Groups of interacting active particles, insects, or humans can form clusters that hinder the goals of the collective; therefore, development of robust strategies for control of such clogs is essential, particularly in confined environments. Our biological and robophysical excavation experiments, supported by computational and theoretical models, reveal that digging performance can be robustly optimized within the constraints of narrow tunnels by individual idleness and retreating. Tools from the study of dense particulate ensembles elucidate how idleness reduces the frequency of flow-stopping clogs and how selective retreating reduces cluster dissolution time for the rare clusters that still occur. Our results point to strategies by which dense active matter and swarms can become task capable without sophisticated sensing, planning, and global control of the collective.

Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kinesin-8 motors affect the length of dynamic microtubules in cells is less clear. We study the more biologically realistic problem of microtubule dynamic instability modulated by a motor-dependent increase in the filament catastrophe frequency. This leads to a significant decrease in the mean filament length and a narrowing of the filament length distribution. The results improve our understanding of the biophysics of length regulation in cells.

Nonequilibrium active matter made up of self-driven particles with short-range repulsive interactions is a useful minimal system to study active matter as the system exhibits collective motion and nonequilibrium order-disorder transitions. We studied high-aspect-ratio self-propelled rods over a wide range of packing fractions and driving to determine the nonequilibrium state diagram and dynamic properties. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state, the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluidlike behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition that, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped micro-organisms.

Biopolymers serve as one-dimensional tracks on which motor proteins move to perform their biological roles. Motor protein phenomena have inspired theoretical models of one-dimensional transport, crowding, and jamming. Experiments studying the motion of Xklp1 motors on reconstituted antiparallel microtubule overlaps demonstrated that motors recruited to the overlap walk toward the plus end of individual microtubules and frequently switch between filaments. We study a model of this system that couples the totally asymmetric simple exclusion process for motor motion with switches between antiparallel filaments and binding kinetics. We determine steady-state motor density profiles for fixed-length overlaps using exact and approximate solutions of the continuum differential equations and compare to kinetic Monte Carlo simulations. Overlap motor density profiles and motor trajectories resemble experimental measurements. The phase diagram of the model is similar to the single-filament case for low switching rate, while for high switching rate we find a new (to our knowledge) low density-high density-low density-high density phase. The overlap center region, far from the overlap ends, has a constant motor density as one would naïvely expect. However, rather than following a simple binding equilibrium, the center motor density depends on total overlap length, motor speed, and motor switching rate. The size of the crowded boundary layer near the overlap ends is also dependent on the overlap length and switching rate in addition to the motor speed and bulk concentration. The antiparallel microtubule overlap geometry may offer a previously unrecognized mechanism for biological regulation of protein concentration and consequent activity.

Dense cellular aggregates are common in many biological settings, ranging from bacterial biofilms to organoids, cell spheroids and tumors. Motivated by Neisseria gonorrhoeae biofilms as a model system, we present a hydrodynamic theory to study dense, active, viscoelastic cellular aggregates.The dynamics of these aggregates, driven by forces generated by individual cells, is intrinsically out-of-equilibrium. Starting from the force balance at the level of individual cells, we arrive at the dynamic equations for the macroscopic cell number density via a systematic coarse-graining procedure taking into account a nematic tensor of intracellular force dipoles. We describe the basic process of aggregate formation as an active phase separation phenomenon. Our theory furthermore captures how two cellular aggregates coalesce. Merging of aggregates is a complex process exhibiting several time scales and heterogeneous cell behaviors as observed in experiments.In our theory, it emerges as a coalescence of active viscoelastic droplets where the key timescales are linked to the turnover of the active force generation. Our theory provides a general framework to study the rheology and dynamics of dense cellular aggregates out of thermal equilibrium. * vasily.zaburdaev@fau.de