Under investigation in this paper is the Sasa-Satsuma equation, which describes the propagation of ultrashort pulses in a monomode fiber with the third-order dispersion, self-steepening, and stimulated Raman scattering effects. Based on the known bilinear forms, through the modified expanded formulas and symbolic computation, we construct the bright two-soliton solutions. Through classifying the interactions under different parameter conditions, we reveal six cases of interactions between the two solitons via an asymptotic analysis. With the help of the analytic and graphic analysis, we find that such interactions are different from those of the nonlinear Schrödinger equation and Hirota equation. When those solitons interact with each other, the singular-I soliton is shape-preserving, while the singular-II and nonsingular solitons may be shape preserving or shape changing. Such elastic and inelastic interaction phenomena in a scalar equation might enrich the knowledge of soliton behavior, which could be expected to be experimentally observed.

The Griffiths phase has been proposed to induce a stretched critical regime that facilitates self-organizing of brain networks for optimal function. This phase stems from the intrinsic structural heterogeneity of brain networks, i.e., the hierarchical modular structure. In this work, the Griffiths phase is studied in modified hierarchical networks with small-world connections based on the 3-regular Hanoi network. Through extensive simulations, the hierarchical level-dependent inter-module wiring probabilities are identified to determine the emergence of the Griffiths phase. Numerical results and the complementary spectral analysis of the relevant networks can be helpful for a deeper understanding of the essential structural characteristics of finite-dimensional networks to support the Griffiths phase.

Spatiotemporal disorder has been recently associated to the occurrence of anomalous nonergodic diffusion of molecular components in biological systems, but the underlying microscopic mechanism is still unclear. We introduce a model in which a particle performs continuous Brownian motion with changes of diffusion coefficients induced by transient molecular interactions with diffusive binding partners. In spite of the exponential distribution of waiting times, the model shows subdiffusion and nonergodicity similar to the heavy-tailed continuous time random walk. The dependence of these properties on the density of binding partners is analyzed and discussed. Our work provides an experimentally testable microscopic model to investigate the nature of nonergodicity in disordered media.

For short-range attractive colloids, the phase diagram of the kinetic glass transition is studied by time-convolutionless mode-coupling theory (TMCT). Using numerical calculations, TMCT is shown to recover all the remarkable features predicted by the mode-coupling theory for attractive colloids: the glass-liquid-glass reentrant, the glass-glass transition, and the higher-order singularities. It is also demonstrated through the comparisons with the results of molecular dynamics for the binary attractive colloids that TMCT improves the critical values of the volume fraction. In addition, a schematic model of three control parameters is investigated analytically. It is thus confirmed that TMCT can describe the glass-glass transition and higher-order singularities even in such a schematic model.

A binary mixture of superparamagnetic colloidal particles is confined between glass plates such that the large particles become fixed and provide a two-dimensional disordered matrix for the still mobile small particles, which form a fluid. By varying fluid and matrix area fractions and tuning the interactions between the superparamagnetic particles via an external magnetic field, different regions of the state diagram are explored. The mobile particles exhibit delocalized dynamics at small matrix area fractions and localized motion at high matrix area fractions, and the localization transition is rounded by the soft interactions [T. O. E. Skinner et al., Phys. Rev. Lett. 111, 128301 (2013)]. Expanding on previous work, we find the dynamics of the tracers to be strongly heterogeneous and show that molecular dynamics simulations of an ideal gas confined in a fixed matrix exhibit similar behavior. The simulations show how these soft interactions make the dynamics more heterogeneous compared to the disordered Lorentz gas and lead to strong non-Gaussian fluctuations.

We examine the long-term behavior of nonintegrable, energy-conserved, one-dimensional systems of macroscopic grains interacting via a contact-only generalized Hertz potential and held between stationary walls. Such systems can be set up to have no phononic background excitation and represent examples of a sonic vacuum. Existing dynamical studies showed the absence of energy equipartitioning in such systems, hence their long-term dynamics was described as quasiequilibrium. Here we show that these systems do in fact reach thermal equilibrium at sufficiently long times, as indicated by the calculated heat capacity. As a by-product, we show how fluctuations of system quantities, and thus the distribution functions, are influenced by the Hertz potential. In particular, the variance of the system's kinetic energy probability density function is reduced by a factor related to the contact potential.

We use direct numerical simulations to compute structure functions, scaling exponents, probability density functions, and effective transport coefficients of passive scalars in turbulent rotating helical and nonhelical flows. We show that helicity affects the inertial range scaling of the velocity and of the passive scalar when rotation is present, with a spectral law consistent with $\sim k_{\perp }^{-1.4}$ for the passive scalar variance spectrum. This scaling law is consistent with a phenomenological argument [P. Rodriguez Imazio and P. D. Mininni, Phys. Rev. E 83, 066309 (2011)] for rotating nonhelical flows, which follows directly from Kolmogorov-Obukhov scaling and states that if energy follows a $E\left(k\right)\sim k^{-n}$ law, then the passive scalar variance follows a law $V\left(k\right)\sim k^{-n_{\theta }}$ with $n_{\theta }=(5-n)/2$. With the second-order scaling exponent obtained from this law, and using the Kraichnan model, we obtain anomalous scaling exponents for the passive scalar that are in good agreement with the numerical results. Multifractal intermittency models are also considered. Intermittency of the passive scalar is stronger than in the nonhelical rotating case, a result that is also confirmed by stronger non-Gaussian tails in the probability density functions of field increments. Finally, Fick's law is used to compute the effective diffusion coefficients in the directions parallel and perpendicular to rotation. Calculations indicate that horizontal diffusion decreases in the presence of helicity in rotating flows, while vertical diffusion increases. A simple mean field argument explains this behavior in terms of the amplitude of velocity fluctuations.

In this paper, an alternative approach to implement initial and boundary conditions in the lattice Boltzmann method is presented. The main idea is to approximate the nonequilibrium component of distribution functions as a third-order power series in the lattice velocities and formulate a procedure to determine boundary node distributions by using fluid variables, consistent with such an expansion. The velocity shift associated with the body force effects is included in this scheme, along with an approximation to determine the mass density in complex geometries. Different strategies based on the present scheme are developed to implement velocity and pressure conditions for arbitrarily shaped boundaries, using the D2Q9, D3Q15, D3Q19 and D3Q27 lattices, in two and three space dimensions, respectively. The proposed treatment is tested against several well-established problems, showing second-order spatial accuracy and often improved behavior as compared to various existing methods, with no appreciable computational overhead.

We thoroughly describe a class of models recently presented by Fisher and coworkers [Phys. Rev. Lett. 116, 040601 (2016)]. The crucial feature of such models, termed compressible cell gases (CCGs), is that the individual cell volumes of a lattice gas are allowed to fluctuate. They are studied via the seldom-used ($\mu$, $p$, $T$) ensemble, which leads to their exact mapping onto the Ising model. Remarkably, CCGs obey complete scaling, a formulation for the thermodynamic behavior of fluids near the gas-liquid critical point that accommodates features inherent to the asymmetric nature of this phase transition like the Yang-Yang (YY) and singular coexistence-curve diameter anomalies. The ${\mathrm{CCG}}_0$ models generated when volumes vary freely reveal local free volume fluctuations as the origin of these phenomena. Local energy-volume coupling is found to be another relevant microscopic factor. Furthermore, the CCG class is greatly extended by using the decoration transformation, with an interesting example being the Sastry-Debenedetti-Sciortino-Stanley model for hydrogen bonding in low-temperature water. The magnitude of anomalies is characterized by a single parameter, the YY ratio, which for the models so far considered here ranges from $-\infty$ to $\frac{1}{2}$.

We characterize the influence that external noise, with both spatial and temporal correlations, has on the scale dependence of the reaction parameters of a cubic autocatalytic reaction diffusion (CARD) system. Interpreting the CARD model as a primitive reaction scheme for a living system, the results indicate that power-law correlations in environmental fluctuations can either decrease or increase the rates of nutrient decay and the rate of autocatalysis (replication) on small spatial and temporal scales.

In the present work, we revisit two-component Bose-Einstein condensates in their fully three-dimensional (3D) form. Motivated by earlier studies of dark-bright solitons in the 1D case, we explore the stability of these structures in their fully 3D form in two variants. In one the dark soliton is planar and trapping a planar bright (disk) soliton. In the other case, a dark spherical shell soliton creates an effective potential in which a bright spherical shell of atoms is trapped in the second component. We identify these solutions as numerically exact states (up to a prescribed accuracy) and perform a Bogolyubov–de Gennes linearization analysis that illustrates that both structures can be dynamically stable in suitable intervals of sufficiently low chemical potentials. We corroborate this finding theoretically by analyzing the stability via degenerate perturbation theory near the linear limit of the system. When the solitary waves are found to be unstable, we explore their dynamical evolution via direct numerical simulations which, in turn, reveal wave forms that are more robust. Finally, using the $\mathrm{SO}\left(2\right)$ symmetry of the model, we produce multi-dark-bright planar or shell solitons involved in pairwise oscillatory motion.

Atomistic simulations of binary amorphous systems with over 4 million atoms are performed. Systems of two interatomic potentials of the Lennard-Jones type, LJ12-6 and LJ9-6, are simulated. The athermal quasistatic shearing protocol is adopted, where the shear strain is applied in a stepwise fashion with each step followed by energy minimization. For each avalanche event, the shear stress drop $\left(\mathrm{\Delta }\sigma \right)$, the hydrostatic pressure drop $\left(\mathrm{\Delta }{\sigma }_h\right)$, and the potential energy drop $\left(\mathrm{\Delta }E\right)$ are computed. It is found that, with the avalanche size increasing, the three become proportional to each other asymptotically. The probability distributions of avalanche sizes are obtained and values of scaling exponents fitted. In particular, the distributions follow a power law, $P\left(\mathrm{\Delta }U\right)\sim \mathrm{\Delta }{U}^{-\tau }$, where $\mathrm{\Delta }U$ is a measure of avalanche sizes defined based on shear stress drops. The exponent $\tau$ is $1.25\pm 0.1$ for the LJ12-6 systems, and $1.15\pm 0.1$ for the LJ9-6 systems. The value of $\tau$ for the LJ12-6 systems is consistent with that from an earlier atomistic simulation study by Robbins et al. [Phys. Rev. Lett. 109, 105703 (2012)], but the fitted values of other scaling exponents differ, which may be because the shearing protocol used here differs from that in their study.

We study the role of the tail and the range of interaction in a spatially structured population of two-state on-off units governed by Markovian transition rates. The coupling among the oscillators is evidenced by the dependence of the transition rates of each unit on the states of the units to which it is coupled. Tuning the tail or range of the interactions, we observe a transition from an ordered global state (long-range interactions) to a disordered one (short-range interactions). Depending on the interaction kernel, the transition may be smooth (second order) or abrupt (first order). We analyze the transient, which may present different routes to the steady state with vastly different time scales.

To understand, predict, and control complex networked systems, a prerequisite is to reconstruct the network structure from observable data. Despite recent progress in network reconstruction, binary-state dynamics that are ubiquitous in nature, technology, and society still present an outstanding challenge in this field. Here we offer a framework for reconstructing complex networks with binary-state dynamics by developing a universal data-based linearization approach that is applicable to systems with linear, nonlinear, discontinuous, or stochastic dynamics governed by monotonic functions. The linearization procedure enables us to convert the network reconstruction into a sparse signal reconstruction problem that can be resolved through convex optimization. We demonstrate generally high reconstruction accuracy for a number of complex networks associated with distinct binary-state dynamics from using binary data contaminated by noise and missing data. Our framework is completely data driven, efficient, and robust, and does not require any a priori knowledge about the detailed dynamical process on the network. The framework represents a general paradigm for reconstructing, understanding, and exploiting complex networked systems with binary-state dynamics.

Many natural and social networks evolve in time and their structures are dynamic. In most networks, nodes are heterogeneous, and their roles in the evolution of structure differ. This paper focuses on the role of individual attributes on the temporal dynamics of network structure. We focus on a basic model for growing networks that incorporates node attributes (which we call “quality”), and we focus on the problem of forecasting the structural properties of the network in arbitrary times for an arbitrary initial network. That is, we address the following question: If we are given a certain initial network with given arbitrary structure and known node attributes, then how does the structure change in time as new nodes with given distribution of attributes join the network? We solve the model analytically and obtain the quality-degree joint distribution and degree correlations. We characterize the role of individual attributes in the position of individual nodes in the hierarchy of connections. We confirm the theoretical findings with Monte Carlo simulations.

Cell migration is essential to cell segregation, playing a central role in tissue formation, wound healing, and tumor evolution. Considering random mixtures of two cell types, it is still not clear which cell characteristics define clustering time scales. The mass of diffusing clusters merging with one another is expected to grow as $t^{d/d+2}$ when the diffusion constant scales with the inverse of the cluster mass. Cell segregation experiments deviate from that behavior. Explanations for that could arise from specific microscopic mechanisms or from collective effects, typical of active matter. Here we consider a power law connecting diffusion constant and cluster mass to propose an analytic approach to model cell segregation where we explicitly take into account finite-size corrections. The results are compared with active matter model simulations and experiments available in the literature. To investigate the role played by different mechanisms we considered different hypotheses describing cell-cell interaction: differential adhesion hypothesis and different velocities hypothesis. We find that the simulations yield normal diffusion for long time intervals. Analytic and simulation results show that (i) cluster evolution clearly tends to a scaling regime, disrupted only at finite-size limits; (ii) cluster diffusion is greatly enhanced by cell collective behavior, such that for high enough tendency to follow the neighbors, cluster diffusion may become independent of cluster size; (iii) the scaling exponent for cluster growth depends only on the mass-diffusion relation, not on the detailed local segregation mechanism. These results apply for active matter systems in general and, in particular, the mechanisms found underlying the increase in cell sorting speed certainly have deep implications in biological evolution as a selection mechanism.

A phase-field model of an oxide relevant to corrosion resistant alloys for film thicknesses below the Debye length $L_D$, where charge neutrality in the oxide does not occur, is formulated. The phase-field model is validated in the Wagner limit using a sharp interface Gouy-Chapman model for the electrostatic double layer. The phase-field simulations show that equilibrium oxide films below the Wagner limit are charged throughout due to their inability to electrostatically screen charge over the length of the film, $L$. The character of the defect and charge distribution profiles in the oxide vary depending on whether reduced oxygen adatoms are present on the gas-oxide interface. The Fermi level in the oxide increases for thinner films, approaching the Fermi level of the metal in the limit $L/L_D\to 0$, which increases the driving force for adsorbed oxygen reduction at the gas-oxide interface.

We investigate the drag experienced by a spherical intruder moving through a medium consisting of granular hydrogels immersed in water as a function of its depth, size, and speed. The medium is observed to display a yield stress with a finite force required to move the intruder in the quasistatic regime at low speeds before rapidly increasing at high speeds. In order to understand the relevant time scales that determine drag, we estimate the inertial number $I$ given by the ratio of the time scales required to rearrange grains due to the overburden pressure and imposed shear and the viscous number $J$ given by the ratio of the time scales required to sediment grains in the interstitial fluid and imposed shear. We find that the effective friction ${\mu }_e$ encountered by the intruder can be parametrized by $I=\sqrt{{\rho }_g/P_p}{v}_i$, where ${\rho }_g$ is the density of the granular hydrogels, $v_i$ is the intruder speed, and $P_p$ is the overburden pressure due to the weight of the medium, over a wide range of $I$ where the Stokes number $\text{St}=I^2/J\gg 1$. We then show that ${\mu }_e$ can be described by the function ${\mu }_e\left(I\right)={\mu }_0+\alpha I^{\beta }$, where ${\mu }_0$, $\alpha$, and $\beta$ are constants that depend on the medium. This formula can be used to predict the drag experienced by an intruder of a different size at a different depth in the same medium as a function of its speed.

We rigorously show that the truncation at low wave numbers always leads to background scalar-level anisotropy at large scales. Neither the resolution nor the spectral low-pass filter is dominant for this anisotropy, while the shape of the energy spectrum at low wave numbers is an important influence factor. Quantitative results are shown to provide references to the statistics in future postprocessing studies. Also, a simplified analytical model is introduced to explain the single-mode effects for this anisotropy.