Chemotaxis – from Basic Physics to Biology

This study delves into the intricate dynamics underlying the self-organisation of active matter systems, elucidating the fundamental role of non-equilibrium thermodynamics in shaping their structure and stability. We investigate the formation of catalytic aggregates of Janus particles in heterogeneous environments, characterised by concentration gradients and fluid flow induced by particle activity. By incorporating hydrodynamic interactions (HI) in our analysis, we reveal the influence of these interactions on the mobility and arrangement of the aggregate constituents, revealing a richer spectrum of structural features compared to systems lacking such interactions. Despite the observed decrease in energy conversion efficiency in the presence of hydrodynamic interactions, their presence facilitates the emergence of complex structures, amplifying the thermodynamic stability of the system. Furthermore, our examination of the energetic cost of structure formation, exploiting the entropy production rate and the out-of-equilibrium chemical potential, reveals distinct self-assembly regimes governed by the interplay of particle dynamics and fuel concentration gradients. This holistic thermodynamic framework provides valuable insights into the principles governing the formation and stability of active matter structures, shedding light on their relevance to natural phenomena and engineered systems.

The motile response of bacteria to chemical profiles that change in both space and time is not well understood. Recent work has highlighted the importance of accounting for temporal variations of chemical landscapes in determining the fundamental limits of bacterial chemo-sensing. However, this has not been incorporated into a continuum model of chemotaxis. Critically, an expression for how the chemotactic drift velocity depends on both spatial and temporal gradients has not been derived. Here, using Monte Carlo Simulations we simulate different bacterial paths and average over these paths to obtain an expression for the mean drift velocity, which accounts for both temporal and spatial gradients. Using this newly-derived drift velocity, we use a continuum model of chemotaxis to explore a series of dynamic chemical environments, inspired by microfluidic experiments.

Using Ludwig, an open-source hybrid Lattice-Boltzmann+free-energy code, we develop a model to represent photo-catalytically active Pacman-shaped colloid, such as the one proposed here (https://onlinelibrary.wiley.com/doi/full/10.1002/aisy.202200091). Our model captures the main features of the experiments including vertical confinement, directional photo-catalytic activity, chemo-phoretic effects, and the unique "Pacman" colloid in its viscous fluid environment. As a simplified version of the real setup, it provides 1) a "mirror" to compare observations with theoretical predictions, a useful tool to rationalize the mechanism at play at the difficult-to-probe nano-scales. It is also interesting to 2) understand the model in itself, free from experimental constraints, to derive theoretical principles associated with the active motion of colloids of complex shape. Here, we propose a mechanism to explain the experimental fact that Pacman have a preferred orientation when sedimented on horizontal substrate, and under bottom-up illumination. We also provide some insights into their chemo-phoretic behavior in bulk fluid.

The capacity of cells to perceive and react to chemical signals in their surroundings is vital for their survival and adaptability, making chemotaxis a decisive phenomenon in evolution. Our investigation explored the essential elements required for observing chemotaxis within a protocell model. This model comprised a liposome with an encapsulated enzyme and a transmembrane protein, specifically α-hemolysin. By employing this setup, we simplified the fundamental constituents of a cell to their bare minimum: the compartmentalization of a chemical reaction within a lipidic bilayer membrane. The α-hemolysin assembles into a heptametric pore within the liposome membrane, facilitating the transport of substrate and products into and out of the liposome. Consequently, when a liposome containing an encapsulated enzyme is situated in an environment with the corresponding substrate, an asymmetrical distribution of products emerges along its surface, promoting active motion. Our focus extended to examining the motion of liposomes encapsulating glucose oxidase and urease, exposed to glucose and urea concentration gradients, respectively. The drift velocities were obtained by tracking single liposomes in a microfluidic device (μ-slide chemotaxis Ibidi) using a Confocal microscope. Parallel experiments, tracking polystyrene beads with diverse surface chemistries, allowed us to assess fluid flows induced by the concentration gradient in the microfluidic device. Observations revealed that high-concentration gradients induced advective flows, while low-concentration gradients led to flows induced by diffusion osmosis. The direction of diffusioosmotic flows depends on the interaction potential between the solute and the channel walls; glucose exhibited a positive interaction potential, while urea displayed a negative potential. The concentration gradient was limited to the range with no advective flows to track liposomes accurately. The liposome drift results from diffusioosmophoresis and chemotaxis. The chemotactic component is absent for liposomes with no pores, as there is no asymmetry in the system. Liposomes lacking pores, encapsulating glucose oxidase, and urease showed a drift towards low substrate concentration, explained by diffusioosmophoresis. Introducing pores resulted in a diminished velocity drift towards lower concentrations, implying in positive chemotaxis component. Notably, liposomes encapsulating urease with an α-hemolysin-to-lipids ratio of 0.5 (by mass) exhibited a reversal of drift toward higher urea concentrations. Our minimal chemotactic cell model showcased the achievement of chemotaxis by simply incorporating an enzyme and a transmembrane protein into liposomes. Furthermore, the chemotactic component showed an increase, corresponding to the increased concentration of α-hemolysin.

Flagellar swimming allows bacteria to travel long distances. When a mobile bacterium approaches a surface, hydrodynamic interactions cause its trajectory to become circular. However, the bacterium's path is marked by periodic reorientations and pauses resulting from changes in the rotational direction of the flagellar bundle. This directional shift occurs at regular intervals, approximately every second, lasting about 100 milliseconds in the case of the bacterium E. coli. These sporadic reorientations enable bacteria to enhance their effective diffusion near surfaces, facilitating environmental exploration. Bacterial chemotaxis takes advantage of a frequency bias in reorientation, allowing the redistribution of bacterial populations to evade toxic environments and move towards favorable regions. Our research focuses on the impact of known chemorepellent substances, such as Ni2+ cations, on bacterial redistribution. Experimental investigations into bacterial motility under varied chemical conditions in microfluidic channels are carried out using dark-field video microscopy. The chemorepulsive diffusion profile of Ni2+ and other cations generates an asymmetric wave. Notably, individual bacteria exhibit a biased motion aligned with the direction of the wave's propagation. The surface behavior of the wave differs from its bulk counterpart. A minimal model, integrating Ni2+ diffusion and chemotactically enhanced bacterial displacement, successfully replicates the asymmetrical shape of the wave and its average speed. The colonization pattern is marked by collective movement in large groups within the bulk and scattering at the surface.

Inspired by adaptation in the swarming behaviour of bacteria and slime molds, we study experimental synthetic systems that display quorum sensing-like behavior and emergent pattern formation. Specifically, we are interested in the self-organizing behaviour of motile droplets that are driven by surface tension imbalances (Marangoni effect). We employ simple pH gradients and pH sensitive surfactants to generate these surface tension imbalances at air-water interfaces. As a consequence, the droplets that float at such an interface become motile and depending on the intensity of the chemical gradient and on the mutual interactions with neigboring droplets display clustering or more complex pattern formation. First, we show an example of floating emulsion droplets that only cluster when sufficient signalling molecules are generated by the droplets, reminiscent of quorum sensing in Dictyostelium discoideum colonies. Furthermore, we incorporate a chemical reaction that leads to a luminescence response upon collective clustering, similar to the bioluminescence generated by Vibrio fischeri. Second, we demonstrate floating surfactant droplets that self-generate local Marangoni flow, revealed by the protrusion of so-called myelin filaments. When an external pH gradient is applied to a swarm of these droplets, the competition between the global and local surface tension gradients lead to emergent patterning that is under control of the total amount of acid added to the system.

Neutrophils, as primary responders to tissue damage, exhibit a transition from motile patrolling to coordinated swarming upon detecting a wound. This dynamic shift is crucial for the rapid and effective containment of potential infections and the initiation of the healing process. However, the underlying mechanisms governing this transition and the subsequent swarm dynamics remain incompletely understood. Here, we introduce a mathematical model that simulates neutrophil behavior from individual motility to collective swarming in response to wounding-induced signaling. Our model incorporates the complex interplay between chemotactic signaling, neutrophil-neutrophil interactions, and the evolving wound environment. Through this framework, we provide key insights into the growth and dynamics of neutrophil swarms, highlighting the critical factors that drive the formation and maintenance of these swarms. Our findings offer a deeper understanding of the self-organized nature of neutrophil responses to tissue damage and present a quantitative tool for exploring the implications of neutrophil dynamics in wound healing and inflammation. This work not only advances our knowledge of immune cell behavior but also opens avenues for developing targeted interventions to modulate the inflammatory response for improved healing outcomes.

Artificial chemotaxis is achieved by using the popular Janus particle, composed of a catalytic half and an inert half. This system breaks the symmetry of the particle and allows it the ability to swim. TiO2 pacmen particles are a single material but have an asymmetric structure, with a crack along one side. This physical asymmetry allows pac-men particles to catalyze hydrogen peroxide at different rates along their structure. This method allows a simple method to produce a self-asymmetric catalytic particle that can swim in hydrogen peroxide under a UV light. The current research seeks to establish if these particles perform any form of taxis in a gradient of fuel.

Nanorobots receive great attention for their move-sense-and-act capabilities. Autonomous movement enables the micro/nanorobots to navigate within complex environments1 and perform encoded tasks. Among the designs, chemically-powered micro/nanomotors can harness the catalytic power of enzymes that convert chemical fuels to motion. The motion is often induced by catalytic decomposition of the fuel, but the efficiency of fuel conversion of these nanomachines remains low. In the past decade, single atom engineering has demonstrated exceptional efficiency in catalysis, energy-related technologies, and medicine. Downsizing functional nanoparticles to single atoms2 not only enhances catalytic activities and metal utilization efficiency but also facilitates the possibility of coupling cascade reactions in one confinement with structural simplicity3. In this study, we present a novel approach involving point defect engineering and the incorporation of single atoms and atomic level species onto the surface of dioxide-based nanomaterials. We investigate the impact of catalytic single atoms on the propulsion capabilities of nanorobots. Single atom decorated nanorobots demonstrated enhanced motion due to maximized catalytic effect of dispersed catalyst species. The developed nanorobots have demonstrated remarkable efficiency toward biomedical and environmental applications, offering promising advances in related technologies. Acknowledgement: This work is supported by ERDF/ESF project TECHSCALE (No. CZ.02.01.01/00/22_008/0004587), Czech Republic. This work is also produced with the support of the NCK project for industrial 3D printing, reg. no. TN02000033, which is co-financed with state support from the Technology Agency of the Czech Republic under the National Centres of Competence Programme. References: [1] Oral, C. M. & Pumera, M. In vivo applications of micro/nanorobots. Nanoscale, 15, 8491-8507 (2023). [2] Lang, R. et al. Single-atom catalysts based on the metal–oxide interaction. Chemical Reviews, 120, 11986-12043 (2020). [3] Du, X. et al. pH-switchable nanozyme cascade catalysis: a strategy for spatial-temporal modulation of pathological wound microenvironment to rescue stalled healing in diabetic ulcer. Journal of Nanobiotechnology, 20, 12 (2022).

Bacterial contamination is an important issue in industrial manufacturing and there is a need to detect and identify bacteria in a label-free and a cost-effective manner. A particular challenge is in-line detection, i.e. the detection directly in an industrial process plant without the ability to take samples to a remote laboratory, which is the goal of this project. We use autofluorescence, because bacteria contain biomolecules such as flavins and porphyrins that autofluoresce in the green and red spectral region, respectively. Initial experiments were performed on Escherichia coli and Halomonas, both of which show strong autofluorescence in the green and weaker signals in the red. We also aim to resonantly enhance this autofluorescence signal using guided mode resonances (GMR). The future goal is to attach a miniaturized set-up directly to the process pipes that can detect and identify bacterial contamination.

The chemotactic response of flagellated bacteria is based on the understanding of the different biochemical pathways that drive the rotation of rotary motors hooked to propelling flagella. The resulting complex stochastic process often describes as a compound of run and tumble sequences, will emerge macroscopically as a mean chemotactic drift taking place along the chemical gradients. However in general, this picture is influenced by many factors such as internal stochasticity borne in the sensory pathways that provides the internal adaptation dynamics as well as the presence of geometrical disorder that may “disorient “ the bacterium and finally provide a mean chemotactic drift depending strongly on various environmental geometrical features. To clarify this question, we carried out several experiments in which we obtained bacterial trajectories and chemotactic biases under different controlled situations. The first experiment allows us to study the effect of internal chemotactic circuitry with different transmembrane receptors. To do this, we use a microfluidic device that creates a linear gradient of attractant (glucose, serine, aspartate) in which we monitor individual bacteria trajectories. In this study, we quantify the role of surfaces in the chemotactic drift and separate the bulk/surfaces contributions. We studied another chemotactic circuit - energy taxis - which is an internal measurement of bacterial metabolism that causes bacteria to migrate to more energetically favorable areas. To do this, we used a microfluidic setup in which we can create uniform concentrations, or gradients, of oxygen (aerotaxis). Both experiments use two different methods of observation. Either an Eulerian view, where the observation area is fixed and many bacteria are tracked over a short period of time. Or we use a 3D Lagrangian tracking method where we can follow one bacterium over a long period of time, giving access to time resolved behavioral variations.

Motor proteins are unique in their ability to convert chemical energy into mechanical work, enabling life to move by using the cytoskeleton as a railway. Kinesins which move along microtubules stand out for their role in intracellular transport and mitosis. During mitosis, kinesins orchestrate the arrangement of microtubule bundles within the spindle apparatus by sliding them against each other. Notably, certain kinesins display an intriguing behavior where they not only move linearly but also traverse sideways to neighboring microtubule protofilaments, tracing helical trajectories around the microtubules. This sidestepping phenomenon could induce torque within the filament bundles, resulting in a twist of the spindle structure, as observed in HeLa and RPE-1 cell lines. This torsional motion can be modulated by the regulation of various kinesins as well as the passive crosslinker PRC1. Kinesin-5 is the key regulator, because it contributes to the separation of spindle poles during late anaphase when spindle twist is most pronounced. We studied human kinesin-5 (KIF11) in an in vitro 3D sliding assay and found that it drives regular right-handed helical motion of microtubules around each other. These motions remained stable when varying the motor number in the overlaps. Furthermore, resolved the individual orientation of microtubules and correlated it with the arrangement of motors in the overlap. By titrating the passive crosslinker PRC1 into the KIF11 sliding assay, we could halt microtubule movement, and by adding the minus-end directed kinesin-14 (HSET), we could even reverse the direction of movement, depending on the HSET:KIF11 ratio. Thus, our study provides a detailed examination of microtubule bundle rotations by motor proteins and elucidates the intricate interplay of sliding regulation by motors and passive crosslinkers in vitro.

The controlled transport of sub-micron colloidal particles within a confined environment, such as a porous medium or a dead end channel, is a key feature in several technological applications (e.g., drug delivery, diagnostics) as well as in living systems (e.g., mass transport in tissues and capillaries). Recently, we demonstrated how solute gradients in steady-state continuous flows past a microgrooved surface can be exploited to induce the controlled and reversible trapping of sub-micron particles within the dead-end grooves. The trapping mechanism is governed by diffusiophoresis, which drives particle motion along a solute gradient. In this study, we investigate how the particle trapping is affected by the groove geometry, channel surface chemistry and solute gradient intensity, thereby determining the conditions for enhancing the particle trapping performance. The microfluidic devices, featuring a 3-inlet junction for generating the salt gradients, are made of an optical glue (NOA-81) layer, laid on a silicon microgrooved substrate. The proposed approach for particle transport in lab-on-a-chip devices has potential applications in point-of-care, drug delivery and biosensing industry

We have developed a synthetic system of motile Escherichia coli bacteria encapsulated inside giant lipid vesicles. Forces exerted by the bacteria on the inner side of the membrane are sufficient to extrude membrane tubes filled with one or several bacteria. We have shown that a physical coupling between the membrane tube and the flagella of the enclosed cells transforms the tube into an effective helical flagellum propelling the vesicle (Le Nagard et al., PNAS 119(34), 2022). Our current work focuses on realising a directed vesicle motion in pH gradients. We study how externally imposed pH gradients transmit across the vesicle membrane and are being sensed and enacted by the encapsulated bacteria in guiding the motion of the whole vesicle. The chemotactic motion can be additionally coupled to a source of nutrients and lipids, hence allowing our bio-hybrid system to move, grow and multiply.

Unlike bacteria, eukaryotic cells are large enough to sense a chemical gradient across their cell body. However, chemotaxis of an entire cell requires a mechanism for coordinating competing protrusions. The slime mold Physarum polycephalum is a giant unicellular organism built in the form of a fluid-filled tubular network. Its strong and large-scale cytoplasmic flows make it an ideal model organism to study the role of fluid flows in coordinating the collective behavior of competing protrusions during morphological changes during chemotaxis. We perform experiments, analyze trajectories and protrusion dynamics, and simulate fluid flows to elucidate the mechanism that coordinates the chemotaxis of this macroscopic cell.

One of the fundamental requirements for self diffusiophoresis in a particle is the presence of catalytic asymmetry. Common methods to introduce such asymmetry involve procedures such as deposition of metals, passive elements or masking with wax among others. Here we present a simpler approach using MXenes, based on their 2D layered structure. MXenes are a class of two-dimensional transition metal carbides, nitrides, and carbonitrides that exhibit a range of remarkable properties which has enabled diverse applications across various branches of electrochemistry. Their unique layered structure, combined with excellent electrical conductivity, mechanical strength, and surface chemistry, makes them highly versatile materials. In addition, MXene based micromotors have been previously demonstrated for nano plastic removal from water. Given the layered structure, solvent based chemical modification methods allow for direct asymmetric modification as the inner surface is masked until the structure is delaminated. This approach not only simplifies the creation of catalytic asymmetry in self-diffusiophoretic particles but also paves the way for scalable environmental and biomedical applications involving micromotors.

Due to their small size, artificial micro-motors struggle to accommodate automated control devices, thus limiting their practical application in real environments. Consequently, developing self-propelled artificial micro-motors is a key academic focus. Currently, reports indicate Janus micro-motors can generate torque in gradients, aligning motion with gradients for directed movement. However, as micro-motor size decreases, larger gradient fields are needed to counter enhanced Brownian motion and sustain directional movement. Physicochemical field gradients are small in practical scenarios due to mass transfer, heat transfer, and light scattering, hindering self-propulsion in small micro-motors. Thus, new mechanisms are essential for stable self-propulsion in low-gradient environments. Microorganisms in nature (e.g., light-responsive algae, nutrient-responsive E. coli) achieve stable orientation via rotation and translation. To address challenges in micro-motor self-propulsion under low-gradient or small-sized conditions, this study integrates rotational and translational motions using biomimetic strategies. Compound motion patterns aim to enhance micro-motors' autonomous navigation effectively. The study verify that the composite motion mode can maintain the autonomous navigation characteristics under lower physicochemical gradient conditions by Brownian dynamics simulations, and desigh a novel micro-motor that can independently control both translational and rotational parameters by optimizing the structural geometry and material design, and demonstrate the characteristics of its navigational behaviors in low gradient environments. Additionally, A correlation model between the rotation rate and the degree and rate of navigation is also developed based on experimental results using the theory of physical statistics.The successful implementation of this study will provide new strategies for the design of self-propelled artificial nanomachines. The resulting self-propelled motors hold promise for applications in regional drug delivery and sensor detection.