Searching for Effective Forces in Laboratory Insect Swarms

Collective animal behaviour is often modeled by systems of agents that interact via effective social forces, including short-range repulsion and long-range attraction. We search for evidence of such effective forces by studying laboratory swarms of the flying midge Chironomus riparius. Using multi-camera stereoimaging and particle-tracking techniques, we record three-dimensional trajectories for all the individuals in the swarm. Acceleration measurements show a clear short-range repulsion, which we confirm by considering the spatial statistics of the midges, but no conclusive long-range interactions. Measurements of the mean free path of the insects also suggest that individuals are on average very weakly coupled, but that they are also tightly bound to the swarm itself. Our results therefore suggest that some attractive interaction maintains cohesion of the swarms, but that this interaction is not as simple as an attraction to nearest neighbours

On the transition to turbulence of wall-bounded flows in general, and plane Couette flow in particular

The main part of this contribution to the special issue of EJM-B/Fluids dedicated to Patrick Huerre outlines the problem of the subcritical transition to turbulence in wall-bounded flows in its historical perspective with emphasis on plane Couette flow, the flow generated between counter-translating parallel planes. Subcritical here means discontinuous and direct, with strong hysteresis. This is due to the existence of nontrivial flow regimes between the global stability threshold Re_g, the upper bound for unconditional return to the base flow, and the linear instability threshold Re_c characterized by unconditional departure from the base flow. The transitional range around Re_g is first discussed from an empirical viewpoint ({\S}1). The recent determination of Re_g for pipe flow by Avila et al. (2011) is recalled. Plane Couette flow is next examined. In laboratory conditions, its transitional range displays an oblique pattern made of alternately laminar and turbulent bands, up to a third threshold Re_t beyond which turbulence is uniform. Our current theoretical understanding of the problem is next reviewed ({\S}2): linear theory and non-normal amplification of perturbations; nonlinear approaches and dynamical systems, basin boundaries and chaotic transients in minimal flow units; spatiotemporal chaos in extended systems and the use of concepts from statistical physics, spatiotemporal intermittency and directed percolation, large deviations and extreme values. Two appendices present some recent personal results obtained in plane Couette flow about patterning from numerical simulations and modeling attempts.Comment: 35 pages, 7 figures, to appear in Eur. J. Mech B/Fluid

Band-collision gel electrophoresis.

Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species loaded into the same well. However, shift assays can access only a subset of reaction possibilities that could be otherwise seen if separate bands of reagent species might instead be collisionally reacted. Here, we adapt gel electrophoresis by fabricating two or more wells in the same lane, loading these wells with different reagent species, and applying an electric field, thereby producing collisional reactions between propagating pulse-like bands of these species, which we image optically. For certain pairs of anionic and cationic dyes, propagating bands pass through each other unperturbed; yet, for other pairs, we observe complexing and precipitation reactions, indicating strong attractive interactions. We generalize this band-collision gel electrophoresis (BCGE) approach to other reaction types, including acid-base, ligand exchange, and redox, as well as to colloidal species in passivated large-pore gels

Cherenkov radiation control via self-accelerating wave-packets

Cherenkov radiation is a ubiquitous phenomenon in nature. It describes electromagnetic radiation from a charged particle moving in a medium with a uniform velocity larger than the phase velocity of light in the same medium. Such a picture is typically adopted in the investigation of traditional Cherenkov radiation as well as its counterparts in different branches of physics, including nonlinear optics, spintronics and plasmonics. In these cases, the radiation emitted spreads along a “cone”, making it impractical for most applications. Here, we employ a self-accelerating optical pump wave-packet to demonstrate controlled shaping of one type of generalized Cherenkov radiation - dispersive waves in optical fibers. We show that, by tuning the parameters of the wave-packet, the emitted waves can be judiciously compressed and focused at desired locations, paving the way to such control in any physical system

Data-based stochastic model reduction for the Kuramoto--Sivashinsky equation

The problem of constructing data-based, predictive, reduced models for the Kuramoto-Sivashinsky equation is considered, under circumstances where one has observation data only for a small subset of the dynamical variables. Accurate prediction is achieved by developing a discrete-time stochastic reduced system, based on a NARMAX (Nonlinear Autoregressive Moving Average with eXogenous input) representation. The practical issue, with the NARMAX representation as with any other, is to identify an efficient structure, i.e., one with a small number of terms and coefficients. This is accomplished here by estimating coefficients for an approximate inertial form. The broader significance of the results is discussed.Comment: 23 page, 7 figure

Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient

In the acute inflammatory phase following tissue damage, cells of the innate immune system are rapidly recruited to sites of injury by pro-inflammatory mediators released at the wound site. Although advances in live imaging allow us to directly visualize this process in vivo, the precise identity and properties of the primary immune damage attractants remain unclear, as it is currently impossible to directly observe and accurately measure these signals in tissues. Here, we demonstrate that detailed information about the attractant signals can be extracted directly from the in vivo behavior of the responding immune cells. By applying inference-based computational approaches to analyze the in vivo dynamics of the Drosophila inflammatory response, we gain new detailed insight into the spatiotemporal properties of the attractant gradient. In particular, we show that the wound attractant is released by wound margin cells, rather than by the wounded tissue per se, and that it diffuses away from this source at rates far slower than those of previously implicated signals such as H2O2 and ATP, ruling out these fast mediators as the primary chemoattractant. We then predict, and experimentally test, how competing attractant signals might interact in space and time to regulate multi-step cell navigation in the complex environment of a healing wound, revealing a period of receptor desensitization after initial exposure to the damage attractant. Extending our analysis to model much larger wounds, we uncover a dynamic behavioral change in the responding immune cells in vivo that is prognostic of whether a wound will subsequently heal or not

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.

The regulation of transcription requires the coordination of numerous activities on DNA, yet how transcription factors mediate these activities remains poorly understood. Here, we use lattice light-sheet microscopy to integrate single-molecule and high-speed 4D imaging in developing Drosophila embryos to study the nuclear organization and interactions of the key transcription factors Zelda and Bicoid. In contrast to previous studies suggesting stable, cooperative binding, we show that both factors interact with DNA with surprisingly high off-rates. We find that both factors form dynamic subnuclear hubs, and that Bicoid binding is enriched within Zelda hubs. Remarkably, these hubs are both short lived and interact only transiently with sites of active Bicoid-dependent transcription. Based on our observations, we hypothesize that, beyond simply forming bridges between DNA and the transcription machinery, transcription factors can organize other proteins into hubs that transiently drive multiple activities at their gene targets.Editorial noteThis article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter)

Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments

Biological and Soft Matter Physic

Phase transitions during fruiting body formation in Myxococcus xanthus

The formation of a collectively moving group benefits individuals within a population in a variety of ways such as ultra-sensitivity to perturbation, collective modes of feeding, and protection from environmental stress. While some collective groups use a single organizing principle, others can dynamically shift the behavior of the group by modifying the interaction rules at the individual level. The surface-dwelling bacterium Myxococcus xanthus forms dynamic collective groups both to feed on prey and to aggregate during times of starvation. The latter behavior, termed fruiting-body formation, involves a complex, coordinated series of density changes that ultimately lead to three-dimensional aggregates comprising hundreds of thousands of cells and spores. This multi-step developmental process most likely involves several different single-celled behaviors as the population condenses from a loose, two-dimensional sheet to a three-dimensional mound. Here, we use high-resolution microscopy and computer vision software to spatiotemporally track the motion of thousands of individuals during the initial stages of fruiting body formation. We find that a combination of cell-contact-mediated alignment and internal timing mechanisms drive a phase transition from exploratory flocking, in which cell groups move rapidly and coherently over long distances, to a reversal-mediated localization into streams, which act as slow-spreading, quasi-one-dimensional nematic fluids. These observations lead us to an active liquid crystal description of the myxobacterial development cycle.Comment: 16 pages, 5 figure