Session A29: Active Matter in Complex Environments I

Clogging and Depinning of Active Matter Systems in Disordered Media

We numerically examine the transport of active run-and-tumble particles with steric particle-particle interactions driven with a drift force over random disordered landscapes comprised of fixed obstacles. For increasing run lengths, the net particle transport initially increases before reaching a maximum and decreasing at larger run lengths. The transport reduction is associated with the formation of cluster states that become locally jammed or clogged by the obstacles. We also find that the system dynamically jams at lower particle densities when the run length is increased. Our results indicate that there is an optimal activity level for transport of run-and-tumble type active matter through quenched disorder, and could be important for understanding biological transport in complex environments or for applications of active matter particles in random media.   

Flocking through disorder

We address the robustness of flocking motion to challenging environments.
The emergence of collective motion in groups of motile bodies arises from the competition between rotational diffusion and polar interactions in ensemble of active particles.This minimal picture was successfully employed to account for the large scale dynamics of systems as diverse as starling flocks and self-propelled colloids.
Building on model experiments based on Quincke rollers, I will show how colloidal flocks lose their orientational order when cruising through disordered lattices. I will present a series of quantitative experiments that elucidate the existence of a novel state of active matter that supports orientational order (through a sparse rivers network) but no net transport. In particular, I will show that this state can be seen as a glass of topological defects.
  

Enhanced bacterial motility in colloidal media

The study of the locomotion of biological and artificial microswimmers in Newtonian and non-Newtonian fluids is gaining rapid momentum with applications in many areas such as pathogenicity, bioremediation, and drug delivery. Here, we experimentally investigate the motility of Escherichia coli, a flagellated bacterium, in colloidal media. We systematically vary the size of passive colloidal particles in the mixture from 20 nm to 1 μm and the volume fraction up to 20%. Using confocal microscopy, we image the motion of fluorescent-labeled bacteria and implement an in-house tracking algorithm to obtain the speeds of bacteria. We observe a substantial increase in bacterial speeds (up to 74%) as the colloid volume fraction increases to 3%, followed by a decrease at higher volume fractions. Additionally, we find that increasing the size of colloidal particles results in larger speed enhancement. We construct a model that qualitatively explains our experiments. Our study highlights the unusual locomotion of swimming microorganisms in colloidal suspensions and illustrates the rich dynamics that arises from swimmers’ interactions with their environment.   

Theoretical Framework to Describe Traveling Waves of Bacteria in Porous Media

How bacteria move in porous media like tissues and soil underlies processes like infection and bioremediation. However, existing models of how bacteria coordinate their motion at the population scale cannot fully explain collective migration inside porous media. To address this gap in knowledge, we use confocal microscopy to directly track bacteria deep inside transparent porous media. Similar to the case of free liquid, we find that the cells move together in directed, traveling waves following self-generated nutrient gradients. However, unlike the case of free liquid, the wave speed and shape are also regulated by the structure of the porous medium itself. By analyzing the single cell tracks, we characterize how biased “hopping and trapping” of the individual cells generates traveling waves; surprisingly, in stark contrast to the case of chemotaxis in free liquid, we find that hop length bias is not the dominant contributor to this mode of collective migration. Further, we show how the statistical features of single cell motion can be used to develop a continuum model that can describe collective migration in a porous medium over large length and time scales. Together, our work provides new principles to predict and possibly control bacterial migration in complex environments.   

The role of diversity for collective bacterial migration through diverse environments

Chemotactic bacteria form expanding wave fronts that allow populations to achieve directed expansion towards new territory (Adler J. Science 1966), which can enhance total population growth. But even isogenic populations exhibit phenotypic heterogeneity in their chemotactic properties, and it has been unclear how this affects their directed expansion with growth. We recently showed that diverse cells can travel together in the expanding front by sorting themselves by chemotactic ability, which compensates for their differences by matching ability to the local chemotactic signal (Fu, Kato et al. Nature Communications 2018). However, this places the lowest-performing cells at the back of the wave and at highest risk of falling behind. Here, through a combination of simulations and theory, we demonstrate the conditions in which diversity is valuable (or not) for collectively-migrating populations that grow and encounter varying environments during travel.
  

Light-Sensing Microbes in Complex Geometries: Surface Adhesion, Gliding Motility and Self-Organization

Life on Earth has evolved under the exposure of sunlight and many microbes are equipped with photoreceptors enabling them to perceive light. The microhabitats of such light-sensing microbes include liquid-infused soil, porous rocks and microdroplets, featuring complex geometric architectures that induce strong spatial and temporal fluctuations of light exposure. In these confined environments the cells frequently encounter and interact with interfaces. We discovered that Chlamydomonas reinhardtii, a soil-dwelling photoactive microorganism and biological model system, can reversibly switch its adhesion to surfaces on and off by light (Kreis et al., Nature Physics, 2018). The adhesiveness is regulated by a blue-light photoreceptor and mediated by their two flagella. Once they are attached to a surface, gliding motility sets in and enables the microbes to maneuver on the surface. Based on cell tracking and statistical analysis, we study the surface adsorption and gliding motility of light-sensing microbes and demonstrate how surface gliding, in conjunction with cell-cell interactions, may control the emergence of microbial self-organization in confinement.   

Active Brownian filaments: deviations from blob scaling theory and dynamics inside cavities

Active filaments have become the subject of intense scrutiny in recent years because of their biological implications, and their role as a minimal model where the competition between thermal, elastic and active forces can be systematically studied.

Scaling arguments used to predict the radius of gyration of passive self-avoiding flexible polymers have been shown to hold even under the influence of active fluctuations. Via a numerical study we establish how the standard blob scaling theory representations of a polymer breaks down when dealing with active polymers under confinement. We find that the predicted exponents hold only whenever the persistence length generated on the polymer by the active forces is much smaller than the size of the characteristic blob in the scaling theory. Further, when the activity is directed along the backbone of a semi-flexible filament, while confined in a spherical cavity, a highly dynamic scenario emerges. The filament is capable of escaping local and global energy minima and sample, in a quasi-periodic fashion, an ensemble of conformations usually associated to higher bending energies, and previously observed for passive filaments only under very different degrees of confinement or identified as glassy metastable states.   

Fitness of cell colonies to navigate obstacles

We confront confluent epithelial cells with the need to adapt from wide-channel to narrow-channel growth. Upconversion from single cell, the colony self-organizes to facilitate migration with greater efficiency than that would be accomplished by fluid hydrodynamics. This is traced to long-range mechanical signaling. Stretched leader cells trigger acceleration of the whole group; the resulting velocity difference, in turn, reinforces stretching of the leaders and establishes positive feedback between cell morphology and mechanical strength, as we confirm by direct visualization of F-actin expression, cadherin localization, and the shapes of cells and their nuclei. The relevance is to show how mechanical signaling promotes a 'smart' group navigation strategy in which adaptations of individual cells to the local environment propagate over long distances to benefit the whole colony.   

Anomalous size-dependence of bacterial diffusion in a micropillar array

Microorganisms are endowed with phenotypic variations, including diversities in sizes within the same species, which are crucial to their adaptation to living habitats. Here, we investigate how such size variations affect the transport of bacteria in a structured medium, using an array of microscale pillars and a smooth-swimming mutant of Escherichia coli. In contrast to the common belief that a smaller object can navigate solid obstacles more efficiently, we find that the long-time diffusion of individual E. coli actually decreases with decreasing cell size. By varying the pillar geometries, we determine that such anomalous diffusion is governed by the cell size relative to the pillar curvature: cells with smaller sizes relative to the pillar radius are more easily attracted to the pillar surface and are thus effectively “trapped.” We show that such an attractiveness can be well characterized by a size-dependent residency time that the bacterium spends near the pillar surfaces. We develop an agent-based model that purely relies on the geometry of the micropillars, bacteria and residency time. The numerical model agrees reasonably well with our experimental observations, suggesting that solid structures can affect bacterial transport by purely geometric mechanisms.   

Colloidal random-walkers for probing anomalous diffusion in heterogeneous micro-environments

The natural habitat of many microorganisms is not a simple homogeneous environment. A ubiquitous observation is that diffusion becomes anomalous with nonlinear scaling between mean-squared displacement and time. A major challenge in biological sciences and condensed matter physics is to uncover these links to gain insight paramount for design of efficient filter membranes, medical diagnostics and drug delivery, and micro-robots operated in heterogeneous environments.
Building on our recently developed tunable colloidal random walker, we combine microfluidics experiments with theory to characterize and quantify the degree of anomalous diffusion. We define high-order measurable microstructural descriptors which carry information on connectivity and clustering of the designed obstacles that offer a convenient platform to test the theoretical predictions. Results reveal a complex nature of interactions between the colloidal random walker and obstacles which goes beyond a simple correlation between the diffusive behavior and obstacle volume fraction. Using scaling analysis, we provide new quantitative measures for predicting how anomalous diffusion emerges in a heterogeneous micro-environment with known morphological information.   

Transport properties of circle microswimmers in heterogeneous media

Microswimmers are exposed in nature to crowded media and their transport properties depend in a subtle way on the interaction with obstacles. Here, we investigate a model for a single circle swimmer exploring a two-dimensional disordered array of impenetrable obstacles. The microswimmer follows the surface of an obstacle for a certain time upon collision. An ideal microswimmer [1] can display long-range transport or be localized in a finite region depending on the obstacle density and the radius of circular orbits. Close to the transition lines from two localized states to a diffusive state the transport becomes subdiffusive, which is rationalized as a dynamic critical phenomenon. We determine the non-equilibrium state diagram and evaluate the diffusivities. For the microswimmer subjected to angular noise [2] increasing the noise tends to amplify diffusion, yet large randomness leads to a strong suppression of transport. We rationalize the suppression and amplification of transport by comparing the relevant time scales of the free motion to the mean-free path time between collisions with obstacles.

1. O. Chepizhko, T. Franosch, Soft Matter, 2019, 15, 452
2. O. Chepizhko, T. Franosch, submitted   

Escape of a Nanoparticle from Cavities in a Porous Matrix

Translocation from one cavity to another through a narrow constriction (i.e. a “hole”) represents the fundamental elementary process underlying hindered mass transport of nanoparticles and macromolecules within many natural and synthetic porous materials, including intracellular environments. This process is complex, and may be influenced by long-range (e.g. electrostatic) particle-wall interactions, transient adsorption/desorption, surface diffusion, and hydrodynamic effects. Here, we used a three-dimensional (3D) tracking method to explicitly visualize the process of passive Brownian nanoparticle and self-propelled Janus particle diffusion within periodic porous nanostructures. Specifically, we quantified the spatial dependence of particle motion and the residence times of individual particles in the interconnected confined cavities, allowing us to test hypotheses regarding the effects of self-propulsion on mass transport in confined porous environments.