arXiv subjects

Gil Ariel

Publications and source records attributed to Gil Ariel.

At least 19 recordsLinked to original sources

arXiv2026

Perspective: Measuring physical entropy out of equilibrium

Entropy is one of the key thermodynamic variables reflecting changes in the state of matter. Unlike other thermodynamic variables, it is well-defined also for nonequilibrium steady states through its relation to information. Applying this relation to physical systems is an ongoing challenge, as it requires knowledge of microscopic high-dimensional continuous distributions which is generally unattainable. A set of new approaches for the measurement of entropy in nonequilibrium steady or absorbing states have been developed and successfully applied to identify dynamic structures and transitions in diverse systems, ranging from jammed packings to swarming bacteria. We briefly review these approaches, emphasizing why applications to physical systems, including those out of equilibrium, is substantially different from the general statistical challenge of entropy estimation and inference. We point at promising current and future directions.

cond-mat.stat-mech↗

arXiv2025

Irreversibility and symmetry breaking in the creation and annihilation of defects in active living matter

Active living matter continuously creates and annihilates topological defects in a process that remains poorly understood. Here, we investigate these dynamics in two distinct active living systems: swarming bacteria and human bronchial epithelial cells. Despite their entirely different evolutionary origins, biological functions, and physical scales, both systems exhibit half-integer defects, consistent with the nematic phase. However, in contrast to active nematic theory, we find that defect creation and annihilation undergoes spatial symmetry breaking. We propose that these results stem from a fundamental dualism between nematic structural organization and generated polar forces, which are intrinsic to living systems. Furthermore, estimation of entropy production reveals that creation and annihilation are not reversed processes. Our findings challenge conventional nematic models and emphasize the role of defect-mediated dynamics in non-equilibrium biological systems as a major source of entropy production.

physics.bio-ph↗

arXiv2024

Immobility of isolated swarmer cells due to local liquid depletion

Bacterial swarming is a complex phenomenon in which thousands of self-propelled rod-shaped cells move coherently on surfaces, providing an excellent example of active matter. However, bacterial swarming is different from most studied examples of active systems because single isolated cells do not move, while clusters do. The biophysical aspects underlying this behavior are unclear. In this work we explore the case of low local cell densities, where single cells become temporarily immobile. We show that immobility is related to local depletion of liquid. In addition, it is also associated with the state of the flagella. Specifically, the flagellar bundles at (temporarily) liquid depleted regions are completely spread-out. Our results suggest that dry models of self-propelled agents, which only consider steric alignments and neglect hydrodynamic effects, are oversimplified and are not sufficient to describe swarming bacteria.

cond-mat.soft↗

arXiv2024

Second Law of Thermodynamics without Einstein Relation

Materials that are constantly driven out of thermodynamic equilibrium, such as active and living systems, typically violate the Einstein relation. This may arise from active contributions to particle fluctuations which are unrelated to the dissipative resistance of the surrounding medium. We show that in these cases the widely used relation between informatic entropy production and heat dissipation does not hold. Consequently, fluctuation relations for the mechanical work, such as the Jarzynski and Crooks theorems, are invalid. We relate the breaking of the correspondence between entropy production and heat dissipation to departure from the fluctuation-dissipation theorem. We propose a temperaturelike variable that restores this correspondence and gives rise to a generalized second law of thermodynamics, whereby the dissipated heat is necessarily non-negative and vanishes at equilibrium. The Clausius inequality, Carnot maximum efficiency theorem, and relation between the extractable work and the change of free energy are recovered as well.

cond-mat.stat-mech↗

arXiv2024

Consistent expansion of the Langevin propagator with application to entropy production

Stochastic thermodynamics is a developing theory for systems out of thermal equilibrium. It allows to formulate a wealth of nontrivial relations among thermodynamic quantities such as heat dissipation, excess work, and entropy production in generic nonequilibrium stochastic processes. A key quantity for the derivation of these relations is the propagator - the probability to observe a transition from one point in phase space to another after a given time. Here, applying stochastic Taylor expansions, we devise a formal expansion procedure for the propagator of overdamped Langevin dynamics. The three leading orders are obtained explicitly. The technique resolves the shortcomings of the current mathematical machinery for the calculation of the propagator. For the evaluation of the first two displacement cumulants, the leading order Gaussian propagator is sufficient. However, some functionals of the propagator, such as the entropy production, which we refer to as "first derivatives of the trajectory", need to be evaluated to a previously-unrecognized higher order. The method presented here can be extended to arbitrarily higher orders in order to accurately compute any other functional of the propagator.

cond-mat.stat-mech↗

arXiv2024

Topological defects in multi-layered swarming bacteria

Topological defects, which are singular points in a director field, play a major role in shaping active systems. Here, we experimentally study topological defects and the flow patterns around them, that are formed during the highly rapid dynamics of swarming bacteria. The results are compared to the predictions of two-dimensional active nematics. We show that, even though some of the assumptions underlying the theory do not hold, the swarm dynamics is in agreement with two-dimensional nematic theory. In particular, we look into the multi-layered structure of the swarm, which is an important feature of real, natural colonies, and find a strong coupling between layers. Our results suggest that the defect-charge density is hyperuniform, i.e., that long range density-fluctuations are suppressed.

cond-mat.soft↗

arXiv2023

Detecting and characterizing phase transitions in active matter using entropy

A major challenge in the study of active matter lies in quantitative characterization of phases and transitions between them. We show how the entropy of a collection of active objects can be used to classify regimes and spatial patterns in their collective behavior. Specifically, we estimate the contributions to the total entropy from correlations between the degrees of freedom of position and orientation. This analysis pin-points the flocking transition in the Vicsek model while clarifying the physical mechanism behind the transition. When applied to experiments on swarming Bacillus subtilis with different cell aspect ratios and overall bacterial area fractions, the entropy analysis reveals a rich phase diagram with transitions between qualitatively different swarm statistics. We discuss physical and biological implications of these findings.

cond-mat.soft↗

arXiv2022

Universal Relation between Entropy and Kinetics

Relating thermodynamic and kinetic properties is a conceptual challenge with many practical benefits. Here, based on first principles, we derive a rigorous inequality relating the entropy and the dynamic propagator of particle configurations. It is universal and applicable to steady states arbitrarily far from thermal equilibrium. Applying the general relation to diffusive dynamics yields a relation between the entropy and the (normal or anomalous) diffusion coefficient. The relation can be used to obtain useful bounds for the late-time diffusion coefficient from the calculated steady-state entropy or, conversely, to estimate the entropy based on measured diffusion coefficients. We demonstrate the validity and usefulness of the relation through several examples and discuss its broad range of applications, in particular, for systems far from equilibrium.

cond-mat.stat-mech↗

arXiv2022

Pair correlation function based on Voronoi topology

The pair correlation function (PCF) has proven an effective tool for analyzing many physical systems due to its simplicity and its applicability to simulated and experimental data. However, as an averaged quantity, the PCF can fail to capture subtle structural differences in particle arrangements, even when those differences can have a major impact on system properties. Here, we use Voronoi topology to introduce a discrete version of the PCF that highlights local inter-particle topological configurations. The advantages of the Voronoi PCF are demonstrated in several examples including crystalline, hyperuniform, and active systems showing clustering and giant number fluctuations.

cond-mat.dis-nn↗

arXiv2022

Resolving entropy contributions in nonequilibrium transitions

We derive a functional for the entropy contributed by any microscopic degrees of freedom as arising from their measurable pair correlations. Applicable both in and out of equilibrium, this functional yields the maximum entropy which a system can have given a certain correlation function. When applied to different correlations, the method allows us to identify the degrees of freedom governing a certain physical regime, thus capturing and characterizing dynamic transitions. The formalism applies also to systems whose translational invariance is broken by external forces and whose number of particles may vary. We apply it to experimental results for jammed bidisperse emulsions, capturing the crossover of this nonequilibrium system from crystalline to disordered hyperuniform structures as a function of mixture composition. We discover that the cross-correlations between the positions and sizes of droplets in the emulsion play the central role in the formation of the disordered hyperuniform states. We discuss implications of the approach for entropy estimation out of equilibrium and for characterizing transitions in disordered systems.

cond-mat.stat-mech↗

arXiv2022

Physical characteristics of mixed-species swarming colonies

In nature, bacterial collectives typically consist of multiple species, which are interacting both biochemically and physically. Nonetheless, past studies on the physical properties of swarming bacteria were focused on axenic (single species) populations. In bacterial swarming, intricate interactions between the individuals lead to clusters, rapid jets and vortices that depend on cell characteristics such as speed and length. In this work, we show the first results of rapidly swarming mixed-species populations of {\sl Bacillus subtilis} and {\sl Serratia marcescens}, two model swarm species that are known to swarm well in axenic situations. In mixed liquid cultures, both species have higher reproduction rates. We show that the mixed population swarms together well and that the fraction between the species determines all dynamical scales - from the microscopic (e.g. speed distribution), mesoscopic (vortex size) and macroscopic (colony size structure). Understanding mixed-species swarms is essential for a comprehensive understanding of the bacterial swarming phenomenon and its biological and evolutionary implications.

physics.bio-ph↗

arXiv2021

Biophysics underlying the swarm to biofilm transition

Bacteria organize in a variety of collective states, from swarming, which has been attributed to rapid surface exploration, to biofilms, which are highly dense immobile communities attributed to stress resistance. It has been suggested that biofilm and swarming are oppositely controlled, making this transition particularly interesting for understanding the ability of bacterial colonies to adapt to challenging environments. Here, the swarm to biofilm transition is studied experimentally by analyzing the bacterial dynamics both on the individual and collective scales. We show that both biological and physical processes facilitate the transition - a few individual cells that initiate the biofilm program cause nucleation of large, scale-free stationary aggregates of trapped swarm cells. Around aggregates, cells continue swarming almost unobstructed, while inside, trapped cells slowly transform to biofilm. While our experimental findings rule out previously suggested purely physical effects as a trigger for biofilm formation, they show how physical processes, such as clustering and jamming, accelerate biofilm formation.

physics.bio-ph↗

arXiv2021

Turbulence-induced clustering in compressible active fluids

We study a novel phase of active polar fluids, which is characterized by the continuous creation and destruction of dense clusters due to self-sustained turbulence. This state arises due to the interplay of the self-advection of the aligned swimmers and their defect topology. The typical cluster size is determined by the characteristic vortex size. Our results are obtained by investigating a continuum model of compressible polar active fluids, which incorporates typical experimental observations in bacterial suspensions by assuming a non-monotone dependence of speed on density.

cond-mat.soft↗

arXiv2021

Self-driven criticality in a stochastic epidemic model

We present a generic epidemic model with stochastic parameters, in which the dynamics self-organize to a critical state with suppressed exponential growth. More precisely, the dynamics evolve into a quasi-steady-state, where the effective reproduction rate fluctuates close to the critical value one, as observed for different epidemics. The main assumptions underlying the model are that the rate at which each individual becomes infected changes stochastically in time with a heavy-tailed steady state. The critical regime is characterized by an extremely long duration of the epidemic. Its stability is analyzed both numerically and analytically.

nlin.AO↗

arXiv2020

Heterogeneous bacterial swarms with mixed lengths

Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly significant for understanding realistic bacterial swarms, which typically develop heterogeneities even when grown from a single cell. Here, mixed swarms of cells with different aspect ratios are studied both experimentally and in simulations. In contrast with previous theory, there is no macroscopic phase segregation. However, locally, long cells act as nucleation cites, around which ordered clusters of short, rapidly moving cells can form, resulting in enhanced swarming speeds. On the other hand, high fractions of long cells form a bottle-neck for efficient swarming. Our results suggest a new physical advantage for the spontaneous heterogeneity of bacterial swarm populations.

cond-mat.soft↗

arXiv2020

Motility-Induced Clustering and Meso-Scale Turbulence in Active Polar Fluids

Meso-scale turbulence was originally observed experimentally in various suspensions of swimming bacteria, as well as in the collective motion of active colloids. The corresponding large-scale dynamical patterns were reproduced in a simple model of a polar fluid, assuming a constant density of active particles. Recent, more detailed experimental studies revealed additional interesting aspects, such as anomalous velocity statistics and clustering phenomena. Those phenomena cannot be explained by currently available models for active polar fluids. Herein, we extend the continuum model suggested by Dunkel et al. to include density variations and a feedback between the local density and self-propulsion speed of the active particles. If the velocity decreases strong enough with the density, a linear stability analysis of the resulting model shows that, in addition to the short-wavelength instability of the original model, a long-wavelength instability occurs. This is typically observed for high densities of polar active particles and is analogous to the well-known phenomenon of motility-induced phase separation (MIPS) in scalar active matter. We determine a simple phase diagram indicating the linear instabilities and perform systematic numerical simulations for the various regions in the corresponding parameter space. The interplay between the well understood short-range instability and the long-range instability leads to interesting dynamics and novel phenomena concerning nucleation and coarsening processes. Our simulation results display a rich variety of novel patterns, including phase separation into domains with dynamically changing irregularly shaped boundaries. Anomalous velocity statistics are observed in all phases where the system segregates into regions of high and low densities. This offers a simple explanation for their occurrence in recent experiments with bacterial suspensions.

cond-mat.soft↗

arXiv2020

Inferring entropy from structure

The thermodynamic definition of entropy can be extended to nonequilibrium systems based on its relation to information. To apply this definition in practice requires access to the physical system's microstates, which may be prohibitively inefficient to sample or difficult to obtain experimentally. It is beneficial, therefore, to relate the entropy to other integrated properties which are accessible out of equilibrium. We focus on the structure factor, which describes the spatial correlations of density fluctuations and can be directly measured by scattering. The information gained by a given structure factor regarding an otherwise unknown system provides an upper bound for the system's entropy. We find that the maximum-entropy model corresponds to an equilibrium system with an effective pair-interaction. Approximate closed-form relations for the effective pair-potential and the resulting entropy in terms of the structure factor are obtained. As examples, the relations are used to estimate the entropy of an exactly solvable model and two simulated systems out of equilibrium. The focus is on low-dimensional examples, where our method, as well as a recently proposed compression-based one, can be tested against a rigorous direct-sampling technique. The entropy inferred from the structure factor is found to be consistent with the other methods, superior for larger system sizes, and accurate in identifying global transitions. Our approach allows for extensions of the theory to more complex systems and to higher-order correlations.

cond-mat.stat-mech↗

arXiv2019

Estimating differential entropy using recursive copula splitting

A method for estimating the Shannon differential entropy of multidimensional random variables using independent samples is described. The method is based on decomposing the distribution into a product of the marginal distributions and the joint dependency, also known as the copula. The entropy of marginals is estimated using one-dimensional methods. The entropy of the copula, which always has a compact support, is estimated recursively by splitting the data along statistically dependent dimensions. Numerical examples demonstrate that the method is accurate for distributions with compact and non-compact supports, which is imperative when the support is not known or of mixed type (in different dimensions). At high dimensions (larger than 20), our method is not only more accurate, but also significantly more efficient than existing approaches.

cond-mat.stat-mech↗