The effect of crowding on the run-and-tumble dynamics of swimmers such as bacteria is studied using a discrete lattice model of mutually excluding particles that move with constant velocity along a direction that is randomized at a rate $α$. In stationary state, the system is found to break into dense clusters in which particles are trapped or stopped from moving. The characteristic size of these clusters predominantly scales as $α^{-0.5}$ both in 1D and 2D. For a range of densities, due to cooperative effects, the stopping time scales as ${\cal T}_{1d}^{0.85}$ and as ${\cal T}_{2d}^{0.8}$, where ${\cal T}_d$ is the diffusive time associated with the motion of cluster boundaries. Our findings might be helpful in understanding the early stages of biofilm formation.
The persistent character of the motion of active particles gives rise to accumulation at boundaries. I investigate the problem of run-and-tumble swimmers confined in a 1D box with hard walls, reporting expressions for the particles probability distribution and wall pressure. A crossover box length value is found below which the initial value of the pressure turns out to be higher than the asymptotic one, indicating a bounce effect of the active "wave" of swimmers. The case of attracting and repelling boundaries are also investigated using two different tumble rates for particles in the bulk an…
Suitable asymmetric microstructures can be used to control the direction of motion in microorganism populations. This rectification process makes it possible to accumulate swimmers in a region of space or to sort different swimmers. Here we study numerically how the separation process depends on the specific motility strategies of the microorganisms involved. Crucial properties such as the separation efficiency and the separation time for two bacterial strains are precisely defined and evaluated. In particular, the sorting of two bacterial populations inoculated in a box consisting of a series…
Micro-swimmers such as bacteria perform random walks known as run-and-tumbles to move up chemo-attractant gradients and as a result aggregate with others. It is also known that such micro-swimmers can self-organize into macroscopic patterns due to interactions with neighboring cells through the fluidic environment they live in. While the pattern formation resulting from chemotactic and hydrodynamic interactions separately and together have been previously investigated, the effect of the anisotropy in the tumbles of micro-swimmers has been unexplored. Here we show through linear analysis and fu…
Run-and-tumble dynamics is a wide-spread mechanism of swimming bacteria. The accumulation of run-and-tumble microswimmers near impermeable surfaces is studied theoretically and numerically in the low-density limit in two and three spatial dimensions. Both uni-modal and exponential distributions of the run lengths are considered. Constant run lengths lead to {peaks and depletions regions} in the density distribution of particles near the surface, in contrast to {exponentially-distributed run lengths}. Finally, we present a universal accumulation law for large channel widths, which applies not o…
In our article we present a computational model for the simulation of self-propelled anisotropic bacteria. To this end we use a self-propelled particle model and augment it with a statistical algorithm for the run-and-tumble motion. We derive an equation for the distribution of reorientations of the bacteria that we use to analyze the statistics of the random walk and that allows us to tune the behavior of our model to the characteristics of an E.coli bacterium. We validate our implementation in terms of a single swimmer and demonstrate that our model is capable of reproducing E.coli's run-and…
The run-and-tumble (RT) dynamics followed by bacterial swimmers gives rise first to a ballistic motion due to their persistence, and later, through consecutive tumbles, to a diffusive process. Here we investigate how long it takes for a dilute swimmer suspension to reach the diffusive regime as well as what is the amplitude of the deviations from the diffusive dynamics. A linear time dependence of the mean-squared displacement (MSD) is insufficient to characterize diffusion and thus we also focus on the excess kurtosis of the displacement distribution. Four swimming strategies are considered: …
We consider the tracer diffusion $D_{rr}$ that arises from the run-and-tumble motion of low Reynolds number swimmers, such as bacteria. In unbounded dilute suspensions, where the dipole swimmers move in uncorrelated runs of length $λ$, an exact solution showed that $D_{rr}$ is independent of $λ$. Here we verify this result in numerical simulations for a particular model swimmer, the spherical squirmer. We also note that in confined microenvironments, such as microscopic droplets, microfluidic devices and bacterial microzones in marine ecosystems, the size of the system can be comparable to $λ$…
The spatial and orientational distribution in a dilute active suspension of non-Brownian run-and-tumble spherical swimmers confined between two planar hard walls is calculated theoretically. Using a kinetic model based on coupled bulk/surface probability density functions, we demonstrate the existence of a concentration wall boundary layer with thickness scaling with the run length, the absence of polarization throughout the channel, and the presence of sharp discontinuities in the bulk orientation distribution in the neighborhood of orientations parallel to the wall in the near-wall region. O…
Magnetotactic swimmers tend to align along magnetic field lines against stochastic reorientations. We show that the swimming strategy, e.g. active Brownian motion versus run-and-tumble dynamics, strongly affects the orientation statistics. The latter can exhibit a velocity condensation whereby the alignment probability density diverges. As a consequence, we find that the swimming strategy affects the nature of the phase transition to collective motion, indicating that Lévy run-and-tumble walks can outperform active Brownian processes as strategies to trigger collective behavior.
Most classical work on the hydrodynamics of low-Reynolds-number swimming addresses deterministic locomotion in quiescent environments. Thermal fluctuations in fluids are known to lead to a Brownian loss of the swimming direction. As most cells or synthetic swimmers are immersed in external flows, we consider theoretically in this paper the stochastic dynamics of a model active particle (a self-propelled sphere) in a steady general linear flow. The stochasticity arises both from translational diffusion in physical space, and from a combination of rotary diffusion and run-and-tumble dynamics in …
It has been shown that a nanoliter chamber separated by a wall of asymmetric obstacles can lead to an inhomogeneous distribution of self-propelled microorganisms. Although it is well established that this rectification effect arises from the interaction between the swimmers and the non-centrosymmetric pillars, here we demonstrate numerically that its efficiency is strongly dependent on the detailed dynamics of the individual microorganism. In particular, for the case of run-and-tumble dynamics, the distribution of run lengths, the rotational diffusion and the partial preservation of run orient…
We consider the tracer diffusion $D_{rr}$ that arises from the run-and-tumble motion of low Reynolds number swimmers, such as bacteria. Assuming a dilute suspension, where the bacteria move in uncorrelated runs of length $λ$, we obtain an exact expression for $D_{rr}$ for dipolar swimmers in three dimensions, hence explaining the surprising result that this is independent of $λ$. We compare $D_{rr}$ to the contribution to tracer diffusion from entrainment.
Cooperation is vital for the survival of a swarm$^1$. Large scale cooperation allows murmuring starlings to outmaneuver preying falcons$^2$, shoaling sardines to outsmart sea lions$^3$, and homo sapiens to outlive their Pleistocene peers$^4$. On the micron-scale, bacterial colonies show excellent resilience thanks to the individuals' ability to cooperate even when densely packed, mitigating their internal flow pattern to mix nutrients, fence the immune system, and resist antibiotics$^{5-14}$. Production of an artificial swarm on the micro-scale faces a serious challenge $\frac{\;\;}{\;\;}$ whi…
We numerically examine run-and-tumble active matter particles in Casimir geometries composed of two finite parallel walls. We find that there is an attractive force between the two walls of a magnitude that increases with increasing run length. The attraction exhibits an unusual exponential dependence on the wall separation, and it arises due to a depletion of swimmers in the region between the walls by a combination of the motion of the particles along the walls and a geometric shadowing effect. This attraction is robust as long as the wall separation is comparable to or smaller than the swim…
Experiments have recently shown the feasibility of utilising bacteria as micro-scale robotic devices, with special attention paid to the development of bacteria-driven micro-swimmers taking advantage of built-in actuation and sensing mechanisms of cells. Here we propose a stochastic fluid dynamic model to describe analytically and computationally the dynamics of microscopic particles driven by the motion of surface-attached bacteria undergoing run-and-tumble motion. We compute analytical expressions for the rotational diffusion coefficient, the swimming speed and the effective diffusion coeffi…
The microalga Chlamydomonas Reinhardtii (CR) is used here as a model system to study the effect of complex environments on the swimming of micro-organisms. Its motion can be modelled by a run and tumble mechanism so that it describes a persistent random walk from which we can extract an effective diffusion coefficient for the large-time dynamics. In our experiments, the complex medium consists in a series of pillars that are designed in a regular lattice using soft lithography microfabrication. The cells are then introduced in the lattice, and their trajectories within the pillars are tracked …
Wavelet Monte Carlo dynamics simulations are used to study the dynamics of passive particles in the presence of microswimmers, taking account of the often-omitted thermal motion alongside the hydrodynamic flows generated by the swimmers. Although the Péclet numbers considered are large, we find the thermal motion to have a significant effect on the dynamics of our passive particles, and can be included as a decorrelation factor in the velocity autocorrelation with a decay time proportional to the Péclet number. Similar decorrelation factors come from swimmer rotations, e.g.~run and tumble moti…
Even though making artificial micrometric swimmers has been made possible by using various propulsion mechanisms, guiding their motion in the presence of thermal fluctuations still remains a great challenge. Such a task is essential in biological systems, which present a number of intriguing solutions that are robust against noisy environmental conditions as well as variability in individual genetic makeup. Using synthetic Janus particles driven by an electric field, we present a feedback-based particle guiding method, quite analogous to the "run-and-tumbling" behavior of Escherichia coli but …
We present a novel approach for characterizing the properties and performance of active matter in dilute suspension as well as in crowded environments. We use Super-Heterodyne Laser-Doppler-Velocimetry (SH-LDV) to study large ensembles of catalytically active Janus particles moving under UV-illumination. SH-LDV facilitates a model-free determination of the swimming speed and direction, with excellent ensemble averaging. In addition we obtain in-formation on the distribution of the catalytic activity. Moreover, SH-LDV operates away from walls and permits a facile correction for multiple scatter…
Self-propelled swimmers such as bacteria agglomerate into clusters as a result of their persistent motion. In 1D, those clusters do not coalesce macroscopically and the stationary cluster size distribution (CSD) takes an exponential form. We develop a minimal lattice model for active particles in narrow channels to study how clustering is affected by the interplay between self-propulsion speed diversity and confinement. A mixture of run-and-tumble particles with a distribution of self-propulsion speeds is simulated in 1D. Particles can swap positions at rates proportional to their relative sel…
