arXiv subjects

Jochen Arlt

Publications and source records attributed to Jochen Arlt.

15 recordsLinked to original sources

arXiv2025

Bacteria collective motion is scale-free

Suspensions of swimming bacteria interact hydrodynamically over long ranges, organizing themselves into collective states that drive large-scale chaotic flows, often referred to as "bacterial turbulence". Despite extensive experimental and theoretical work, it remains unclear whether an intrinsic length scale underlies the observed patterns. To shed light on the mechanism driving active turbulence, we investigate the emergence of large-scale flows in E. coli suspensions confined within cylindrical chambers, systematically varying confinement height over more than two orders of magnitude. We first demonstrate that the critical density for the onset of collective motion scales inversely with this confinement height without saturation, even for the smallest densities observed. Near the onset, both the observed length and time scales increase sharply, with the length scale bounded only by the vertical confinement. Importantly, both scales exhibit clear power-law dependence on the confinement height, demonstrating the absence of an intrinsic length scale in bacterial collective motion. This holds up to scales nearly 10,000 times the size of a single bacterium, as evidenced by transient coherent vortices spanning the full chamber width near the onset. Our experimental results demonstrating that bacterial turbulence is scale-free provide important constraints for theories aiming to capture the dynamics of wet active matter.

cond-mat.soft↗

arXiv2025

Self-diffusion in isotropic and liquid crystalline phases of fd virus colloidal rods: a combined single particle tracking and differential dynamic microscopy study

In this article, we investigate the dynamics of self-organised suspensions formed by rod-like fd virus colloids. Two methods have been employed for analysing fluorescence microscopy movies: single particle tracking (SPT) in direct space and differential dynamic microscopy (DDM) in reciprocal space. We perform a quantitative analysis on this anisotropic system with complex diffusion across different self-assembled states, ranging from dilute and semi-dilute liquids to nematic and smectic organisations. By leveraging the complementary strengths of SPT and DDM, we provide new insights in the dynamics of viral colloidal rods, such as long time diffusion coefficients in the smectic phase. We further discuss the advantages and limitations of both methods for studying the intricate dynamics of anisotropic colloidal systems.

cond-mat.soft↗

arXiv2023

Sizing multimodal suspensions with differential dynamic microscopy

Differential dynamic microscopy (DDM) can be used to extract mean particle size from videos of suspensions. However, many suspensions have multimodal particle size distributions (PSDs), for which this is not a sufficient description. After clarifying how different particle sizes contribute to the signal in DDM, we show that standard DDM analysis can extract the mean sizes of two populations in a bimodal suspension given prior knowledge of the sample's bimodality. Further, the use of the CONTIN algorithm obviates the need for such prior knowledge. Finally, we show that by selectively analysing portions of the DDM images, we can size a trimodal suspension where the large particles would otherwise dominate the signal, again without prior knowledge of the trimodality.

cond-mat.soft↗

arXiv2022

Quantitative characterization of run-and-tumble statistics in bulk bacterial suspensions

We introduce a numerical method to extract the parameters of run-and-tumble dynamics from experimental measurements of the intermediate scattering function. We show that proceeding in Laplace space is unpractical and employ instead renewal processes to work directly in real time. We first validate our approach against data produced using agent-based simulations. This allows us to identify the length and time scales required for an accurate measurement of the motility parameters, including tumbling frequency and swim speed. We compare different models for the run-and-tumble dynamics by accounting for speed variability at the single-cell and population level, respectively. Finally, we apply our approach to experimental data on wild-type Escherichia coli obtained using differential dynamic microscopy.

physics.bio-ph↗

arXiv2022

Characterization and Control of the Run-and-Tumble Dynamics of {\it Escherichia Coli}

We characterize the full spatiotemporal gait of populations of swimming {\it Escherichia coli} using renewal processes to analyze the measurements of intermediate scattering functions. This allows us to demonstrate quantitatively how the persistence length of an engineered strain can be controlled by a chemical inducer and to report a controlled transition from perpetual tumbling to smooth swimming. For wild-type {\it E.~coli}, we measure simultaneously the microscopic motility parameters and the large-scale effective diffusivity, hence quantitatively bridging for the first time small-scale directed swimming and macroscopic diffusion.

cond-mat.soft↗

arXiv2021

Exploring particle dynamics in flowing complex fluids using differential dynamic microscopy

Microscopic dynamics reveal the origin of the bulk rheological response in complex fluids. In model systems particle motion can be tracked, but for industrially relevant samples this is often impossible. Here we adapt differential dynamic microscopy (DDM) to study flowing highly-concentrated samples without particle resolution. By combining an investigation of oscillatory flow, using a novel "echo-DDM" analysis, and steady shear, through flow-DDM, we characterise the yielding of a silicone oil emulsion on both the microscopic and bulk level. Through measuring the rate of shear-induced droplet rearrangements and the flow velocity, the transition from a solid-like to liquid-like state is shown to occur in two steps: with droplet mobilisation marking the limit of linear visco-elasticity, followed by the development of shear localisation and macroscopic yielding. Using this suite of techniques, such insight could be developed for a wide variety of challenging complex fluids.

cond-mat.soft↗

arXiv2021

Run-to-Tumble Variability Controls the Surface Residence Times of ${\it E.~coli}$ Bacteria

Motile bacteria are known to accumulate at surfaces, eventually leading to changes in bacterial motility and bio-film formation. We use a novel two-colour, three-dimensional Lagrangian tracking technique, to follow simultaneously the body and the flagella of a wild-type ${\it Escherichia~coli}$. We observe long surface residence times and surface escape corresponding mostly to immediately antecedent tumbling. A motility model accounting for a large behavioural variability in run-time duration, reproduces all experimental findings and gives new insights into surface trapping efficiency.

cond-mat.soft↗

arXiv2021

Particle sizing for flowing colloidal suspensions using flow-differential dynamic microscopy

Particle size is a key variable in understanding the behaviour of the particulate products that underpin much of our modern lives. Typically obtained from suspensions at rest, measuring the particle size under flowing conditions would enable advances for in-line testing during manufacture and high-throughput testing during development. However, samples are often turbid, multiply scattering light and preventing the direct use of common sizing techniques. Differential dynamic microscopy (DDM) is a powerful technique for analysing video microscopy of such samples, measuring diffusion and hence particle size without the need to resolve individual particles while free of substantial user input. However, when applying DDM to a flowing sample, diffusive dynamics are rapidly dominated by flow effects, preventing particle sizing. Here, we develop "flow-DDM", a novel analysis scheme that combines optimised imaging conditions, a drift-velocity correction and modelling of the impact of flow. Flow-DDM allows a decoupling of flow from diffusive motion that facilitates successful particle size measurements at flow speeds an order of magnitude higher than for DDM. We demonstrate the generality of the technique by applying flow-DDM to two separate microscopy methods and flow geometries.

cond-mat.soft↗

arXiv2019

Dynamics-dependent density distribution in active suspensions

Self-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behavior in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, $v(x)$, then their density $\rho(x)$ satisfies $\rho(x) = \rho(0)v(0)/v(x)$, where $x = 0$ is an arbitrary reference point. Such a dependence of steady-state $\rho(x)$ on the particle dynamics, which was the qualitative basis of recent work demonstrating how to `paint' with bacteria, is forbidden in thermal equilibrium. We verify this prediction quantitatively by constructing bacteria that swim with an intensity-dependent speed when illuminated. A spatial light pattern therefore creates a speed profile, along which we find that, indeed, $\rho(x)v(x) = \mathrm{constant}$, provided that steady state is reached.

cond-mat.soft↗

arXiv2018

Dynamic optical rectification and delivery of active particles

We use moving light patterns to control the motion of {\it Escherichia coli} bacteria whose motility is photo-activated. Varying the pattern speed controls the magnitude and direction of the bacterial flux, and therefore the accumulation of cells in up- and down-stream reservoirs. We validate our results with two-dimensional simulations and a 1-dimensional analytic model, and use these to explore parameter space. We find that cell accumulation is controlled by a competition between directed flux and undirected, stochastic transport. We articulate design principles for using moving light patterns and light-activated micro-swimmers to achieve particular experimental goals.

cond-mat.soft↗

arXiv2017

Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy

We demonstrate differential dynamic microscopy and particle tracking for the characterization of the spatiotemporal behavior of active Janus colloids in terms of the intermediate scattering function (ISF). We provide an analytical solution for the ISF of the paradigmatic active Brownian particle model and find striking agreement with experimental results from the smallest length scales, where translational diffusion and self-propulsion dominate, up to the largest ones, which probe effective diffusion due to rotational Brownian motion. At intermediate length scales, characteristic oscillations resolve the crossover between directed motion to orientational relaxation and allow us to discriminate active Brownian motion from other reorientation processes, e.g., run-and-tumble motion. A direct comparison to theoretical predictions reliably yields the rotational and translational diffusion coefficients of the particles, the mean and width of their speed distribution, and the temporal evolution of these parameters.

cond-mat.soft↗

arXiv2017

Painting with bacteria: Smart templated self assembly using motile bacteria

External control of the swimming speed of `active particles' can be used to self assemble designer structures in situ on the micrometer to millimeter scale. We demonstrate such reconfigurable templated active self assembly in a fluid environment using light powered strains of Escherichia coli. The physics and biology controlling the sharpness and formation speed of patterns is investigated using a bespoke fast-responding strain.

cond-mat.soft↗

arXiv2015

Escherichia coli as a model active colloid: a practical introduction

The flagellated bacterium Escherichia coli is increasingly used experimentally as a self-propelled swimmer. To obtain meaningful, quantitative results that are comparable between different laboratories, reproducible protocols are needed to control, `tune' and monitor the swimming behaviour of these motile cells. We critically review the knowledge needed to do so, explain methods for characterising the colloidal and motile properties of E.coli, cells, and propose a protocol for keeping them swimming at constant speed at finite bulk concentrations. In the process of establishing this protocol, we use motility as a high-throughput probe of aspects of cellular physiology via the coupling between swimming speed and the proton motive force.

cond-mat.soft↗

arXiv2013

Switching of swimming modes in Magnetospirillium gryphiswaldense

The microaerophilic magnetotactic bacterium Magnetospirillum gryphiswaldense swims along magnetic field lines using a single flagellum at each cell pole. It is believed that this magnetotactic behavior enables cells to seek optimal oxygen concentration with maximal efficiency. We analyse the trajectories of swimming M. gryphiswaldense cells in external magnetic fields larger than the earth's field, and show that each cell can switch very rapidly (in < 0.2 s) between a fast and a slow swimming mode. Close to a glass surface, a variety of trajectories was observed, from straight swimming that systematically deviates from field lines to various helices. A model in which fast (slow) swimming is solely due to the rotation of the trailing (leading) flagellum can account for these observations. We determined the magnetic moment of this bacterium using a new method, and obtained a value of (2.0 $\pm$ 0.6) $\times$ $10^{-16}$ Am$^2$. This value is found to be consistent with parameters emerging from quantitative fitting of trajectories to our model.

physics.bio-ph↗

arXiv2011

Colloids in a bacterial bath: simulations and experiments

We present a joint experimental and computational study of the effect of bacterial motion on micron-scale colloids contained in a two-dimensional suspension of Bacillus subtilis. With respect to previous work using E. coli, here we introduce a novel experimental set-up that allows us to realise a two-dimensional bacterial suspension insensitive to either evaporation or fluid flow. By analysing the mean square displacements of both bacteria and colloids, we confirm the existence of a crossover from super-diffusive behaviour at short time scales to normal diffusion at longer times. We also study the same two-dimensional system by means of numerical simulations, using a suspension of self-propelled dumbbells or the Vicsek model, which has been previously used to study the dynamics of active particles. Our numerical results obtained with both models are in broad agreement with the experimental trends, but only the dumbbell simulations can match the experimental data quantitatively. The level of agreement we find suggest that steric interactions due to collisions are important players in determining collective motion of the bacterial bath, and should complement hydrodynamic interactions in experiments.

cond-mat.soft↗