We theoretically study the kinetics of photoinduced reordering triggered by linearly polarized (LP) reorienting light in thin azo-dye films that were initially illuminated with LP ultraviolet pumping beam. The process of reordering is treated as a rotational diffusion of molecules in the light intensity-dependent mean-field potential. The two-dimensional diffusion model which is based on the free energy rotational Fokker-Planck equation and describes the regime of in-plane reorientation is generalized to analyze the dynamics of the azo-dye order parameter tensor at varying polarization azimuth of the reorienting light. It is found that, in the photosteady state, the intensity of LP reorienting light determines the scalar order parameter (the largest eigenvalue of the order parameter tensor), whereas the steady state orientation of the corresponding eigenvector (the in-plane principal axis) depends solely on the polarization azimuth. We show that, under certain conditions, reorientation takes place only if the reorienting light intensity exceeds its critical value. Such threshold behavior is predicted to occur in the bistability region provided that the initial principal axis lies in the polarization plane of reorienting light. The model is used to interpret the experimental data on the light-induced azimuthal gliding of the liquid-crystal easy axis on photoaligned azo-dye substrates.

Pulses having a temporal Lorentzian shape arise naturally from topological changes in flow trajectories or phase-space orbits associated with deterministic chaos. The pulses can appear as random intermittent events in the time series of observable quantities, and they are the cause of exponential frequency power spectra previously observed in magnetically confined plasmas and various nonlinear systems.

Modularity maximization is extensively used to detect communities in complex networks. It has been shown, however, that this method suffers from a resolution limit: Small communities may be undetectable in the presence of larger ones even if they are very dense. To alleviate this defect, various modifications of the modularity function have been proposed as well as multiresolution methods. In this paper we systematically study a simple model (proposed by Pons and Latapy [Theor. Comput. Sci. 412, 892 (2011)] and similar to the parametric model of Reichardt and Bornholdt [Phys. Rev. E 74, 016110 (2006)]) with a single parameter $\alpha$ that balances the fraction of within community edges and the expected fraction of edges according to the configuration model. An exact algorithm is proposed to find optimal solutions for all values of $\alpha$ as well as the corresponding successive intervals of $\alpha$ values for which they are optimal. This algorithm relies upon a routine for exact modularity maximization and is limited to moderate size instances. An agglomerative hierarchical heuristic is therefore proposed to address parametric modularity detection in large networks. At each iteration the smallest value of $\alpha$ for which it is worthwhile to merge two communities of the current partition is found. Then merging is performed and the data are updated accordingly. An implementation is proposed with the same time and space complexity as the well-known Clauset-Newman-Moore (CNM) heuristic [Phys. Rev. E 70, 066111 (2004)]. Experimental results on artificial and real world problems show that (i) communities are detected by both exact and heuristic methods for all values of the parameter $\alpha$; (ii) the dendrogram summarizing the results of the heuristic method provides a useful tool for substantive analysis, as illustrated particularly on a Les Misérables data set; (iii) the difference between the parametric modularity values given by the exact method and those given by the heuristic is moderate; (iv) the heuristic version of the proposed parametric method, viewed as a modularity maximization tool, gives better results than the CNM heuristic for large instances.

We investigate the collective dynamics of bursting neurons on clustered networks. The clustered network model is composed of subnetworks, each of them presenting the so-called small-world property. This model can also be regarded as a network of networks. In each subnetwork a neuron is connected to other ones with regular as well as random connections, the latter with a given intracluster probability. Moreover, in a given subnetwork each neuron has an intercluster probability to be connected to the other subnetworks. The local neuron dynamics has two time scales (fast and slow) and is modeled by a two-dimensional map. In such small-world network the neuron parameters are chosen to be slightly different such that, if the coupling strength is large enough, there may be synchronization of the bursting (slow) activity. We give bounds for the critical coupling strength to obtain global burst synchronization in terms of the network structure, that is, the probabilities of intracluster and intercluster connections. We find that, as the heterogeneity in the network is reduced, the network global synchronizability is improved. We show that the transitions to global synchrony may be abrupt or smooth depending on the intercluster probability.

We report the nature of transitions from the nonsynchronous to a complete synchronization (CS) state in arrays of time-delay systems, where the systems are coupled with instantaneous diffusive coupling. We demonstrate that the transition to CS occurs distinctly for different coupling configurations. In particular, for unidirectional coupling, locally (microscopically) synchronization transition occurs in a very narrow range of coupling strength but for a global one (macroscopically) it occurs sequentially in a broad range of coupling strength preceded by an intermittent synchronization. On the other hand, in the case of mutual coupling, a very large value of coupling strength is required for local synchronization and, consequently, all the local subsystems synchronize immediately for the same value of the coupling strength and, hence, globally, synchronization also occurs in a narrow range of the coupling strength. In the transition regime, we observe a type of synchronization transition where long intervals of high-quality synchronization which are interrupted at irregular times by intermittent chaotic bursts simultaneously in all the systems and which we designate as global intermittent synchronization. We also relate our synchronization transition results to the above specific types using unstable periodic orbit theory. The above studies are carried out in a well-known piecewise linear time-delay system.

We study spontaneous breakdown of chiral symmetry during the nonlinear evolution of the Tayler instability. We start with an initial steady state of zero helicity. Within linearized perturbation calculations, helical perturbations of this initial state have the same growth rate for either sign of helicity. Direct numerical simulations (DNS) of the fully nonlinear equations, however, show that an infinitesimal excess of one sign of helicity in the initial perturbation gives rise to a saturated helical state. We further show that this symmetry breaking can be described by weakly nonlinear finite-amplitude equations with undetermined coefficients which can be deduced solely from symmetry consideration. By fitting solutions of the amplitude equations to data from DNS, we further determine the coefficients of the amplitude equations.

Although many gas-phase microfluidic devices contain curved surfaces, relatively little research has been conducted on the degree of slip over nonplanar surfaces. The present study demonstrates the influence of the surface shape (i.e., convex/concave) on the velocity slip and formation of the Knudsen layer. In addition, the study reveals that there is a simple relationship between the shear stress exerted on the surface and the velocity defect in the Knudsen layer.

We study block copolymers (BCPs) on patterned substrates, where the top polymer film surface is not constrained but is free and can adapt its shape self-consistently. In particular, we investigate the combined effect of free interface undulations with wetting of the BCP film as induced by nanopatterned substrates. Under wetting conditions and for a finite volume of BCP material, we find equilibrium droplets composed of coexisting perpendicular and parallel lamellar domains. The self-assembly of BCPs on topographic patterned substrates is also investigated and it is found that the free interface induces mixed morphologies of parallel and perpendicular domains coupled with a nonflat free interface. Our study has some interesting consequences for experimental setups of graphoepitaxy and nanoimprint lithography.

We present a shear-transformation-zone (STZ) theoretical analysis of molecular-dynamics simulations of a rapidly sheared metallic glass. These simulations are especially revealing because, although they are limited to high strain rates, they span temperatures ranging from well below to well above the glass transition. With one important discrepancy, the simplified STZ theory used here reproduces the simulation data, including the way in which those data can be made to collapse approximately onto simple curves by a scaling transformation. The STZ analysis implies that the system's behavior at high strain rates is controlled primarily by effective-temperature thermodynamics, as opposed to system-specific details of the molecular interactions. The discrepancy between theory and simulations occurs at the lower strain rates for temperatures near the glass transition. We argue that this discrepancy can be resolved by the same multispecies generalization of STZ theory that has been proposed recently for understanding frequency-dependent viscoelastic responses, Stokes-Einstein violations, and stretched-exponential relaxation in equilibrated glassy materials.

We present an exhaustive account of phases and phase transitions that can be stabilized in the recently introduced generalized Lebwohl-Lasher model with quadrupolar and octupolar microscopic interactions [L. Longa, G. Pająk, and T. Wydro, Phys. Rev. E 79, 040701(R) (2009)]. A complete mean-field analysis of the model, along with Monte Carlo simulations allows us to identify four distinct classes of the phase diagrams with a number of multicritical points where, in addition to the standard uniaxial and biaxial nematic phases, the other nematic like phases are stabilized. These involve, among the others, tetrahedratic ($T$), nematic tetrahedratic ($N_T$), and chiral nematic tetrahedratic ($N_T^{*}$) phases of global $T_d$, $D_{2d}$, and $D_2$ symmetry, respectively. Molecular order parameters and correlation functions in these phases are determined. We conclude with generalizations of the model that give a simple molecular interpretation of macroscopic regions with opposite optical activity (ambidextrous chirality), observed, e.g., in bent-core systems. An estimate of the helical pitch in the $N_T^{*}$ phase is also given.

We calculate the density of photon states (DOS) of the normal modes in dye-doped chiral nematic liquid crystal (LC) cells in the presence of various loss mechanisms. Losses and gain are incorporated into the transmission characteristics through the introduction of a small imaginary part in the dielectric constant perpendicular and along the director, for which we assume no frequency dispersion. Theoretical results are presented on the DOS in the region of the photonic band gap for a range of values of the loss coefficient and different values of the optical anisotropy. The obtained values of the DOS at the photonic band gap edges predict a reversal of the dominant modes in the structure. Our results are found to be in good agreement with the experimentally obtained excitation thresholds in chiral nematic LC lasers. The behavior of the DOS is also discussed for amplifying LC cells providing additional insight to the lasing mechanism of these structures.

Polymer models tied together by constraints of looping and confinement have been used to explain many of the observed organizational characteristics of interphase chromosomes. Here we introduce a simple lattice animal representation of interphase chromosomes that combines the features of looping and confinement constraints into a single framework. We show through Monte Carlo simulations that this model qualitatively captures both the leveling off in the spatial distance between genomic markers observed in fluorescent in situ hybridization experiments and the inverse decay in the looping probability as a function of genomic separation observed in chromosome conformation capture experiments. The model also suggests that the collapsed state of chromosomes and their segregation into territories with distinct looping activities might be a natural consequence of confinement.

Particle-based simulation represents a powerful approach to modeling physical systems in electronics, molecular biology, and chemical physics. Accounting for the interactions occurring among charged particles requires an accurate and efficient solution of Poisson's equation. For a system of discrete charges with inhomogeneous dielectrics, i.e., a system with discontinuities in the permittivity, the boundary element method (BEM) is frequently adopted. It provides the solution of Poisson's equation, accounting for polarization effects due to the discontinuity in the permittivity by computing the induced charges at the dielectric boundaries. In this framework, the total electrostatic potential is then found by superimposing the elemental contributions from both source and induced charges. In this paper, we present a comparison between two BEMs to solve a boundary-integral formulation of Poisson's equation, with emphasis on the BEMs' suitability for particle-based simulations in terms of solution accuracy and computation speed. The two approaches are the collocation and qualocation methods. Collocation is implemented following the induced-charge computation method of D. Boda et al. [J. Chem. Phys. 125, 034901 (2006)]. The qualocation method is described by J. Tausch et al. [IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 20, 1398 (2001)]. These approaches are studied using both flat and curved surface elements to discretize the dielectric boundary, using two challenging test cases: a dielectric sphere embedded in a different dielectric medium and a toy model of an ion channel. Earlier comparisons of the two BEM approaches did not address curved surface elements or semiatomistic models of ion channels. Our results support the earlier findings that for flat-element calculations, qualocation is always significantly more accurate than collocation. On the other hand, when the dielectric boundary is discretized with curved surface elements, the two methods are essentially equivalent; i.e., they have comparable accuracies for the same number of elements. We find that ions in water—charges embedded in a high-dielectric medium—are harder to compute accurately than charges in a low-dielectric medium.

The study of open quantum billiards has gained popularity in the last decades, including different common and uncommon geometries such as the circular and stadium billiards. We present an extensive analysis of the elliptic quantum billiard with hyperbolic channels. We concentrate on the tunneling through an elliptic resonator-like structure. We analyze three different variations of the system: the first configuration has horizontal channels, then we study the system with vertical leads, and finally we displace both channels by the same angle to gain a more general perspective. We observed a very unusual phase distribution in the resonator cavity when there is no tunneling through the system.

We investigate stimulated scattering instabilities of coherent circularly polarized electromagnetic (CPEM) waves carrying orbital angular momentum (OAM) in dense quantum plasmas with degenerate electrons and nondegenerate ions. For this purpose, we employ the coupled equations for the CPEM wave vector potential and the driven (by the ponderomotive force of the CPEM waves) equations for the electron and ion plasma oscillations. The electrons are significantly affected by the quantum forces (viz., the quantum statistical pressure, the quantum Bohm potential, as well as the electron exchange and electron correlations due to electron spin), which are included in the framework of the quantum hydrodynamical description of the electrons. Furthermore, our investigation of the stimulated Brillouin instability of coherent CPEM waves uses the generalized ion momentum equation that includes strong ion coupling effects. The nonlinear equations for the coupled CPEM and quantum plasma waves are then analyzed to obtain nonlinear dispersion relations which exhibit stimulated Raman, stimulated Brillouin, and modulational instabilities of CPEM waves carrying OAM. The present results are useful for understanding the origin of scattered light off low-frequency density fluctuations in high-energy density plasmas where quantum effects are eminent.

We present a method for the reconstruction of the dynamics of processes with discrete time. The time series from such a system is described by a stochastic recurrence equation, the continuous form of which is known as the Langevin equation. The deterministic $f$ and stochastic $g$ components of the stochastic equation are directly extracted from the measurement data with the assumption that the noise has finite moments and has a zero mean and a unit variance. No other information about the noise distribution is needed. This is contrary to the usual Langevin description, in which the additional assumption that the noise is Gaussian ($\delta$-correlated) distributed as necessary. We test the method using one dimensional deterministic systems (the tent and logistic maps) with Gaussian and with Gumbel noise. In addition, results for human heart rate variability are presented as an example of the application of our method to real data. The differences between cardiological cases can be observed in the properties of the deterministic part $f$ and of the reconstructed noise distribution.

In dynamical models of cortical networks, the recurrent connectivity can amplify the input given to the network in two distinct ways. One is induced by the presence of near-critical eigenvalues in the connectivity matrix $\mathit{W}$, producing large but slow activity fluctuations along the corresponding eigenvectors (dynamical slowing). The other relies on $\mathit{W}$ not being normal, which allows the network activity to make large but fast excursions along specific directions. Here we investigate the trade-off between non-normal amplification and dynamical slowing in the spontaneous activity of large random neuronal networks composed of excitatory and inhibitory neurons. We use a Schur decomposition of $\mathit{W}$ to separate the two amplification mechanisms. Assuming linear stochastic dynamics, we derive an exact expression for the expected amount of purely non-normal amplification. We find that amplification is very limited if dynamical slowing must be kept weak. We conclude that, to achieve strong transient amplification with little slowing, the connectivity must be structured. We show that unidirectional connections between neurons of the same type together with reciprocal connections between neurons of different types, allow for amplification already in the fast dynamical regime. Finally, our results also shed light on the differences between balanced networks in which inhibition exactly cancels excitation and those where inhibition dominates.

Electrical signaling via voltage-gated ion channels depends upon the function of a voltage sensor (VS), identified with the S1–S4 domain in voltage-gated K${}^{+}$ channels. Here we investigate some energetic aspects of the sliding-helix model of the VS using simulations based on VS charges, linear dielectrics, and whole-body motion. Model electrostatics in voltage-clamped boundary conditions are solved using a boundary element method. The statistical mechanical consequences of the electrostatic configurational energy are computed to gain insight into the sliding-helix mechanism and to predict experimentally measured ensemble properties such as gating charge displaced by an applied voltage. Those consequences and ensemble properties are investigated for two alternate S4 configurations, $\alpha$ and $3_{10}$ helical. Both forms of VS are found to have an inherent electrostatic stability. Maximal charge displacement is limited by geometry, specifically the range of movement where S4 charges and countercharges overlap in the region of weak dielectric. Charge displacement responds more steeply to voltage in the $\alpha$-helical than in the 3${}_{10}$-helical sensor. This difference is due to differences on the order of 0.1 eV in the landscapes of electrostatic energy. As a step toward integrating these VS models into a full-channel model, we include a hypothetical external load in the Hamiltonian of the system and analyze the energetic input-output relation of the VS.

We performed experiments to investigate slow fracture in thin rubber films under uniaxial tension using high-viscosity oils. In this system we observed an oscillating instability in slowly propagating cracks for small applied strains. The transition between oscillatory and straight patterns occurred near the characteristic strain at which rubber exhibits a nonlinear stress-strain relation. This suggests that nonlinear elasticity plays an important role in the formation of the observed pattern. This was confirmed by numerical simulation for neo-Hookean and linear elasticity models.