arXiv subjects

Raphaël Jeanneret

Publications and source records attributed to Raphaël Jeanneret.

14 recordsLinked to original sources

arXiv2026

Controlling microalgae populations by phototactic memory

Understanding how microorganisms navigate in complex environments is a central question in active matter and biological physics. Phototaxis - the ability to use light as a navigation cue - is a widespread strategy in motile microalgae to optimise photosynthesis and avoid light-induced stress. The microalga Chlamydomonas reinhardtii is a model system for studying this behaviour, where navigation is classically attributed to a photosensitive organelle named eyespot. While this mechanism enables cells to sense the direction of incoming light, their response to light intensity gradients remains less understood. Here we show that structured light landscapes can guide microalgae populations and localise them in defined spatial regions. By analysing single-cell trajectories, we find that cells actively steer relative to the local light gradient, and a comparison with a minimal theoretical model shows that a short-time memory of light exposure acting on the transition between positive and negative phototaxis is necessary to reproduce the observed accumulation. At longer times, we observe a gradual decrease in cell number density within the trapping region, consistent with phototactic adaptation. Beyond controlling population dynamics, our results reveal new aspects of phototactic behaviour, highlighting gradient-aligned steering together with temporal integration as central mechanisms for navigation in structured environments.

cond-mat.soft↗

arXiv2025

Pure hydrodynamic instabilities in active jets of "puller" microalgae

Active fluids can develop spontaneous flow instabilities and complex patterns. However, spatio-temporal control of active particles has remained challenging, despite its relevance in biological and applied contexts. Here, we harnessed phototaxis to steer millions of swimming ``puller" Chlamydomonas reinhardtii algae to create active jets and control both pearling and buckling instabilities through the preferential orientation of the cells. Our experiments, supported by a full analytical model and simulations, confirm long-standing predictions that self-generated flows can lead to jet destabilization. Our results further indicate that pullers can behave analogously to pushers when their orientation is properly tuned, and demonstrate how light enables efficient control of active fluids.

cond-mat.soft↗

arXiv2025

Hydrodynamic Instabilities of Active Jets

Using a combination of theory, experiments, and numerical simulations, we investigate the stability of coherent structures in a suspension of strongly aligned active swimmers. We show that a dilute jet of pullers undergoes a pearling instability, while a jet of pushers exhibits a helical (or, in two dimensions, zigzag) instability. We further characterise the nonlinear evolution of these instabilities, deriving exact and approximate solutions for the spreading and mutual attraction of puller clusters, as well as the wavelength coarsening of the helical instability. Our theoretical predictions closely match the experimentally observed wavelengths, timescales, and flow fields in suspensions of photophobic algae, as well as results from direct numerical simulations. These findings reveal the intrinsic instability mechanisms of aligned active suspensions and demonstrate that coherent structures can be destabilised by the flows they generate.

cond-mat.soft↗

arXiv2025

Phototactic Decision-Making by Micro-Algae

We study how simple eukaryotic organisms make decisions in response to competing stimuli in the context of phototaxis by the unicellular alga $Chlamydomonas~reinhardtii$. While negatively phototactic cells swim directly away from a collimated light beam, when presented with two beams of adjustable intersection angle and intensities, we find that cells swim in a direction given by an intensity-weighted average of the two light propagation vectors. This geometrical law is a fixed point of an adaptive model of phototaxis and minimizes the average light intensity falling on the anterior pole of the cell. At large angular separations, subpopulations of cells swim away from one source or the other, or along the direction of the geometrical law, with some cells stochastically switching between the three directions. This behavior is shown to arise from a population-level distribution of photoreceptor locations that breaks front-back symmetry of photoreception.

cond-mat.soft↗

arXiv2024

Light-induced phase separation with finite wavelength selection in photophobic micro-algae

As for many motile micro-algae, the freshwater species Chlamydomonas reinhardtii can detect light sources and adapt its motile behavior in response. Here, we show that suspensions of photophobic cells can be unstable to density fluctuations, as a consequence of shading interactions mediated by light absorption. In a circular illumination geometry this mechanism leads to the complete phase separation of the system into transient branching patterns, providing the first experimental evidence of finite wavelength selection in an active phase-separating system without birth and death processes. The finite wavelength selection, that can be captured in a simple drift-diffusion framework, is a consequence of a vision-based interaction length scale set by the illumination geometry and depends on global cell density, light intensity and medium viscosity. Finally we show that this active phase separation shields individual cells from the deleterious effects of high light intensity, demonstrating that phototaxis can efficiently contribute to photoprotection through collective behaviors on short timescales.

cond-mat.soft↗

arXiv2021

Confinement-induced accumulation and spontaneous de-mixing of microscopic active-passive mixtures

Understanding the out-of-equilibrium properties of noisy microscale systems and the extent to which they can be modulated externally, is a crucial scientific and technological challenge. It holds the promise to unlock disruptive new technologies ranging from targeted delivery of chemicals within the body to directed assembly of new materials. Here we focus on how active matter can be harnessed to transport passive microscopic systems in a statistically predictable way. Using a minimal active-passive system of weakly Brownian particles and swimming microalgae, we show that spatial confinement leads to a complex non-monotonic steady-state distribution of colloids, with a pronounced peak at the boundary. The particles' emergent active dynamics is well captured by a space-dependent Poisson process resulting from the space-dependent motion of the algae. Based on our findings, we then realise experimentally the spontaneous de-mixing of the active-passive suspension, opening the way for manipulating colloidal objects via controlled activity fields.

cond-mat.soft↗

arXiv2020

Stereo Darkfield Interferometry : a versatile localization method for subnanometer force spectroscopy of single molecules and 3D-tracking of single cells

Super-resolutive 3D tracking, such as PSF engineering or evanescent field imaging has long been used to track microparticles and to enhance the throughput of single molecules force spectroscopic measurements. However, current methods present two drawbacks. First, they lack precision compared with optical tweezers or AFM. Second, the dependence of their signal upon the position is complex creating the need for a time-consuming calibration step. Here, we introduce a new optical technique that circumvents both issues and allows for a simple, versatile and efficient 3D tracking of diluted particles while offering a sub-nanometer frame-to-frame precision in all three spatial directions. The principle is to combine stereoscopy and interferometry, such that the z (axial) position is measured through the distance between two interferometric fringe patterns. The linearity of this stereoscopy technique alleviates the need for lookup tables while the structured interferometric pattern enhances precision. On the other hand, the extended spatial footprint of this PSF maximizes the number of photons detected per frame without the need of fancy cameras, nor the need for complex hardware. Hence, thanks to its simplicity and versatility, we believe that SDI (Stereo Darkfield Interferometry) technology has the potential to significantly enhance the spreading of 3D tracking. We demonstrate the efficiency of this technique on various single-molecule measurements thanks to magnetic tweezers. In particular we demonstrate the precise quantification of two-state dynamics involving axial steps as short as 1 nm. We then show that SDI can be directly embedded in a commercial objective providing a means to track multiple single cells in 3D .

physics.bio-ph↗

arXiv2019

Confinement enhances the diversity of microbial flow fields

Despite their importance in many biological, ecological and physical processes, microorganismal fluid flows under tight confinement have not been investigated experimentally. Strong screening of Stokelets in this geometry suggests that the flow fields of different microorganisms should be universally dominated by the 2D source dipole from the swimmer's finite-size body. Confinement therefore is poised to collapse differences across microorganisms, that are instead well-established in bulk. Here we combine experiments and theoretical modelling to show that, in general, this is not correct. Our results demonstrate that potentially minute details like microswimmers' spinning and the physical arrangement of the propulsion appendages have in fact a leading role in setting qualitative topological properties of the hydrodynamic flow fields of micro-swimmers under confinement. This is well captured by an effective 2D model, even under relatively weak confinement. These results imply that active confined hydrodynamics is much richer than in bulk, and depends in a subtle manner on size, shape and propulsion mechanisms of the active components.

physics.bio-ph↗

arXiv2017

Universal entrainment mechanism governs contact times with motile cells

Contact between particles and motile cells underpins a wide variety of biological processes, from nutrient capture and ligand binding, to grazing, viral infection and cell-cell communication. The window of opportunity for these interactions is ultimately determined by the physical mechanism that enables proximity and governs the contact time. Jeanneret et al. (Nat. Comm. 7: 12518, 2016) reported recently that for the biflagellate microalga Chlamydomonas reinhardtii contact with microparticles is controlled by events in which the object is entrained by the swimmer over large distances. However, neither the universality of this interaction mechanism nor its physical origins are currently understood. Here we show that particle entrainment is indeed a generic feature for microorganisms either pushed or pulled by flagella. By combining experiments, simulations and analytical modelling we reveal that entrainment length, and therefore contact time, can be understood within the framework of Taylor dispersion as a competition between advection by the no slip surface of the cell body and microparticle diffusion. The existence of an optimal tracer size is predicted theoretically, and observed experimentally for C. reinhardtii. Spatial organisation of flagella, swimming speed, swimmer and tracer size influence entrainment features and provide different trade-offs that may be tuned to optimise microbial interactions like predation and infection.

physics.bio-ph↗

arXiv2016

A brief introduction to the model microswimmer {\it Chlamydomonas reinhardtii}

The unicellular biflagellate green alga {\it Chlamydomonas reinhardtii} has been an important model system in biology for decades, and in recent years it has started to attract growing attention also within the biophysics community. Here we provide a concise review of some of the aspects of {\it Chlamydomonas} biology and biophysics most immediately relevant to physicists that might be interested in starting to work with this versatile microorganism.

q-bio.CB↗

arXiv2016

Entrainment dominates the interaction of microalgae with micron-sized objects

The incessant activity of swimming microorganisms has a direct physical effect on surrounding microscopic objects, leading to enhanced diffusion far beyond the level of Brownian motion with possible influences on the spatial distribution of non-motile planktonic species and particulate drifters. Here we study in detail the effect of eukaryotic flagellates, represented by the green microalga Chlamydomonas reinhardtii, on microparticles. Macro- and micro-scopic experiments reveal that microorganism-colloid interactions are dominated by rare close encounters leading to large displacements through direct entrainment. Simulations and theoretical modelling show that the ensuing particle dynamics can be understood in terms of a simple jump-diffusion process, combining standard diffusion with Poisson-distributed jumps. This heterogeneous dynamics is likely to depend on generic features of the near-field of swimming microorganisms with front-mounted flagella.

physics.bio-ph↗

arXiv2015

Emergent hyperuniformity in periodically-driven emulsions

We report the emergence of large-scale hyperuniformity in microfluidic emulsions. Upon periodic driving confined emulsions undergo a first-order transition from a reversible to an irreversible dynamics. We evidence that this dynamical transition is accompanied by structural changes at all scales yielding macroscopic yet finite hyperuniform structures. Numerical simulations are performed to single out the very ingredients responsible for the suppression of density fluctuations. We show that as opposed to equilibrium systems the long-range nature of the hydrodynamic interactions are not required for the formation of hyperuniform patterns, thereby suggesting a robust relation between reversibility and hyperuniformity which should hold in a broad class of periodically driven materials.

cond-mat.soft↗

arXiv2014

Geometrically-protected reversibility in hydrodynamic Loschmidt-echo experiments

We demonstrate an archetypal Loschmidt-echo experiment involving thousands of droplets which interact in a reversible fashion via a viscous fluid. Firstly, we show that, unlike equilibrium systems, periodically driven microfluidic emulsions self-organize and geometrically protect their macroscopic reversibility. Self-organization is not merely dynamical; we show that it has a clear structural signature akin to that found in a mixture of molecular liquids. Secondly, we show that, above a maximal shaking amplitude, structural order and reversibility are lost simultaneously in the form of a first order non-equilibrium phase transition. We account for this discontinuous transition in terms of a memory-loss process. Finally, we suggest potential applications of microfluidic echo as a robust tool to tailor colloidal self-assembly at large scales.

cond-mat.soft↗

arXiv2011

Hamiltonian traffic dynamics in microfluidic-loop networks

Recent microfluidic experiments revealed that large particles advected in a fluidic loop display long-range hydrodynamic interactions. However, the consequences of such couplings on the traffic dynamics in more complex networks remain poorly understood. In this letter, we focus on the transport of a finite number of particles in one-dimensional loop networks. By combining numerical, theoretical, and experimental efforts, we evidence that this collective process offers a unique example of Hamiltonian dynamics for hydrodynamically interacting particles. In addition, we show that the asymptotic trajectories are necessarily reciprocal despite the microscopic traffic rules explicitly break the time reversal symmetry. We exploit these two remarkable properties to account for the salient features of the effective three-particle interaction induced by the exploration of fluidic loops.

cond-mat.soft↗