Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session F05: Active Matter in Complex EnvironmentsFocus Live
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Sponsoring Units: DSOFT DBIO GSNP DFD Chair: Sujit Datta, Princeton University; Tapomoy Bhattacharjee, Princeton University Room: 05 |
Tuesday, March 16, 2021 11:30AM - 12:06PM Live |
F05.00001: Clogging Dynamics of Active and Passive Disks in Complex Environments Invited Speaker: Cynthia Reichhardt Directional locking occurs when a particle moving over a periodic substrate can travel only along certain substrate symmetry directions. We study the directional locking and clogging of passive disks and active run-and-tumble particles interacting with a periodic array of obstacles. In the absence of an external biasing force, the active particle motion locks to various symmetry directions of the substrate when the run time between tumbles is large. The number of possible locking directions depends on the array density and the relative size of the obstacles. For large obstacles under biased driving, a trapping behavior occurs that is non-monotonic as a function of increasing run length or increasing self-propulsion force, and the trapping diminishes when the run length is sufficiently large. Passive disks exhibit a drive-direction-dependent clogging behavior when the disk density is sufficiently large. The clogged states are fragile and can be unclogged by changing the driving angle. For large obstacle sizes, we find a uniform clogged state that is distinct from the collective clogging regime. Within the clogged phases, depinning transitions can occur as a function of increasing driving force, with strongly intermittent motion appearing just above the depinning threshold. |
Tuesday, March 16, 2021 12:06PM - 12:18PM Live |
F05.00002: Breakdown of Ergodicity and Self-Averaging in Polar Flocks with Quenched Disorder Yu Duan, Benoît Mahault, Xiaqing Shi, Hugues Chate We show that quenched disorder affects polar active matter in ways more complex and far-reaching than believed heretofore. Using simulations of the 2D Vicsek model subjected to random couplings or a disordered scattering field, we find in particular that ergodicity is lost in the ordered phase, the nature of which we show to depend qualitatively on the type of quenched disorder: for random couplings, it remains long-range order as in the pure case. For random scatterers, polar order varies with system size but we find strong non-self-averaging, with sample-to-sample fluctuations dominating asymptotically, which prevents us from elucidating the asymptotic status of order. |
Tuesday, March 16, 2021 12:18PM - 12:30PM Live |
F05.00003: Life in a tight spot: How bacteria move in porous media Tapomoy Bhattacharjee, Daniel Amchin, Jenna Ott, Felix Sebastian Kratz, Sujit Datta Diverse processes in healthcare, agriculture, and the environment rely on bacterial motility in heterogeneous porous media; indeed, most bacterial habitats—e.g. biological gels, tissues, soils, and sediments—are porous media. However, while bacterial motility is well-studied in homogeneous environments, how confinement in a porous environment impacts bacterial transport remains poorly understood. To address this gap in knowledge, we combine microscopy, materials fabrication, and microbiology to investigate how E. coli moves in 3D porous media. By probing single cells, we demonstrate that the paradigm of run-and-tumble motility is dramatically altered by pore-scale confinement. Instead, we find a new mode of motility in which cells are intermittently and transiently trapped as they navigate the pore space; analysis of these dynamics enables prediction of bacterial transport over large length and time scales. Further, by developing a new 3D printing approach, we design multi-cellular communities with precise control over the spatial distribution of bacteria. Using this approach, we show that concentrated populations can collectively migrate through a porous medium—despite being strongly confined—and develop principles to predict and direct this behavior. |
Tuesday, March 16, 2021 12:30PM - 12:42PM Live |
F05.00004: Chemotaxis strategies of bacteria with multiple run modes in complex environments Zahra Alirezaeizanjani, Robert Großmann, Veronika Pfeifer, Marius Hintsche, Carsten Beta Elucidating the principles of bacterial motility and navigation is key to understand many important phenomena such as the spreading of infectious diseases. One of the prime challenges of swimming bacteria is to purposefully navigate to find food or flee from poisons in their natural habitat, e.g. the soil, which constitutes a complex, structured environment. Many bacterial species were recently reported to exhibit several distinct swimming modes—the flagella may, for example, push the cell body or wrap around it [1]. How do the different run modes shape the chemotaxis strategy of a multimode swimmer in complex environments? Here, we discuss the chemotactic motion of the bacterium Pseudomonas putida as a model organism [2]. By simultaneously tracking the position of the cell body and the configuration of its flagella, we demonstrate that individual run modes show different chemotactic responses in nutrition gradients and, thus, constitute distinct behavioral states. On the basis of an active particle model, we demonstrate that switching between multiple run states that differ in their speed and responsiveness provides the basis for robust and efficient chemotaxis in complex natural habitats. |
Tuesday, March 16, 2021 12:42PM - 12:54PM Live |
F05.00005: Chemotaxis of cargo-carrying self-propelled particles Hidde Vuijk, Holger Merlitz, Michael Lang, Abhinav Sharma, Jens-Uwe Sommer Active particles with their characteristic feature of self-propulsion are regarded as the simplest models for motility in living systems. The accumulation of active particles in low activity regions has led to the general belief that chemotaxis requires additional features and at least a minimal ability to process information and to control motion. We show that self-propelled particles display chemotaxis and move into regions of higher activity, if the particles perform work on passive objects, or cargo, to which they are bound. The origin of this cooperative chemotaxis is the exploration of the activity gradient by the active particle when bound to a load. We theoretically capture the most relevant features of these active-passive dimers, and predict the crossover between anti-chemotactic and chemotactic behaviour. Moreover we show that connecting active particles in chains is sufficient to obtain the crossover from anti-chemotaxis to chemotaxis with increasing chain length. The observed transition is of significance to proto-forms of life enabling them to locate a source of nutrients even in the absence of any supporting sensomotoric apparatus. |
Tuesday, March 16, 2021 12:54PM - 1:06PM Live |
F05.00006: Active Matter Commensuration and Frustration Effects on Periodic Substrates Charles Reichhardt, Cynthia Reichhardt We show that self-driven particles coupled to a periodic obstacle array exhibit novel active matter commensuration effects that are absent in the Brownian limit. As the obstacle size is varied for sufficiently large activity, a series of commensuration effects appear in which the motility induced phase separation produces commensurate crystalline states, while for other obstacle sizes we find frustrated or amorphous states. The commensuration effects are associated with peaks in the amount of six-fold ordering and the maximum cluster size. When a drift force is added to the system, the mobility contains peaks and dips similar to those found in transport studies for commensuration effects in superconducting vortices and colloidal particles. |
Tuesday, March 16, 2021 1:06PM - 1:18PM Live |
F05.00007: Trapping in porous microstructure suppresses magnetotactic bacterial transport Amin Dehkharghani, Nicolas Waisbord, Jeffrey S Guasto Swimming magnetotactic bacteria thrive in porous sediments of marine environments, which they navigate by orienting relative to Earth’s magnetic field. While their motility is well-studied in bulk media, the physical mechanisms regulating magnetotactic bacterial motility in porous environments are not clear. Using microfluidic experiments complemented by Langevin simulations, we investigate the effect of porous microstructure and the role of disorder in dictating cell transport. Cell-surface scattering from solid boundaries provides an effective cell reorientation mechanism that yields diffusive, random walks in the absence of a magnetic field for both ordered and disordered media. In the presence of a strong magnetic field, cell alignment leads to ballistic transport and enhanced cell propagation in an ordered lattice of obstacles. However, trapping in concave pore geometries significantly hinders their mobility in disordered media. Combined with the known weak cell alignment to Earth’s ambient magnetic field, our findings suggest that cell-surface scattering may provide an escape mechanism to help avoid trapping, while still facilitating cell dispersal in naturally disordered porous geometries. |
Tuesday, March 16, 2021 1:18PM - 1:30PM Live |
F05.00008: Enhanced bacterial motility in colloidal media Shashank Kamdar, Seunghwan Shin, Youngjun Kim, Lorraine F. Francis, Xiang Cheng Understanding the locomotion of microorganisms in complex fluids is crucial for gaining insights into their behaviors in natural habitats. Here, we investigate the motility of E. coli, a flagellated bacterium, in colloidal media. We systematically vary the size of colloidal particles in the mixture from 20 nm to 1 μm and the volume fraction up to 20%. We image the motion of fluorescent bacteria using confocal microscopy and characterize the speed and wobble angle of bacteria. A substantial increase in bacterial speeds (up to 81%) is observed as the colloid volume fraction increases to 3%, followed by a decrease at higher volume fractions. The speed enhancement coincides with a decrease in bacteria’s wobble angle. Larger sized particles lead to higher speeds and smaller wobble angles. We reveal the microscopic origin of the speed enhancement via optical trapping of a colloidal particle and demonstrate the important role of discrete flagella-particle interactions. This work highlights the unusual swimming behavior of microorganisms in colloidal media and provides a unifying picture for understanding the effect of discrete interactions on bacterial locomotion in various complex fluids. |
Tuesday, March 16, 2021 1:30PM - 1:42PM Live |
F05.00009: Emergence of collective states in suspensions of swimming bacteria in confined geometries Dipanjan Ghosh, Xiang Cheng Geometric confinement is known to alter the swimming behavior of individual microswimmers as well as the interactions between them. This is relevant in biological systems such as swimming of bacteria in pores of soil and of spermatozoa in the confines of the cervical canal. To understand how confinement affects the collective behavior of microswimmers, we conduct experiments with suspensions of genetically modified Escherichia coli with tunable swimming velocity, in Hele-Shaw cells with a gap thickness of 7 microns. Imaging these suspensions using bright-field microscopy, we observe the emergence of three distinct collective states, dependent on the density of bacteria and their swimming velocity: a disordered state, a state characterized by lanes with long-ranged orientational nematic order, and a state of swarming clusters with short-ranged polar order. Using kinetic theory, we investigate the role of binary collisions in bringing about a transition from the disordered state to the orientationally ordered state. Thus, our experiments demonstrate how geometric confinement can give rise to novel collective states of microswimmers and help us understand the nature of interactions that are responsible for the emergence of these states. |
Tuesday, March 16, 2021 1:42PM - 1:54PM Live |
F05.00010: Attractors in disordered active matter and using disorder to control active matter Fernando Peruani First, we will discuss old [*] and new theoretical results that show the existence of multiple attractors in disordered active matter for flocks flying through the same realization of quenched disorder, meaning that the fate and history of the flock are strongly dependent on the initial condition. Second, we will discuss how the disorder can be used to control active matter. |
Tuesday, March 16, 2021 1:54PM - 2:06PM Live |
F05.00011: Separating Motile and Immotile Bacteria through Confined Chemotaxis SHANG-HUAN CHIU, Francesca Zumpano, Enkeleida Lushi The majority of bacteria move in complex porous materials such as tissues or soil, yet their motion and chemotaxis in confinement is not yet completely understood. We will present a model that couples individual run-and-tumble bacterial motion to the chemical gradient while the entire colony is inside a circular confinement. We will discuss the states observed for various parameters, and also the phase separation in an initially random mixture of motile and immotile bacteria. |
Tuesday, March 16, 2021 2:06PM - 2:18PM Live |
F05.00012: Aligning self-propelling particles in confinement Enkeleida Lushi, Katherine Wall, Nathaniel Netznik, Shang-Huan Chiu We present a model for self-propelling aligning particles and look at the collective motion for such swimmers in non-trivial confined domains. We discuss the complex behavior in circular convex domains and racetracks for a variety of densities, confinement sizes and alignment distances. Phase diagrams for different geometries summarize the behavior and give insight into the dynamics. Lastly, we compare the results to experiments in active matter systems such as motile colloids, swimming bacteria or larva fish, and note the qualitative similarities and differences. |
Tuesday, March 16, 2021 2:18PM - 2:30PM On Demand |
F05.00013: Bacterial motion and spread in porous media Yasser Almoteri, Enkeleida Lushi We will present a continuum model that describes the collective dynamics of micro-swimmers such as bacteria through a porous wet material. The motion of the swimmer suspension is coupled to the fluid dynamics that is modeled through a Stokes-Brinkman equation with an added active stress. The linear stability of the uniform isotropic state reveals that the suspension transitions from a long-wave instability to a mid-range one where the collective bacterial chaotic motion is weakened. Simulations of the full nonlinear system confirm the analytical results. We discuss the spread of an initial accumulation of bacteria and show the speed of the resulting waves depends non-trivially on the medium porosity. Lastly, we will discuss the dynamics of a bacterial suspension through a structured surface. |
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