Macroscopic waves, biological clocks and morphogenesis driven by light in a giant unicellular green alga.

A hallmark of self-organisation in living systems is their capacity to stabilise their own dynamics, often appearing to anticipate and act upon potential outcomes. Caulerpa brachypus is a marine green alga consisting of differentiated organs resembling leaves, stems and roots. While an individual can exceed a metre in size, it is a single multinucleated giant cell. Thus Caulerpa presents the mystery of morphogenesis on macroscopic scales in the absence of cellularization. The experiments reported here reveal self-organised waves of greenness - chloroplasts - that propagate throughout the alga in anticipation of the day-night light cycle. Using dynamical systems analysis we show that these waves are coupled to a self-sustained oscillator, and demonstrate their entrainment to light. Under constant conditions light intensity affects the natural period and drives transition to temporal disorder. Moreover, we find distinct morphologies depending on light temporal patterns, suggesting waves of chlorophyll could link biological oscillators to metabolism and morphogenesis in this giant single-celled organism.

Calcium signals are necessary to establish auxin transporter polarity in a plant stem cell niche.

In plants mechanical signals pattern morphogenesis through the polar transport of the hormone auxin and through regulation of interphase microtubule (MT) orientation. To date, the mechanisms by which such signals induce changes in cell polarity remain unknown. Through a combination of time-lapse imaging, and chemical and mechanical perturbations, we show that mechanical stimulation of the SAM causes transient changes in cytoplasmic calcium ion concentration (Ca2+) and that transient Ca2+ response is required for downstream changes in PIN-FORMED 1 (PIN1) polarity. We also find that dynamic changes in Ca2+ occur during development of the SAM and this Ca2+ response is required for changes in PIN1 polarity, though not sufficient. In contrast, we find that Ca2+ is not necessary for the response of MTs to mechanical perturbations revealing that Ca2+ specifically acts downstream of mechanics to regulate PIN1 polarity response.

On the role of initial velocities in pair dispersion in a microfluidic chaotic flow.

Chaotic flows drive mixing and efficient transport in fluids, as well as the associated beautiful complex patterns familiar to us from our every day life experience. Generating such flows at small scales where viscosity takes over is highly challenging from both the theoretical and engineering perspectives. This can be overcome by introducing a minuscule amount of long flexible polymers, resulting in a chaotic flow dubbed 'elastic turbulence'. At the basis of the theoretical frameworks for its study lie the assumptions of a spatially smooth and random-in-time velocity field. Previous measurements of elastic turbulence have been limited to two-dimensions. Using a novel three-dimensional particle tracking method, we conduct a microfluidic experiment, allowing us to explore elastic turbulence from the perspective of particles moving with the flow. Our findings show that the smoothness assumption breaks already at scales smaller than a tenth of the system size. Moreover, we provide conclusive experimental evidence that 'ballistic' separation prevails in the dynamics of pairs of tracers over long times and distances, exhibiting a memory of the initial separation velocities. The ballistic dispersion is universal, yet it has been overlooked so far in the context of small scales chaotic flows.Elastic turbulence, a random-in-time flow, can drive efficient mixing in microfluidics. Using a 3D particle tracking method, the authors show that the smoothness assumption breaks at scales far smaller than believed and the ballistic pair dispersion holds over much longer distances than expected.

Oscillatory elastic instabilities in an extensional viscoelastic flow.

Dilute polymer solutions are known to exhibit purely elastic instabilities even when the fluid inertia is negligible. Here we report the quantitative evidence of two consecutive oscillatory elastic instabilities in an elongation flow of a dilute polymer solution as realized in a T-junction geometry with a long recirculating cavity. The main result reported here is the observation and characterization of the first transition as a forward Hopf bifurcation resulted in a uniformly oscillating state due to breaking of time translational invariance. This unexpected finding is in contrast with previous experiments and numerical simulations performed in similar ranges of the Wi and Re numbers, where the forward fork-bifurcation into a steady asymmetric flow due to the broken spatial inversion symmetry was reported. We discuss the plausible discrepancy between our findings and previous studies that could be attributed to the long recirculating cavity, where the length of the recirculating cavity plays a crucial role in the breaking of time translational invariance instead of the spatial inversion. The second transition is manifested via time aperiodic transverse fluctuations of the interface between the dyed and undyed fluid streams at the channel junction and advected downstream by the mean flow. Both instabilities are characterized by fluid discharge-rate and simultaneous imaging of the interface between the dyed and undyed fluid streams in the outflow channel.

Robust and highly performant ring detection algorithm for 3d particle tracking using 2d microscope imaging.

Three-dimensional particle tracking is an essential tool in studying dynamics under the microscope, namely, fluid dynamics in microfluidic devices, bacteria taxis, cellular trafficking. The 3d position can be determined using 2d imaging alone by measuring the diffraction rings generated by an out-of-focus fluorescent particle, imaged on a single camera. Here I present a ring detection algorithm exhibiting a high detection rate, which is robust to the challenges arising from ring occlusion, inclusions and overlaps, and allows resolving particles even when near to each other. It is capable of real time analysis thanks to its high performance and low memory footprint. The proposed algorithm, an offspring of the circle Hough transform, addresses the need to efficiently trace the trajectories of many particles concurrently, when their number in not necessarily fixed, by solving a classification problem, and overcomes the challenges of finding local maxima in the complex parameter space which results from ring clusters and noise. Several algorithmic concepts introduced here can be advantageous in other cases, particularly when dealing with noisy and sparse data. The implementation is based on open-source and cross-platform software packages only, making it easy to distribute and modify. It is implemented in a microfluidic experiment allowing real-time multi-particle tracking at 70 Hz, achieving a detection rate which exceeds 94% and only 1% false-detection.

Characteristic spatial scale of vesicle pair interactions in a plane linear flow.

We report the experimental studies on interaction of two vesicles trapped in a microfluidic four-roll mill, where a plane linear flow is realized. We found that the dynamics of a vesicle in tank-treading motion is significantly altered by the presence of another vesicle at separation distances up to 3.2-3.7 times of the vesicle effective radius. This result is supported by measurement of a single vesicle back-reaction on the velocity field. Thus the experiment provides the upper bound for the volume fraction φ = 0.08-0.13 of noninteracting vesicle suspensions.