A Stokes layer, which is a flow pattern that arises in a viscous fluid adjacent to an oscillatory boundary, was observed in an experiment using a two-dimensional strongly coupled dusty plasma. Liquid conditions were maintained using laser heating, while a separate laser manipulation applied an oscillatory shear that was localized and sinusoidal. The evolution of the resulting flow was analyzed using space-time diagrams. These figures provide an intuitive visualization of a Stokes layer, including features such as the depth of penetration and wavelength. Another feature, the characteristic speed for the penetration of the oscillatory flow, also appears prominently in space-time diagrams. To model the experiment, the Maxwell-fluid model of a Stokes layer was generalized to describe a two-phase liquid. In our experiment, the phases were gas and dust, where the dust cloud was viscoelastic due to strong Coulomb coupling. The model is found to agree with the experiment, in the appearance of the space-time diagrams, and in the values of the characteristic speed, depth of penetration, and wavelength.

We study a system involving a single quantum degree of freedom per site of the lattice interacting with a few neighbors (up to second neighbors), with the interactions chosen so as to produce frustration. At zero temperature, this system undergoes several quantum phase transitions from both gapped to gapless and gapless to gapless phases, providing a very rich phase structure with disordered, homogeneous, and modulated ordered phases meeting in a quantum Lifshitz point. The gapless phases spontaneously break spatial lattice translations as well as internal symmetries of the form $\text{U}{\left(1\right)}^{{\mathsf{N}}_c}$, where ${\mathsf{N}}_c$ is the number of independent pitch vectors that arise in the homogeneous and modulated ordered phases. We carry out a detailed analysis of the quantum critical behavior, discussing the mechanism leading to the phase transitions. We also discuss a proper characterization of all the gapless phases as well as the nature of the Goldstone excitations. We study the behavior of the correlation functions and identify regions in the phase diagram where the system exhibits generalized symmetries such as polynomial shift symmetry. This type of symmetry plays an important role in the so-called fractonic phase, which is an exotic form of matter recently discovered.

We introduce a general formulation of the fluctuation-dissipation relations (FDRs) holding also in far-from-equilibrium stochastic dynamics. A great advantage of this version of the FDR is that it does not require explicit knowledge of the stationary probability density function. Our formula applies to Markov stochastic systems with generic noise distributions: When the noise is additive and Gaussian, the relation reduces to those known in the literature; for multiplicative and non-Gaussian distributions (e.g., Cauchy noise) it provides exact results in agreement with numerical simulations. Our formula allows us to reproduce, in a suitable small-noise limit, the response functions of deterministic, strongly nonlinear dynamical models, even in the presence of chaotic behavior: This could have important practical applications in several contexts, including geophysics and climate. As a case of study, we consider the Lorenz ‘63 model, which is paradigmatic for the chaotic properties of deterministic dynamical systems.

In several pathological conditions, such as coronavirus infections, multiple sclerosis, Alzheimer's and Parkinson's diseases, the physiological shape of axons is altered and a periodic sequence of bulges appears. Experimental evidences suggest that such morphological changes are caused by the disruption of the microtubules composing the cytoskeleton of the axon. In this paper, we develop a mathematical model of damaged axons based on the theory of continuum mechanics and nonlinear elasticity. The axon is described as a cylinder composed of an inner passive part, called axoplasm, and an outer active cortex, composed mainly of F-actin and able to contract thanks to myosin-II motors. Through a linear stability analysis we show that, as the shear modulus of the axoplasm diminishes due to the disruption of the cytoskeleton, the active contraction of the cortex makes the cylindrical configuration unstable to axisymmetric perturbations, leading to a beading pattern. Finally, the nonlinear evolution of the bifurcated branches is investigated through finite element simulations.

The random Lorentz gas (RLG) is a minimal model for transport in disordered media. Despite the broad relevance of the model, theoretical grasp over its properties remains weak. For instance, the scaling with dimension $d$ of its localization transition at the void percolation threshold is not well controlled analytically nor computationally. A recent study [Biroli et al., Phys. Rev. E 103, L030104 (2021)] of the caging behavior of the RLG motivated by the mean-field theory of glasses has uncovered physical inconsistencies in that scaling that heighten the need for guidance. Here we first extend analytical expectations for asymptotic high-$d$ bounds on the void percolation threshold and then computationally evaluate both the threshold and its criticality in various $d$. In high-$d$ systems, we observe that the standard percolation physics is complemented by a dynamical slowdown of the tracer dynamics reminiscent of mean-field caging. A simple modification of the RLG is found to bring the interplay between percolation and mean-field-like caging down to $d=3$.

Chromatin loop extrusion by structural maintenance of chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop extrusion by SMCs, such as cohesin and condensin complexes, we introduce and characterize theoretically a composite loop extrusion factor (composite LEF) model. In addition to an SMC complex that creates a chromatin loop by encircling two threads of DNA, this model includes a remodeling complex that relocates or removes nucleosomes as it progresses along the chromatin, and nucleosomes that block SMC translocation along the DNA. Loop extrusion is enabled by SMC motion along nucleosome-free DNA, created in the wake of the remodeling complex, while nucleosome rebinding behind the SMC acts as a ratchet, holding the SMC close to the remodeling complex. We show that, for a wide range of parameter values, this collection of factors constitutes a composite LEF that extrudes loops with a velocity, comparable to the velocity of remodeling complex translocation on chromatin in the absence of SMC, and much faster than loop extrusion by an isolated SMC that is blocked by nucleosomes.

At high concentration, free swimming nematodes known as vinegar eels (Turbatrix aceti), collectively exhibit metachronal waves near a boundary. We find that the frequency of the collective traveling wave is lower than that of the freely swimming organisms. We explore models based on a chain of oscillators with nearest-neighbor interactions that inhibit oscillator phase velocity. The phase of each oscillator represents the phase of the motion of the eel's head back and forth about its mean position. A strongly interacting directed chain model mimicking steric repulsion between organisms robustly gives traveling wave states and can approximately match the observed wavelength and oscillation frequency of the observed traveling wave. We predict body shapes assuming that waves propagate down the eel body at a constant speed. The phase oscillator model that impedes eel head overlaps also reduces close interactions throughout the eel bodies.

The forest fire model in statistical physics represents a paradigm for systems close to but not completely at criticality. For large tree growth probabilities $p$ we identify periodic attractors, where the tree density $\rho$ oscillates between discrete values. For lower $p$ this self-organized multistability persists with incrementing numbers of states. Even at low $p$ the system remains quasiperiodic with a frequency $\approx p$ on the way to chaos. In addition, the power-spectrum shows $1/f^2$ scaling (Brownian noise) at the low frequencies $f$, which turns into white noise for very long simulation times.

When two resonantly interacting modes are in contact with a thermostat, their statistics is exactly Gaussian and the modes are statistically independent despite strong interaction. Considering a noise-driven system, we show that when one mode is pumped and another dissipates, the statistics of such cascades is never close to Gaussian, no matter what is the relation between interaction and noise. One finds substantial phase correlation in the limit of strong interaction or weak noise. Surprisingly, the mutual information between modes increases and entropy decreases when interaction strength decreases. We use the model to elucidate the fundamental problem of far-from equilibrium physics: where the information, or entropy deficit, is encoded, and how singular measures form. For an instability-driven system, such as laser, even a small added noise leads to large fluctuations of the relative phase near the stability threshold, while far from the equilibrium the conversion into the second harmonic is weakly affected by noise.

We study the two-dimensional motion of colloidal dimers by single-particle tracking and compare the experimental observations obtained by bright-field microscopy to theoretical predictions for anisotropic diffusion. The comparison is based on the mean-square displacements in the laboratory and particle frame as well as generalizations of the self-intermediate scattering functions, which provide insights into the rotational dynamics of the dimer. The diffusional anisotropy leads to a measurable translational-rotational coupling that becomes most prominent by aligning the coordinate system with the initial orientation of the particles. In particular, we find a splitting of the time-dependent diffusion coefficients parallel and perpendicular to the long axis of the dimer which decays over the orientational relaxation time. Deviations of the self-intermediate scattering functions from pure exponential relaxation are small but can be resolved experimentally. The theoretical predictions and experimental results agree quantitatively.

Scientists have observed and studied diffusive waves in contexts as disparate as population genetics and cell signaling. Often, these waves are propagated by discrete entities or agents, such as individual cells in the case of cell signaling. For a broad class of diffusive waves, we characterize the transition between the collective propagation of diffusive waves, in which the wave speed is well described by continuum theory, and the propagation of diffusive waves by individual agents. We show that this transition depends heavily on the dimensionality of the system in which the wave propagates and that disordered systems yield dynamics largely consistent with lattice systems. In some system dimensionalities, the intuition that closely packed sources more accurately mimic a continuum can be grossly violated.

Synchronization has been the subject of intense research during decades mainly focused on determining the structural and dynamical conditions driving a set of interacting units to a coherent state globally stable. However, little attention has been paid to the description of the dynamical development of each individual networked unit in the process towards the synchronization of the whole ensemble. In this paper we show how in a network of identical dynamical systems, nodes belonging to the same degree class, differentiate in the same manner, visiting a sequence of states of diverse complexity along the route to synchronization independently on the global network structure. In particular, we observe, just after interaction starts pulling orbits from the initially uncoupled attractor, a general reduction of the complexity of the dynamics of all units being more pronounced in those with higher connectivity. In the weak-coupling regime, when synchronization starts to build up, there is an increase in the dynamical complexity, whose maximum is achieved, in general, first in the hubs due to their earlier synchronization with the mean field. For very strong coupling, just before complete synchronization, we found a hierarchical dynamical differentiation with lower degree nodes being the ones exhibiting the largest complexity departure. We unveil how this differentiation route holds for several models of nonlinear dynamics, including toroidal chaos and how it depends on the coupling function. This study provides insights to understand better strategies for network identification or to devise effective methods for network inference.

Cell division times in microbial populations display significant fluctuations that impact the population growth rate in a nontrivial way. If fluctuations are uncorrelated among different cells, the population growth rate is predicted by the Euler-Lotka equation, which is a classic result in mathematical biology. However, cell division times can be significantly correlated, due to physical properties of cells that are passed through generations. In this Letter, we derive an equation remarkably similar to the Euler-Lotka equation which is valid in the presence of correlations. Our exact result is based on large deviation theory and does not require particularly strong assumptions on the underlying dynamics. We apply our theory to a phenomenological model of bacterial cell division in E. coli and to experimental data. We find that the discrepancy between the growth rate predicted by the Euler-Lotka equation and our generalized version is relatively small, but large enough to be measurable by our approach.

The large deviation statistics of dynamical observables is encoded in the spectral properties of deformed Markov generators. Recent works have shown that tensor network methods are well suited to compute accurately the relevant leading eigenvalues and eigenvectors. However, the efficient generation of the corresponding rare trajectories is a harder task. Here, we show how to exploit the matrix product state approximation of the dominant eigenvector to implement an efficient sampling scheme which closely resembles the optimal (so-called “Doob”) dynamics that realizes the rare events. We demonstrate our approach on three well-studied lattice models, the Fredrickson-Andersen and East kinetically constrained models, and the symmetric simple exclusion process. We discuss how to generalize our approach to higher dimensions.

The unconstrained ensemble describes completely open systems whose control parameters are the chemical potential, pressure, and temperature. For macroscopic systems with short-range interactions, thermodynamics prevents the simultaneous use of these intensive variables as control parameters, because they are not independent and cannot account for the system size. When the range of the interactions is comparable with the size of the system, however, these variables are not truly intensive and may become independent, so equilibrium states defined by the values of these parameters may exist. Here, we derive a Monte Carlo algorithm for the unconstrained ensemble and show that simulations can be performed using the chemical potential, pressure, and temperature as control parameters. We illustrate the algorithm by applying it to physical systems where either the system has long-range interactions or is confined by external conditions. The method opens up an avenue for the simulation of completely open systems exchanging heat, work, and matter with the environment.

The Fluctuation-Dissipation Theorem (FDT) is a powerful tool to estimate the thermal noise of physical systems in equilibrium. In general, however, thermal equilibrium is an approximation or cannot be assumed at all. A more general formulation of the FDT is then needed to describe the behavior of the fluctuations. In our experiment we study a microcantilever brought out of equilibrium by a strong heat flux generated by the absorption of the light of a laser. While the base is kept at cryogenic temperatures, the tip is heated up to the melting point, thus creating the highest temperature difference the system can sustain. We independently estimate the temperature profile of the cantilever and its mechanical fluctuations as well as its dissipation. We then demonstrate how the thermal fluctuations of all the observed degrees of freedom, though increasing with the heat flux, are much lower than what is expected from the average temperature of the system. We interpret these results using a minimal extension of the FDT: this dearth of thermal noise arises from a dissipation shared between clamping losses and distributed damping.

Plants have a special structure, torus-margo (TM) pit, which comprises a thickened torus at the center encircled by a highly porous margo. It is regarded as a key evolutionary structure to enable stable water transport, minimizing the air spread in the vessels. However, its valve-like dynamics to regulate two-phase flows still remains unclear even at a single pit level. Here, we study the air spreading dynamics using a bioinspired model of this soft pit valve. We divide it into the initial onset and the consecutive air-spreads, and propose the criteria of TM structures as the valve-like function. To delay the onset of air spread, the margo region should be thin and deformable enough to seal the pit aperture with the torus before the air penetration. Even after the onset, the membranes whose maximum pore size is smaller than its thickness can avoid continuous air-spread. The criteria also fit properly into botanical data on the morphologies of TM pits, implying that their valve-like behaviors may alleviate the tradeoff between hydraulic safety and efficiency at the single pit level. Our study would help to understand of the mechanistic pit-level strategy and also can provide insight into fluidic systems to control interfacial phenomena.

The colocalization of density modulations and particle polarization is a characteristic emergent feature of motile active matter in activity gradients. We employ the active-Brownian-particle model to derive precise analytical expressions for the density and polarization profiles of a single Janus-type swimmer in the vicinity of an abrupt activity step. Our analysis allows for an optional (but not necessary) orientation-dependent propulsion speed, as often employed in force-free particle steering. The results agree well with measurement data for a thermophoretic microswimmer presented in the companion paper [Söker et al., Phys. Rev. Lett. 126, 228001 (2021)], and they can serve as a template for more complex applications, e.g., to motility-induced phase separation or studies of physical boundaries. The essential physics behind our formal results is robustly captured and elucidated by a schematic two-species “run-and-tumble” model.

We show that the Bose-glass phase of a one-dimensional disordered Bose fluid exhibits a chaotic behavior, i.e., an extreme sensitivity to external parameters. Using bosonization, the replica formalism and the nonperturbative functional renormalization group, we find that the ground state is unstable to any modification of the disorder configuration (“disorder” chaos) or variation of the Luttinger parameter (“quantum” chaos, analog to the “temperature” chaos in classical disordered systems). This result is obtained by considering two copies of the system, with slightly different disorder configurations or Luttinger parameters, and showing that intercopy statistical correlations are suppressed at length scales larger than an overlap length ${\xi }_{\mathrm{ov}}\sim {\left|\epsilon \right|}^{-1/\alpha }$ ($\left|\epsilon \right|\ll 1$ is a measure of the difference between the disorder distributions or Luttinger parameters of the two copies). The chaos exponent $\alpha$ can be obtained by computing ${\xi }_{\mathrm{ov}}$ or by studying the instability of the Bose-glass fixed point for the two-copy system when $\epsilon \ne 0$. The renormalized, functional, intercopy disorder correlator departs from its fixed-point value—characterized by “cuspy” singularities—via a chaos boundary layer, in the same way as it approaches the Bose-glass fixed point when $\epsilon =0$ through a quantum boundary layer. Performing a linear analysis of perturbations about the Bose-glass fixed point, we find $\alpha =1$.

Elastic materials with holes and inclusions are important in a large variety of contexts ranging from construction material to biological membranes. More recently, they have also been exploited in mechanical metamaterials, where the geometry of highly deformable structures is responsible for their unusual properties, such as negative Poisson's ratio, mechanical cloaking, and tunable phononic band gaps. Understanding how such structures deform in response to applied external loads is thus crucial for designing novel mechanical metamaterials. Here we present a method for predicting the linear response of infinite 2D solid structures with circular holes and inclusions by employing analogies with electrostatics. Just like an external electric field induces polarization (dipoles, quadrupoles, and other multipoles) of conductive and dielectric objects, external stress induces elastic multipoles inside holes and inclusions. Stresses generated by these induced elastic multipoles then lead to interactions between holes and inclusions, which induce additional polarization and thus additional deformation of holes and inclusions. We present a method that expands the induced polarization in a series of elastic multipoles, which systematically takes into account the interactions of inclusions and holes with the external stress field and also between them. The results of our method show good agreement with both linear finite element simulations and experiments.