Diffusive transport without detailed balance in motile bacteria: does microbiology need statistical physics?

Phases and correlations in active nematic granular systems

We investigate the statistical behavior of a system comprising fore-aft symmetric rods confined between two vertically vibrating plates using numerical simulations closely resembling the experimental setup studied by V. Narayan et al., Science, 2007, 317, 105-108. Our focus lies in studying the phase transition of the system from an isotropic phase to a nematic phase as we increase either the rod length or the rod concentration. Our simulations confirm the presence of long-range ordering in the ordered phase. Furthermore, we identify a phase characterized by a periodic ordering profile that disrupts translation symmetry. We also provide a detailed analysis of the translational and rotational diffusive dynamics of the rods. Interestingly, the translational diffusivity of the rods is found to increase with the rod concentration.

Electrically activated ferroelectric nematic microrobots

Ferroelectric nematic liquid crystals are fluids exhibiting spontaneous electric polarization, which is coupled to their long range orientational order. Due to their inherent property of making bound and surface charges, the free surface of ferroelectric nematics becomes unstable in electric fields. Here we show that ferroelectric liquid bridges between two electrode plates undergo distinct interfacial instabilities. In a specific range of frequency and voltage, the ferroelectric fluid bridges move as active interacting particles resembling living organisms like swarming insects, microbes or microrobots. The motion is accompanied by sound emission, as a consequence of piezoelectricity and electrostriction. Statistical analysis of the active particles reveals that the movement can be controlled by the applied voltage, which implies the possible application of the system in new types of microfluidic devices.

Collective dynamics of active dumbbells near a circular obstacle

In this article, we present the collective dynamics of active dumbbells in the presence of a static circular obstacle using Brownian dynamics simulation. The active dumbbells aggregate on the surface of a circular obstacle beyond a critical radius. The aggregation is non-uniform along the circumference, and the aggregate size increases with the activity (Pe) and the curvature radius (Ro). The dense aggregate of active dumbbells displays persistent rotational motion with a certain angular speed, which linearly increases with activity. Furthermore, we show a strong polar ordering of the active dumbbells within the aggregate. The polar ordering exhibits long-range correlation, with the correlation length corresponding to the aggregate size. Additionally, we show that the residence time of an active dumbbell on the obstacle surface increases rapidly with area fraction due to many-body interactions that lead to a slowdown of the rotational diffusion. This article further considers the dynamical behavior of a tracer particle in the solution of active dumbbells. Interestingly, the speed of the passive tracer particle displays a crossover from monotonically decreasing to increasing with the size of the tracer particle upon increasing the dumbbells' speed. Furthermore, the effective diffusion of the tracer particle displays non-monotonic behavior with the area fraction; the initial increase in diffusivity is followed by a decrease for a larger area fraction.

Experimental and numerical study of a second-order transition in the behavior of confined self-propelled particles

In this paper, we conduct experimental investigations on the behavior of confined self-propelled particles within a circular arena, employing small commercial robots capable of locomotion, communication, and information processing. These robots execute circular trajectories, which can be clockwise or counterclockwise, based on two internal states. Using a majority-based stochastic decision algorithm, each robot can reverse its direction based on the states of two neighboring robots. By manipulating a control parameter governing the interaction, the system exhibits a transition from a state where all robots rotate randomly to one where they rotate uniformly in the same direction. Moreover, this transition significantly impacts the trajectories of the robots. To extend our findings to larger systems, we introduce a mathematical model enabling characterization of the order transition type and the resulting trajectories. Our results reveal a second-order transition from active Brownian to chiral motion.

Confined run-and-tumble particles with non-Markovian tumbling statistics

Confined active particles constitute simple, yet realistic, examples of systems that converge into a nonequilibrium steady state. We investigate a run-and-tumble particle in one spatial dimension, trapped by an external potential, with a given distribution g(t) of waiting times between tumbling events whose mean value is equal to τ. Unless g(t) is an exponential distribution (corresponding to a constant tumbling rate), the process is non-Markovian, which makes the analysis of the model particularly challenging. We use an analytical framework involving effective position-dependent tumbling rates to develop a numerical method that yields the full steady-state distribution (SSD) of the particle's position. The method is very efficient and requires modest computing resources, including in the large-deviation and/or small-τ regime, where the SSD can be related to the the large-deviation function, s(x), via the scaling relation P_{st}(x)∼e^{-s(x)/τ}.

Diffusion of active Brownian particles under quenched disorder

The motion of a single active particle in one dimension with quenched disorder under the external force is investigated. Within the tailored parameter range, anomalous diffusion that displays weak ergodicity breaking is observed, i.e., non-ergodic subdiffusion and non-ergodic superdiffusion. This non-ergodic anomalous diffusion is analyzed through the time-dependent probability distributions of the particle's velocities and positions. Its origin is attributed to the relative weights of the locked state (predominant in the subdiffusion state) and running state (predominant in the superdiffusion state). These results may contribute to understanding the dynamical behavior of self-propelled particles in nature and the extraordinary response of nonlinear dynamics to the externally biased force.

Learning how to find targets in the micro-world: the case of intermittent active Brownian particles

Finding the best strategy to minimize the time needed to find a given target is a crucial task both in nature and in reaching decisive technological advances. By considering learning agents able to switch their dynamics between standard and active Brownian motion, here we focus on developing effective target-search behavioral policies for microswimmers navigating a homogeneous environment and searching for targets of unknown position. We exploit projective simulation, a reinforcement learning algorithm, to acquire an efficient stochastic policy represented by the probability of switching the phase, i.e. the navigation mode, in response to the type and the duration of the current phase. Our findings reveal that the target-search efficiency increases with the particle's self-propulsion during the active phase and that, while the optimal duration of the passive case decreases monotonically with the activity, the optimal duration of the active phase displays a non-monotonic behavior.

Optimal escapes in active matter

The out-of-equilibrium character of active particles, responsible for accumulation at boundaries in confining domains, determines not-trivial effects when considering escape processes. Non-monotonous behavior of exit times with respect to tumbling rate (inverse of mean persistent time) appears, as a consequence of the competing processes of exploring the bulk and accumulate at boundaries. By using both 1D analytical results and 2D numerical simulations of run-and-tumble particles with different behaviours at boundaries, we scrutinize this very general phenomenon of active matter, evidencing the role of accumulation at walls for the existence of optimal tumbling rates for fast escapes.

Transition from scattering to orbiting upon increasing the fuel concentration for an active Janus colloid moving at an obstacle-decorated interface

Efficient exploration of space is a paramount motive for active colloids in practical applications. Yet, introducing activity may lead to surface-bound states, hindering efficient space exploration. Here, we show that the interplay between self-motility and fuel-dependent affinity for surfaces affects how efficiently catalytically-active Janus microswimmers explore both liquid-solid and liquid-fluid interfaces decorated with arrays of similarly-sized obstacles. In a regime of constant velocity vs. fuel concentration, we find that microswimmer-obstacle interactions strongly depend on fuel concentration, leading to a counter-intuitive decrease in space exploration efficiency with increased available fuel for all interfaces. Using experiments and theoretical predictions, we attribute this phenomenon to a largely overlooked change in the surface properties of the microswimmers' catalytic cap upon H2O2 exposure. Our findings have implications in the interpretation of experimental studies of catalytically active colloids, as well as in providing new handles to control their dynamics in complex environments.

Generalized disorder averages and current fluctuations in run and tumble particles

We present exact results for the fluctuations in the number of particles crossing the origin up to time t in a collection of noninteracting run and tumble particles in one dimension. In contrast to passive systems, such active particles are endowed with two inherent degrees of freedom, positions and velocities, which can be used to construct density and magnetization fields. We introduce generalized disorder averages associated with both these fields and perform annealed and quenched averages over various initial conditions. We show that the variance σ^{2} of the current in annealed versus quenched magnetization situations exhibits a surprising difference at short times, σ^{2}∼t vs σ^{2}∼t^{2}, respectively, with a sqrt[t] behavior emerging at large times. Our analytical results demonstrate that in the strictly quenched scenario, where both the density and magnetization fields are initially frozen, the fluctuations in the current are strongly suppressed. Importantly, these anomalous fluctuations cannot be obtained solely by freezing the density field.

Microswimmers under the spotlight: interplay between agents with different levels of activity

The ability of active matter to assemble into reconfigurable nonequilibrium structures has drawn considerable interest in recent years. We investigate how active fluids respond to spatial light patterns through simulations and experiments on light-activated self-propelled colloidal particles. We examine the processes of inverse templated assembly, which involves creating a region without active particles through a bright pattern, and templated assembly, which promotes the formation of dense particle regions through a dark pattern. We identify scaling relations for the characteristic times for both processes that quantify the interplay between the dimension of the applied pattern and the intrinsic properties of the active fluid. We also explore the assembly mechanism and dynamics of large clusters and show how assembly and inverse assembly can be combined to create any arbitrarily complex template. In addition to providing protocols for templated assembly via light patterning, our results demonstrate how the local packing fraction can be fine-tuned by modulation of the light intensity. The protocol so obtained exceeds the capabilities of conventional assembly strategies, in which packing fraction is dictated by thermodynamics, and opens the door to arbitrarily precise and programmable nonequilibrium assembly strategies in active matter.

Chemotactic Motility-Induced Phase Separation

Collectives of actively moving particles can spontaneously separate into dilute and dense phases-a fascinating phenomenon known as motility-induced phase separation (MIPS). MIPS is well-studied for randomly moving particles with no directional bias. However, many forms of active matter exhibit collective chemotaxis, directed motion along a chemical gradient that the constituent particles can generate themselves. Here, using theory and simulations, we demonstrate that collective chemotaxis strongly competes with MIPS-in some cases, arresting or completely suppressing phase separation, or in other cases, generating fundamentally new dynamic instabilities. We establish principles describing this competition, thereby helping to reveal and clarify the rich physics underlying active matter systems that perform chemotaxis, ranging from cells to robots.

Collective behavior and self-organization in neural rosette morphogenesis

Neural rosettes develop from the self-organization of differentiating human pluripotent stem cells. This process mimics the emergence of the embryonic central nervous system primordium, i.e., the neural tube, whose formation is under close investigation as errors during such process result in severe diseases like spina bifida and anencephaly. While neural tube formation is recognized as an example of self-organization, we still do not understand the fundamental mechanisms guiding the process. Here, we discuss the different theoretical frameworks that have been proposed to explain self-organization in morphogenesis. We show that an explanation based exclusively on stem cell differentiation cannot describe the emergence of spatial organization, and an explanation based on patterning models cannot explain how different groups of cells can collectively migrate and produce the mechanical transformations required to generate the neural tube. We conclude that neural rosette development is a relevant experimental 2D in-vitro model of morphogenesis because it is a multi-scale self-organization process that involves both cell differentiation and tissue development. Ultimately, to understand rosette formation, we first need to fully understand the complex interplay between growth, migration, cytoarchitecture organization, and cell type evolution.

Efficient control protocols for an active Ornstein-Uhlenbeck particle

Designing a protocol to efficiently drive a stochastic system is an active field of research. Here we extend such control theory to an active Ornstein-Uhlenbeck particle (AOUP) in a bistable potential, driven by a harmonic trap. We find that protocols designed to minimize the excess work (up to linear response) perform better than naive protocols with constant velocity for a wide range of protocol durations.

Nonequilibrium steady state of trapped active particles

We consider an overdamped particle with a general physical mechanism that creates noisy active movement (e.g., a run-and-tumble particle or active Brownian particle, etc.), that is confined by an external potential. Focusing on the limit in which the correlation time τ of the active noise is small, we find the nonequilibrium steady-state distribution P_{st}(X) of the particle's position X. While typical fluctuations of X follow a Boltzmann distribution with an effective temperature that is not difficult to find, the tails of P_{st}(X) deviate from a Boltzmann behavior: In the limit τ→0, they scale as P_{st}(X)∼e^{-s(X)/τ}. We calculate the large-deviation function s(X) exactly for arbitrary trapping potential and active noise in dimension d=1, by relating it to the rate function that describes large deviations of the position of the same active particle in absence of an external potential at long times. We then extend our results to d>1 assuming rotational symmetry.

Mechanism for giant enhancement of transport induced by active fluctuations

Understanding the role of active fluctuations in physics is a problem in statu nascendi appearing both as a hot topic and a major challenge. The reason for this is the fact that they are inherently nonequilibrium. This feature opens a landscape of phenomena yet to be explored that are absent in the presence of thermal fluctuations alone. Recently a paradoxical effect has been briefly communicated in which a free-particle transport induced by active fluctuations in the form white Poisson shot noise can be enormously boosted when the particle is additionally subjected to a periodic potential. In this work we considerably extend the original predictions and investigate the impact of statistics of active noise on the occurrence of this effect. We construct a toy model of the jump-relaxation process that allow us to identify different regimes of the free-particle transport boost and explain their corresponding mechanisms. Moreover, we formulate and interpret the conditions for statistics of active fluctuations that are necessary for the emergence of giant enhancement of the free-particle transport induced by the periodic potential. Our results are relevant not only for microscopic physical systems but also for biological ones such as, e.g., living cells where fluctuations generated by metabolic activities are active by default.

Active Brownian particles in a circular disk with an absorbing boundary

We solve the time-dependent Fokker-Planck equation for a two-dimensional active Brownian particle exploring a circular region with an absorbing boundary. Using the passive Brownian particle as basis states and dealing with the activity as a perturbation, we provide a matrix representation of the Fokker-Planck operator and we express the propagator in terms of the perturbed eigenvalues and eigenfunctions. Alternatively, we show that the propagator can be expressed as a combination of the equilibrium eigenstates with weights depending only on time and on the initial conditions, and obeying exact iterative relations. Our solution allows also obtaining the survival probability and the first-passage time distribution. These latter quantities exhibit peculiarities induced by the nonequilibrium character of the dynamics; in particular, they display a strong dependence on the activity of the particle and, to a less extent, also on its rotational diffusivity.

Single active particle in a harmonic potential: Question about the existence of the Jarzynski relation

The interest in active matter stimulates the need to generalize thermodynamic description and relations to active matter systems, which are intrinsically out of equilibrium. One important example is the Jarzynski relation, which links the exponential average of work done in an arbitrary process connecting two equilibrium states with the difference of the free energies of these states. Using a simple model system, a single thermal active Ornstein-Uhlenbeck particle in a harmonic potential, we show that if the standard stochastic thermodynamics definition of work is used, the Jarzynski relation is not generally valid for processes connecting stationary states of active matter systems.

Inertial active ratchet: Simulation versus theory

We present the inertial active dynamics of an Ornstein-Uhlenbeck particle in a piecewise sawtooth ratchet potential. Using the Langevin simulation and matrix continued fraction method (MCFM), the particle transport, steady-state diffusion, and coherence in transport are investigated in different parameter regimes of the model. Spatial asymmetry is found to be a key criterion for the possibility of directed transport in the ratchet. The MCFM results for net particle current of overdamped dynamics of the particle agree well with the simulation results. The simulated particle trajectories for the inertial dynamics and the corresponding position and velocity distribution functions reveal that the system passes through an activity-induced transition in the transport from the running phase to the locked phase of the dynamics. This is further corroborated by the mean square displacement (MSD) calculations, where the MSD gets suppressed with increase in the persistent duration of activity or self-propulsion in the medium and finally approaches zero for a very large value of self propulsion time. The nonmonotonic behavior of the particle current and Péclet number with self-propulsion time confirms that the particle transport and its coherence can be enhanced or reduced by fine tuning the persistent duration of activity. Moreover, for intermediate ranges of self-propulsion time as well as mass of the particle, even though the particle current shows a pronounced unusual maximum with mass, there is no enhancement in the Péclet number, instead the Péclet number decreases with mass, confirming the degradation of coherence in transport.

Activity-assisted barrier crossing of self-propelled colloids over parallel microgrooves

We report a systematic study of the dynamics of self-propelled particles (SPPs) over a one-dimensional periodic potential landscape U_{0}(x), which is fabricated on a microgroove-patterned polydimethylsiloxane (PDMS) substrate. From the measured nonequilibrium probability density function P(x;F_{0}) of the SPPs, we find that the escape dynamics of the slow rotating SPPs across the potential landscape can be described by an effective potential U_{eff}(x;F_{0}), once the self-propulsion force F_{0} is included into the potential under the fixed angle approximation. This work demonstrates that the parallel microgrooves provide a versatile platform for a quantitative understanding of the interplay among the self-propulsion force F_{0}, spatial confinement by U_{0}(x), and thermal noise, as well as its effects on activity-assisted escape dynamics and transport of the SPPs.

3D Active Brownian Motion of Single Dust Particles Induced by a Laser in a DC Glow Discharge

The active Brownian motion of single dust particles of various types in the 3D electrostatic DC discharge trap under the action of laser radiation is studied experimentally. Spherical dust particles with a homogeneous surface, as well as Janus particles, are used in the experiment. The properties of the active Brownian motion of all types of dust particles are studied. In particular, the 3D analysis of trajectories of microparticles is carried out, well as an analysis of their root mean square displacement. The mean kinetic energy of motion of the dust particle of various types in a 3D trap is determined for different laser powers. Differences in the character of active Brownian motion in electrostatic traps with different spatial dimensions are found.

Periodic potential can enormously boost free-particle transport induced by active fluctuations

Active fluctuations are detected in a growing number of systems due to self-propulsion mechanisms or collisions with an active environment. They drive the system far from equilibrium and can induce phenomena that are forbidden at equilibrium states by, e.g., fluctuation-dissipation relations and detailed balance symmetry. Understanding their role in living matter is emerging as a challenge for physics. Here we demonstrate a paradoxical effect in which a free-particle transport induced by active fluctuations can be boosted by many orders of magnitude when the particle is additionally subjected to a periodic potential. In contrast, within the realm of only thermal fluctuations, the velocity of a free particle exposed to a bias is reduced when the periodic potential is switched on. The presented mechanism is significant for understanding nonequilibrium environments such as living cells, where it can explain from a fundamental point of view why spatially periodic structures known as microtubules are necessary to generate impressively effective intracellular transport. Our findings can be readily corroborated experimentally, e.g., in a setup comprising a colloidal particle in an optically generated periodic potential.

Bouncing dynamics of inertial self-propelled particles reveals directional asymmetry

This study aims to examine experimental conditions in which active particles are forced by their surroundings to move forward and backward in a continuous oscillatory manner. The experimental design is based on using a vibrating self-propelled toyrobot called hexbug, which is placed inside a narrow channel closed on one end by a rigid moving wall. Using the end-wall velocity as a controlling factor, the main forward mode of the hexbug movement can be turned to mostly rearward mode. We investigate the bouncing hexbug motion on both experimental and theoretical grounds. The Brownian model of active particles with inertia is employed in the theoretical framework. The model itself uses a pulsed Langevin equation in order to simulate abrupt changes in velocity that mimic hexbug propulsion in the moments when its legs make contact with the base plate. Significant directional asymmetry is caused by the legs bending backward. We demonstrate that the simulation successfully reproduces the experimental characteristics of hexbug motion after regressing the spatial and temporal statistical characteristics, especially when directional asymmetry is under consideration.

Mode-coupling theory for the dynamics of dense underdamped active Brownian particle system

We present a theory to study the inertial effect on glassy dynamics of the underdamped active Brownian particle (UABP) system. Using the assumption of the nonequilibrium steady-state, we obtain an effective Fokker-Planck equation for the probability distribution function (PDF) as a function of positions and momentums. With this equation, we achieve the evolution equation of the intermediate scattering function through the Zwanzig-Mori projection operator method and the mode-coupling theory (MCT). Theoretical analysis shows that the inertia of the particle affects the memory function and corresponding glass transition by influencing the structure factor and a velocity correlation function. The theory provides theoretical support and guidance for subsequent simulation work.

Diffusion Coefficient of a Brownian Particle in Equilibrium and Nonequilibrium: Einstein Model and Beyond

The diffusion of small particles is omnipresent in many processes occurring in nature. As such, it is widely studied and exerted in almost all branches of sciences. It constitutes such a broad and often rather complex subject of exploration that we opt here to narrow our survey to the case of the diffusion coefficient for a Brownian particle that can be modeled in the framework of Langevin dynamics. Our main focus centers on the temperature dependence of the diffusion coefficient for several fundamental models of diverse physical systems. Starting out with diffusion in equilibrium for which the Einstein theory holds, we consider a number of physical situations outside of free Brownian motion and end by surveying nonequilibrium diffusion for a time-periodically driven Brownian particle dwelling randomly in a periodic potential. For this latter situation the diffusion coefficient exhibits an intriguingly non-monotonic dependence on temperature.

Mechanochemical subcellular-element model of crawling cells

Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due to the law of action and reaction. The typical mechanics of cell crawling involve periodic changes in the cell shape and in the adhesion characteristics of the cell to the substrate. However, the basic physical mechanisms by which a single cell coordinates these processes cooperatively to achieve autonomous migration are not yet well understood. To obtain a clearer grasp of how the intracellular force is converted to directional motion, we develop a basic mechanochemical model of a crawling cell based on subcellular elements with the focus on the dependence of the protrusion and contraction as well as the adhesion and de-adhesion processes on intracellular biochemical signals. By introducing reaction-diffusion equations that reproduce traveling waves of local chemical concentrations, we clarify that the chemical dependence of the cell-substrate adhesion dynamics determines the crawling direction and distance with one chemical wave. Finally, we also perform multipole analysis of the traction force to compare it with the experimental results. Our present work sheds light on how intracellular chemical reactions are converted to a directional cell migration under the force-free condition. Although the detailed mechanisms of actual cells are far more complicated than our simple model, we believe that this mechanochemical model is a good prototype for more realistic models.

Exact position distribution of a harmonically confined run-and-tumble particle in two dimensions

We consider an overdamped run-and-tumble particle in two dimensions, with self-propulsion in an orientation that stochastically rotates by 90^{∘} at a constant rate, clockwise or counterclockwise with equal probabilities. In addition, the particle is confined by an external harmonic potential of stiffness μ, and possibly diffuses. We find the exact time-dependent distribution P(x,y,t) of the particle's position, and in particular, the steady-state distribution P_{st}(x,y) that is reached in the long-time limit. We also find P(x,y,t) for a "free" particle, μ=0. We achieve this by showing that, under a proper change of coordinates, the problem decomposes into two statistically independent one-dimensional problems, whose exact solution has recently been obtained. We then extend these results in several directions, to two such run-and-tumble particles with a harmonic interaction, to analogous systems of dimension three or higher, and by allowing stochastic resetting.

Analytic Solution of an Active Brownian Particle in a Harmonic Well

We provide an analytical solution for the time-dependent Fokker-Planck equation for a two-dimensional active Brownian particle trapped in an isotropic harmonic potential. Using the passive Brownian particle as basis states we show that the Fokker-Planck operator becomes lower diagonal, implying that the eigenvalues are unaffected by the activity. The propagator is then expressed as a combination of the equilibrium eigenstates with weights obeying exact iterative relations. We show that for the low-order correlation functions, such as the positional autocorrelation function, the recursion terminates at finite order in the Péclet number, allowing us to generate exact compact expressions and derive the velocity autocorrelation function and the time-dependent diffusion coefficient. The nonmonotonic behavior of latter quantities serves as a fingerprint of the nonequilibrium dynamics.

Hamiltonian active particles in an environment

We examine a Hamiltonian system which represents an active particle that can move against an opposing external force by drawing energy from an internal depot while immersed in a noisy and dissipative environment. The Hamiltonian consists of two subsystems, one representing the active particle's motion and the other its depot of "fuel." We show that although the active particle loses some of its energy to dissipation from the environment, dissipation can also help to stabilize the dynamical process that makes the particle active. This raises the possibility that the internal mechanisms of active particles may not only be able to operate in noisy and dissipative environments, but may actually rely on the environment for their control.

Heterogeneous run-and-tumble motion accounts for transient non-Gaussian super-diffusion in haematopoietic multi-potent progenitor cells

Multi-potent progenitor (MPP) cells act as a key intermediary step between haematopoietic stem cells and the entirety of the mature blood cell system. Their eventual fate determination is thought to be achieved through migration in and out of spatially distinct niches. Here we first analyze statistically MPP cell trajectory data obtained from a series of long time-course 3D in vivo imaging experiments on irradiated mouse calvaria, and report that MPPs display transient super-diffusion with apparent non-Gaussian displacement distributions. Second, we explain these experimental findings using a run-and-tumble model of cell motion which incorporates the observed dynamical heterogeneity of the MPPs. Third, we use our model to extrapolate the dynamics to time-periods currently inaccessible experimentally, which enables us to quantitatively estimate the time and length scales at which super-diffusion transitions to Fickian diffusion. Our work sheds light on the potential importance of motility in early haematopoietic progenitor function.

Spatial population genetics with fluid flow

The growth and evolution of microbial populations is often subjected to advection by fluid flows in spatially extended environments, with immediate consequences for questions of spatial population genetics in marine ecology, planktonic diversity and origin of life scenarios. Here, we review recent progress made in understanding this rich problem in the simplified setting of two competing genetic microbial strains subjected to fluid flows. As a pedagogical example we focus on antagonsim, i.e., two killer microorganism strains, each secreting toxins that impede the growth of their competitors (competitive exclusion), in the presence of stationary fluid flows. By solving two coupled reaction-diffusion equations that include advection by simple steady cellular flows composed of characteristic flow motifs in two dimensions (2D), we show how local flow shear and compressibility effects can interact with selective advantage to have a dramatic influence on genetic competition and fixation in spatially distributed populations. We analyze several 1D and 2D flow geometries including sources, sinks, vortices and saddles, and show how simple analytical models of the dynamics of the genetic interface can be used to shed light on the nucleation, coexistence and flow-driven instabilities of genetic drops. By exploiting an analogy with phase separation with nonconserved order parameters, we uncover how thesegeneticdrops harness fluid flows for novel evolutionary strategies, even in the presence of number fluctuations, as confirmed by agent-based simulations as well.

Colossal Power Extraction from Active Cyclic Brownian Information Engines

Brownian information engines can extract work from thermal fluctuations by utilizing information. To date, the studies on Brownian information engines consider the system in a thermal bath; however, many processes in nature occur in a nonequilibrium setting, such as the suspensions of self-propelled microorganisms or cellular environments called an active bath. Here, we introduce an archetypal model for a Maxwell-demon type cyclic Brownian information engine operating in a Gaussian correlated active bath capable of extracting more work than its thermal counterpart. We obtain a general integral fluctuation theorem for the active engine that includes additional mutual information gained from the active bath with a unique effective temperature. This effective description modifies the generalized second law and provides a new upper bound for the extracted work. Unlike the passive information engine operating in a thermal bath, the active information engine extracts colossal power that peaks at the finite cycle period. Our study provides fundamental insights into the design and functioning of synthetic and biological submicrometer motors in active baths under measurement and feedback control.

Anomalous Transport of Tracers in Active Baths

We derive the long-time dynamics of a tracer immersed in a one-dimensional active bath. In contrast to previous studies, we find that the damping and noise correlations possess long-time tails with exponents that depend on the tracer symmetry. For generic tracers, shape asymmetry induces ratchet effects that alter fluctuations and lead to superdiffusion and friction that grows with time when the tracer is dragged at a constant speed. In the singular limit of a completely symmetric tracer, we recover normal diffusion and finite friction. Furthermore, for small symmetric tracers, the active contribution to the friction becomes negative: active particles enhance motion rather than oppose it. These results show that, in low-dimensional systems, the motion of a passive tracer in an active bath cannot be modeled as a persistent random walker with a finite correlation time.

Active random walks in one and two dimensions

We investigate active lattice walks: biased continuous time random walks which perform orientational diffusion between lattice directions in one and two spatial dimensions. We study the occupation probability of an arbitrary site on the lattice in one and two dimensions and derive exact results in the continuum limit. Next, we compute the large deviation free-energy function in both one and two dimensions, which we use to compute the moments and the cumulants of the displacements exactly at late times. Our exact results demonstrate that the cross-correlations between the motion in the x and y directions in two dimensions persist in the large deviation function. We also demonstrate that the large deviation function of an active particle with diffusion displays two regimes, with differing diffusive behaviors. We verify our analytic results with kinetic Monte Carlo simulations of an active lattice walker in one and two dimensions.

Competing effects of rotational diffusivity and activity on finite-sized clusters

Colloidal particles interacting via short-range attraction and long-range repulsion are known to stabilize finite-sized clusters under equilibrium conditions. In this work, the effect of self-propulsion speed (activity) and rotational diffusivity (D_r) on the phase behavior of such particles is investigated using Brownian dynamics simulations. The system exhibits rich phase behavior consisting of clusters of different kinds. The cluster size varies non-monotonically with activity: increasing first and decreasing at higher activity, thus driving cluster-to-fluid phase transition. Rotational diffusivity also facilitates the formation of clusters. Larger clusters could be stabilized at lowD_rvalues while at highD_rvalues, clusters are stable even at higher activities. The analysis of the static structure factor of the system confirms that rotational diffusivity delays the cluster-to-fluid transition driven by activity.

Brownian motion in a growing population of ballistic particles

We investigate the motility of a growing population of cells in a idealized setting: We consider a system of hard disks in which new particles are added according to prescribed growth kinetics, thereby dynamically changing the number density. As a result, the expected Brownian motion of the hard disks is modified. We compute the density-dependent friction of the hard disks and insert it in an effective Langevin equation to describe the system, assuming that the intercollision time is smaller than the timescale of the growth. We find that the effective Langevin description captures the changes in motility, in agreement with the simulation results. Our framework can be extended to other systems in which the transport coefficient varies with time.

Diffusion of chiral active particles in a Poiseuille flow

We study the diffusive behavior of chiral active (self-propelled) Brownian particles in a two-dimensional microchannel with a Poiseuille flow. Using numerical simulations, we show that the behavior of the transport coefficients of particles, for example, the average velocity v and the effective diffusion coefficient D_{eff}, strongly depends on flow strength u_{0}, translational diffusion constant D_{0}, rotational diffusion rate D_{θ}, and chirality of the active particles Ω. It is demonstrated that the particles can exhibit upstream drift, resulting in a negative v, for the optimal parameter values of u_{0}, D_{θ}, and Ω. Interestingly, the direction of v can be controlled by tuning these parameters. We observe that for some optimal values of u_{0} and Ω, the chiral particles aggregate near a channel wall and the corresponding D_{eff} are enhanced. However, for the nonchiral particles (Ω=0), D_{eff} is suppressed by the presence of Poiseuille flow. It is expected that these findings have a great potential for developing microfluidic and lab-on-a-chip devices for separating the active particles.

Premelting controlled active matter in ice

Self-propelled particles can undergo complex dynamics due to a range of bulk and surface interactions. When a particle is embedded in a host solid near its bulk melting temperature, the latter may melt at the surface of the former in a process known as interfacial premelting. The thickness of the melt film depends on the temperature, impurities, material properties and geometry. A temperature gradient is accompanied by a thermomolecular pressure gradient that drives the interfacial liquid from high to low temperatures and hence the particle from low to high temperatures, in a process called thermal regelation. When the host material is ice and the embedded particle is a biological entity, one has a particularly different form of active matter, which addresses interplay between a wide range of problems, from extremophiles of both terrestrial and exobiological relevance to ecological dynamics in Earth's cryosphere. Of basic importance in all such settings is the combined influence of biological activity and thermal regelation in controlling the redistribution of bioparticles. Therefore, we recast this class of regelation phenomena in the stochastic framework of active Ornstein-Uhlenbeck dynamics and make predictions relevant to this and related problems of interest in biological and geophysical problems. We examine how thermal regelation compromises paleoclimate studies in the context of ice core dating and we find that the activity influences particle dynamics during thermal regelation by enhancing the effective diffusion coefficient. Therefore, accurate dating relies on a quantitative treatment of both effects.

Unified analysis of topological defects in 2D systems of active and passive disks

We provide a comprehensive quantitative analysis of localized and extended topological defects in the steady state of 2D passive and active repulsive Brownian disk systems. We show that, both in and out-of-equilibrium, the passage from the solid to the hexatic is driven by the unbinding of dislocations, in quantitative agreement with the KTHNY singularity. Instead, extended clusters of defects largely dominate below the solid-hexatic critical line. The latter percolate in the liquid phase very close to the hexatic-liquid transition, both for continuous and discontinuous transitions, in the homogeneous liquid regime. At critical percolation the clusters of defects are fractal with statistical and geometric properties that are independent of the activity and compatible with the universality class of uncorrelated critical percolation. We also characterize the spatial organization of point-like defects and we show that the disclinations are not free, but rather always very near more complex defect structures. At high activity, the bulk of the dense phase generated by Motility-Induced Phase Separation is characterized by a density of point-like defects, and statistics and morphology of defect clusters, set by the amount of activity and not the packing fraction. Hexatic domains within the dense phase are separated by grain-boundaries along which a finite network of topological defects resides, interrupted by gas bubbles in cavitation. This structure is dynamic in the sense that the defect network allows for an unzipping mechanism that leaves free space for gas bubbles to appear, close, and even be released into the dilute phase.

Migration of active filaments under Poiseuille flow in a microcapillary tube

We present a comprehensive study of active filaments confined in a cylindrical channel under Poiseuille flow. The activity drives the filament towards the channel boundary, whereas external fluid flow migrates the filament away from the boundary. This migration further shifts towards the centre for higher flow strength. The migration behaviour of the filaments is presented in terms of the alignment order parameter that shows the alignment grows with shear and activity. Further, we have also addressed the role of length of filament on the migration behaviour, which suggests higher migration for larger filaments. Moreover, we discuss the polar ordering of filaments as a function of distance from the centre of channel that displays upstream motion near the boundary and downstream motion at the centre of the tube.

Density fluctuations and energy spectra of 3D bacterial suspensions

Giant number fluctuations are often considered as a hallmark of the emergent nonequilibrium dynamics of active fluids. However, these anomalous density fluctuations have only been reported experimentally in two-dimensional dry active systems heretofore. Here, we investigate density fluctuations of bulk Escherichia coli suspensions, a paradigm of three-dimensional (3D) wet active fluids. Our experiments demonstrate the existence and quantify the scaling relation of giant number fluctuations in 3D bacterial suspensions. Surprisingly, the anomalous scaling persists at small scales in low-concentration suspensions well before the transition to active turbulence, reflecting the long-range nature of hydrodynamic interactions of 3D wet active fluids. To illustrate the origin of the density fluctuations, we measure the energy spectra of suspension flows and explore the density-energy coupling in both the steady and transient states of active turbulence. A scale-invariant density-independent correlation between density fluctuations and energy spectra is uncovered across a wide range of length scales. In addition, our experiments show that the energy spectra of bacterial turbulence exhibit the scaling of 3D active nematic fluids, challenging the common view of dense bacterial suspensions as active polar fluids.

Multiple functions of flagellar motility and chemotaxis in bacterial physiology

Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.

Stationary nonequilibrium bound state of a pair of run and tumble particles

We study two interacting identical run-and-tumble particles (RTPs) in one dimension. Each particle is driven by a telegraphic noise and, in some cases, also subjected to a thermal white noise with a corresponding diffusion constant D. We are interested in the stationary bound state formed by the two RTPs in the presence of a mutual attractive interaction. The distribution of the relative coordinate y indeed reaches a steady state that we characterize in terms of the solution of a second-order differential equation. We obtain the explicit formula for the stationary probability P(y) of y for two examples of interaction potential V(y). The first one corresponds to V(y)∼|y|. In this case, for D=0 we find that P(y) contains a δ function part at y=0, signaling a strong clustering effect, together with a smooth exponential component. For D>0, the δ function part broadens, leading instead to weak clustering. The second example is the harmonic attraction V(y)∼y^{2} in which case, for D=0, P(y) is supported on a finite interval. We unveil an interesting relation between this two-RTP model with harmonic attraction and a three-state single-RTP model in one dimension, as well as with a four-state single-RTP model in two dimensions. We also provide a general discussion of the stationary bound state, including examples where it is not unique, e.g., when the particles cannot cross due to an additional short-range repulsion.

Dependency of active pressure and equation of state on stiffness of wall

Autonomous motion and motility are hallmarks of active matter. Active agents, such as biological cells and synthetic colloidal particles, consume internal energy or extract energy from the environment to generate self-propulsion and locomotion. These systems are persistently out of equilibrium due to continuous energy consumption. It is known that pressure is not always a state function for generic active matter. Torque interaction between active constituents and confinement renders the pressure of the system a boundary-dependent property. The mechanical pressure of anisotropic active particles depends on their microscopic interactions with a solid wall. Using self-propelled dumbbells confined by solid walls as a model system, we perform numerical simulations to explore how variations in the wall stiffness influence the mechanical pressure of dry active matter. In contrast to previous findings, we find that mechanical pressure can be independent of the interaction of anisotropic active particles with walls, even in the presence of intrinsic torque interaction. Particularly, the dependency of pressure on the wall stiffness vanishes when the stiffness is above a critical level. In such a limit, the dynamics of dumbbells near the walls are randomized due to the large torque experienced by the dumbbells, leading to the recovery of pressure as a state variable of density.

Durotaxis of Passive Nanoparticles on Elastic Membranes

The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in nonuniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically nonuniform elastic membrane. We observe a nonmonotonic affinity of the particle to the membrane as a function of the membrane's rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.

Durotaxis of Passive Nanoparticles on Elastic Membranes

The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in nonuniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically nonuniform elastic membrane. We observe a nonmonotonic affinity of the particle to the membrane as a function of the membrane's rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.

Heat fluctuations in a harmonic chain of active particles

One of the major challenges in stochastic thermodynamics is to compute the distributions of stochastic observables for small-scale systems for which fluctuations play a significant role. Hitherto much theoretical and experimental research has focused on systems composed of passive Brownian particles. In this paper, we study the heat fluctuations in a system of interacting active particles. Specifically we consider a one-dimensional harmonic chain of N active Ornstein-Uhlenbeck particles, with the chain ends connected to heat baths of different temperatures. We compute the moment-generating function for the heat flow in the steady state. We employ our general framework to explicitly compute the moment-generating function for two example single-particle systems. Further, we analytically obtain the scaled cumulants for the heat flow for the chain. Numerical Langevin simulations confirm the long-time analytical expressions for first and second cumulants for the heat flow for a two-particle chain.

Optimal navigation strategy of active Brownian particles in target-search problems

We investigate exploration patterns of a microswimmer, modeled as an active Brownian particle, searching for a target region located in a well of an energy landscape and separated from the initial position of the particle by high barriers. We find that the microswimmer can enhance its success rate in finding the target by tuning its activity and its persistence in response to features of the environment. The target-search patterns of active Brownian particles are counterintuitive and display characteristics robust to changes in the energy landscape. On the contrary, the transition rates and transition-path times are sensitive to the details of the specific energy landscape. In striking contrast to the passive case, the presence of additional local minima does not significantly slow down the active-target-search dynamics.

Ordering kinetics in the active model B

We undertake a detailed numerical study of the Active Model B proposed by Wittkowski et al., [Nature Commun. 5, 4351 (2014)]2041-172310.1038/ncomms5351. We find that the introduction of activity has a drastic effect on the ordering kinetics. First, the domain growth law shows a crossover from the usual Lifshitz-Slyozov growth law for phase separation (L∼t^{1/3}, where t is the time) to a novel growth law (L∼t^{1/4}) at late times. Second, the equal-time correlation function of the density field exhibits dynamical scaling for a given activity strength λ, but the scaling function depends on λ.

C. elegans colony formation as a condensation phenomenon

Phase separation at the molecular scale affects many biological processes. The theoretical requirements for phase separation are fairly minimal, and there is growing evidence that analogous phenomena occur at other scales in biology. Here we examine colony formation in the nematode C. elegans as a possible example of phase separation by a population of organisms. The population density of worms determines whether a colony will form in a thresholded fashion, and a simple two-compartment ordinary differential equation model correctly predicts the threshold. Furthermore, small, round colonies sometimes fuse to form larger, round colonies, and a phenomenon akin to Ostwald ripening – a coarsening process seen in many systems that undergo phase separation – also occurs. These findings support the emerging view that the principles of microscopic phase separation can also apply to collective behaviors of living organisms.

Phase separation phenomena have emerged as being of critical importance in biology. Here, using colony formation in C. elegans as model, the authors demonstrate that the basic concepts that underpin phase separation at a molecular level also apply to collective phenomena at the level of a population of organisms.