Geometrical statistics of the vorticity vector and the strain rate tensor in rotating turbulence

We report results on the geometrical statistics of the vorticity vector obtained from experiments in electromagnetically forced rotating turbulence. A range of rotation rates $\Omega$ is considered, from non-rotating to rapidly rotating turbulence with a maximum background rotation rate of $\Omega=5$ rad/s (with Rossby number much smaller than unity). Typically, in our experiments ${\rm{Re}}_{\lambda}\approx 100$. The measurement volume is located in the centre of the fluid container above the bottom boundary layer, where the turbulent flow can be considered locally statistically isotropic and horizontally homogeneous for the non-rotating case, see van Bokhoven et al., Phys. Fluids 21, 096601 (2009). Based on the full set of velocity derivatives, measured in a Lagrangian way by 3D Particle Tracking Velocimetry, we have been able to quantify statistically the effect of system rotation on several flow properties. The experimental results show how the turbulence evolves from almost isotropic 3D turbulence ($\Omega\lesssim 0.2$ rad/s) to quasi-2D turbulence ($\Omega\approx 5.0$ rad/s) and how this is reflected by several statistical quantities. In particular, we have studied the orientation of the vorticity vector with respect to the three eigenvectors of the local strain rate tensor and with respect to the vortex stretching vector. Additionally, we have quantified the role of system rotation on the self-amplification terms of the enstrophy and strain rate equations and the direct contribution of the background rotation on these evolution equations. The main effect is the strong reduction of extreme events and related (strong) reduction of the skewness of PDFs of several quantities such as, for example, the intermediate eigenvalue of the strain rate tensor and the enstrophy self-amplification term.Comment: 17 pages, 6 figures, 3 table

Short-range interaction vs long-range correlation in bird flocks

Bird flocks are a paradigmatic example of collective motion. One of the prominent experimental traits discovered about flocks is the presence of long range velocity correlations between individuals, which allow them to influence each other over the large scales, keeping a high level of group coordination. A crucial question is to understand what is the mutual interaction between birds generating such nontrivial correlations. Here we use the Maximum Entropy (ME) approach to infer from experimental data of natural flocks the effective interactions between birds. Compared to previous studies, we make a significant step forward as we retrieve the full functional dependence of the interaction on distance and find that it decays exponentially over a range of a few individuals. The fact that ME gives a short-range interaction even though its experimental input is the long-range correlation function, shows that the method is able to discriminate the relevant information encoded in such correlations and single out a minimal number of effective parameters. Finally, we show how the method can be used to capture the degree of anisotropy of mutual interactions.Comment: 21 pages, 7 figures, 1 tabl

Emergence of collective changes in travel direction of starling flocks from individual birds fluctuations

One of the most impressive features of moving animal groups is their ability to perform sudden coherent changes in travel direction. While this collective decision can be a response to an external perturbation, such as the presence of a predator, recent studies show that such directional switching can also emerge from the intrinsic fluctuations in the individual behaviour. However, the cause and the mechanism by which such collective changes of direction occur are not fully understood yet. Here, we present an experimental study of spontaneous collective turns in natural flocks of starlings. We employ a recently developed tracking algorithm to reconstruct three-dimensional trajectories of each individual bird in the flock for the whole duration of a turning event. Our approach enables us to analyze changes in the individual behavior of every group member and reveal the emergent dynamics of turning. We show that spontaneous turns start from individuals located at the elongated edges of the flocks, and then propagate through the group. We find that birds on the edges deviate from the mean direction of motion much more frequently than other individuals, indicating that persistent localized fluctuations are the crucial ingredient for triggering a collective directional change. Finally, we quantitatively show that birds follow equal radius paths during turning allowing the flock to change orientation and redistribute risky locations among group members. The whole process of turning is a remarkable example of how a self-organized system can sustain collective changes and reorganize, while retaining coherence.Comment: 18 pages, 2 Videos adde

A singular nitric oxide synthase with a globin domain found in Synechococcus PCC 7335 mobilizes N from arginine to nitrate

The enzyme nitric oxide synthase (NOS) oxidizes L-arginine to NO and citrulline. In this work, we characterise the NOS from the cyanobacteria Synechococcus PCC 7335 (SyNOS). SyNOS possesses a canonical mammalian NOS architecture consisting of oxygenase and reductase domains. In addition, SyNOS possesses an unusual globin domain at the N-terminus. Recombinant SyNOS expressed in bacteria is active, and its activity is suppressed by the NOS inhibitor L-NAME. SyNOS allows E. coli to grow in minimum media containing L-arginine as the sole N source, and has a higher growth rate during N deficiency. SyNOS is expressed in Synechococcus PCC 7335 where NO generation is dependent on L-arginine concentration. The growth of Synechococcus is dramatically inhibited by L-NAME, suggesting that SyNOS is essential for this cyanobacterium. Addition of arginine in Synechococcus increases the phycoerythrin content, an N reservoir. The role of the novel globin domain in SyNOS is discussed as an evolutionary advantage, conferring new functional capabilities for N metabolism.Fil: Correa Aragunde, Maria Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; Argentina. Universidad Nacional de Mar del Plata; ArgentinaFil: Foresi, Noelia Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; Argentina. Universidad Nacional de Mar del Plata; ArgentinaFil: del Castello, Fiorella Paola. Universidad Nacional de Mar del Plata; ArgentinaFil: Lamattina, Lorenzo. Universidad Nacional de Mar del Plata; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; Argentin

Flocking and turning: a new model for self-organized collective motion

Birds in a flock move in a correlated way, resulting in large polarization of velocities. A good understanding of this collective behavior exists for linear motion of the flock. Yet observing actual birds, the center of mass of the group often turns giving rise to more complicated dynamics, still keeping strong polarization of the flock. Here we propose novel dynamical equations for the collective motion of polarized animal groups that account for correlated turning including solely social forces. We exploit rotational symmetries and conservation laws of the problem to formulate a theory in terms of generalized coordinates of motion for the velocity directions akin to a Hamiltonian formulation for rotations. We explicitly derive the correspondence between this formulation and the dynamics of the individual velocities, thus obtaining a new model of collective motion. In the appropriate overdamped limit we recover the well-known Vicsek model, which dissipates rotational information and does not allow for polarized turns. Although the new model has its most vivid success in describing turning groups, its dynamics is intrinsically different from previous ones in a wide dynamical regime, while reducing to the hydrodynamic description of Toner and Tu at very large length-scales. The derived framework is therefore general and it may describe the collective motion of any strongly polarized active matter system.Comment: Accepted for the Special Issue of the Journal of Statistical Physics: Collective Behavior in Biological Systems, 17 pages, 4 figures, 3 video

Chimera of Globin/Nitric Oxide Synthase: Toward Improving Nitric Oxide Homeostasis and Nitrogen Recycling and Availability

As a result of anthropogenic activities, there are regions suffering extreme climate changes (hot temperatures, droughts, floods), that generate serious and harmful environmental and socio-economic consequences (Hoegh-Guldberg et al., 2018). Climate change has a strong impact on agriculture, mainly by increasing soil degradation and reducing land productivity (Olsson et al., 2019). Desertification decreases soil macronutrients as organic carbon (OC), phosphorus (P) and nitrogen (N) (Shang et al., 2013; Tang et al., 2015). Considerable reductions of OC, P and N are caused by a decline in soil water, vegetation and wind erosion. It is estimated that when soil water is less than 30%, OC and N decrease approximately 50% (Shang et al., 2013). The intensity and frequency of extreme climate events predicted will increase the competition for nutrients, notably N among plants and soil microorganisms (Bennett and Klironomos, 2019; Pugnaire et al., 2019).N availability is essential for net primary production and determines changes in total vegetation biomass and soil OC (Tharammal et al., 2019). Approximately 150 Tg/yr of N is spilled to the land surface as a result of industrial activities and fossil fuel combustion (Schlesinger, 2009). Huge amounts of N fertilizers are used to increase crop productivity, but only 25%?30% are retained in plant biomass (Nadelhoffer et al., 1999; Schlesinger, 2009). The excess of N is then transported to aquatic environments resulting in eutrophication and reduction of dissolved O2, percolated to the groundwater or loss to the atmosphere, increasing greenhouse gas (GHG) emissions such as nitrogen oxides (NOx) (Schlesinger, 2009; Breitburg et al., 2018). In this context, bio/technological solutions like genetic modification of crops are required to avoid, reduce and reverse GHG emissions and water eutrophication, contributing to climate change mitigation. New biotechnological strategies developed for the agriculture to increase N use efficiency (NUE) in crops would help to fulfill this purpose. In this opinion, we will discuss some studies of nitric oxide (NO) synthases (NOS) and nitrate reductase (NR) enzymes playing a collaborative role with globin (Hb) proteins, leading to NO and/or nitrate (NO3-) homeostasis in different organisms. We propose that chimeric globin-NOS such as the NOS from Synechococcus PCC 7335 (SyNOS) may have evolved in photosynthetic microorganisms contributing to a more efficient N recycling and sustaining growth in N fluctuating conditions. Engineered crops that maximize NUE would result in a better adaptation to changing climatic conditions with less N fertilization, preserving aquatic ecosystems and atmosphere.Fil: del Castello, Fiorella Paola. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Nejamkin, Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Foresi, Noelia Pamela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Lamattina, Lorenzo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Correa Aragunde, Maria Natalia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Biológicas. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; Argentin

GReTA - a novel Global and Recursive Tracking Algorithm in three dimensions

Tracking multiple moving targets allows quantitative measure of the dynamic behavior in systems as diverse as animal groups in biology, turbulence in fluid dynamics and crowd and traffic control. In three dimensions, tracking several targets becomes increasingly hard since optical occlusions are very likely, i.e. two featureless targets frequently overlap for several frames. Occlusions are particularly frequent in biological groups such as bird flocks, fish schools, and insect swarms, a fact that has severely limited collective animal behavior field studies in the past. This paper presents a 3D tracking method that is robust in the case of severe occlusions. To ensure robustness, we adopt a global optimization approach that works on all objects and frames at once. To achieve practicality and scalability, we employ a divide and conquer formulation, thanks to which the computational complexity of the problem is reduced by orders of magnitude. We tested our algorithm with synthetic data, with experimental data of bird flocks and insect swarms and with public benchmark datasets, and show that our system yields high quality trajectories for hundreds of moving targets with severe overlap. The results obtained on very heterogeneous data show the potential applicability of our method to the most diverse experimental situations.Comment: 13 pages, 6 figures, 3 tables. Version 3 was slightly shortened, and new comprative results on the public datasets (thermal infrared videos of flying bats) by Z. Wu and coworkers (2014) were included. in A. Attanasi et al., "GReTA - A Novel Global and Recursive Tracking Algorithm in Three Dimensions", IEEE Trans. Pattern Anal. Mach. Intell., vol.37 (2015

Information transfer and behavioural inertia in starling flocks

Collective decision-making in biological systems requires all individuals in the group to go through a behavioural change of state. During this transition fast and robust transfer of information is essential to prevent cohesion loss. The mechanism by which natural groups achieve such robustness, however, is not clear. Here we present an experimental study of starling flocks performing collective turns. We find that information about direction changes propagates across the flock with a linear dispersion law and negligible attenuation, hence minimizing group decoherence. These results contrast starkly with present models of collective motion, which predict diffusive transport of information. Building on spontaneous symmetry breaking and conservation-law arguments, we formulate a theory that correctly reproduces linear and undamped propagation. Essential to this framework is the inclusion of the birds? behavioural inertia. The theory not only explains the data, but also predicts that information transfer must be faster the stronger the group’s orientational order, a prediction accurately verified by the data. Our results suggest that swift decision-making may be the adaptive drive for the strong behavioural polarization observed in many living groups.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada