A discrete-time dynamics of a non-Markovian random walker is analyzed using a minimal model where memory of the past drives the present dynamics. In recent work [N. Kumar et al., Phys. Rev. E 82, 021101 (2010)] we proposed a model that exhibits asymptotic superdiffusion, normal diffusion, and subdiffusion with the sweep of a single parameter. Here we propose an even simpler model, with minimal options for the walker: either move forward or stay at rest. We show that this model can also give rise to diffusive, subdiffusive, and superdiffusive dynamics at long times as a single parameter is varied. We show that in order to have subdiffusive dynamics, the memory of the rest states must be perfectly correlated with the present dynamics. We show explicitly that if this condition is not satisfied in a unidirectional walk, the dynamics is only either diffusive or superdiffusive (but not subdiffusive) at long times.

This study proposes a delay-coupled system based on the logistic equation that models the interaction of a population with its varying environment. The integro-diferential equations of the model are presented in terms of a distributed time-delayed coupled logistic-capacity equation. The model eliminates the need for a prior knowledge of the maximum saturation environmental carrying capacity value. Therefore the dynamics toward the final attractor in a distributed time-delayed coupled logistic-capacity model is studied. Exact results are presented, and analytical conclusions have been done in terms of the two parameters of the model.

The Boltzmann equation for inelastic and rough hard spheres is considered as a model of a dilute granular gas. In this model, the collisions are characterized by constant coefficients of normal and tangential restitution, and hence the translational and rotational degrees of freedom are coupled. A normal solution to the Boltzmann equation is obtained by means of the Chapman-Enskog method for states near the homogeneous cooling state. The analysis is carried out to first order in the spatial gradients of the number density, the flow velocity, and the granular temperature. The constitutive equations for the momentum and heat fluxes and for the cooling rate are derived, and the associated transport coefficients are expressed in terms of the solutions of linear integral equations. For practical purposes, a first Sonine approximation is used to obtain explicit expressions of the transport coefficients as nonlinear functions of both coefficients of restitution and the moment of inertia. Known results for purely smooth inelastic spheres and perfectly elastic and rough spheres are recovered in the appropriate limits.

In contrast to the predictions of the standard theory of electroconvection (EC), our experiments showed that the action of superposed ac and dc voltages rather inhibits pattern formation than favors the emergence of instabilities; the patternless region may extend to much higher voltages than the individual ac or dc thresholds. The pattern formation induced by such asymmetrical voltage was explored in a nematic liquid crystal in a wide frequency range. The findings could be qualitatively explained for the conductive EC, but represent a challenging problem for the dielectric EC.

At low temperatures, some lattice spin models with simple ferromagnetic or antiferromagnetic interactions (for example, nearest-neighbor interaction being isotropic in spin space on a bipartite three-dimensional lattice) produce orientationally ordered phases exhibiting nematic (second-rank) order, in addition to the primary first-rank one; on the other hand, in the literature, they have been rather seldom investigated in this respect. Here we study the thermodynamic properties of a three-dimensional model with dipolar-like interaction. Its ground state is found to exhibit full orientational order with respect to a suitably defined staggered magnetization (polarization), but no nematic second-rank order. Extensive Monte Carlo simulations, in conjunction with finite-size scaling analysis, have been used for characterizing its critical behavior; on the other hand, it has been found that nematic order does indeed set in at low temperatures, via a mechanism of order by disorder.

In order to test the application of the “nanoparticle” concept to viruses in terms of low-frequency dynamics, large viruses (140–190 nm) were compared to similar-sized polymer colloids using ultra-small-angle x-ray scattering and very-low-frequency Raman or Brillouin scattering. While both viruses and polymer colloids show comparable highly defined morphologies, with comparable abilities of forming self-assembled structures, their respective abilities to confine detectable acoustic vibrations, as expected for such monodisperse systems, differed. Possible reasons for these different behaviors are discussed.

Allostery is a rapid and efficient way in many biological processes to regulate protein functions, where binding of an effector at the allosteric site alters the activity and function at a distant active site. Allosteric regulation of protein biological functions provides a promising strategy for novel drug design. However, how to effectively identify the allosteric sites remains one of the major challenges for allosteric drug design. In the present work, a thermodynamic method based on the elastic network model was proposed to predict the allosteric sites on the protein surface. In our method, the thermodynamic coupling between the allosteric and active sites was considered, and then the allosteric sites were identified as those where the binding of an effector molecule induces a large change in the binding free energy of the protein with its ligand. Using the proposed method, two proteins, i.e., the 70 kD heat shock protein (Hsp70) and GluA2 alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptor, were studied and the allosteric sites on the protein surface were successfully identified. The predicted results are consistent with the available experimental data, which indicates that our method is a simple yet effective approach for the identification of allosteric sites on proteins.

In this paper we develop a model for the evolution of multiple networks which is able to replicate the concentrated and sparse nature of world trade data. Our model is an extension of the preferential attachment growth model to the case of multiple networks. Countries trade a variety of goods of different complexity. Every country progressively evolves from trading less sophisticated to high-tech goods. The probabilities of capturing more trade opportunities at a given level of complexity and of starting to trade more complex goods are both proportional to the number of existing trade links. We provide a set of theoretical predictions and simulative results. A calibration exercise shows that our model replicates the same concentration level of world trade as well as the sparsity pattern of the trade matrix. We also discuss a set of numerical solutions to deal with large multiple networks.

Systems of FitzHugh–Nagumo units with different coupling topologies are capable of self-generating and -terminating strong deviations from their regular dynamics that can be regarded as extreme events due to their rareness and recurrent occurrence. Here we demonstrate the crucial role of an interior crisis in the emergence of extreme events. In parameter space we identify this interior crisis as the organizing center of the dynamics by employing concepts of mixed-mode oscillations and of leaking chaotic systems. We find that extreme events occur in certain regions in parameter space, and we show the robustness of this phenomenon with respect to the system size.

We obtain exact solutions for kinks in ${\varphi }^8$, ${\varphi }^{10}$, and ${\varphi }^{12}$ field theories with degenerate minima, which can describe a second-order phase transition followed by a first-order one, a succession of two first-order phase transitions and a second-order phase transition followed by two first-order phase transitions, respectively. Such phase transitions are known to occur in ferroelastic and ferroelectric crystals and in meson physics. In particular, we find that the higher-order field theories have kink solutions with algebraically decaying tails and also asymmetric cases with mixed exponential-algebraic tail decay, unlike the lower-order ${\varphi }^4$ and ${\varphi }^6$ theories. Additionally, we construct distinct kinks with equal energies in all three field theories considered, and we show the coexistence of up to three distinct kinks (for a ${\varphi }^{12}$ potential with six degenerate minima). We also summarize phonon dispersion relations for these systems, showing that the higher-order field theories have specific cases in which only nonlinear phonons are allowed. For the ${\varphi }^{10}$ field theory, which is a quasiexactly solvable model akin to ${\varphi }^6$, we are also able to obtain three analytical solutions for the classical free energy as well as the probability distribution function in the thermodynamic limit.

We show that the relaxation dynamics near a glass transition with continuous ergodicity breaking can be endowed with a geometric interpretation based on percolation theory. At the mean-field level this approach is consistent with the mode-coupling theory (MCT) of type-A liquid-glass transitions and allows one to disentangle the universal and nonuniversal contributions to MCT relaxation exponents. Scaling predictions for the time correlation function are successfully tested in the ${\mathsf{F}}_{12}$ schematic model and facilitated spin systems on a Bethe lattice. Our approach immediately suggests the extension of MCT scaling laws to finite spatial dimensions and yields predictions for dynamic relaxation exponents below an upper critical dimension of 6.

We study the conditions for persistent cooperation in an off-lattice model of mobile agents playing the Prisoner's Dilemma game with pure, unconditional strategies. Each agent has an exclusion radius $r_P$, which accounts for the population viscosity, and an interaction radius $r_{\mathrm{int}}$, which defines the instantaneous contact network for the game dynamics. We show that, differently from the $r_P=0$ case, the model with finite-sized agents presents a coexistence phase with both cooperators and defectors, besides the two absorbing phases, in which either cooperators or defectors dominate. We provide, in addition, a geometric interpretation of the transitions between phases. In analogy with lattice models, the geometric percolation of the contact network (i.e., irrespective of the strategy) enhances cooperation. More importantly, we show that the percolation of defectors is an essential condition for their survival. Differently from compact clusters of cooperators, isolated groups of defectors will eventually become extinct if not percolating, independently of their size.

Reliable forecasts of extreme but rare events, such as earthquakes, financial crashes, and epileptic seizures, would render interventions and precautions possible. Therefore, forecasting methods have been developed which intend to raise an alarm if an extreme event is about to occur. In order to statistically validate the performance of a prediction system, it must be compared to the performance of a random predictor, which raises alarms independent of the events. Such a random predictor can be obtained by bootstrapping or analytically. We propose an analytic statistical framework which, in contrast to conventional methods, allows for validating independently the sensitivity and specificity of a forecasting method. Moreover, our method accounts for the periods during which an event has to remain absent or occur after a respective forecast.

This paper studies the signal-to-noise ratio (SNR) gain of a parallel array of nonlinear elements that transmits a common input composed of a periodic signal and external noise. Aiming to further enhance the SNR gain, each element is injected with internal noise components or high-frequency sinusoidal vibrations. We report that the SNR gain exhibits two maxima at different values of the internal noise level or of the sinusoidal vibration amplitude. For the addition of internal noise to an array of threshold-based elements, the condition for occurrence of stochastic resonance is analytically investigated in the limit of weak signals. Interestingly, when the internal noise components are replaced by high-frequency sinusoidal vibrations, the SNR gain displays the vibrational multiresonance phenomenon. In both considered cases, there are certain regions of the internal noise intensity or the sinusoidal vibration amplitude wherein the achieved maximal SNR gain can be considerably beyond unity for a weak signal buried in non-Gaussian external noise. Due to the easy implementation of sinusoidal vibration modulation, this approach is potentially useful for improving the output SNR in an array of nonlinear devices.

We develop a mean-field approach for multicomponent stochastic spatially extended systems and use it to obtain a multivariate nonlinear self-consistent Fokker-Planck equation defining the probability density of the state of the system, which describes a well-known model of autocatalytic chemical reaction (brusselator) with spatially correlated multiplicative noise, and to study the evolution of probability density and statistical characteristics of the system in the process of spatial pattern formation. We propose the finite-difference method for the numerical solving of a general class of multivariate nonlinear self-consistent time-dependent Fokker-Planck equations. We illustrate the accuracy and reliability of the method by applying it to an exactly solvable nonlinear Fokker-Planck equation (NFPE) for the Shimizu-Yamada model [Prog. Theor. Phys. 47, 350 (1972)] and nonlinear Fokker-Planck equation [Desai and Zwanzig, J. Stat. Phys. 19, 1 (1978)] obtained for a nonlinear stochastic mean-field model introduced by Kometani and Shimizu [J. Stat. Phys. 13, 473 (1975)]. Taking the problems indicated above as an example, the accuracy of the method is compared with the accuracy of Hermite distributed approximating functional method [Zhang et al., Phys. Rev. E 56, 1197 (1997)]. Numerical study of the NFPE solutions for a stochastic brusselator shows that in the region of Turing bifurcation several types of solutions exist if noise intensity increases: unimodal solution, transient bimodality, and an interesting solution which involves multiple “repumping” of probability density through bimodality. Additionally, we study the behavior of the order parameter of the system under consideration and show that the second type of solution arises in the supercritical region if noise intensity values are close to the values appropriate for the transition from bimodal stationary probability density for the order parameter to the unimodal one.

Thermal fluctuations, geometric exclusion, and external driving all govern the mechanical response of dense particulate suspensions. Here, we measure the stress-strain response of quasi-two-dimensional flow-stabilized microsphere heaps in a regime in which all three effects are present using a microfluidic device. We observe that the elastic modulus and the mean interparticle separation of the heaps are tunable via the confining stress provided by the fluid flow. Furthermore, the measured stress-strain curves exhibit a universal nonlinear shape, which can be predicted from a thermal van der Waals equation of state with excluded volume. This analysis indicates that many-body interactions contribute a significant fraction of the stress supported by the heap.

We report that light beams, guided along liquid crystal defect lines, can be transformed into vector beams with various polarization profiles. Using finite-difference time-domain numerical solving of Maxwell equations, we confirm that the defect in the orientational order of the liquid crystal induces a defect in the light field with twice the winding number of the liquid crystal defect, coupling the topological invariants of both fields. For example, it is possible to transform uniformly polarized light into light with a radial polarization profile. Our approach also correctly yields a zero-intensity region near the defect core, which is always present in areas of discontinuous light polarization or phase. Using circularly polarized incident light, we show that defects with noninteger winding numbers can be obtained, where topological constants are preserved by phase vortices, demonstrating coupling between the light's spin, orbital angular momentum, and polarization profile. Further, we find that an ultrafast femtosecond laser pulse traveling along a defect line splits into multiple intensity regions, again depending on the defect's winding number, allowing applications in beam steering and filtering. Finally, our approach describing the generation of complex optical fields via coupling with topological defect lines in optically birefringent nematic fluids can be easily extended to high-intensity beams that affect nematic ordering.

Liquid crystals displays with tailoring electrodes exhibit complex spatiotemporal dynamics when a large voltage is applied. We report experimental observations of the appearance of a programmable zig-zag lattice using an in-plane-switching cell filled with a nematic liquid crystal. Applying a small voltage to a wide range of frequencies, the system exhibits an Ising wall lattice. Increasing the voltage, this lattice presents a spatial instability generating an undulating wall lattice, and to higher voltages it becomes zig-zag type. Experimentally, we characterize the bifurcations and phase diagram of the wall lattice. Theoretically, we develop, from first principles, a descriptive model. This model has a good qualitative agreement with experimental observations.

Boolean networks are discrete dynamical systems for modeling regulation and signaling in living cells. We investigate a particular class of Boolean functions with inhibiting inputs exerting a veto (forced zero) on the output. We give analytical expressions for the sensitivity of these functions and provide evidence for their role in natural systems. In an intracellular signal transduction network [Helikar et al., Proc. Natl. Acad. Sci. USA 105, 1913 (2008)], the functions with veto are over-represented by a factor exceeding the over-representation of threshold functions and canalyzing functions in the same system. In Boolean networks for control of the yeast cell cycle [Li et al., Proc. Natl. Acad. Sci. USA 101, 4781 (2004); Davidich et al., PLoS ONE 3, e1672 (2008)], no or minimal changes to the wiring diagrams are necessary to formulate their dynamics in terms of the veto functions introduced here.