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Surrogate-based ensemble data assimilation for reducing uncertainty in large-eddy simulation of microscale pollutant dispersion
No full textInternational audienceBy capturing the physical complexity of the interactions between atmospheric flows and the built environment, Large-Eddy Simulations (LES) could provide detailed information for risk assessment and mitigation in case of environmental emergency. However, to account for LES uncertainties and cover the range of plausible scenarios in order to support decision making, it is necessary to go beyond deterministic simulation capability. This study introduces a novel ensemble-based data assimilation algorithm to correct the LES meteorological forcing and thereby improve LES spatial predictions of pollutant concentration by making use of available measurements. This approach is demonstrated through the MUST field-scale experiment. Results show that the ensemble smoother with multiple data assimilation (ESMDA) algorithm is a good candidate to address parameter interaction effects in the relationship between uncertain meteorological forcing and LES field quantities. This iterative algorithm is computationally feasible when the LES model is replaced with a machine learning-based surrogate model, from which robust ensemble statistics can be extracted. This surrogate-based data assimilation approach can then be used to examine observability in the system. Results show that the estimation outcome is highly sensitive to the design of the observation network, and that this sensitivity may be underestimated in idealized experiments. It is therefore important to use real data assimilation to optimize sensor placement and extract informative data for modeling, thus improving our ability to monitor accidental dispersion events
Synthesis and structural characterization of β-phosphonated thiosemicarbazones: Investigation of their Z/E interconversion by NMR and DFT computing
No full textInternational audienceThis work aims to present the synthesis of thiosemicarbazones (TSCs) bearing a Ph2P(=O)CH2- moiety, a yet unknown subclass of TSCs, along with their crystal structures and the Z/E interconversion occurring in solution. For this purpose, eight new phosphonated thiosemicarbazones Ph2P(=O)CH2{C=N-NH(C=S)-NH-R}CH3 (4a R = Ph; 4b R = p-FC6H4; 4c R = p-ClC6H4; 4d R = 3,5-Me2C6H3; 4e R = 2,5-(MeO)2C6H3; 4f R = CH2C6H5; 4g R = C6H11; 4h R = CH2-CHdouble bondCH2) were prepared by nucleophilic addition of β-phosphonated hydrazone Ph2P(=O)CH2(C=N-H2)CH3 2 across various aromatic and aliphatic isothiocyanates R-N=C=S. The synthesis of 4 is accompanied by competing formation of the phosphonated azine Ph2P(=O)CH2{C(Me)=N-N=C(Me)}CH2P(=O)Ph2 3 and of bis(N-arylthioureas) or bis(N-alkylhexylthioureas) 5, lowering the overall yield of 4. All products were characterized by multinuclear NMR, FT-IR spectroscopy and UV–vis spectroscopy. NMR spectroscopy of 4 at variable temperature indicates the coexistence of E and Z-isomers in solution with respect to the relative position of the substituents around the hydrazonic –C=N–NH- array. Several crystal structure determinations by single crystal X-ray diffraction (SC-XRD) reveal that in the solid state exclusively the E isomer is present, except for 4e which adopts a Z configuration due to an intramolecular C-O···H-N and P=O···H-N hydrogen bonding. For all derivatives, also an intramolecular N-H···N bonding is evidenced. The individual molecules of 4a, 4b, 4d, 4f, 4g and 4h are associated by strong intermolecular P=O···H-N hydrogen bonding in form of supramolecular macrocyclic dimers or 1D chains. These secondary interactions were further examined by a Hirshfeld surface analysis of 4f. For a comparison of the experimental SC-XRD parameters with the theoretical calculated ones and the preferred configuration, DFT calculations at the B3LYP/6–311+G (d, p) level were performed both in solution and in the gas phase. A computing of the Intrinsic Reaction Coordinates (IRC) revealed that the E-isomer of 4a is energetically more stable than the Z-isomer, since there is less steric crowding
How to integrate biology, physics and chemistry for a better description of soil water dynamics?
No full textInternational audienceNumerous and diverse edaphic organisms have the capacity to modify several physical and chemical soil characteristics that influence water transfers. Considering these modifications in modeling approaches would make for more accurate descriptions and modeling of water fluxes in soils. Some impacts of biological activity on soil physical aspects (e.g. modification of the pore space) have been described for 5-10 years now, and are being increasingly accounted for in water transfer models.However, the situation is not the same for biologically-driven chemical modifications linked to the secretion of organic molecules by soil organisms: modeling their consequences on pore space chemical properties and water transfers has just started. We here shortly survey prominent effects of biological activity on water-transfer related soil properties, and describe their coupling with existing water transfer models. We then propose possible ways for a better integration of biological soil modifications into such models. Among these, we point out that an energy-based theoretical framework would not only be consistent with the basic principles of thermodynamics, but would also foster synergies between ecologists, physicists and chemists, to better describe and predict water dynamics in soils and interactions with the soil biota. This would pave the way to model the evolution, on the scale of a few decades, of the water flow regulation services provided by soils</p
Marine Model Organisms for Mechanobiology Studies
No full textInternational audienceMarine invertebrate species have been used as model organisms in evo-devo studies for over a century. These species provided a great advantage in seminal microscopic studies because of the large size of their eggs and embryos and the easy accessibility to the first embryological processes afforded by their external fertilization and development. This review provides a historical perspective on the use of marine invertebrates—including echinoderms, ascidians, and spiralians—in the study of embryo mechanics. Here, we highlight the key contributions of marine invertebrates to the understanding of cortical and cytoplasmic mechanics, the implementation of early cleavage patterns, and tissue mechanics. We also examine the emergence of different blastula shapes in metazoans and focus on the clear dichotomy between compact and hollow embryos, suggesting a canalization of a compact embryo shape in taxa that display invariant cleavage patterns such as nematodes, spiralians, and ascidians.With recent advances in high-resolution imaging, computational modeling, and the development of modern genetic and genomic tools, marine invertebrate model organisms continue to be at the forefront of evolutionary developmental biology and mechanobiology. Their contribution to these fields not only provides invaluable insights into the fundamental principles of morphogenesis but also offers an ideal comparative framework that allows the exploration of the evolution of mechanical and biological processes across metazoans
Thiosemicarbazone derivatives bearing a dioxaphosphorinane ring: Synthesis, crystal structure, DFT calculation, in vitro antiproliferative activity against colorectal cancer cells, in silico docking and ADMET investigations
No full textInternational audienceTo design promising new bioactive compounds endowed with anti-tumor activity, we synthesized a series ofisomeric phosphonated thiosemicarbazones (TSCs) 2 bearing a six-membered dioxaphosphorinane cycle. Thetargeted TSCs were obtained in satisfying yields under mild conditions by reaction between β-cyclo-alkoxyphosphonated hydrazones 1 of type R1R2C(CH2O)2P(=O)CH2-C{=N-N(H)R5}C(H)R3R4 (1a R1 = R2 = H,R3 = Me, R4 = Ph; 1b R1 = R2 = H, R3 = R4 =Me; 1c R1 = R2 = Me, R3 = H, R4 = Bn) and various aliphatic andaromatic isothiocyanates. The formula of the synthesized TSCs correspond to R1R2C(CH2O)2P(=O)CH2{C=N-NH(C=S)-N(H)R5}C(H)R3R4 (2a R1 = R2 = H, R3 = Me, R4 = R5 = Ph; 2b R1 = R2 = H, R3 = Me, R4 = Ph, R5 = Cy;2c R1 = R2 = H, R3 = Me, R4 = Ph, R5 = Bn; 2d R1 = R2 = H, R3 = R4 = Me, R5 = Ph; 2e R1 = R2 = Me, R3 = H,R4 = R5 = Ph). The chemical structures of the novel thiosemicarbazones were assessed in solution by 31P, 13C, 1HNMR and IR spectroscopy. Since several derivates occur as mixtures of Z/E isomers in solution, the structuralanalysis was further extended by mechanistic elucidation, single-crystal X-ray diffraction analysis (SC-XRD),Hirshfeld surface analysis and computational investigation. The global reactivity parameters of TSCs 2a, 2d and2e were determined using Frontier Molecular Orbital (FMO) analysis. Compounds 2a, 2b, 2c and 2e were thenscreened for their in vitro antiproliferative activity against two human colorectal HT29 and LS174 tumor celllines. Cell viability studies revealed that compound 2b exhibits the most potent antiproliferative activity. To gaininsight into the mechanism of action of TSCs 2, an in silico docking study of derivatives 2a-d with DNA topo-isomerase IIα was conducted. Furthermore, an in silico ADME/Tox profile was established, indicating adequatevalues in accordance with the Lipinsky rules of five. The druglikeness levels and bioavailability were alsoinvestigated
Element mobilities during serpentinization: Insights from the Ronda Massif, Spain
No full textInternational audienceSerpentinization is a widespread hydrothermal alteration of ultramafic rocks, particularly peridotites, resulting in the formation of serpentinite through hydration processes. While the behavior of fluid-mobile elements (FME; e.g. B, Li, Cl, As, Sb, Pb, U, Th, Cs, Sr, Ba) during serpentinization is well documented, the mobility of other elements (e.g., base metals) remains poorly constrained. We analyzed bulk rock compositions of pairs of poorly and highly serpentinized peridotite rocks from the Ronda Massif (Spain), complemented by in situ LA-ICP-MS mineral analyses. The loss on ignition (LOI) content of whole rock represents a good proxy for serpentinization intensity. Ca, Al, Cu, V, and Ti are increasingly mobilized during the initial stages of pervasive serpentinization. In a second stage corresponding to total serpentinization along cm-wide, several meters-long corridors, a systematic loss in Ca, Al, Rb, Sr, REE Hf, Ti, Cu, and V was observed. In contrast, during the third stage of serpentinization corresponding to late faulting only Ca and Cu were leached. The trace element composition of J o u r n a l P r e -p r o o fJournal Pre-proof serpentine minerals, including Ti, V, and Zn, is influenced by the primary mineral assemblage, particularly olivine and pyroxenes. In contrast, the mobility of Al and Ca from millimeter to meter scale is notably linked to the bastite-pyroxene and serpentine mesh texture-olivine transformation. Co, Ni, Zn, and Cr depletion in serpentine within veins is compensated by their significant incorporation into magnetite. Copper is systematically leached from serpentinized rocks, suggesting that serpentinization likely serves as a significant source for Cu-rich hydrothermal metallogenic systems hosted in ultramafic rocks</div
Turbulence-Driven Corrugation of Collisionless Fast-Magnetosonic Shocks
No full textInternational audienceCollisionless fast-magnetosonic shocks are often treated as smooth, planar boundaries, yet observations point to organized corrugation of the shock surface. A plausible driver is upstream turbulence. Broadband fluctuations arriving at the front can continually wrinkle it, changing the local shock geometry and, in turn, conditions for particle injection and radiation. We develop a linear-MHD formulation that treats the shock as a moving interface rather than a fixed boundary. In this approach the shock response can be summarized by an effective impedance determined by the Rankine-Hugoniot base state and the shock geometry, while the upstream turbulence enters only through its statistics. This provides a practical mapping from an assumed incident spectrum to the corrugation amplitude, its drift along the surface, and a coherence scale set by weak damping or leakage. The response is largest when the transmitted downstream fast mode propagates nearly parallel to the shock in the shock frame, which produces a Lorentzian-type enhancement controlled by the downstream normal group speed. We examine how compression, plasma , and obliquity affect these corrugation properties and discuss implications for fine structure in heliospheric and supernova-remnant shock emission
Co-culturing with bacteria modulates fatty acid composition in benthic diatom biofilms for lipid-based biotechnologies: A case study of Amphora sp.
No full textInternational audienceDespite being recognized as promising oleaginous microalgal resources, benthic diatom biofilms remain overlooked in microalgal biotechnology. To enhance their industrial potential, bacterial interactions can exploit to boost biomass, increase lipid yields and tailor lipid profiles. Given the complexity of natural biofilms, our study adopted a reductionist approach to investigate the impact of bacteria on the metabolism of a marine benthic diatom, Amphora sp., through binary co-cultures. Bacteria were isolated from non-axenic Amphora sp. biofilm cultures during the exponential phase in a lab-scale porous substrate biofilm photobioreactor. A bacterial biofilm assay was conducted to select biofilm-forming strains, followed by co-culturing them with Amphora sp. in bottle culture flasks, assuming these strains would persist and interact within the Amphora biofilm. All cultures were maintained for 6 days in F/2-enriched artificial seawater at 16 • C, under a 12:12 light:dark cycle (100 μmol photons.m -2 .s -1 ). Biomass and lipid contents were quantified using the gravimetric method, while fatty acid profiles were analysed using GC-MS. Results showed that some bacterial strains reduced Amphora sp. biomass, while Nitratireductor sp. and Sulfitobacter sp. had no noticeable effect. However, significant shifts in fatty acid profile of Amphora sp. were observed in most co-cultures while none of the individual bacterial strains substantially affected lipid production compared to its axenic and non-axenic counterparts. Co-cultures with Nitratireductor sp. and Sulfitobacter sp. yielded 50-55 % saturated, 40-50 % monounsaturated, and 1-6 % polyunsaturated fatty acids, indicating favourable biodiesel properties. Thus, modifying the microbiome of microalgal biofilms could be an innovative strategy for tailoring fatty acid composition for lipid-based applications
Born to be alive. Isotopic evidence of investment in the survival of immature individuals in the Neolithic period, ecological influences and the construction of social identities
No full textInternational audienc
Turbulence and far-from-equilibrium equation of state of Bogoliubov waves in Bose-Einstein Condensates
No full textBogoliubov waves are fundamental excitations of Bose-Einstein Condensates (BECs). They emerge from a perturbed ground state and interact nonlinearly, triggering turbulent cascades. Here, we study turbulent BECs theoretically and numerically using the 3D Gross-Pitaevskii model and its associated wave-kinetic equations. We derive a new Kolmogorov-like stationary spectrum for short Bogoliubov waves and find a complete analytical expression for the spectrum in the long-wave acoustic regime. We then use our predictions to explain the BEC equation of state reported in [Dora et al. Nature 620,521 (2023)], and to suggest new experimental settings