Steering self-organisation through confinement.

Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units' translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.

Myosin II Filament Dynamics in Actin Networks Revealed with Interferometric Scattering Microscopy.

The plasma membrane and the underlying cytoskeletal cortex constitute active platforms for a variety of cellular processes. Recent work has shown that the remodeling acto-myosin network modifies local membrane organization, but the molecular details are only partly understood because of difficulties with experimentally accessing the relevant time and length scales. Here, we use interferometric scattering microscopy to investigate a minimal acto-myosin network linked to a supported lipid bilayer membrane. Using the magnitude of the interferometric contrast, which is proportional to molecular mass, and fast acquisition rates, we detect and image individual membrane-attached actin filaments diffusing within the acto-myosin network and follow individual myosin II filament dynamics. We quantify myosin II filament dwell times and processivity as functions of ATP concentration, providing experimental evidence for the predicted ensemble behavior of myosin head domains. Our results show how decreasing ATP concentrations lead to both increasing dwell times of individual myosin II filaments and a global change from a remodeling to a contractile state of the acto-myosin network.

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, which are instead well established in bulk. We combine experiments and theoretical modeling to show that, in general, this is not correct. Our results demonstrate that potentially minute details like microswimmer 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 microswimmers 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 the size, shape, and propulsion mechanisms of the active components.

Light Control of Localized Photobioconvection.

Microorganismal motility is often characterized by complex responses to environmental physico-chemical stimuli. Although the biological basis of these responses is often not well understood, their exploitation already promises novel avenues to directly control the motion of living active matter at both the individual and collective level. Here we leverage the phototactic ability of the model microalga Chlamydomonas reinhardtii to precisely control the timing and position of localized cell photoaccumulation, leading to the controlled development of isolated bioconvective plumes. This novel form of photobioconvection allows a precise, fast, and reconfigurable control of the spatiotemporal dynamics of the instability and the ensuing global recirculation, which can be activated and stopped in real time. A simple continuum model accounts for the phototactic response of the suspension and demonstrates how the spatiotemporal dynamics of the illumination field can be used as a simple external switch to produce efficient bio mixing.

Ciliary contact interactions dominate surface scattering of swimming eukaryotes.

Interactions between swimming cells and surfaces are essential to many microbiological processes, from bacterial biofilm formation to human fertilization. However, despite their fundamental importance, relatively little is known about the physical mechanisms that govern the scattering of flagellated or ciliated cells from solid surfaces. A more detailed understanding of these interactions promises not only new biological insights into structure and dynamics of flagella and cilia but may also lead to new microfluidic techniques for controlling cell motility and microbial locomotion, with potential applications ranging from diagnostic tools to therapeutic protein synthesis and photosynthetic biofuel production. Due to fundamental differences in physiology and swimming strategies, it is an open question of whether microfluidic transport and rectification schemes that have recently been demonstrated for pusher-type microswimmers such as bacteria and sperm cells, can be transferred to puller-type algae and other motile eukaryotes, because it is not known whether long-range hydrodynamic or short-range mechanical forces dominate the surface interactions of these microorganisms. Here, using high-speed microscopic imaging, we present direct experimental evidence that the surface scattering of both mammalian sperm cells and unicellular green algae is primarily governed by direct ciliary contact interactions. Building on this insight, we predict and experimentally verify the existence of optimal microfluidic ratchets that maximize rectification of initially uniform Chlamydomonas reinhardtii suspensions. Because mechano-elastic properties of cilia are conserved across eukaryotic species, we expect that our results apply to a wide range of swimming microorganisms.

Microalgae Scatter off Solid Surfaces by Hydrodynamic and Contact Forces.

Interactions between microorganisms and solid boundaries play an important role in biological processes, such as egg fertilization, biofilm formation, and soil colonization, where microswimmers move within a structured environment. Despite recent efforts to understand their origin, it is not clear whether these interactions can be understood as being fundamentally of hydrodynamic origin or hinging on the swimmer's direct contact with the obstacle. Using a combination of experiments and simulations, here we study in detail the interaction of the biflagellate green alga Chlamydomonas reinhardtii, widely used as a model puller microorganism, with convex obstacles, a geometry ideally suited to highlight the different roles of steric and hydrodynamic effects. Our results reveal that both kinds of forces are crucial for the correct description of the interaction of this class of flagellated microorganisms with boundaries.

Antiphase synchronization in a flagellar-dominance mutant of Chlamydomonas.

Groups of beating flagella or cilia often synchronize so that neighboring filaments have identical frequencies and phases. A prime example is provided by the unicellular biflagellate Chlamydomonas reinhardtii, which typically displays synchronous in-phase beating in a low-Reynolds number version of breaststroke swimming. We report the discovery that ptx1, a flagellar-dominance mutant of C. reinhardtii, can exhibit synchronization in precise antiphase, as in the freestyle swimming stroke. High-speed imaging shows that ptx1 flagella switch stochastically between in-phase and antiphase states, and that the latter has a distinct waveform and significantly higher frequency, both of which are strikingly similar to those found during phase slips that stochastically interrupt in-phase beating of the wild-type. Possible mechanisms underlying these observations are discussed.

Hydrodynamic synchronization and metachronal waves on the surface of the colonial alga Volvox carteri.

From unicellular ciliates to the respiratory epithelium, carpets of cilia display metachronal waves, long-wavelength phase modulations of the beating cycles, which theory suggests may arise from hydrodynamic coupling. Experiments have been limited by a lack of organisms suitable for systematic study of flagella and the flows they create. Using time-resolved particle image velocimetry, we report the discovery of metachronal waves on the surface of the colonial alga Volvox carteri, whose large size and ease of visualization make it an ideal model organism for these studies. An elastohydrodynamic model of weakly coupled compliant oscillators, recast as interacting phase oscillators, reveals that orbit compliance can produce fast, robust synchronization in a manner essentially independent of boundary conditions, and offers an intuitive understanding of a possible mechanism leading to the emergence of metachronal waves.

Confinement-induced accumulation and 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 de-mixing of the active-passive suspension, opening the way for manipulating colloidal objects via controlled activity fields.

Microbial pioneers of plastic colonisation in coastal seawaters.

Plastics, when entering the environment, are immediately colonised by microorganisms. This modifies their physico-chemical properties as well as their transport and fate in natural ecosystems, but whom pioneers this colonisation in marine ecosystems? Previous studies have focused on microbial communities that develop on plastics after relatively long incubation periods (i.e., days to months), but very little data is available regarding the earliest stages of colonisation on buoyant plastics in marine waters (i.e., minutes or hours). We conducted a preliminary study where the earliest hours of microbial colonisation on buoyant plastics in marine coastal waters were investigated by field incubations and amplicon sequencing of the prokaryotic and eukaryotic communities. Our results show that members of the Bacteroidetes group pioneer microbial attachment to plastics but, over time, their presence is masked by other groups - Gammaproteobacteria at first and later by Alphaproteobacteria. Interestingly, the eukaryotic community on plastics exposed to sunlight became dominated by phototrophic organisms from the phylum Ochrophyta, diatoms at the start and brown algae towards the end of the three-day incubations. This study defines the pioneering microbial community that colonises plastics immediately when entering coastal marine environments and that may set the seeding Plastisphere of plastics in the oceans.

Emergence of synchronized beating during the regrowth of eukaryotic flagella.

A fundamental issue in the biology of eukaryotic flagella is the origin of synchronized beating observed in tissues and organisms containing multiple flagella. Recent studies of the biflagellate unicellular alga Chlamydomonas reinhardtii provided the first evidence that the interflagellar coupling responsible for synchronization is of hydrodynamic origin. To investigate this mechanism in detail, we study here synchronization in Chlamydomonas as its flagella slowly regrow after mechanically induced self-scission. The duration of synchronized intervals is found to be strongly dependent on flagellar length. Analysis within a stochastic model of coupled phase oscillators is used to extract the length dependence of the interflagellar coupling and the intrinsic beat frequencies of the two flagella. Physical and biological considerations that may explain these results are proposed.

Swarming bacteria undergo localized dynamic phase transition to form stress-induced biofilms.

Self-organized multicellular behaviors enable cells to adapt and tolerate stressors to a greater degree than isolated cells. However, whether and how cellular communities alter their collective behaviors adaptively upon exposure to stress is largely unclear. Here, we investigate this question using Bacillus subtilis, a model system for bacterial multicellularity. We discover that, upon exposure to a spatial gradient of kanamycin, swarming bacteria activate matrix genes and transit to biofilms. The initial stage of this transition is underpinned by a stress-induced multilayer formation, emerging from a biophysical mechanism reminiscent of motility-induced phase separation (MIPS). The physical nature of the process suggests that stressors which suppress the expansion of swarms would induce biofilm formation. Indeed, a simple physical barrier also induces a swarm-to-biofilm transition. Based on the gained insight, we propose a strategy of antibiotic treatment to inhibit the transition from swarms to biofilms by targeting the localized phase transition.

Pili allow dominant marine cyanobacteria to avoid sinking and evade predation.

How oligotrophic marine cyanobacteria position themselves in the water column is currently unknown. The current paradigm is that these organisms avoid sinking due to their reduced size and passive drift within currents. Here, we show that one in four picocyanobacteria encode a type IV pilus which allows these organisms to increase drag and remain suspended at optimal positions in the water column, as well as evade predation by grazers. The evolution of this sophisticated floatation mechanism in these purely planktonic streamlined microorganisms has important implications for our current understanding of microbial distribution in the oceans and predator-prey interactions which ultimately will need incorporating into future models of marine carbon flux dynamics.

Direct measurement of the flow field around swimming microorganisms.

Swimming microorganisms create flows that influence their mutual interactions and modify the rheology of their suspensions. While extensively studied theoretically, these flows have not been measured in detail around any freely-swimming microorganism. We report such measurements for the microphytes Volvox carteri and Chlamydomonas reinhardtii. The minute (∼0.3%) density excess of V. carteri over water leads to a strongly dominant Stokeslet contribution, with the widely-assumed stresslet flow only a correction to the subleading source dipole term. This implies that suspensions of V. carteri have features similar to suspensions of sedimenting particles. The flow in the region around C. reinhardtii where significant hydrodynamic interaction is likely to occur differs qualitatively from a puller stresslet, and can be described by a simple three-Stokeslet model.

Noise and synchronization in pairs of beating eukaryotic flagella.

It has long been conjectured that hydrodynamic interactions between beating eukaryotic flagella underlie their ubiquitous forms of synchronization; yet there has been no experimental test of this connection. The biflagellate alga Chlamydomonas is a simple model for such studies, as its two flagella are representative of those most commonly found in eukaryotes. Using micromanipulation and high-speed imaging, we show that the flagella of a C. reinhardtii cell present periods of synchronization interrupted by phase slips. The dynamics of slips and the statistics of phase-locked intervals are consistent with a low-dimensional stochastic model of hydrodynamically coupled oscillators, with a noise amplitude set by the intrinsic fluctuations of single flagellar beats.

Autocalibrated colloidal interaction measurements with extended optical traps.

We describe an efficient technique for measuring the effective interaction potential for pairs of colloidal particles. The particles to be tested are confined in an extended optical trap, also known as a line tweezer, that is projected with the holographic optical trapping technique. Their diffusion along the line reflects not only their intrinsic interactions with each other, but also the influence of the line's potential energy landscape and interparticle interactions mediated by scattered light. We demonstrate that measurements of the particles' trajectories at just two laser powers can be used to correct explicitly for optically induced forces and that statistically optimal analysis for optically induced forces yields autocalibrated measurements of the particles' intrinsic interactions with remarkably few statistically independent measurements of the particles' separation.

Transitions in synchronization states of model cilia through basal-connection coupling.

Despite evidence for a hydrodynamic origin of flagellar synchronization between different eukaryotic cells, recent experiments have shown that in single multi-flagellated organisms, coordination hinges instead on direct basal body connections. The mechanism by which these connections lead to coordination, however, is currently not understood. Here, we focus on the model biflagellate Chlamydomonas reinhardtii, and propose a minimal model for the synchronization of its two flagella as a result of both hydrodynamic and direct mechanical coupling. A spectrum of different types of coordination can be selected, depending on small changes in the stiffness of intracellular couplings. These include prolonged in-phase and anti-phase synchronization, as well as a range of multi-stable states induced by spontaneous symmetry breaking of the system. Linking synchrony to intracellular stiffness could lead to the use of flagellar dynamics as a probe for the mechanical state of the cell.

Critical behavior of the Chayes-Machta-Swendsen-Wang dynamics.

We study the dynamic critical behavior of the Chayes-Machta dynamics for the Fortuin-Kasteleyn random-cluster model, which generalizes the Swendsen-Wang dynamics for the q-state Potts model to noninteger q, in two and three spatial dimensions, by Monte Carlo simulation. We show that the Li-Sokal bound z >or= alpha/nu is close to but probably not sharp in d = 2 and is far from sharp in d = 3, for all q. The conjecture z >or= beta/nu is false (for some values of q) in both d = 2 and d = 3.

Colloidal electrostatic interactions near a conducting surface.

Like-charged colloidal spheres dispersed in de-ionized water are supposed to repel each other. Instead, artifact-corrected video microscopy measurements reveal an anomalous long-ranged like-charge attraction in the interparticle pair potential when the spheres are confined to a layer by even a single-charged glass surface. These attractions can be masked by electrostatic repulsions at low ionic strengths. Coating the bounding surfaces with a conducting gold layer suppresses the attraction. These observations suggest a possible mechanism for the anomalous confinement-induced attractions.