuations contained in vulcanization theory, associated with a subtle form of spontaneous symmetry breaking that is associated with the liquid-to-random-solid transition. The resulting free energy of this Goldstone sector can be reinterpreted as arising from a phenomenological description of an elastic medium with quenched disorder. Through this comparison, we arrive at the statistics of the quenched disorder of the elasticity of soft random solids in terms of residual stress and Lamé-coefficient fields. In particular, there are large residual stresses in the equilibrium reference state, and the disorder correlators involving the residual stress are found to be long ranged and governed by a universal parameter that also gives the mean shear modulus.

Motivated by recent experiments, we develop a model for DNA toroids under external tension. We find that tori are the equilibrium states for our model up to a critical tension, above which they become only metastable. Above this tension, we find a cascade of transitions between discrete toroid states that successively lower the winding number, until the ground state (rod) is reached. In this process, this model predicts a nearly constant force plateau as a function of extension, in agreement with experiment.

We investigate a two-level model with a large number of open decay channels in order to describe avoided level crossing statistics in open chaotic billiards. This model allows us to describe the fundamental changes in the probability distribution of the avoided level crossings compared with the closed case. Explicit expressions are derived for systems with preserved and broken time-reversal symmetry. We find that the decay process induces a modification at small spacings of the probability distribution of the avoided level crossings due to an attraction of the resonances. The theoretical predictions are in complete agreement with the recent experimental results of Dietz et al. [Phys. Rev. E 73, 035201 (2006)].

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

An investigation of dissipative forces for Lagrangian computational fluid dynamics is conducted from Hamiltonian considerations including energy dissipation for macroscopic systems. It is shown that discrete forces must fulfill particular rules to be in agreement with the fundamentals of Physics. Those rules are specified in the case of the smoothed particle hydrodynamics (SPH) numerical approach, leading to a clear treatment of friction forces in connection with energy dissipation. In particular, it is proved that the kernel function, which is at the heart of interpolation in SPH, must satisfy some constraints in order to be consistent with the dissipative properties of a real fluid. A numerical example is given to illustrate the abovementioned considerations.

We investigate the morphology of the spatial pattern resulting from the division of land into the parcels that is observed in the centers of the cities, by analyzing the distribution function of the parcel areas. A simple model based on a two-dimensional bond percolation is employed to mimic the process of the formation of the city. The model reproduces the empirical distribution of the parcel areas that is found to exhibit the power law with the exponent $\tau =2.0$. We argue that the city emerges from a collection of separated settlements in a process that can be described as a structural phase transition.

Effects of the nonthermal distribution of electrons as well as the polarity of the net dust-charge number density on nonplanar (viz. cylindrical and spherical) dust-ion-acoustic solitary waves (DIASWs) are investigated by employing the reductive perturbation method. It is found that the basic features of the DIASWs are significantly modified by the effects of nonthermal electron distribution, polarity of net dust-charge number density, and nonplanar geometry. The implications of our results in some space and laboratory dusty plasma environments are briefly discussed.

We demonstrate the possibility to build a thermoelectric engine using a one-dimensional gas of molecules with unequal masses and hard-point interaction. Most importantly, we show that the efficiency of this engine is determined by a parameter $YT$ which is different from the well known figure of merit $ZT$. Even though the efficiency of this particular model is low, our results shed light on the problem and open the possibility to build efficient thermoelectric engines.

Kramers-Moyal coefficients provide a simple and easily visualized method with which to analyze nonlinear stochastic time series. One mechanism that can affect the estimation of the coefficients is geometric projection effects. For some biologically inspired examples, these effects are predicted and explored with a nonstochastic projection operator method and compared with direct numerical simulation of the systems’ Langevin equations. General features and characteristics are identified, and the utility of the Kramers-Moyal method is discussed. Projections of a system are in general non-Markovian, but here the Kramers-Moyal method remains useful, and in any case the primary examples considered are found to be close to Markovian.

Methods for understanding classical disordered spin systems with interactions conforming to some idealized graphical structure are well developed. The equilibrium properties of the Sherrington-Kirkpatrick model, which has a densely connected structure, have become well understood. Many features generalize to sparse Erdös-Rényi graph structures above the percolation threshold and to Bethe lattices when appropriate boundary conditions apply. In this paper, we consider spin states subject to a combination of sparse strong interactions with weak dense interactions, which we term a composite model. The equilibrium properties are examined through the replica method, with exact analysis of the high-temperature paramagnetic, spin-glass, and ferromagnetic phases by perturbative schemes. We present results of replica symmetric variational approximations, where perturbative approaches fail at lower temperature. Results demonstrate re-entrant behaviors from spin glass to ferromagnetic phases as temperature is lowered, including transitions from replica symmetry broken to replica symmetric phases. The nature of high-temperature transitions is found to be sensitive to the connectivity profile in the sparse subgraph, with regular connectivity a discontinuous transition from the paramagnetic to ferromagnetic phases is apparent.

Using even driven simulations, we show that homogeneously sheared inelastic dumbbells in two dimensions are randomly orientated in the limit of low density. As the packing fraction is increased, particles first tend to orient along the extensional axis, and then as the packing fraction is further increased, the alignment shifts closer to the flow axis. The orientational order parameter displays a continuous increase with packing fraction and does not appear to exhibit a universal scaling with elongation. Except at the highest packing fractions, the orientational distribution function can be reconstructed with only the first coefficient of the Fourier expansion.

We report a detailed comparison of a slow gravity-driven sheared granular flow with a discrete-element simulation performed in the same geometry. In the experiments, grains flow inside a silo with a rectangular cross section and are sheared by a rough boundary on one side and smooth boundaries on the other sides. Individual grain position and motion are measured using a particle index-matching imaging technique where a fluorescent dye is added to the interstitial liquid which has the same refractive index as the glass beads. The simulations use a Cundall-Strack contact model between the grains using contact parameters that have been used in many other previous studies and ignore the hydrodynamic effects of the interstitial liquid. Computations are performed to understand the effect of particle coefficient of friction, elasticity, contact model, and polydispersity on mean flow properties. We then perform a detailed comparison of the particle fluctuation properties as measured by the displacement probability distribution function and the mean square displacement. All in all, our study suggests a high level of quantitative agreement between the simulations and experiments.

We investigate a gas of wet granular particles covered by a thin liquid film. The dynamic evolution is governed by two-particle interactions, which are mainly due to interfacial forces in contrast to dry granular gases. When two wet grains collide, a capillary bridge is formed and stays intact up to a certain distance of withdrawal when the bridge ruptures, dissipating a fixed amount of energy. A freely cooling system is shown to undergo a nonequilibrium dynamic phase transition from a state with mainly single particles and fast cooling to a state with growing aggregates such that bridge rupture becomes a rare event and cooling is slow. In the early stage of cluster growth, aggregation is a self-similar process with a fractal dimension of the aggregates approximately equal to $D_{\text{f}}\approx 2$. At later times, a percolating cluster is observed which ultimately absorbs all the particles. The final cluster is compact on large length scales, but fractal with $D_{\text{f}}\approx 2$ on small length scales.

The shear rate dependence of the slip length in thin polymer films confined between atomically flat surfaces is investigated by molecular dynamics simulations. The polymer melt is described by the bead-spring model of linear flexible chains. We found that at low shear rates the velocity profiles acquire a pronounced curvature near the wall and the absolute value of the negative slip length is approximately equal to the thickness of the viscous interfacial layer. At higher shear rates, the velocity profiles become linear and the slip length increases rapidly as a function of shear rate. The gradual transition from no-slip to steady-state slip flow is associated with faster relaxation of the polymer chains near the wall evaluated from decay of the time autocorrelation function of the first normal mode. We also show that at high melt densities the friction coefficient at the interface between the polymer melt and the solid wall follows a power-law decay as a function of the slip velocity. At large slip velocities the friction coefficient is determined by the product of the surface-induced peak in the structure factor, the temperature, and the contact density of the first fluid layer near the solid wall.

We have carried out a numerical study of a system of hydrodynamic equations including director reorientation, fluid flow, and temperature redistribution across a two-dimensional (2D) hybrid-oriented liquid-crystal (HOLC) cell under the influence of a heat flow directed normal to the upper bounding surface, whereas on the rest boundaries the temperature is kept constant. Calculations based upon the nonlinear extension of the classical Ericksen-Leslie theory shows that the HOLC material under the influence of the heat flow, after some time, more than the time of relaxation, for instance, of the director field in the HOLC cell, settles down to the rest state regime, where the horizontal and vertical components of the velocity vector are equal to zero, and the temperature field across the LC cell finally reaches the value of temperature on the lower and two lateral bounding surfaces. The role of hydrodynamic flow in the relaxation processes of the temperature field to its equilibrium distribution across the 2D HOLC cell, containing $4-\text{n}-\text{pentyl}-4^{\prime }-\text{cyanobiphenyl}$, has been investigated, for a number of dynamic regimes.

Motivated by measurements on stretched double-stranded DNA in the presence of multivalent cations, we develop a statistical mechanical model for the compaction of an insoluble semiflexible polymer under tension. Using a mean-field approach, we determine the order of the extended-to-compact transition and provide an interpretation for the magnitude and interval of tensions over which compaction takes place. In the simplest thermodynamic limit of an infinitely long homogeneous polymer, compaction is a first-order transition that occurs at a single value of tension. For finite length chains or for heterogeneous polymers, the transition progresses over an interval of tension. Our theory provides an interpretation for the result of single-molecule experiments in terms of microscopic parameters such as persistence length and free energy of condensation.

We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and understanding the nature of the noise in gene expression. We analyze the dispersion of the process, i.e., the ratio of the variance to the mean at arbitrary time, and introduce a measure, the fractional protein distribution, which can be used to probe the phase of transcription of DNA into mRNA.

Nonperiodic tunable quantum echoes have been observed in experiments with an open microwave billiard whose geometry under certain conditions provides Fibonacci-like sequences of classical delay times. These sequences combined with the reflection at the opening induced by the wave character of the experiment and the size of the opening allow to shape quantum pulses. The pulses are obtained by response of an integrable scattering system.