arXiv subjects

Arnold J. T. M. Mathijssen

Publications and source records attributed to Arnold J. T. M. Mathijssen.

At least 19 recordsLinked to original sources

arXiv2026

Multiflagellarity facilitates bacterial upstream motility

Upstream swimming drives bacterial spreading and surface colonization. Many pathogens encounter fluid flows as they infect the intestines, lungs, and urinary tract, so how bacteria use their flagella to counter these flows matters for disease and treatment. Yet how morphology and flagellar arrangement govern motility against flow remains unknown. Here, we investigate the biophysical determinants of rheotaxis by combining microfluidics, directed evolution, genetics, holography, and hydrodynamics simulations. Using upstream swimming competitions, we find that peritrichous E. coli and S. enterica rapidly outcompete monotrichous P. aeruginosa and V. cholerae, accumulating upstream at densities up to five orders of magnitude higher, even though Vibrio swims three times as fast. Motility selection experiments show that rheotaxis increases with flagellar number and length, confirmed by overexpressing the master regulator flhD/C. Three-dimensional holography and single-cell tracking reveal that multiflagellarity stabilizes surface residence and promotes the weathervane effect that reorients cells upstream, a mechanism further supported by simulations that fully resolve flagellar arrangement and fluid-structure interactions. These results establish multiflagellarity as a key facilitator of upstream navigation, governed by near-wall residence and shear-driven reorientation rather than by swimming speed.

physics.bio-ph↗

arXiv2026

Elongation suppresses rheotaxis and enables microfluidic enrichment of \b{eta}-lactam-resistant bacteria

Antimicrobial resistance (AMR) complicates the treatment of diseases including lung and urinary tract infections (UTIs), which are among the most common bacterial infections worldwide. Motile pathogens can use rheotaxis to swim upstream against fluid flows, potentially promoting access to upper regions of anatomical tracts. However, it remains unclear how antibiotic exposure and resistance influence this transport process. Here, using single-cell tracking microscopy, we investigate how elongation induced by \b{eta}-lactam antibiotics affects the rheotactic migration of E. coli in confined microfluidic channels. Remarkably, we find that rheotaxis can be inhibited 100-fold by antibiotics, even if the susceptible elongated cells remain fully motile. However, resistant bacteria remain short and retain upstream migration under the same conditions. Using genetically engineered bacteria with tunable cell length, we show that the underlying mechanism that governs rheotaxis is the coupling between cell morphology and flow vorticity, where elongated cells are rapidly rotated downstream. Finally, we exploit this length-dependent transport difference to separate short and elongated cells under flow and enrich ampicillin-resistant cells from mixed populations. Together, these results establish bacterial elongation as a key control parameter for rheotactic transport, and provide a proof-of-concept strategy for enriching \b{eta}-lactam-resistant bacteria for potential use in rapid AMR detection.

physics.bio-ph↗

arXiv2026

Active diffusion enhances plankton carbon capture and phycosphere radius

Plankton fix about 40 gigatons of carbon annually, using photosynthesis to convert $\text{CO}_2$ into $\text{O}_2$ and carbohydrates. These solutes are exchanged with the ocean in a diffusive boundary layer around the organism called the phycosphere. Here, we study how organisms can increase their carbon influx and outflux by actively mixing the surrounding fluid. By developing exact analytical expressions validated by stochastic simulations, we determine the enhanced diffusivity of phycosphere particles as a function of mixing activity, and their resulting fluxes and concentration fields. Hence, we find that plankton can significantly increase their uptake and photosynthetic turnover. Moreover, we find that the phycosphere radius is enlarged both by increased metabolism and by increased diffusive transport further from the organism. These results provide new biophysical insights into marine microbial ecology, with important implications for global carbon capture and climate change.

physics.bio-ph↗

arXiv2026

Surfing on metachronal waves: ciliary transport by inertial coasting

Motile cilia drive biological fluid transport through whip-like beating motions that synchronize into metachronal waves. The lengths of these cilia span three orders of magnitude, from microns in human airways to millimeters in ctenophores. While recent studies have considered ciliary flows at intermediate Reynolds numbers, the effect of inertia on coordinated particle transport remains unexplored. Here, we address this gap using "Pufflets," the inertial counterparts of Stokeslets. These Pufflets describe rapidly accelerating flows generated by short-lived impulses, encoded by spatiotemporally singular momentum injections. To produce such rapid impulses experimentally, we designed an Atwood machine that generates long-lived Pufflet flows, which we capture with high-speed PIV measurements that agree well with analytical theory and simulations. Moreover, we find that pairs of equal and opposite Pufflets can drive net particle displacements and mixing due to time reversal symmetry breaking, which would be impossible in Stokes flow. Finally, we consider metachronal waves of Pufflets. Remarkably, we discover that particles can surf on these waves by coasting inertially from one cilium to the next, leading to highly efficient particle transport. This work paves the way toward understanding rapidly accelerating flows and collective transport driven by biological and artificial cilia.

physics.bio-ph↗

arXiv2025

Selective trapping of bacteria in porous media by cell length

Bacteria commonly inhabit porous environments such as host tissues, soil, and marine sediments, where complex geometries constrain and redirect their motion. Although bacterial motility has been studied in porous media, the roles of cell length and pore shape in navigating these environments remain poorly understood. Here, we investigate how cell morphology and pore architecture jointly determine bacterial spreading behavior. Using genetically engineered E. coli with tunable cell length, we performed single-cell tracking in microfluidic devices that mimic ordered and disordered porous structures. We find that elongated bacteria traverse ordered pore networks more effectively than short cells, exhibiting straighter paths, greater directional persistence, and enhanced exploration efficiency. In contrast, in disordered porous media, elongated bacteria become trapped in dead-end regions for extended periods, resulting in markedly reduced navigational efficiency. Together, these results reveal how cell shape and environmental geometry interact to govern bacterial transport. Moreover, we suggest a new mechanism for separating antimicrobial-resistant (AMR) bacteria from elongated susceptible cells in designer porous media.

cond-mat.soft↗

arXiv2025

Collective transport efficiency of microswimmer swarms optimized by tactic run-tumble dynamics

The collective motion of microorganisms and microrobots can be used for particle delivery, especially when guided by external magnetic fields, phototaxis, or chemotaxis. This cargo transport is enhanced significantly by hydrodynamic entrainment, where the surrounding fluid and any dissolved molecules or suspended cargo particles are dragged along with a collectively moving swarm. However, it remains unclear how this directed entrainment is affected by stochastic run-tumble motion, and how such motility patterns couple to particle dispersion. Here, we combine theory and simulations to compute the entrainment velocity and diffusivity for different degrees of swimmer directedness. Surprisingly, we find that the transport efficiency Péclet number, the ratio of advective to diffusive transport, is optimal for intermediate directedness values, so perfectly guided active suspensions perform worse than those with stochastic reorientations. These results could have implications for microrobotic drug delivery and nutrient transport in microbial environments.

cond-mat.soft↗

arXiv2024

Enhancement of bacterial rheotaxis in non-Newtonian fluids

Bacteria often exhibit upstream swimming, which can cause the contamination of biomedical devices and the infection of organs including the urethra or lungs. This process, called rheotaxis, has been studied extensively in Newtonian fluids. However, most microorganisms thrive in non-Newtonian fluids that contain suspended polymers such as mucus and biofilms. Here, we investigate the rheotatic behavior of E. coli near walls in non-Newtonian fluids. Our experiments demonstrate that bacterial upstream swimming is enhanced by an order of magnitude in shear-thinning polymeric fluids relative to Newtonian fluids. This result is explained by direct numerical simulations, revealing a torque that promotes the alignment of bacteria against the flow. From this analysis, we develop a theoretical model that accurately describes experimental rheotatic data in both Newtonian and shear-thinning fluids.

physics.flu-dyn↗

arXiv2024

Giant enhancement of bacterial upstream swimming in macromolecular flows

Many bacteria live in natural and clinical environments with abundant macromolecular polymers. Macromolecular fluids commonly display viscoelasticity and non-Newtonian rheological behavior; it is unclear how these complex-fluid properties affect bacterial transport in flows. Here we combine high-resolution microscopy and numerical simulations to study bacterial response to shear flows of various macromolecular fluids. In stark contrast to the case in Newtonian shear flows, we found that flagellated bacteria in macromolecular flows display a giant capacity of upstream swimming (a behavior resembling fish swimming against current) near solid surfaces: The cells can counteract flow washing at shear rates up to ~65 $s^{-1}$, one order of magnitude higher than the limit for cells swimming in Newtonian flows. The significant enhancement of upstream swimming depends on two characteristic complex-fluid properties, namely viscoelasticity and shear-thinning viscosity; meanwhile, increasing the viscosity with a Newtonian polymer can prevent upstream motion. By visualizing flagellar bundles and modeling bacterial swimming in complex fluids, we explain the phenomenon as primarily arising from the augmentation of a "weathervane effect" in macromolecular flows due to the presence of a viscoelastic lift force and a shear-thinning induced azimuthal torque promoting the alignment of bacteria against the flow direction. Our findings shed light on bacterial transport and surface colonization in macromolecular environments, and may inform the design of artificial helical microswimmers for biomedical applications in physiological conditions.

cond-mat.soft↗

arXiv2024

Floating active carpets drive transport and aggregation in aquatic ecosystems

Communities of swimming microorganisms often thrive near liquid-air interfaces. We study how such `active carpets' shape their aquatic environment by driving biogenic transport in the water column beneath them. The hydrodynamic stirring that active carpets generate leads to diffusive upward fluxes of nutrients from deeper water layers, and downward fluxes of oxygen and carbon. Combining analytical theory and simulations, we examine the biogenic transport by studying fundamental metrics, including the single and pair diffusivity, the first passage time for particle pair encounters, and the rate of particle aggregation. Our findings reveal that the hydrodynamic fluctuations driven by active carpets have a region of influence that reaches orders of magnitude further in distance than the size of the organisms. These nonequilibrium fluctuations lead to a strongly enhanced diffusion of particles, which is anisotropic and space-dependent. Fluctuations also facilitate encounters of particle pairs, which we quantify by analysing their velocity pair correlation functions as a function of distance between the particles. We found that the size of the particles plays a crucial role in their encounter rates, with larger particles situated near the active carpet being more favourable for aggregation. Overall, this research broadens our comprehension of aquatic systems out of equilibrium and how biologically driven fluctuations contribute to the transport of fundamental elements in biogeochemical cycles.

cond-mat.soft↗

arXiv2024

Active Carpets in floating viscous films

Earth's aquatic environments are inherently stratified layered systems where interfaces between layers serve as ecological niches for microbial swimmers, forming colonies known as Active Carpet (AC). Previous theoretical studies have explored the hydrodynamic fluctuations exerted by ACs in semi-infinite fluid media, demonstrating their capability to enhance thermal diffusion and mass transport in aquatic systems. Yet, little is understood about the fluid dynamics and impact of ACs residing in confined layered environments, like slicks floating on water bodies. In this study, we report novel solutions for the hydrodynamic fluctuations induced by ACs geometrically confined between a free surface and a fluid-fluid interface characterized by a jump in fluid viscosity. Combining theory and numerical experiments, we investigate the topology of the biogenic hydrodynamic fluctuations in a confined, thin fluid environment. We reveal that within this thin layer, ACs gives shape to three characteristic regions: Region I is the closest zone to the AC and the fluid-fluid interface, where hydrodynamic fluctuations are dominantly vertical; Region II is further up from the AC and is characterized by isotropic hydrodynamic fluctuations; Region III is the furthest region, near the free surface and is dominated by horizontal flow fluctuations. We demonstrate that the extent of these regions depends strongly on the degree of confinement, i.e. the layer thickness and the strength of the viscosity jump. Lastly, we show that confinement fosters the emergence of large-scale flow structures within the layer housing the ACs--not previously reported. Our findings shed light on the complex interplay between confinement and hydrodynamics in floating viscous film biological systems, providing valuable insights with implications spanning from ecological conservation to bio-inspired engineering.

physics.flu-dyn↗

arXiv2024

Tuning upstream swimming of micro-robots by shape and cargo size

The navigation of micro-robots in complex flow environments is controlled by rheotaxis, the reorientation with respect to flow gradients. Here we demonstrate how payloads can be exploited to enhance the motion against flows. Using fully resolved hydrodynamic simulations, the mechanisms are described that allow micro-robots of different shapes to reorient upstream. We find that cargo pullers are the fastest at most flow strengths, but pushers feature a non-trivial optimum as a function of the counter flow strength. Moreover, the rheotactic performance can be maximised by tuning the micro-robot shape or cargo size. These results may be used to control micro-swimmer navigation, but they also apply to rheotaxis in microbial ecology and the prevention of bacterial contamination dynamics.

cond-mat.soft↗

arXiv2022

Interfacial activity dynamics of confined active droplets

Active emulsions can spontaneously form self-propelled droplets or phoretic micropumps. It has been predicted that the interaction with their self-generated chemical fields can lead to multistable higher-order flows and chemodynamic phenomena. However, it remains unclear how such reaction-advection-diffusion instabilities can emerge from the interplay between chemical reactions and interfacial hydrodynamics. Here, we simultaneously measure the flow fields and the chemical concentration fields using dual-channel microscopy for oil droplets that dynamically solubilize in a supramicellar aqueous surfactant solution. We developed an experimentally tractable setup with micropumps, droplets that are pinned between the top and bottom surfaces of a microfluidic reservoir, which we compare directly to predictions from a Brinkman squirmer model to account for the confinement. With increasing droplet radius, we observe (i) a migration of vortex flows from the posterior to the anterior of the droplet, analogous to a transition from pusher- to puller-type swimmers, (ii) a bistability between dipolar and quadrupolar flow modes, and, eventually, (iii) a transition to multipolar modes. We also investigate how the dynamics evolve over long time periods. Together, our observations suggest that a local build-up of chemical products leads to a saturation of the surface, which controls the propulsion mechanism. These multistable dynamics can be explained by the competing time scales of slow micellar diffusion governing the chemical buildup and faster molecular diffusion powering the underlying transport mechanism. Our results are directly relevant to phoretic micropumps, but also shed light on the interfacial activity dynamics of self-propelled droplets and other active emulsion systems

cond-mat.soft↗

arXiv2022

Culinary fluid mechanics and other currents in food science

Innovations in fluid mechanics are leading to better food since ancient history, while creativity in cooking inspires applied and fundamental science. Here, we review how recent advances in hydrodynamics are changing food science, and we highlight how the surprising phenomena that arise in the kitchen lead to discoveries and technologies across the disciplines, including rheology, soft matter, biophysics and molecular gastronomy. This review is structured like a menu, where each course highlights different aspects of culinary fluid mechanics. Our main themes include multiphase flows, complex fluids, thermal convection, hydrodynamic instabilities, viscous flows, granular matter, porous media, percolation, chaotic advection, interfacial phenomena, and turbulence. For every topic, we first provide an introduction accessible to food professionals and scientists in neighbouring fields. We then assess the state-of-the-art knowledge, the open problems, and likely directions for future research. New gastronomic ideas grow rapidly as the scientific recipes keep improving too.

physics.pop-ph↗

arXiv2021

Amphibious Transport of Fluids and Solids by Soft Magnetic Carpets

One of the major challenges in modern robotics is controlling micromanipulation by active and adaptive materials. In the respiratory system, such actuation enables pathogen clearance by means of motile cilia. While various types of artificial cilia have been engineered recently, they often involve complex manufacturing protocols and focus on transporting liquids only. Here, we create soft magnetic carpets via an easy self-assembly route based on the Rosensweig instability. These carpets can transport liquids but also solid objects that are larger and heavier than the artificial cilia, using a crowd-surfing effect. This amphibious transportation is locally and reconfigurably tuneable by simple micromagnets or advanced programmable magnetic fields with a high degree of spatial resolution. We identify and model two surprising cargo reversal effects due to collective ciliary motion and non-trivial elastohydrodynamics. While our active carpets are generally applicable to integrated control systems for transport, mixing and sorting, these effects could also be exploited for microfluidic viscosimetry and elastometry.

physics.app-ph↗

arXiv2021

Collective entrainment and confinement amplify transport by schooling micro-swimmers

Micro-swimmers can serve as cargo carriers that move deep inside complex flow networks. When a school collectively entrains the surrounding fluid, their transport capacity can be enhanced. This effect is quantified with good agreement between experiments with self-propelled droplets and a confined Brinkman squirmer model. The volume of liquid entrained can be much larger than the droplet itself, amplifying the effective cargo capacity over an order of magnitude, even for dilute schools. Hence, biological and engineered swimmers can efficiently transport materials into confined environments.

cond-mat.soft↗

arXiv2020

Towards an analytical description of active microswimmers in clean and in surfactant-covered drops

Geometric confinements are frequently encountered in the biological world and strongly affect the stability, topology, and transport properties of active suspensions in viscous flow. Based on a far-field analytical model, the low-Reynolds-number locomotion of a self-propelled microswimmer moving inside a clean viscous drop or a drop covered with a homogeneously distributed surfactant, is theoretically examined. The interfacial viscous stresses induced by the surfactant are described by the well-established Boussinesq-Scriven constitutive rheological model. Moreover, the active agent is represented by a force dipole and the resulting fluid-mediated hydrodynamic couplings between the swimmer and the confining drop are investigated. We find that the presence of the surfactant significantly alters the dynamics of the encapsulated swimmer by enhancing its reorientation. Exact solutions for the velocity images for the Stokeslet and dipolar flow singularities inside the drop are introduced and expressed in terms of infinite series of harmonic components. Our results offer useful insights into guiding principles for the control of confined active matter systems and support the objective of utilizing synthetic microswimmers to drive drops for targeted drug delivery applications.

physics.flu-dyn↗

arXiv2019

Membrane penetration and trapping of an active particle

The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrates through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing to accurately predict most of our results analytically. This analytical theory helps identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict mechanical properties of synthetic minimal membranes.

cond-mat.soft↗

arXiv2018

Nutrient transport driven by microbial active carpets

We demonstrate that active carpets of bacteria or self-propelled colloids generate coherent flows towards the substrate, and propose that these currents provide efficient pathways to replenish nutrients that feed back into activity. A full theory is developed in terms of gradients in the active matter density and velocity, and applied to bacterial turbulence, topological defects and clustering. Currents with complex spatiotemporal patterns are obtained, which are tuneable through confinement. Our findings show that diversity in carpet architecture is essential to maintain biofunctionality.

cond-mat.soft↗