Arnold J. T. M. Mathijssen’s research while affiliated with University of Pennsylvania and other places

Coffee is one of the most consumed beverages in the world. However, issues such as climate change threaten the growth of the temperature-sensitive Coffea arabica plant, more commonly known as Arabica coffee. Therefore, it is crucial to make beverages more efficient by using less coffee while still meeting the high demand for the beverage. Here, we explore pour-over filter coffees, in which a water jet impinges on a water layer above a granular bed. To reveal its internal dynamics, we first substitute opaque coffee grounds with silica gel particles in a glass cone, imaged with a laser sheet and a high-speed camera. We discover an avalanche effect that leads to strong mixing at various pour heights, even with a gentle pour-over jet. We also find that this mixing is not significantly impacted by a layer of floating grains, which is often present in pour-overs. Next, we perform experiments with real coffee grounds to measure the extraction yield of total dissolved solids. Together, these results indicate that the extraction of the coffee can be tuned by prolonging the mixing time with slower but more effective pours using avalanche dynamics. This suggests that instead of increasing the amount of beans, the sensory profile and the strength of the beverage can be adjusted by varying the flow rate and the pour height. In this way, the extraction efficiency could be better controlled to help alleviate the demand on coffee beans worldwide.

In Earth's aquatic environments and the human body, microbial swimmers often accumulate at interfaces within layered systems, forming colonies known as . These bioactive layers enhance mass transport and diffusion in fluid media. Here we study the hydrodynamic behavior induced by within confined semi-infinite fluid layers, such as the one found in the sea surface microlayer. By deriving analytical expressions and performing numerical simulations, we explore how geometrical and viscous confinement (layer thickness and viscosity ratio) influence hydrodynamic fluctuations and passive tracer dynamics. Our findings reveal anisotropic distributions of fluctuations, characterized by three distinct regions: near the and fluid-fluid interface (Region I), vertical fluctuations dominate; in an intermediate region (Region II), fluctuations become isotropic; and near the free surface (Region III), horizontal fluctuations prevail. The results also demonstrate the emergence of coherent vortical structures in highly confined systems, with roll-like patterns governed by the thickness of the confined layer and the sharpness in viscosity transitions. The insights provided by this work have implications for understanding biogenic flow patterns and transport processes in natural and engineered environments, offering potential applications in areas such as microbial ecology, biofilm management, and microfluidic technologies. Published by the American Physical Society 2025

Many microorganisms exhibit upstream swimming, which is important to many biological processes and can cause contamination of biomedical devices and the infection of organs. 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 rheotactic behavior of Escherichia coli near walls in non-Newtonian fluids. Our experiments demonstrate that bacterial upstream swimming is enhanced by an order of magnitude in shear-thinning (ST) 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 rheotactic data in both Newtonian and ST fluids.

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 non-equilibrium 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.

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.

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.

To determine why SARS-CoV-2 appears to thrive specifically well in meat packaging plants, we used SARS-CoV-2 Delta variant and meat packaging plant drain samples to develop mixed-species biofilms on materials commonly found within meat packaging plants (stainless steel (SS), PVC, and ceramic tile). Our data provides evidence that SARS-CoV-2 Delta variant remained viable on all the surfaces tested with and without an environmental biofilm after the virus was inoculated with the biofilm for 5 days at 7°C. We observed that SARS-CoV-2 Delta variant was able to remain infectious with each of the environmental biofilms by conducting plaque assay and qPCR experiments, however, we detected a significant reduction in viability post-exposure to Plant B biofilm on SS, PVC, and on ceramic tile chips, and to Plant C biofilm on SS and PVC chips. The numbers of viable SARS-CoV-2 Delta viral particles was 1.81–4.57-fold high than the viral inoculum incubated with the Plant B and Plant C environmental biofilm on SS, and PVC chips. We did not detect a significant difference in viability when SARS-CoV-2 Delta variant was incubated with the biofilm obtained from Plant A on any of the materials tested and SARS-CoV-2 Delta variant had higher plaque numbers when inoculated with Plant C biofilm on tile chips, with a 2.75-fold difference compared to SARS-CoV-2 Delta variant on tile chips by itself. In addition, we detected an increase in the biofilm biovolume in response to SARS-CoV-2 Delta variant which is also a concern for food safety due to the potential for foodborne pathogens to respond likewise when they come into contact with the virus. These results indicate a complex virus-environmental biofilm interaction which correlates to the different bacteria found in each biofilm. Our results also indicate that there is the potential for biofilms to protect SARS-CoV-2 from disinfecting agents and remaining prevalent in meat packaging plants.

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 the active carpet. The collective flows that these organisms generate lead 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 key transport 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 non-equilibrium fluctuations lead to a strongly enhanced diffusion of particles, which is anisotropic and space-dependent. The fluctuations also facilitate encounters of particle pairs, which we quantify by analyzing 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 has broadened our comprehension of aquatic systems out of equilibrium, particularly how biologically driven fluctuations contribute to the transport of fundamental elements in biogeochemical cycles.

Active emulsions can spontaneously form self-propelled droplets or phoretic micropumps. However, it remains unclear how these active systems interact with their self-generated chemical fields, which can lead to emergent chemodynamic phenomena and multistable interfacial flows. Here, we simultaneously measure the flow and chemical concentration fields using dual-channel fluorescence microscopy for active micropumps, i.e. immobilised oil droplets that dynamically solubilise in a supramicellar aqueous surfactant solution. With increasing droplet radius, we observe (i) a migration of vortices from the posterior to the anterior, analogous to a transition from pusher- to puller-type swimmers, (ii) a bistability between dipolar and quadrupolar flows and, eventually, (iii) a transition to multipolar modes. We also investigate the long-time dynamics. 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.