The local shear stress of non-Brownian suspensions was investigated using the lattice Boltzmann method coupled with the smoothed profile method. Previous studies have only focused on the bulk rheology of complex fluids because the local rheology of complex fluids was not accessible due to technical limitations. In this study, the local shear stress of two-dimensional solid particle suspensions in Couette flow was investigated with the method of planes to correlate non-Newtonian fluid behavior with the structural evolution of concentrated particle suspensions. Shear thickening was successfully captured for highly concentrated suspensions at high particle Reynolds number, and both the local rheology and local structure of the suspensions were analyzed. It was also found that the linear correlation between the local particle stress and local particle volume fraction was dramatically reduced during shear thickening. These results clearly show how the change in local structure of suspensions influences the local and bulk rheology of the suspensions.

We study the interaction between two cracks propagating quasistatically during the tearing of a thin brittle sheet. We show that the cracks attract each other following a path described by a power law resulting from the competition between elastic and fracture energies. The power law exponent $(8/11)$ is in close agreement with experiments. We also show that a second (asymptotic) regime, with an exponent of $9/8$, emerges for small distances between the two crack tips due to the finite transverse curvature of the elastic ridge joining them.

Electrical actuation is investigated in two kinds of chiral smectic liquid-crystal elastomers (LCEs) with different domain structures LCE1 and LCE2: The latter is better than the former in orientational order. Tracking fluorescent beads dispersed on the samples enables us to measure the two-dimensional strain tensors in ferroelectric elastomer films. It turns out that the electric-field-induced strain is polarity dependent and the type of molecular orientation responsible for the strain is specified. In LCE1 the shear strain is dominant, whereas in LCE2 it is comparable to the elongation strain, which is explained by the rotation of the principal axes. The essential differences of the two elastomers are observed in the eigenvalues of the strain tensors. The absolute values for LCE1 are larger than those for LCE2. The difference is discussed on the basis of the domain structures.

The de Gennes' blob model is extensively used in different problems of polymer physics. This model is theoretically applicable when the number of monomers inside each blob is large enough. For confined flexible polymers, this requires the confining geometry to be much larger than the monomer size. In this paper, the opposite limit of polymer in nanoslits with one to several monomers width is studied, using molecular dynamics simulations. Extension of the polymer inside nanoslits, confinement force on the plates, and the effective spring constant of the confined polymer are investigated. Despite the theoretical limitations of the blob model, the simulation results are explained with the blob model very well. The agreement is observed for the static properties and the dynamic spring constant of the polymer. A theoretical description of the conditions under which the dynamic spring constant of the polymer is independent of the small number of monomers inside blobs is given. Our results on the limit of applicability of the blob model can be useful in the design of nanotechnology devices.

When a self-localized quasiparticle excitation propagates along a discrete one-dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy no longer enables the excitation to cross over the minimum energy barrier between neighboring sites, and the excitation becomes localized within a lattice cell. In the case of a protein, the lattice structure consists of the ${\mathrm{C}}^{\alpha }$ backbone. The self-localized quasiparticle excitation is the elemental building block of loops. It can be modeled by a kink that solves a variant of the discrete nonlinear Schrödinger equation. We study the propagation of such a kink in the case of the protein G related albumin-binding domain, using the united residue coarse-grained molecular-dynamics force field. We estimate the height of the energy barriers that the kink needs to cross over in order to propagate along the backbone lattice. We analyze how these barriers give rise to both stresses and reliefs, which control the kink movement. For this, we deform a natively folded protein structure by parallel translating the kink along the backbone away from its native position. We release the transposed kink, and we follow how it propagates along the backbone toward the native location. We observe that the dissipative forces that are exerted on the kink by the various energy barriers have a pivotal role in determining how a protein folds toward its native state.

We investigate collective dynamics of branched actin networks growing against a rigid movable wall constrained by a resistive force. Computing the force velocity relations, we show that the stall force of such networks depends not only on the average number of filaments touching the wall, but also on the amount of fluctuation of the leading edge of the network. These differences arise due to differences in the network architecture, namely, distance between two adjacent branching points and the initial distance of the starting filament from the wall, with their relative magnitudes influencing the nature of the force velocity curves (convex versus concave). We also show that the introduction of branching results in nonmonotonic diffusion constant, a quantity that measures the growth in length fluctuation of the leading edge of the network, as a function of externally applied force. Together our results demonstrate how the collective dynamics of a branched network differs from that of a parallel filament network.

Many graph clustering quality functions suffer from a resolution limit, namely the inability to find small clusters in large graphs. So-called resolution-limit-free quality functions do not have this limit. This property was previously introduced for hard clustering, that is, graph partitioning. We investigate the resolution-limit-free property in the context of non-negative matrix factorization (NMF) for hard and soft graph clustering. To use NMF in the hard clustering setting, a common approach is to assign each node to its highest membership cluster. We show that in this case symmetric NMF is not resolution-limit free, but that it becomes so when hardness constraints are used as part of the optimization. The resulting function is strongly linked to the constant Potts model. In soft clustering, nodes can belong to more than one cluster, with varying degrees of membership. In this setting resolution-limit free turns out to be too strong a property. Therefore we introduce locality, which roughly states that changing one part of the graph does not affect the clustering of other parts of the graph. We argue that this is a desirable property, provide conditions under which NMF quality functions are local, and propose a novel class of local probabilistic NMF quality functions for soft graph clustering.

Different definitions of links in climate networks may lead to considerably different network topologies. We construct a network from climate records of surface level atmospheric temperature in different geographical sites around the globe using two commonly used definitions of links. Utilizing detrended fluctuation analysis, shuffled surrogates, and separation analysis of maritime and continental records, we find that one of the major influences on the structure of climate networks is due to the autocorrelation in the records, which may introduce spurious links. This may explain why different methods could lead to different climate network topologies.

Threshold cascade models have been used to describe the spread of behavior in social networks and cascades of default in financial networks. In some cases, these networks may have multiple kinds of interactions, such as distinct types of social ties or distinct types of financial liabilities; furthermore, nodes may respond in different ways to influence from their neighbors of multiple types. To start to capture such settings in a stylized way, we generalize a threshold cascade model to a multiplex network in which nodes follow one of two response rules: some nodes activate when, in at least one layer, a large enough fraction of neighbors is active, while the other nodes activate when, in all layers, a large enough fraction of neighbors is active. Varying the fractions of nodes following either rule facilitates or inhibits cascades. Near the inhibition regime, global cascades appear discontinuously as the network density increases; however, the cascade grows more slowly over time. This behavior suggests a way in which various collective phenomena in the real world could appear abruptly yet slowly.

We provide appropriate tools for the analysis of dynamics and chaos for one-dimensional systems with periodic boundary conditions. Our approach allows for the investigation of the dependence of the largest Lyapunov exponent on various initial conditions of the system. The method employs an effective approach for defining the phase-space distance appropriate for systems with periodic boundaries and allows for an unambiguous test-orbit rescaling in the phase space required to calculate the Lyapunov exponents. We elucidate our technique by applying it to investigate the chaotic dynamics of a one-dimensional plasma with periodic boundaries. Exact analytic expressions are derived for the electric field and potential using Ewald sums, thereby making it possible to follow the time evolution of the plasma in simulations without any special treatment of the boundary. By employing a set of event-driven algorithms, we calculate the largest Lyapunov exponent, the radial distribution function, and the pressure by following the evolution of the system in phase space without resorting to numerical manipulation of the equations of motion. Simulation results are presented and analyzed for the one-dimensional plasma with a view to examining the dynamical and chaotic behavior exhibited by small and large versions of the system.

We explore the classical dynamics of atoms in an optical dipole trap formed by two identical Gaussian beams propagating in perpendicular directions. The phase space is a mixture of regular and chaotic orbits, the latter becoming dominant as the energy of the atoms increases. The trapping capabilities of these perpendicular Gaussian beams are investigated by considering an atomic ensemble in free motion. After a sudden turn on of the dipole trap, a certain fraction of atoms in the ensemble remains trapped. The majority of these trapped atoms has energies larger than the escape channels, which can be explained by the existence of regular and chaotic orbits with very long escape times.

The embedding of a time series provides a basic tool to analyze dynamical properties of the underlying chaotic system. To this purpose, the choice of the embedding dimension and lag is crucial. Although several methods have been devised to tackle the issue of the optimal setting of these parameters, a conclusive criterion to make the most appropriate choice is still lacking. An accepted procedure to rank different embedding methods relies on the evaluation of the maximum Lyapunov exponent (MLE) out of embedded time series that are generated by chaotic systems with explicit analytic representation. The MLE is evaluated as the local divergence rate of nearby trajectories. Given a system, embedding methods are ranked according to how close such MLE values are to the true MLE. This is provided by the so-called standard method in a way that exploits the mathematical description of the system and does not require embedding. In this paper we study the dependence of the finite-time MLE evaluated via the divergence rate method on the embedding dimension and lag in the case of time series generated by four systems that are widely used as references in the scientific literature. We develop a completely automatic algorithm that provides the divergence rate and its statistical uncertainty. We show that the uncertainty can provide useful information about the optimal choice of the embedding parameters. In addition, our approach allows us to find which systems provide suitable benchmarks for the comparison and ranking of different embedding methods.

Quantitative characterization of causal couplings from time series is crucial in studies of complex systems of different origin. Various statistical tools for that exist and new ones are still being developed with a tendency to creating a single, universal, model-free quantifier of coupling strength. However, a clear and generally applicable way of interpreting such universal characteristics is lacking. This work suggests a general conceptual framework for causal coupling quantification, which is based on state space models and extends the concepts of virtual interventions and dynamical causal effects. Namely, two basic kinds of interventions (state space and parametric) and effects (orbital or transient and stationary or limit) are introduced, giving four families of coupling characteristics. The framework provides a unifying view of apparently different well-established measures and allows us to introduce new characteristics, always with a definite “intervention-effect” interpretation. It is shown that diverse characteristics cannot be reduced to any single coupling strength quantifier and their interpretation is inevitably model based. The proposed set of dynamical causal effect measures quantifies different aspects of “how the coupling manifests itself in the dynamics,” reformulating the very question about the “causal coupling strength.”

We introduce one- and two-dimensional (1D and 2D) continuum and discrete models for the two-component BEC, with the spin-orbit (SO) coupling of the Rashba type between the components, and attractive cubic interactions, assuming that the condensate is fragmented into a quasidiscrete state by a deep optical-lattice potential. In 1D, it is demonstrated, in analytical and numerical forms, that the ground states of both the discrete system and its continuum counterpart switch from striped bright solitons, featuring deep short-wave modulations of its profile, to smooth solitons, as the strength ratio of the inter- and intracomponent attraction, $\gamma$, changes from $\gamma <1$ to $\gamma >1$. At the borderline, $\gamma =1$, there is a continuous branch of stable solitons, which share a common value of the energy and interpolate between the striped and smooth ones. Unlike the 2D system, the 1D solitons, which do not represent the ground state at given $\gamma$, are nevertheless stable against small perturbations, and they remain stable too in collisions with other solitons. In 2D, a transition between two different types of discrete solitons, which represent the ground state, viz., semivortices and mixed modes, also takes place at $\gamma =1$. A specific property of 2D discrete solitons of both types is their discontinuous transition into a delocalized state at a critical value of the SO-coupling strength. We also address the continuum 2D model in the borderline case of $\gamma =1$, which was not studied previously, and demonstrate the existence of an energy-degenerate branch of dynamically stable solitons connecting the semivortex and the mixed mode. Last, it is demonstrated that 1D and 2D discrete solitons are mobile, in a limited interval of velocities.

The field theoretic renormalization group and the operator product expansion are applied to two models of passive scalar quantities (the density and the tracer fields) advected by a random turbulent velocity field. The latter is governed by the Navier-Stokes equation for compressible fluid, subject to external random force with the covariance $\propto \delta (t-t^{\prime })k^{4-d-y}$, where $d$ is the dimension of space and $y$ is an arbitrary exponent. The original stochastic problems are reformulated as multiplicatively renormalizable field theoretic models; the corresponding renormalization group equations possess infrared attractive fixed points. It is shown that various correlation functions of the scalar field, its powers and gradients, demonstrate anomalous scaling behavior in the inertial-convective range already for small values of $y$. The corresponding anomalous exponents, identified with scaling (critical) dimensions of certain composite fields (“operators” in the quantum-field terminology), can be systematically calculated as series in $y$. The practical calculation is performed in the leading one-loop approximation, including exponents in anisotropic contributions. It should be emphasized that, in contrast to Gaussian ensembles with finite correlation time, the model and the perturbation theory presented here are manifestly Galilean covariant. The validity of the one-loop approximation and comparison with Gaussian models are briefly discussed.

The existence of a buoyancy-dominated scaling range in convective turbulence is a longstanding open question. We investigate this issue by considering the scale-by-scale energy budget in direct numerical simulations of Rayleigh-Bénard convection. We try to minimize the so-called Bolgiano length scale, the length scale at which buoyancy becomes dominant for scaling. Therefore, we deliberately choose modest Rayleigh numbers $\mathrm{Ra}=2.5\times {10}^6$ and $2.5\times {10}^7$. The budget reveals that buoyant forcing, turbulent energy transfer, and dissipation are contributing significantly over a wide range of scales. Thereby neither Kolmogorov-like (balance of turbulent transfer and dissipation) nor Bolgiano-Obukhov-like scaling (balance of turbulent transfer and buoyancy) is expected in the structure functions, which indeed reveal inconclusive scaling behavior. Furthermore, we consider the calculation of the Bolgiano length scale. To account for correlations between the dissipation rates of kinetic energy and thermal variance we propose to average the Bolgiano length scale directly. This gives an estimate, which is one order of magnitude larger than the previous estimate, and actually larger than the domain itself. Rather than studying the scaling of structure functions, we propose that the use of scale-by-scale energy budgets resolving anisotropic contributions is appropriate to consider the energy cascade mechanisms in turbulent convection.

Three-dimensional (3D) numerical simulations are performed on suspensions composed of puller-like microswimmers that are sensitive to light (phototaxis) mimicking microalgae in a Poiseuille flow. Simulations are based on the numerical resolution of the flow equations at low Reynolds numbers discretized on a 3D grid (finite differences). The model reproduces the formation of a central jet of swimmers by self-focusing [Phys. Rev. Lett. 110, 138106 (2013)] but also predicts an instability of the jet, which leads to its fractionation in clusters. We show that this instability is due to hydrodynamic interactions between microswimmers, which attract each other along the flow direction. This effect was not observed in the experiments conducted on dilute suspensions (i.e., where hydrodynamic interactions are weak). This phenomenon is peculiar for pullers for which collective motions are usually not observed on such a time scale. With this modeling, we hope to pave the way toward a better understanding of concentration techniques of algae (a bottleneck challenge in industrial applications).

Molecular-dynamic simulations were performed in order to investigate the melting processes of isotropically confined binary systems. We considered two species of particles, which differ by their amount of electric charge. A Lindemann type of criterion was used to determine the angular melting temperature. We demonstrate that the magic-to-normal cluster transition can evolve in two distinct ways, that is, through a structural phase transition of the first order or via a smooth transition where an increase of the shells' width leads to a continuous decreasing mechanical stability of the system. Moreover, for large systems, we demonstrate that the internal cluster exerts a minor effect on the mechanical stability of the external shell. Furthermore, we show that highly symmetric configurations, such as those found for multiple ring structures, have large mechanical stability, i.e., high angular melting temperature.