The propagation of active-passive interfaces in bacterial swarms

Deep learning-based detection of bacterial swarm motion using a single image

Motility is a fundamental characteristic of bacteria. Distinguishing between swarming and swimming, the two principal forms of bacterial movement, holds significant conceptual and clinical relevance. Conventionally, the detection of bacterial swarming involves inoculating samples on an agar surface and observing colony expansion, which is qualitative, time-intensive, and requires additional testing to rule out other motility forms. A recent methodology that differentiates swarming and swimming motility in bacteria using circular confinement offers a rapid approach to detecting swarming. However, it still heavily depends on the observer's expertise, making the process labor-intensive, costly, slow, and susceptible to inevitable human bias. To address these limitations, we developed a deep learning-based swarming classifier that rapidly and autonomously predicts swarming probability using a single blurry image. Compared with traditional video-based, manually processed approaches, our method is particularly suited for high-throughput environments and provides objective, quantitative assessments of swarming probability. The swarming classifier demonstrated in our work was trained on Enterobacter sp. SM3 and showed good performance when blindly tested on new swarming (positive) and swimming (negative) test images of SM3, achieving a sensitivity of 97.44% and a specificity of 100%. Furthermore, this classifier demonstrated robust external generalization capabilities when applied to unseen bacterial species, such as Serratia marcescens DB10 and Citrobacter koseri H6. This competitive performance indicates the potential to adapt our approach for diagnostic applications through portable devices, which would facilitate rapid, objective, on-site screening for bacterial swarming motility, potentially enhancing the early detection and treatment assessment of various diseases, including inflammatory bowel diseases (IBD) and urinary tract infections (UTI).

Interface Dynamics of Wet Active Systems

We study the roughening of interfaces in phase-separated active suspensions on substrates. At both large length and time scales, we show that the interfacial dynamics belongs to the |q|KPZ universality class discussed in Besse et al. [Phys. Rev. Lett. 130, 187102 (2023)PRLTAO0031-900710.1103/PhysRevLett.130.187102]. This holds despite the presence of long-ranged fluid flows. At early times, however, or for sufficiently small systems, the roughening exponents are the same as those in the presence of a momentum-conserving fluid. Surprisingly, when the effect of substrate friction can be ignored, the interface becomes random beyond a de Gennes-Taupin length scale that depends on the interfacial tension.

Rapid Evaluation of Antimicrobial Potency Through Bacterial Collective Motion Analysis

The growing threat of bacterial resistance is a critical global health concern, necessitating the development of more efficient methods for evaluating antimicrobial efficacy. Here, we introduce a technique based on the sensitivity of bacterial collective motion to environmental changes, using motion trajectory analysis for swift antibiotic susceptibility appraisal within a simple spread-out of bacterial droplet. By single cell tracking in bacterial fluids near the droplet edge or boundary-detection of the colony expansion, we achieved rapid evaluation of antibiotic efficacy in under 60 min. This method is not only faster than traditional assays but also provides insights into drug-bacterial interactions, offering a powerful tool for advancing both diagnostic testing and the development of antimicrobial agents.

Scaling Transition of Active Turbulence from Two to Three Dimensions

Turbulent flows are observed in low-Reynolds active fluids, which display similar phenomenology to the classical inertial turbulence but are of a different nature. Understanding the dependence of this new type of turbulence on dimensionality is a fundamental challenge in non-equilibrium physics. Real-space structures and kinetic energy spectra of bacterial turbulence are experimentally measured from two to three dimensions. The turbulence shows three regimes separated by two critical confinement heights, resulting from the competition of bacterial length, vortex size and confinement height. Meanwhile, the kinetic energy spectra display distinct universal scaling laws in quasi-2D and 3D regimes, independent of bacterial activity, length, and confinement height, whereas scaling exponents transition in two steps around the critical heights. The scaling behaviors are well captured by the hydrodynamic model we develop, which employs image systems to represent the effects of confining boundaries. The study suggests a framework for investigating the effect of dimensionality on non-equilibrium self-organized systems.

Multiplex Detection of Foodborne Pathogens using 3D Nanostructure Swab and Deep Learning-Based Classification of Raman Spectra

Proactive management of foodborne illness requires routine surveillance of foodborne pathogens, which requires developing simple, rapid, and sensitive detection methods. Here, a strategy is presented that enables the detection of multiple foodborne bacteria using a 3D nanostructure swab and deep learning-based Raman signal classification. The nanostructure swab efficiently captures foodborne pathogens, and the portable Raman instrument directly collects the Raman signals of captured bacteria. a deep learning algorithm has been demonstrated, 1D convolutional neural network with binary labeling, achieves superior performance in classifying individual bacterial species. This methodology has been extended to mixed bacterial populations, maintaining accuracy close to 100%. In addition, the gradient-weighted class activation mapping method is used to provide an investigation of the Raman bands for foodborne pathogens. For practical application, blind tests are conducted on contaminated kitchen utensils and foods. The proposed technique is validated by the successful detection of bacterial species from the contaminated surfaces. The use of a 3D nanostructure swab, portable Raman device, and deep learning-based classification provides a powerful tool for rapid identification (≈5 min) of foodborne bacterial species. The detection strategy shows significant potential for reliable food safety monitoring, making a meaningful contribution to public health and the food industry.

Colonization and spreading dynamics of Lactiplantibacillus plantarum spoilage isolates on wet surfaces

The role of lactic acid bacteria, including Lactiplantibacillus plantarum, in food spoilage is well recognized, while the behavior of these non-motile bacteria on wet surfaces, such as those encountered in food processing environments has gained relatively little attention. Here, we observed a fast colony spreading of non-motile L. plantarum spoilage isolates on wet surfaces via passive sliding using solid BHI agar media as a model. We investigated the effect of physical properties of agar hydrogel substrate on the surface spreading of six L. plantarum food isolates FBR1-6 and a model strain WCFS1, using increasing concentrations of agar from 0.25 up to 1.5% (w/v). Our results revealed that L. plantarum strain FBR2 spreads significantly on low agar concentration plates compared to the other strains studied here (with a factor of 50-60 folds higher surface coverage), due to the formation of very soft biofilms with high water content that can float on the surface. The fast-spreading of FBR2 colonies is accompanied by an increased number of cells, elongated cell morphology, and a higher amount of extracellular components. Our finding highlights colonization dynamics and the spreading capacity of non-motile bacteria on surfaces that are relatively wet, thereby revealing an additional hitherto unnoticed parameter for non-motile bacteria that may contribute to contamination of foods by fast surface spreading of these bacteria in food processing environments.

Multi-population dissolution in confined active fluids

Autonomous out-of-equilibrium agents or cells in suspension are ubiquitous in biology and engineering. Turning chemical energy into mechanical stress, they generate activity in their environment, which may trigger spontaneous large-scale dynamics. Often, these systems are composed of multiple populations that may reflect the coexistence of multiple species, differing phenotypes, or chemically varying agents in engineered settings. Here, we present a new method for modeling such multi-population active fluids subject to confinement. We use a continuum multi-scale mean-field approach to represent each phase by its first three orientational moments and couple their evolution with those of the suspending fluid. The resulting coupled system is solved using a parallel adaptive level-set-based solver for high computational efficiency and maximal flexibility in the confinement geometry. Motivated by recent experimental work, we employ our method to study the spatiotemporal dynamics of confined bacterial suspensions and swarms dominated by fluid hydrodynamic effects. Our in silico explorations reproduce observed emergent collective patterns, including features of active dissolution in two-population active-passive swarms, with results clearly suggesting that hydrodynamic effects dominate dissolution dynamics. Our work lays the foundation for a systematic characterization and study of collective phenomena in natural or synthetic multi-population systems such as bacteria colonies, bird flocks, fish schools, colloid swimmers, or programmable active matter.

Dynamic Buckling of a Filament Impacted by a Falling Droplet

We investigate the buckling dynamics of an elastic filament impacted axially by a falling liquid droplet, and identify the buckling modes through a combination of experimental and theoretical analyses. A phase diagram is constructed on a plane defined by two primary parameters: the falling height and the filament length. Two transition boundaries are observed, with one marking the occurrence of dynamic buckling and the other separating the buckling regime into two distinct modes. Notably, the hydrodynamic viscous force of the liquid dominates during the impact, with the dynamic buckling instability predicted by a single elastoviscous number. The critical load is twice the critical static load, which is, however, lower for the deformable droplet utilized in our study, as compared to a solid object. An additional time-dependent simulation on a longer filament exhibits a higher buckling mode, succeeded by a more distinct coarsening process than our experimental observations.

Size-Dependent Diffusion and Dispersion of Particles in Mucin

Mucus, composed significantly of glycosylated mucins, is a soft and rheologically complex material that lines respiratory, reproductive, and gastrointestinal tracts in mammals. Mucus may present as a gel, as a highly viscous fluid, or as a viscoelastic fluid. Mucus acts as a barrier to the transport of harmful microbes and inhaled atmospheric pollutants to underlying cellular tissue. Studies on mucin gels have provided critical insights into the chemistry of the gels, their swelling kinetics, and the diffusion and permeability of molecular constituents such as water. The transport and dispersion of micron and sub-micron particles in mucin gels and solutions, however, differs from the motion of small molecules since the much larger tracers may interact with microstructure of the mucin network. Here, using brightfield and fluorescence microscopy, high-speed particle tracking, and passive microrheology, we study the thermally driven stochastic movement of 0.5-5.0 μm tracer particles in 10% mucin solutions at neutral pH, and in 10% mucin mixed with industrially relevant dust; specifically, unmodified limestone rock dust, modified limestone, and crystalline silica. Particle trajectories are used to calculate mean square displacements and the displacement probability distributions; these are then used to assess tracer diffusion and transport. Complex moduli are concomitantly extracted using established microrheology techniques. We find that under the conditions analyzed, the reconstituted mucin behaves as a weak viscoelastic fluid rather than as a viscoelastic gel. For small- to moderately sized tracers with a diameter of lessthan 2 μm, we find that effective diffusion coefficients follow the classical Stokes-Einstein relationship. Tracer diffusivity in dust-laden mucin is surprisingly larger than in bare mucin. Probability distributions of mean squared displacements suggest that heterogeneity, transient trapping, and electrostatic interactions impact dispersion and overall transport, especially for larger tracers. Our results motivate further exploration of physiochemical and rheological mechanisms mediating particle transport in mucin solutions and gels.

Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology

The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.

Collective behavior of passive and active circle swimming particle mixtures

We present a numerical study on a binary mixture of passive and circle swimming, self-propelling particles which interact via the Lennard-Jones (LJ) potential in two dimensions. Using Brownian Dynamics (BD) simulations, we present state diagrams using the control parameters such as attraction strength, angular velocity, self-propulsion velocity and composition. In a symmetric mixture, the system undergoes a transition from a mixed gel to a rotating passive cluster state and finally to a homogeneous fluid state as translational activity increases. The formation of the rotating cluster of passive particles surrounded by active and passive monomers is attributed to the combined effect of composition, activity and strength of attraction of the active particles. Different phases are characterized using radial distribution functions, bond order parameters, cluster fraction and probability distribution of local volume fractions. The present study addresses comprehensively the intricate role of activity, angular velocity, inter-particle interaction and compositional variation on the phase behavior. The predictions presented in the study can be experimentally realized in synthetic colloidal swimmers and motile bacterial suspensions.

Topological defect-mediated morphodynamics of active-active interfaces

Physical interfaces widely exist in nature and engineering. Although the formation of passive interfaces is well elucidated, the physical principles governing active interfaces remain largely unknown. Here, we combine simulation, theory, and cell-based experiment to investigate the evolution of an active-active interface. We adopt a biphasic framework of active nematic liquid crystals. We find that long-lived topological defects mechanically energized by activity display unanticipated dynamics nearby the interface, where defects perform "U-turns" to keep away from the interface, push the interface to develop local fingers, or penetrate the interface to enter the opposite phase, driving interfacial morphogenesis and cross-interface defect transport. We identify that the emergent interfacial morphodynamics stems from the instability of the interface and is further driven by the activity-dependent defect-interface interactions. Experiments of interacting multicellular monolayers with extensile and contractile differences in cell activity have confirmed our predictions. These findings reveal a crucial role of topological defects in active-active interfaces during, for example, boundary formation and tissue competition that underlie organogenesis and clinically relevant disorders.

Equilibrium morphology of tactoids in elastically anisotropic nematics

We study two dimensional tactoids in nematic liquid crystals by using a Q-tensor representation. A bulk free energy of the Maier-Saupe form with eigenvalue constraints on Q, plus elastic terms up to cubic order in Q are used to understand the effects of anisotropic anchoring and Frank-Oseen elasticity on the morphology of nematic-isotropic domains. Further, a volume constraint is introduced to stabilize tactoids of any size at coexistence. We find that anisotropic anchoring results in differences in interface thickness depending on the relative orientation of the director at the interface, and that interfaces become biaxial for tangential alignment when anisotropy is introduced. For negative tactoids, surface defects induced by boundary topology become sharper with increasing elastic anisotropy. On the other hand, by parametrically studying their energy landscape, we find that surface defects do not represent the minimum energy configuration in positive tactoids. Instead, the interplay between Frank-Oseen elasticity in the bulk, and anisotropic anchoring yields semi-bipolar director configurations with non-circular interface morphology. Finally, we find that for growing tactoids the evolution of the director configuration is highly sensitive to the anisotropic term included in the free energy, and that minimum energy configurations may not be representative of kinetically obtained tactoids at long times.

Dispersion of activity at an active-passive nematic interface

Efficient nutrient mixing is crucial for the survival of bacterial colonies and other living systems known as active nematics. However, the dynamics of this mixing is non-trivial as there is a coupling between nutrients concentration and velocity field. To address this question, we solve the hydrodynamic equation for active nematics to model the bacterial swarms coupled to an advection-diffusion equation for the activity field, which is proportional to the concentration of nutrients. At the interface between active and passive nematics the activity field is transported by the interfacial flows and in turn it modifies them through the generation of active stresses. We find that the dispersion of this conserved activity field is subdiffusive due to the emergence of a barrier of negative defects at the active-passive interface, which hinders the propagation of the motile positive defects.

Dynamics of active liquid interfaces

Controlling interfaces of phase-separating fluid mixtures is key to the creation of diverse functional soft materials. Traditionally, this is accomplished with surface-modifying chemical agents. Using experiment and theory, we studied how mechanical activity shapes soft interfaces that separate an active and a passive fluid. Chaotic flows in the active fluid give rise to giant interfacial fluctuations and noninertial propagating active waves. At high activities, stresses disrupt interface continuity and drive droplet generation, producing an emulsion-like active state composed of finite-sized droplets. When in contact with a solid boundary, active interfaces exhibit nonequilibrium wetting transitions, in which the fluid climbs the wall against gravity. These results demonstrate the promise of mechanically driven interfaces for creating a new class of soft active matter.

Bacterial active matter

Bacteria are among the oldest and most abundant species on Earth. Bacteria successfully colonize diverse habitats and play a significant role in the oxygen, carbon, and nitrogen cycles. They also form human and animal microbiota and may become sources of pathogens and a cause of many infectious diseases. Suspensions of motile bacteria constitute one of the most studied examples of active matter: a broad class of non-equilibrium systems converting energy from the environment (e.g., chemical energy of the nutrient) into mechanical motion. Concentrated bacterial suspensions, often termed active fluids, exhibit complex collective behavior, such as large-scale turbulent-like motion (so-called bacterial turbulence) and swarming. The activity of bacteria also affects the effective viscosity and diffusivity of the suspension. This work reports on the progress in bacterial active matter from the physics viewpoint. It covers the key experimental results, provides a critical assessment of major theoretical approaches, and addresses the effects of visco-elasticity, liquid crystallinity, and external confinement on collective behavior in bacterial suspensions.

Spreading rates of bacterial colonies depend on substrate stiffness and permeability

The ability of bacteria to colonize and grow on different surfaces is an essential process for biofilm development. Here, we report the use of synthetic hydrogels with tunable stiffness and porosity to assess physical effects of the substrate on biofilm development. Using time-lapse microscopy to track the growth of expanding Serratia marcescens colonies, we find that biofilm colony growth can increase with increasing substrate stiffness, unlike what is found on traditional agar substrates. Using traction force microscopy-based techniques, we find that biofilms exert transient stresses correlated over length scales much larger than a single bacterium, and that the magnitude of these forces also increases with increasing substrate stiffness. Our results are consistent with a model of biofilm development in which the interplay between osmotic pressure arising from the biofilm and the poroelastic response of the underlying substrate controls biofilm growth and morphology.

Materials science and mechanosensitivity of living matter

Living systems are composed of molecules that are synthesized by cells that use energy sources within their surroundings to create fascinating materials that have mechanical properties optimized for their biological function. Their functionality is a ubiquitous aspect of our lives. We use wood to construct furniture, bacterial colonies to modify the texture of dairy products and other foods, intestines as violin strings, bladders in bagpipes, and so on. The mechanical properties of these biological materials differ from those of other simpler synthetic elastomers, glasses, and crystals. Reproducing their mechanical properties synthetically or from first principles is still often unattainable. The challenge is that biomaterials often exist far from equilibrium, either in a kinetically arrested state or in an energy consuming active state that is not yet possible to reproduce de novo. Also, the design principles that form biological materials often result in nonlinear responses of stress to strain, or force to displacement, and theoretical models to explain these nonlinear effects are in relatively early stages of development compared to the predictive models for rubberlike elastomers or metals. In this Review, we summarize some of the most common and striking mechanical features of biological materials and make comparisons among animal, plant, fungal, and bacterial systems. We also summarize some of the mechanisms by which living systems develop forces that shape biological matter and examine newly discovered mechanisms by which cells sense and respond to the forces they generate themselves, which are resisted by their environment, or that are exerted upon them by their environment. Within this framework, we discuss examples of how physical methods are being applied to cell biology and bioengineering.

Exploring order in active turbulence: Geometric rule and pairing order transition in confined bacterial vortices

Ordered collective motion emerges in a group of autonomously motile elements (known as active matter) as their density increases. Microswimmers, such as swimming bacteria, have been extensively studied in physics and biology. A dense suspension of bacteria forms seemingly chaotic turbulence in viscous fluids. Interestingly, this active turbulence driven by bacteria can form a hidden ensemble of many vortices. Understanding the active turbulence in a bacterial suspension can provide physical principles for pattern formation and insight into the instability underlying biological phenomena. This review presents recent findings regarding ordered structures causing active turbulence and discusses a physical approach for controlling active turbulence via geometric confinement. When the active matter is confined in a compartment with a size comparable to the correlation length of the collective motion, vortex-like rotation appears, and the vortex pairing order is indicated by the patterns of interacting vortices. Additionally, we outline the design principle for controlling collective motions via the geometric rule of the vortex pairing, which may advance engineering microdevices driven by a group of active matter. This article is an extended version of the Japanese article, Ordered Structure and Geometric Control of Active Matter in Dense Bacterial Suspensions, published in SEIBUTSU BUTSURI Vol. 60, p. 13–18 (2020).

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.

Morphologies and dynamics of the interfaces between active and passive phases

Active matters exhibit interesting collective behaviors and novel phases, which provide an important platform for the study of nonequilibrium physics. Mixtures of active and passive particles have been intensively studied in motility-induced phase separation, but the morphology of the active-passive interface has been poorly explored. In this work, we investigate the interface morphology in two-dimensional mixtures of active and passive particles using Brownian dynamics simulations. By systematically changing the Péclet number (Pe) and area fraction (ρ), we obtain the phase diagram of the active-passive interface, including rough sharp, rough invasive and flat interdiffusive interfaces. For a sharp interface, dynamic scaling analysis in the propagation stage shows that the roughness exponent α, the growth exponent β, the time exponent κ, and the dynamic exponent z satisfy z = α/(β - κ). Such anomalous scaling indicates that the roughening behavior does not belong to the conventional universality classes with Family-Vicsek scaling for the growth of passive interfaces. On the other hand, the interface in the middle-wavelength regime during the morphology relaxation stage can be described by capillary wave theory. The mean interface position propagates with time as t^1/2, which is robust at different ρ and Pe values in the propagation stage and exhibits superdiffusion in the morphology relaxation stage. These similarities and differences between the active-inactive interfaces and passive interfaces cast light on the interfacial growth of active matter.

Director alignment at the nematic-isotropic interface: elastic anisotropy and active anchoring

Activity in nematics drives interfacial flows that lead to preferential alignment that is tangential or planar for extensile systems (pushers) and perpendicular or homeotropic for contractile ones (pullers). This alignment is known as active anchoring and has been reported for a number of systems and described using active nematic hydrodynamic theories. The latter are based on the one-elastic constant approximation, i.e. they assume elastic isotropy of the underlying passive nematic. Real nematics, however, have different elastic constants, which lead to interfacial anchoring. In this paper, we consider elastic anisotropy in multiphase and multicomponent hydrodynamic models of active nematics and investigate the competition between the interfacial alignment driven by the elastic anisotropy of the passive nematic and the active anchoring. We start by considering systems with translational invariance to analyse the alignment at flat interfaces and, then, consider two-dimensional systems and active nematic droplets. We investigate the competition of the two types of anchoring over a wide range of the other parameters that characterize the system. The results of the simulations reveal that the active anchoring dominates except at very low activities, when the interfaces are static. In addition, we found that the elastic anisotropy does not affect the dynamics but changes the active length that becomes anisotropic. This article is part of the theme issue 'Progress in mesoscale methods for fluid dynamics simulation'.

Interparticle Adhesion Regulates the Surface Roughness of Growing Dense Three-Dimensional Active Particle Aggregates

Activity and self-generated motion are fundamental features observed in many living and nonliving systems. Given that interparticle adhesive forces can regulate particle dynamics, we investigate how interparticle adhesion strength controls the boundary growth and roughness of active particle aggregates. Using particle based simulations incorporating both activity (birth, death, and growth) and systematic physical interactions (elasticity and adhesion), we establish that interparticle adhesion strength (f^ad) controls the surface roughness of a densely packed three-dimensional(3D) active particle aggregate expanding into a highly viscous medium. We discover that the surface roughness of a 3D active particle aggregate increases in proportion to the interparticle adhesion strength (f^ad) and show that asymmetry in the radial and transverse active particle mean-squared displacement (MSD) suppresses 3D surface roughness at lower adhesion strengths. By analyzing the statistical properties of particle displacements at the aggregate periphery, we determine that the 3D surface roughness is driven by the movement of active particle toward the core at high interparticle adhesion strengths. Our results elucidate the physics controlling the expansion of adhesive 3D active particle collectives into a highly viscous medium, with implications into understanding stochastic interface growth in active matter systems characterized by self-generation of particles.

Cluster and conquer: the morphodynamics of invasion of a compliant substrate by active rods

The colonisation of a soft passive material by motile cells such as bacteria is common in biology. The resulting colonies of the invading cells are often observed to exhibit intricate patterns whose morphology and dynamics can depend on a number of factors, particularly the mechanical properties of the substrate and the motility of the individual cells. We use simulations of a minimal 2D model of self-propelled rods moving through a passive compliant medium consisting of particles that offer elastic resistance before being plastically displaced from their equilibrium positions. It is observed that the clustering of active (self-propelled) particles is crucial for understanding the morphodynamics of colonisation. Clustering enables motile colonies to spread faster than they would have as isolated particles. The colonisation rate depends non-monotonically on substrate stiffness with a distinct maximum at a non-zero value of substrate stiffness. This is observed to be due to a change in the morphology of clusters. Furrow networks created by the active particles have a fractal-like structure whose dimension varies systematically with substrate stiffness but is less sensitive to particle activity. The power-law growth exponent of the furrowed area is smaller than unity, suggesting that, to sustain such extensive furrow networks, colonies must regulate their overall growth rate.

Confinement discerns swarmers from planktonic bacteria

Powered by flagella, many bacterial species exhibit collective motion on a solid surface commonly known as swarming. As a natural example of active matter, swarming is also an essential biological phenotype associated with virulence, chemotaxis, and host pathogenesis. Physical changes like cell elongation and hyper-flagellation have been shown to accompany the swarming phenotype. Less studied, however, are the contrasts of collective motion between the swarming cells and their counterpart planktonic cells of comparable cell density. Here, we show that confining bacterial movement in circular microwells allows distinguishing bacterial swarming from collective swimming. On a soft agar plate, a novel bacterial strain Enterobacter sp. SM3 in swarming and planktonic states exhibited different motion patterns when confined to circular microwells of a specific range of sizes. When the confinement diameter was between 40 μm and 90 μm, swarming SM3 formed a single-swirl motion pattern in the microwells whereas planktonic SM3 formed multiple swirls. Similar differential behavior is observed across several other species of gram-negative bacteria. We also observed 'rafting behavior' of swarming bacteria upon dilution. We hypothesize that the rafting behavior might account for the motion pattern difference. We were able to predict these experimental features via numerical simulations where swarming cells are modeled with stronger cell-cell alignment interaction. Our experimental design using PDMS microchip disk arrays enabled us to observe bacterial swarming on murine intestinal surface, suggesting a new method for characterizing bacterial swarming under complex environments, such as in polymicrobial niches, and for in vivo swarming exploration.

Extensions of the worm-like-chain model to tethered active filaments under tension

Intracellular elastic filaments such as microtubules are subject to thermal Brownian noise and active noise generated by molecular motors that convert chemical energy into mechanical work. Similarly, polymers in living fluids such as bacterial suspensions and swarms suffer bending deformations as they interact with single bacteria or with cell clusters. Often, these filaments perform mechanical functions and interact with their networked environment through cross-links or have other similar constraints placed on them. Here, we examine the mechanical properties-under tension-of such constrained active filaments under canonical boundary conditions motivated by experiments. Fluctuations in the filament shape are a consequence of two types of random forces-thermal Brownian forces and activity derived forces with specified time and space correlation functions. We derive force-extension relationships and expressions for the mean square deflections for tethered filaments under various boundary conditions including hinged and clamped constraints. The expressions for hinged-hinged boundary conditions are reminiscent of the worm-like-chain model and feature effective bending moduli and mode-dependent non-thermodynamic effective temperatures controlled by the imposed force and by the activity. Our results provide methods to estimate the activity by measurements of the force-extension relation of the filaments or their mean square deflections, which can be routinely performed using optical traps, tethered particle experiments, or other single molecule techniques.

Morphological transitions of active Brownian particle aggregates on porous walls

Motility-induced wall aggregation of Active Brownian Particles (ABPs) is a well-studied phenomenon. Here, we study the aggregation of ABPs on porous walls, which allows the particles to penetrate through at large motility. We show that the active aggregates undergo a morphological transition from a connected dense-phase to disconnected droplets with an increase in wall porosity and the particle self-motility, similar to wetting-dewetting transitions in equilibrium fluids. We show that both morphologically distinct states are stable, and independent of initial conditions at least in some parameter regions. Our analysis reveals that changes in wall porosity affect the intrinsic properties of the aggregates and changes the effective wall-aggregate interfacial tension, consistent with the appearance of the morphological transition. Accordingly, a close analysis of the density, as well as orientational distribution, indicates that the underlying reason for such morphological transitions is not necessarily specific to the systems with porous walls, and it can be possible to observe in a larger class of confined, active systems by tuning the properties of confining walls.

Clustering and Phase Separation in Mixtures of Dipolar and Active Particles in an External Field

Directing the assembly of colloidal particles through the use of external electric or magnetic fields shows promise for the creation of reconfigurable materials. Self-propelled particles can also be used to dynamically drive colloidal systems to nonequilibrium steady states. We investigate colloidal systems that combine both of these methods of directed assembly, simulating mixtures of passive dipolar colloids and active soft spheres in an external magnetic field using Brownian dynamics in two dimensions. In these systems, the dipolar particles align in the direction of the external field, but the active particles are unaffected by the field. The phase behaviors exhibited included a percolated dipolar network, dipolar string-fluid, isotropic fluid, and phase-separated state. We find that the external field allows the dipolar particles to form a percolated network more easily compared to when no external field is present. Additionally, the mixture phase separates at lower active particle velocity in an external field than when no field is present. Our results suggest that combining multiple methods of directing colloidal assembly could lead to new pathways to fabricate reconfigurable materials.

Trapping flocking particles with asymmetric obstacles

Asymmetric obstacles can be exploited to direct the motion and induce sorting of run-and-tumble particles. In this work, we show that flocking particles which follow the Vicsek model aligning rules experience collective trapping in the presence of a wall of funnels made of chevrons, concentrating at the opposite side of the wall of funnels to run-and-tumble particles. Flocking particles can be completely trapped or exhibit a dynamical trapping behaviour; these two regimes open the door to the design of a system with two perpendicular flows of active particles. This systematic study broadens our understanding of the emergence of collective motion of microorganisms in confined environments and directs the design of new microfluidic devices able to control these collective behaviours.

Propagation of active nematic-isotropic interfaces on substrates

Motivated by results for the propagation of active-passive interfaces of bacterial Serratia marcescens swarms [Nat. Commun., 2018, 9, 5373], we used a hydrodynamic multiphase model to investigate the propagation of interfaces of active nematics on substrates. We characterized the active nematic phase of the model through the calculation of the spatial and temporal auto correlation functions and the energy spectrum and discussed its description of the statistical dynamics of the swarms reported in the experiment. We then studied the propagation of circular and flat active-passive interfaces. We found that the closing time of the circular passive domain decays quadratically with the activity and that the structure factor of the flat interface is similar to that reported for the swarms, with an activity dependent exponent. Finally, the effect of the substrate friction was investigated. We found an activity dependent threshold, above which the turbulent active nematic forms isolated islands that shrink until the system becomes isotropic and below which the active nematic expands, with a well defined propagating interface. We also found that the interface becomes static in the presence of a friction gradient.

Buckling instabilities and spatio-temporal dynamics of active elastic filaments

Biological filaments driven by molecular motors tend to experience tangential propulsive forces also known as active follower forces. When such a filament encounters an obstacle, it deforms, which reorients its follower forces and alters its entire motion. If the filament pushes a cargo, the friction on the cargo can be enough to deform the filament, thus affecting the transport properties of the cargo. Motivated by cytoskeletal filament motility assays, we study the dynamic buckling instabilities of a two-dimensional slender elastic filament driven through a dissipative medium by tangential propulsive forces in the presence of obstacles or cargo. We observe two distinct instabilities. When the filament's head is pinned or experiences significant translational but little rotational drag from its cargo, it buckles into a steadily rotating coiled state. When it is clamped or experiences both significant translational and rotational drag from its cargo, it buckles into a periodically beating, overall translating state. Using minimal analytically tractable models, linear stability theory and fully nonlinear computations, we study the onset of each buckling instability, characterize each buckled state, and map out the phase diagram of the system. Finally, we use particle-based Brownian dynamics simulations to show our main results are robust to moderate noise and steric repulsion. Overall, our results provide a unified framework to understand the dynamics of tangentially propelled filaments and filament-cargo assemblies.

Clustering and phase separation in mixtures of dipolar and active particles

The self-assembly of colloidal particles in dynamic environments has become an important field of study because of potential applications in fabricating out-of-equilibrium materials. We investigate the phase behavior of mixtures of passive dipolar colloids and active soft spheres using Brownian dynamics simulations in two dimensions. The phase behaviors exhibited include dipolar percolated network, dipolar string-fluid, isotropic fluid, and a phase-separated state. We find that the clustering of dipolar colloids is enhanced in the presence of slow-moving active particles compared to the clustering of dipolar particles mixed with passive particles. When the active particle motility is high, the chains of dipolar particles are either broken into short chains or pushed into dense clusters. Motility-induced phase separation into dense and dilute phases is also present. The area fraction of particles in the dilute phase increases as the fraction of active particles in the system decreases, while the area fraction of particles in the dense phase remains constant. Our findings are relevant to the development of reconfigurable self-assembled materials.

Active nematic-isotropic interfaces in channels

We use numerical simulations to investigate the hydrodynamic behavior of the interface between nematic (N) and isotropic (I) phases of a confined active liquid crystal. At low activities, a stable interface with constant shape and velocity is observed separating the two phases. For nematics in homeotropic channels, the velocity of the interface at the NI transition increases from zero (i) linearly with the activity for contractile systems and (ii) quadratically for extensile ones. Interestingly, the nematic phase expands for contractile systems while it contracts for extensile ones, as a result of the active forces at the interface. Since both activity and temperature affect the stability of the nematic, for active nematics in the stable regime the temperature can be tuned to observe static interfaces, providing an operational definition for the coexistence of active nematic and isotropic phases. At higher activities, beyond the stable regime, an interfacial instability is observed for extensile nematics. In this regime defects are nucleated at the interface and move away from it. The dynamics of these defects is regular and persists asymptotically for a finite range of activities. We used an improved hybrid model of finite differences and the lattice Boltzmann method with a multi-relaxation-time collision operator, the accuracy of which allowed us to characterize the dynamics of the distinct interfacial regimes.

Stability of the interface of an isotropic active fluid

We study the linear stability of an isotropic active fluid in three different geometries: a film of active fluid on a rigid substrate, a cylindrical thread of fluid, and a spherical fluid droplet. The active fluid is modeled by the hydrodynamic theory of an active nematic liquid crystal in the isotropic phase. In each geometry, we calculate the growth rate of sinusoidal modes of deformation of the interface. There are two distinct branches of growth rates; at long wavelength, one corresponds to the deformation of the interface, and one corresponds to the evolution of the liquid crystalline degrees of freedom. The passive cases of the film and the spherical droplet are always stable. For these geometries, a sufficiently large activity leads to instability. Activity also leads to propagating damped or growing modes. The passive cylindrical thread is unstable for perturbations with wavelength longer than the circumference. A sufficiently large activity can make any wavelength unstable, and again leads to propagating damped or growing modes. Our calculations are carried out for the case of zero Frank elasticity. While Frank elasticity is a stabilizing mechanism as it penalizes distortions of the order parameter tensor, we show that it has a small effect on the instabilities considered here.

Quenching active swarms: effects of light exposure on collective motility in swarming Serratia marcescens

Swarming colonies of the light-responsive bacteria Serratia marcescens grown on agar exhibit robust fluctuating large-scale flows that include arrayed vortices, jets and sinuous streamers. We study the immobilization and quenching of these collective flows when the moving swarm is exposed to intense wide-spectrum light with a substantial ultraviolet component. We map the emergent response of the swarm to light in terms of two parameters-light intensity and duration of exposure-and identify the conditions under which collective motility is impacted. For small exposure times and/or low intensities, we find collective motility to be negligibly affected. Increasing exposure times and/or intensity to higher values suppresses collective motility but only temporarily. Terminating exposure allows bacteria to recover and eventually reestablish collective flows similar to that seen in unexposed swarms. For long exposure times or at high intensities, exposed bacteria become paralysed and form aligned, jammed regions where macroscopic speeds reduce to zero. The effective size of the quenched region increases with time and saturates to approximately the extent of the illuminated region. Post-exposure, active bacteria dislodge immotile bacteria; initial dissolution rates are strongly dependent on duration of exposure. Based on our experimental observations, we propose a minimal Brownian dynamics model to examine the escape of exposed bacteria from the region of exposure. Our results complement studies on planktonic bacteria, inform models of patterning in gradated illumination and provide a starting point for the study of specific wavelengths on swarming bacteria.