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On the Number of Realizations of Certain Henneberg Graphs arising in Protein Conformation
No full textInternational audienceSeveral application fields require finding Euclidean coordinates consistent with a set of distances. More precisely, given a simple undirected edge-weighted graph, we wish to find a realization in a Euclidean space so that adjacent vertices are placed at a distance which is equal to the corresponding edge weight. Realizations of a graph can be either flexible or rigid. In certain cases, rigidity can be seen as a property of the graph rather than the realization. In the last decade, several advances have been made in graph rigidity, but most of these, for applicative reasons, focus on graphs having a unique realization. In this paper we consider a particular type of Henneberg graphs that model protein backbones and show that almost all of them give rise to sets of incongruent realizations whose cardinality is a power of two
Mitigating Phototoxicity during Multiphoton Microscopy of Live Drosophila Embryos in the 1.0–1.2 mm Wavelength Range
No full textInternational audienceLight-induced toxicity is a fundamental bottleneck in microscopic imaging of live embryos. In this article, after a review of photodamage mechanisms in cells and tissues, we assess photo-perturbation under illumination conditions relevant for point-scanning multiphoton imaging of live Drosophila embryos. We use third-harmonic generation (THG) imaging of developmental processes in embryos excited by pulsed near-infrared light in the 1.0–1.2 mm range. We study the influence of imaging rate, wavelength, and pulse duration on the short-term and long-term perturbation of development and define criteria for safe imaging. We show that under illumination conditions typical for multiphoton imaging, photodamage in this system arises through 2-and/or 3-photon absorption processes and in a cumulative manner. Based on this analysis, we derive general guidelines for improving the signal-to-damage ratio in two-photon (2PEF/SHG) or THG imaging by adjusting the pulse duration and/or the imaging rate. Finally, we report label-free time-lapse 3D THG imaging of gastrulating Drosophila embryos with sampling appropriate for the visualisation of morphogenetic movements in wild-type and mutant embryos, and long-term multiharmonic (THG-SHG) imaging of development until hatching. Citation: Débarre D, Olivier N, Supatto W, Beaurepaire E (2014) Mitigating Phototoxicity during Multiphoton Microscopy of Live Drosophila Embryos in the 1.0– 1.2 mm Wavelength Range. PLoS ONE 9(8): e104250
Afforestation in China cools local land surface temperature
No full textInternational audienceChina has the largest afforested area in the world (~62 million hectares in 2008), and these forests are carbon sinks. The climatic effect of these new forests depends on how radiant and turbulent energy fluxes over these plantations modify surface temperature. For instance, a lower albedo may cause warming, which negates the climatic benefits of carbon sequestration. Here, we used satellite measurements of land surface temperature (LST) from planted forests and adjacent grasslands or croplands in China to understand how afforestation affects LST. Afforestation is found to decrease daytime LST by about 1.1 ± 0.5 °C (mean ± 1 SD) and to increase nighttime LST by about 0.2 ± 0.5 °C, on average. The observed daytime cooling is a result of increased evapotranspiration. The nighttime warming is found to increase with latitude and decrease with average rainfall. Afforestation in dry regions therefore leads to net warming, as daytime cooling is offset by nighttime warming. Thus, it is necessary to carefully consider where to plant trees to realize potential climatic benefits in future afforestation projects
Applications des impulsions femtosecondes infrarouges : façonnage programmable et spectroscopie bidimensionnelle
No full textMid-infrared femtosecond lasers have recently provided a new tool to study complex ultrafast dynamics, especially in biological systems such as hemeproteins. Using these lasers, two kind of powerful experiments can be planned. The first type contains optimal control experiments, in which the principle is to find the optimal shape of a pulse in order to reach one desired final state. This approach requires a way to produce an arbitrary shape of pulses, so in a first part we have worked on a new kind of linear programmable acousto-optic pulse-shaper called Mid-infrared Dazzler, which is produced by the company FASLITE. For this sake, we have implemented a new method to measure weak mid-infrared pulses with complex shapes, based on the homodyne detection of a replica of the mid-infrared field into the visible domain. Then, we have produced and measured shaped pulses which exhibit complex shapes like pi-steps in the spectral phase. This demonstrates the ability of the Dazzler to be used in optimal control experiments with hemeproteins. The second type of experiments contain the multidimensional coherent spectroscopy experiments, which are powerful tools to probe ultrafast dynamics since the principle is to measure the complete non-linear response function, which permits to disentangle the different microscopic informations. We have finalized the building of an innovative two-dimensional spectrometer, which exhibits a simple geometry, an excellent spectral resolution in both axes, an iterative and very precise self-calibration method, and a simple and efficient trick to remove the signal from scattering. Our first measurements of the Frequency-frequency correlation function of the CO vibration bound to Hemoglobin shows a promising agreement with recent progress in the modelization of ultrafast fluctuations.La mise au point des lasers femtosecondes, en particulier dans le moyen-infrarouge, a ouvert une voie d’étude des systèmes biologiques, où les couplages et les fluctuations impliquent des déphasages ultra-rapides. Ce travail participe à l’élaboration d’outils pour l’étude de systèmes vibrationnels, ici la carboxy-hémoglobine HbCO. L’approche du contrôle optimal, d’une part, détermine empiriquement le profil optimal d’une impulsion en vue d’un objectif, nécessitant la programmation d’impulsions de formes arbitraires. Nous avons étudié un prototype d’une technologie acousto-optique de façonnage d’impulsions infrarouges, le Dazzler, conçu par la société FASTLITE. Pour cela, une méthode adaptée de mesure du champ, effectuant la mesure homodyne d’une réplique de l’impulsion dans le domaine visible, a été mise au point. Puis, la production et la mesure d’impulsions infrarouges de formes complexes comprenant un saut de phase spectrale, ont été réalisées, montrant l’adéquation du Dazzler pour des expériences de contrôle cohérent dans les hémoprotéines. D’autre part, la spectroscopie multidimensionnelle mesure la réponse non-linéaire d’un échantillon, constituant un outil puissant d’étude de la surface de potentiel. Un spectromètre bidimensionnel a donc été finalisé, qui combine une géométrie simplifiée, une excellente résolution, une procédure d’auto-calibration itérative et précise, et une solution simple pour éliminer la principale source de bruit. Des mesures de la fonction de corrélation à deux temps de la fréquence de résonance du CO ont enfin été comparées à des résultats préliminaires issus d’avancées théoriques récentes, montrant un accord prometteur pour leur validation
Superhydrophobie Active
No full textA droplet of water on a lotus leaf stays spherical as a bead, and rolls very easily without leaving any trace behind; the leaf is thus protected from water and stays dry. This property is called superhydrophobicity, or « Lotus effect ». This thesis is about studying remarkable surperhydrophobic behaviors in nature and understanding their origins to inspire the creation of new materials.A part of this thesis is dedicated to an unusual spider, the Diving Bell spider, which has everything of a terrestrial spider, especially its structure and respiratory system, but that lives its entire life under water. To breath oxygen in the gas form, it constructs itself a bell of air under water by accumulating bubbles that it pulls from the water surface, thanks to its superhydrophobic abdomen. We are interested in the coupling of the superhydrophobic properties of its abdomen and the dynamic of the air cavities pulled by the spider when it leaves an air/water interface.We also design new sensitive and active water repelling materials, inspired by living superhydrophobic sur- faces in nature. It is now well established that the rugosity of a surface plays a crucial role in its wetting properties. The goal is therefore to tune a generally fixed rugosity. A way to do so, is to make the textures with a material that we can modify the mechanical properties of, for example its elasticity. To take it a step further, it is an interesting challenge to create surfaces of which one can modify the structure of the textures by applying external stimuli, so as to tune their wetting properties. Finally, we show that the behavior of a non-wetting drop on such surfaces can depend on its rheological properties, and especially viscosity.Une goutte d'eau posée sur une feuille de lotus reste sphérique, sous forme de perle, et roule très facilement sans laisser de trace derrière elle ; la feuille est ainsi protégée de l'eau. On appelle cette propriété superhydrophobie, ou « effet Lotus ». Cette thèse porte sur l'étude de cas de superhydrophobie originaux rencontrés dans la nature et tente de s'en inspirer pour construire des matériaux nouveaux. Une partie de cette thèse est consacrée à une araignée remarquable, l'Argyronète Aquatique, qui a tout d'une araignée terrestre, en particulier sa structure et son mode respiratoire, mais qui a la particularité de vivre en permanence sous l'eau. Afin de respirer de l'oxygène gazeux, elle se construit un abri sous-marin sous la forme d'une cloche d'air en accumulant des bulles d'air qu'elle tire à la surface de l'eau grâce à son abdomen superhydrophobe. Nous nous intéressons au couplage des propriétés superhydrophobes de l'abdomen avec la dynamique des cavités créées lorsque l'araignée quitte ces interfaces air/eau. Une autre idée est de s'inspirer des propriétés de surfaces superhydrophobes vivantes de la nature pour mettre au point de nouveaux matériaux actifs. Il est maintenant bien établi que la rugosité d'une surface joue un rôle crucial dans ses propriétés de mouillage. L'enjeu est donc de parvenir à modifier une rugosité a priori figée. Nous discutons ainsi comment fabriquer des textures avec un matériau dont on peut moduler les propriétés mécaniques, par exemple son élasticité. Pour aller plus loin, il est possible de mettre au point des surfaces dont on peut modifier la structure des textures par un stimulus extérieur afin d'en varier les propriétés de mouillage. Enfin, nous montrons que le comportement d'une goutte non-mouillante sur de telles surfaces peut dépendre de ses propriétés rhéologiques, et en particulier de sa viscosité
Identification techniques for highly boosted W bosons that decay into hadrons
No full textSubmitted to JHEP, see paper for full list of authorsInternational audienceIn searches for new physics in the energy regime of the LHC, it is becoming increasingly important to distinguish single-jet objects that originate from the merging of the decay products of W bosons produced with high transverse momenta from jets initiated by single partons. Algorithms are defined to identify such W jets for different signals of interest, using techniques that are also applicable to other decays of bosons to hadrons that result in a single jet, such as those from highly boosted Z and Higgs bosons. The efficiency for tagging W jets is measured in data collected with the CMS detector at a center-of-mass energy of 8 TeV, corresponding to an integrated luminosity of 19.7 inverse femtobarns. The performance of W tagging in data is compared with predictions from several Monte Carlo simulators
A global analysis of tonal noise in flows around aerofoils
No full textInternational audienceThe generation of discrete acoustic tones in the compressible flow around an aerofoil is addressed in this work by means of nonlinear numerical simulations and global stability analyses. The nonlinear simulations confirm the appearance of discrete tones in the acoustic spectrum and, for the chosen flow case, the global stability analyses of the mean-flow dynamics reveal that the linearized operator is stable. However, the flow response to incoming disturbances exhibits important transient growth effects that culminate in the onset of aeroacoustic feedback loops, involving instability processes on the suction- and pressure-surface boundary layers together with their cross-interaction by acoustic radiation at the trailing edge. The features of the aeroacoustic feedback loops and the appearance of discrete tones are then related to the features of the least-stable modes in the global spectrum: the spatial structure of the direct modes displays the coupled dynamics of hydrodynamic instabilities on the suction surface and in the near wake. Finally, different families of global modes will be identified and the dynamics that they represent will be discussed
Shooting in a foam
No full textInternational audienceWe study the motion of a solid sphere after its fast impact on a bath of liquid foam. We identify two regimes of deceleration. At short times, the velocity is still large and the foam behaves similar to a Newtonian fluid of constant viscosity. Then we measure a velocity threshold below which the sphere starts experiencing the foam's elasticity. We interpret this behavior using a visco-elasto-plastic model for foam rheology. Finally we discuss the possibility of stopping a projectile in the foam, and evaluate the capture efficiency
TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues
No full textInternational audienceWe describe TmiRUsite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The predicted data find utility in molecular and evolutionary biology studies. They are also used in studying miRNA binding sites in animals and plants.Nous présentons des scripts en python pour l'extraction de séquences de nucléotides de sites de fixation de miRNAs. Les données prédites sont utiles en phylogénie, pour les animaux et les plantes