arXiv subjects

Holger Stark

Publications and source records attributed to Holger Stark.

At least 19 recordsLinked to original sources

arXiv2026

Non-reciprocal torques guide self-assembly of active particles into clusters with controllable function

Self-assembly of constituents determines structure formation in the microscopic world. Attractive forces can assemble active particles into colloidal machines, but they do not fix the particles' orientations, which limits control over the machine's function. We demonstrate that non-reciprocal turn-towards torques not only assemble active particles into clusters, without requiring attractive forces, but also link particle orientations to the cluster configuration. Symmetry then dictates whether the cluster is static, rotates, or translates. In small systems, the particle number uniquely determines the stable configuration and function. In larger systems, there are multiple stable configurations with distinct functions, and tuning the torque strength allows us to bias towards the desired function, such as a run-and-tumble motion. Because the interactions driving assembly can be switched on and off, the clusters self-assemble when needed. For such a "just-in-time" self-assembly to be practical, fast assembly is necessary. We show that stochastic resetting, implemented by briefly turning off propulsion and torque, significantly speeds up self-assembly by avoiding slow pathways. Together, our findings demonstrate that non-reciprocal torques can rapidly assemble active particles into colloidal micromachines with controllable function.

cond-mat.soft↗

arXiv2026

E. coli bacterium near corrugated surfaces: near-surface swimming, escape, and hydrodynamic trapping

Bacteria often swim in complex environments where surfaces are ubiquitous and rarely flat. Surface topography and curvature can strongly affect bacterial motility, with important consequences for surface exploration, adhesion, and biofilm formation. Here, we investigate the swimming of a non-tumbling Escherichia coli bacterium near an undulating no-slip surface using hydrodynamic simulations of a detailed model bacterium. The latter is described by a rigid spherocylindrical cell body and flexible flagella modeled with the Kirchhoff rod theory, while the surrounding fluid is simulated using the method of multi-particle collision dynamics. At low curvatures of the sinusoidal surface modulations, the bacterium exhibits persistent near-surface swimming and clockwise trajectories, consistent with the known behavior near flat no-slip walls. As the curvature increases, bacteria swimming toward a ridge can escape from the surface, which we use to estimate a critical curvature where surface detachment is more likely. At larger curvatures, we find that the surface geometry promotes oscillatory swimming along the groove direction, which reduces escape opportunities and, therefore, enhances bacterial trapping. Indeed, the confinement around the groove reverses the swimming of the bacterium from clockwise to counter-clockwise, as we demonstrate by two minimal models. Thus our work highlights the importance of the three-dimensional surface topography in bacterial surface exploration.

cond-mat.soft↗

arXiv2026

Droplets sitting on thin elastic sheets: A study with the boundary element method

Elasto-capillarity of a droplet wetting an elastic sheet provides an interesting system, both for fundamental and applied research. The droplet sinks into the sheet and assumes the shape of a lens. To determine the equilibrium shape in simulations, we formulate a boundary element method (BEM) extending our earlier approaches, and apply the BEM to three specific protocols for the boundary conditions of the sheet. For a clamped elastic sheet, we use various morphological metrics to demonstrate that the lens shape crucially depends on the sheet thickness. Stretching the sheet isotropically, allows for an additional control parameter to influence the droplet shape and the tension in the sheet, which we quantify by radial profiles of the azimuthal and radial elastic stresses. We further demonstrate how the focal length of a liquid lens can be tuned by varying the applied tension. Finally, stretching the sheet along one direction, elongates the droplet, and the sheet shows folds and dimples.

cond-mat.soft↗

arXiv2025

Spontaneous Emergence of Solitary Waves in Active Flow Networks with Elastic Elements

Flow networks are fundamental for understanding systems such as animal and plant vasculature or power distribution grids. These networks can encode, transmit, and transform information embodied in the spatial and temporal distribution of their flows. In this work, we focus on a minimal yet physically grounded system that allows us to isolate the fundamental mechanisms by which active flow networks generate and regulate emergent dynamics capable of supporting information transmission. The system is composed of active units that pump fluid and elastic units that store volume. From first principles, we derive a discrete model -- an active flow network -- that enables the simulation of large systems with many interacting units. Numerically, we show that the pressure field can develop solitary waves, resulting in the spontaneous creation and transmission of localized packets of information stored in the physical properties of the flow. We characterize how these solitary waves emerge from disordered initial conditions in a one-dimensional network, and how their size and propagation speed depend on key system parameters. Finally, when the elastic units are coupled to their neighbors, the solitary waves exhibit even richer dynamics, with diverse shapes and finite lifetimes that display power-law behaviors that we can predict analytically. Together, these results show how simple fluidic elements can collectively create, shape and transport information, laying the foundations for understanding -- and ultimately engineering -- information processing in active flow systems.

physics.flu-dyn↗

arXiv2025

Mechanical work extraction from an error-prone active dynamic Szilard engine

Isothermal information engines operate by extracting net work from a single heat bath through measurement and feedback control. In this work, we analyze a realistic active Szilard engine operating on a single active particle by means of steric interaction with an externally controlled mechanical element. In particular, we provide a comprehensive study of how finite measurement accuracy affects the engine's work and power output, as well as the cost of operation. Having established the existence of non-trivial optima for work and power output, we study the dependence of their loci on the measurement error parameters and identify conditions for their positivity under one-shot and cyclic engine operation. By computing a suitably defined information efficiency, we also demonstrate that this engine design allows for the violation of Landauer's bound on the efficiency of information-to-work conversion. Notably, the information efficiency for one-shot operation exhibits a discontinuous transition and a non-monotonic dependence on the measurement precision. Finally, we show that cyclic operation improves information efficiency by harvesting residual mutual information between successive measurements.

cond-mat.stat-mech↗

arXiv2025

E. coli bacterium tumbling in bulk and close to surfaces: A simulation study

Motility is fundamental to the survival and proliferation of microorganisms. The E. coli bacterium propels itself using a bundle of rotating helical flagella. If one flagellum reverses its rotational direction, it leaves the bundle, performs a polymorphic transformation, and the bacterium tumbles. The E. coli bacterium is hydrodynamically attracted to surfaces. This prolongs its residence time, while tumbling facilitates surface detachment. We develop a model of E. coli that uses an extended Kirchhoff rod theory to implement flagellar flexibility as well as different polymorphic conformations and perform hydrodynamic simulations with the method of multiparticle collision dynamics (MPCD). To establish a reference case, we determine the distribution of tumble angles in the bulk fluid, which shows good agreement with experiments for a fixed tumble time. Increasing the hook stiffness, narrows the tumble angle distribution and reduces the flagellar dispersion during tumbling. Close to a bounding surface, the tumble angle distribution is shifted to smaller angles, while flagellar dispersion is reduced. Reorientation within the plane favors the forward direction, which might be an explanation for prolonged run times observed in experiments

cond-mat.soft↗

arXiv2025

Emergent collective behavior of cohesive, aligning particles

Collective behavior is all around us, from flocks of birds to schools of fish. These systems are immensely complex, which makes it pertinent to study their behavior through minimal models. We introduce such a minimal model for cohesive and aligning self-propelled particles in which group cohesion is established through additive, non-reciprocal torques. These torques cause constituents to effectively turn towards one another. We additionally incorporate an alignment torque, which competes with the cohesive torque in the same spatial range. By changing the strength and range of these torque interactions, we uncover six states which we distinguish via their static and dynamic properties: a disperse state, a multiple worm state, a line state, a persistent worm state, a rotary worm state, and an aster state. Their occurrence strongly depends on initial conditions and stochasticity, so the model exhibits multistabilities. A number of the states exhibit collective dynamics which are reminiscent of those seen in nature.

cond-mat.soft↗

arXiv2024

Trypanosoma brucei moving in microchannels and through constrictions

Trypanosoma brucei (T. brucei), a single-celled parasite and natural microswimmer, is responsible for fatal sleeping sickness in infected mammals, including humans. Understanding how T. brucei interacts with fluid environments and navigates through confining spaces is crucial not only for medical and clinical applications but also for a fundamental understanding of how life organizes in a confined microscopic world. Using a hybrid multi-particle collision dynamics (MPCD)--molecular dynamics (MD) approach, we present our investigations on the locomotion of an in silico T. brucei in three types of fluid environments: bulk fluid, straight cylindrical microchannels, and microchannels with constrictions. We observe that the helical swimming trajectory of the in silico T. brucei becomes rectified in straight cylindrical channels compared to bulk fluid. The swimming speed for different channel widths is governed by the diameter of the helical trajectory. The speed first slightly increases as the channel narrows and then decreases when the helix diameter is compressed. An optimal swimming speed is achieved, when the channel width is approximately twice the bulk helix diameter. It results from an interplay of the trypanosome's hydrodynamic interactions with the cylindrical channel walls and the high deformability of the parasite. In microchannels with constrictions, the motions of the anterior and posterior ends, the end-to-end distance, and the log-rolling motion of the cell body are characterized and show salient differences compared to the straight-channel case. Depending on the constriction length and width, we observe characteristic slip, stuck, and stuck-slip motions of the model T. brucei within the constriction. Our findings may provide some mechanical insights into how T. brucei moves through blood vessels and tissues, and across the blood-brain barrier.

cond-mat.soft↗

arXiv2024

Mixing in viscoelastic fluids using elastic turbulence

We investigate the influence of elastic turbulence on mixing of a scalar concentration field within a viscoelastic fluid in a two-dimensional Taylor-Couette geometry using numerical solutions of the Oldroyd-B model. The flow state is determined through the secondary-flow order parameter indicating the regime of elastic turbulence. When starting in the turbulent state and subsequently lowering the Weissenberg number, a weakly-chaotic flow occurs below $\mathrm{Wi_c}$. Advection in both the turbulent and weakly-chaotic flow states induces mixing, which we illustrate by the time evolution of the standard deviation of the solute concentration from the uniform distribution. In particular, in the elastic turbulent state mixing is strong and we quantify it by the mixing rate, the mixing time, and the mixing efficiency. All three quantities follow scaling laws. Importantly, we show that the order parameter is strongly correlated to the mixing rate and hence is also a good indication of mixing within the fluid.

physics.flu-dyn↗

arXiv2024

CowScape: Quantitative reconstruction of the conformational landscape of biological macromolecules from cryo-EM data

Cryo-EM data processing typically focuses on the structure of the main conformational state under investigation and discards images that belong to other states. This approach can reach atomic resolution, but ignores vast amounts of valuable information about the underlying conformational ensemble and its dynamics. CowScape analyzes an entire cryo-EM dataset and thereby obtains a quantitative description of structural variability of macromolecular complexes that represents the biochemically relevant conformational space. By combining extensive image classification with principal component analysis (PCA) of the classified 3D volumes and kernel density estimation, CowScape can be used as a quantitative tool to analyze this variability. PCA projects all 3D structures along the major modes spanning a low-dimensional space that captures a large portion of structural variability. The number of particle images in a given state can be used to calculate an energy landscape based on kernel density estimation and Boltzmann inversion. By revealing allosteric interactions in macromolecular complexes, CowScape allows us to distinguish and interpret dynamic changes in macromolecular complexes during function and regulation.

q-bio.BM↗

arXiv2024

Dividing active and passive particles in nonuniform nutrient environments

To explore the coupling between a growing population of microorganisms such as E. coli and a nonuniform nutrient distribution, we formulate a minimalistic model. It consists of active Brownian particles that divide and grow at a nutrient-dependent rate following the Monod equation. The nutrient concentration obeys a diffusion equation with a consumption term and a point source. In this setting the heterogeneity in the nutrient distribution can be tuned by the diffusion coefficient. In particle-based simulations, we demonstrate that passive and weakly active particles form proliferation-induced clusters when the nutrient is localized, without relying on further mechanisms such as chemotaxis or adhesion. In contrast, strongly active particles disperse in the whole system during their lifetime and no clustering is present. The steady population is unaffected by activity or nonuniform nutrient distribution and only determined by the ratio of nutrient influx and bacterial death. However, the transient dynamics strongly depends on the nutrient distribution and activity. Passive particles in almost uniform nutrient profiles display a strong population overshoot, with clusters forming all over the system. In contrast, when slowly diffusing nutrients remain centred around the source, the bacterial population quickly approaches the steady state due to its strong coupling to the nutrient. Conversely, the population overshoot of highly active particles becomes stronger when the nutrient localisation increases. We successfully map the transient population dynamics onto a uniform model where the effect of the nonuniform nutrient and bacterial distributions are rationalized by two effective areas.

physics.bio-ph↗

arXiv2023

Steering droplets on substrates with plane-wave wettability patterns and deformations

Motivated by strategies for targeted microfluidic transport of droplets, we investigate how sessile droplets can be steered toward a preferred direction using travelling waves in substrate wettability or deformations of the substrate. To perform our numerical study, we implement the boundary-element method to solve the governing Stokes equations for the fluid flow field inside the moving droplet. In both cases we find two distinct modes of droplet motion. For small wave speed the droplet surfes with a constant velocity on the wave, while beyond a critical wave speed a periodic wobbling motion occurs, the period of which diverges at the transition. These observation can be rationalized by the nonuniform oscillator model and the transition described by a SNIPER bifurcation. For the travelling waves in wettability the mean droplet velocity in the wobbling state decays with the inverse wave speed. In contrast, for travelling-wave deformations of the substrate it is proportional to the wave speed at large speed values since the droplet always has to move up and down. To rationalize this behavior, the nonuniform oscillator model has to be extended. Since the critical wave speed of the bifurcation depends on the droplet radius, this dependence can be used to sort droplets by size.

physics.flu-dyn↗

arXiv2023

Orientational dynamics and rheology of active suspensions in weakly viscoelastic flows

Microswimmer suspensions in Newtonian fluids exhibit unusual macroscale properties, such as a superfluidic behavior, which can be harnessed to perform work at microscopic scales. Since most biological fluids are non-Newtonian, here we study the rheology of a microswimmer suspension in a weakly viscoelastic shear flow. At the individual level, we find that the viscoelastic stresses generated by activity substantially modify the Jeffery orbits well-known from Newtonian fluids. The orientational dynamics depends on the swimmer type; especially pushers can resist flow-induced rotation and align at an angle with the flow. To analyze its impact on bulk rheology, we study a dilute microswimmer suspension in the presence of random tumbling and rotational diffusion. Strikingly, swimmer activity and its elastic response in polymeric fluids alter the orientational distribution and substantially amplify the swimmer-induced viscosity. This suggests that pusher suspensions reach the superfluidic regime at lower volume fractions compared to a Newtonian fluid with identical viscosity.

cond-mat.soft↗

arXiv2022

Collective motion of active particles exhibiting non-reciprocal orientational interactions

We present a Brownian dynamics study of a 2d bath of active particles interacting among each other through usual steric interactions and, additionally, via non-reciprocal avoidant orientational interactions. We motivate them by the fact that the two flagella of the alga Chlamydomonas interact sterically with nearby surfaces such that a torque acts on the alga. As expected, in most cases such interactions disrupt the motility-induced particle clustering in active baths. Surprisingly, however, we find that the active particles can self-organize into collectively moving flocks if the range of non-reciprocal interactions is close to that of steric interactions. We observe that the flocking motion can manifest itself through a variety of structural forms, spanning from single dense bands to multiple moderately-dense stripes, which are highly dynamic. The flocking order parameter is found to be only weakly dependent on the underlying flock structure. Together with the variance of the local-density distribution, one can clearly group the flocking motion into the two separate band and dynamic-stripes states.

cond-mat.soft↗

arXiv2022

Characterizing elastic turbulence in the three-dimensional von Karman swirling flow using the Oldroyd-B model

We present the full three-dimensional numerical investigation of the von Karman swirling flow between two parallel plates using the Oldroyd-B model and characterize the onset and development of elastic turbulence. We quantify the flow state with the secondary-flow strength, a measure of the average strength of the velocity fluctuations, and then define an order parameter as the time average of the secondary-flow strength. The order parameter displays a subcritical transition from the laminar to a bistable flow that switches between weakly chaotic flow and elastic turbulence. The transition to the bistable flow occurs at the critical Weissenberg number $\mathrm{Wi_c}=12$. Above $\mathrm{Wi_c}$, in the elastic turbulent state, we observe a strong increase in velocity fluctuations and flow resistance, which we define as the total work performed on the fluid. Upon starting simulations in the turbulent state and subsequently lowering $\mathrm{Wi}$ below its critical value, we observe hysteretic behavior in the order parameter and the flow resistance, which is a common feature of a subcritical transition. Hysteresis has also been found in experiments. Additionally, we find power-law scaling in the spatial and temporal power spectra of the velocity fluctuations, characteristic for elastic turbulence. The maximum values of the power-law exponents in our simulations are $α_t= 3.41$ for the temporal exponent and $α_s= 3.17$ for the spatial exponent, which are remarkably close to the values obtained in experiments.

physics.flu-dyn↗

arXiv2022

Gyrotactic cluster formation of bottom-heavy squirmers

Squirmers that are bottom-heavy experience a torque that aligns them along the vertical so that they swim upwards. In a suspension of many squirmers, they also interact hydrodynamically via flow fields that are initiated by their swimming motion and by gravity. Swimming under the combined action of flow field vorticity and gravitational torque is called gyrotaxis. Using the method of multi-particle collision dynamics, we perform hydrodynamic simulations of a many-squirmer system floating above the bottom surface. Due to gyrotaxis they exhibit pronounced cluster formation with increasing gravitational torque. The clusters are more volatile at low values but compactify to smaller clusters at larger torques. The mean distance between clusters is mainly controlled by the gravitational torque and not the global density. Furthermore, we observe that neutral squirmers form clusters more easily, whereas pullers require larger gravitational torques due to their additional force-dipole flow fields. We do not observe clustering for pusher squirmers. Adding a rotlet dipole to the squirmer flow field induces swirling clusters. At high gravitational strengths, the hydrodynamic interactions with the no-slip boundary create an additional vertical alignment for neutral squirmers, which also supports cluster formation.

cond-mat.soft↗

arXiv2021

On the cross-streamline lift of microswimmers in viscoelastic flows

The current work studies the dynamics of a microswimmer in pressure-driven flow of a weakly viscoelastic fluid. Employing the second-order fluid model, we show that the self-propelling swimmer experiences a viscoelastic swimming lift in addition to the well-known passive lift that arises from its resistance to shear flow. Using the reciprocal theorem, we evaluate analytical expressions for the swimming lift experienced by neutral and pusher/puller-type swimmers and show that they depend on the hydrodynamic signature associated with the swimming mechanism. We find that for neutral swimmers focusing towards the centerline is accelerated by two orders of magnitude, while for force-dipole swimmers no net modification in cross-streamline migration occurs.

physics.flu-dyn↗

arXiv2021

How inertial lift affects the dynamics of a microswimmer in Poiseuille flow

We analyze the dynamics of a microswimmer in pressure-driven Poiseuille flow, where fluid inertia is small but non-negligible. Using perturbation theory and the reciprocal theorem, we show that in addition to the classical inertial lift of passive particles, the active nature generates a `swimming lift', which we evaluate for neutral and pusher/puller-type swimmers. Accounting for fluid inertia engenders a rich spectrum of novel complex dynamics including bistable states, where tumbling coexists with stable centerline swimming or swinging. The dynamics is sensitive to the swimmer's hydrodynamic signature and goes well beyond the findings at vanishing fluid inertia. Our work will have non-trivial implications on the transport and dispersion of active suspensions in microchannels.

cond-mat.soft↗