Laboratoire de Dynamique des Fluides

We attribute similarities in the rheology of many soft materials (foams, emulsions, slurries, etc.) to the shared features of structural disorder and metastability. A generic model for the mesoscopic dynamics of ``soft glassy matter'' is introduced, with interactions represented by a mean-field noise temperature $x$. We find power-law fluid behavior either with $(x<1)$ or without $(1<x<2)$ a yield stress. For $1<x<2$, both storage and loss modulus vary with frequency as ${\ensuremath{\omega}}^{x\ensuremath{-}1}$, becoming flat near a glass transition $(x\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1)$. Values of $x\ensuremath{\approx}1$ may result from marginal dynamics as seen in some spin glass models.

An analytical theory is developed for the stability properties of planar fronts of premixed laminar flames freely propagating downwards in a uniform reacting mixture. The coupling between the hydrodynamics and the diffusion process is described for an arbitrary expansion of the gas across the flame. Viscous effects are included with an arbitrary Prandtl number. The flame structure is described for a large value of the reduced activation energy and for a Lewis number close to unity. The flame thickness is assumed to be small compared with the wavelength of the wrinkles of the front, this wavelength being also the characteristic lengthscale of the perturbations of the flow field outside the flame. A two-scale method is then used to solve the problem. The results show that the acceleration of gravity associated with the diffusion mechanisms inside the front can counterbalance the hydrodynamical instability when the laminar-flame velocity is low enough. The theory provides predictions concerning the instability threshold. In particular, the dimensions of the cells are predicted to be large compared with the flame thickness, and thus the basic assumption of the theory is verified. Furthermore, the quantitative predictions are in good agreement with the existing experimental data. The bifurcation is shown to be of a different nature than predicted by the purely diffusive–thermal model. The viscous diffusivities are supposed to be independent of the temperature, and then the viscosity is proved to have no effect at all on the dynamical properties of the flame front.

Abstract One of the critical factors that control the efficiency of CO 2 geological storage process in aquifers and hydrocarbon reservoirs is the capillary‐sealing potential of the caprock. This potential can be expressed in terms of the maximum reservoir overpressure that the brine‐saturated caprock can sustain, i.e. of the CO 2 capillary entry pressure. It is controlled by the brine/CO 2 interfacial tension, the water‐wettability of caprock minerals, and the pore size distribution within the caprock. By means of contact angle measurements, experimental evidence was obtained showing that the water‐wettability of mica and quartz is altered in the presence of CO 2 under pressures typical of geological storage conditions. The alteration is more pronounced in the case of mica. Both minerals are representative of shaly caprocks and are strongly water‐wet in the presence of hydrocarbons. A careful analysis of the available literature data on breakthrough pressure measurements in caprock samples confirms the existence of a wettability alteration by dense CO 2 , both in shaly and in evaporitic caprocks. The consequences of this effect on the maximum CO 2 storage pressure and on CO 2 storage capacity in the underground reservoir are discussed. For hydrocarbon reservoirs that were initially close to capillary leakage, the maximum allowable CO 2 storage pressure is only a fraction of the initial reservoir pressure.

In the early times of isoprenoid research, a single pathway was found for the formation of the C 5 monomer, isopentenyl diphosphate (IPP), and this acetate/mevalonate pathway was supposed to occur ubiquitously in all living organisms. Now, 40 years later, a totally different IPP biosynthesis route has been detected in eubacteria, green algae and higher plants. In this new pathway glyceraldehyde 3‐phosphate (GAP) and pyruvate are precursors of isopentenyl diphosphate, but not acetyl‐CoA and mevalonic acid. In green tissues of three higher plants it was shown that all chloroplastbound isoprenoids (β‐carotene, phytyl chains of chlorophylls and nona‐prenyl chain of plastoquinone‐9) are formed via the GAP/pyruvate pathway, whereas the cytoplasmic sterols are formed via the acetate/mevalonate pathway. Also, isoprene, emitted by various plants at high light conditions by action of the plastid‐bound isoprene synthase, is formed via the new GAP/pyruvate pathway. Thus, in higher plants, there exist two separate and biochemically different IPP biosynthesis pathways: (1) the novel alternative GAP/pyruvate pathway apparently bound to the plastidic compartment and (2) the classical cytoplasmic acetate/mevalonate pathway. This new GAP/pyruvate pathway for IPP formation allows a reasonable interpretation of previous odd results concerning the biosynthesis of chloroplast isoprenoids, which, so far, had mainly been interpreted assuming compartmentation differences. The novel GAP/pyruvate pathway for IPP formation in plastids appears as a heritage of their prokaryotic, endosymbiotic ancestors.

To study effects of flow inhomogeneities on the dynamics of laminar flamelets in turbulent flames, with account taken of influences of the gas expansion produced by heat release, a previously developed theory of premixed flames in turbulent flows, that was based on a diffusive-thermal model in which thermal expansion was neglected, and that applied to turbulence having scales large compared with the laminar flame-thickness, is extended by eliminating the hypothesis of negligible expansion and by adding the postulate of weak-intensity turbulence. The consideration of thermal expansion motivates the formal introduction of multiple-scale methods, which should be useful in subsequent investigations. Although the hydrodynamic-instability mechanism of Landau is not considered, no restriction is imposed on the density change across the flame front, and the additional transverse convection correspondingly induced by the tilted front is described. By allowing the heat-to-reactant diffusivity ratio to differ slightly from unity, clarification is achieved of effects of phenomena such as flame stretch and the flame-relaxation mechanism traceable to transverse diffusive processes associated with flame-front curvature. By carrying the analysis to second order in the ratio of the laminar flame thickness to the turbulence scale, an equation for evolution of the flame front is derived, containing influences of transverse convection, flame relaxation and stretch. This equation explains anomalies recently observed at low frequencies in experimental data on power spectra of velocity fluctuations in turbulent flames. It also shows that, concerning the diffusive-stability properties of the laminar flame, the density change across the flame thickness produces a shift of the stability limits from those obtained in the purely diffusive-thermal model. At this second order, the turbulent correction to the flame speed involves only the mean area increase produced by wrinkling. The analysis is carried to the fourth order to demonstrate the mean-stretch and mean-curvature effects on the flame speed that occur if the diffusivity ratio differs from unity.

We report an experimental investigation of the motion of bed load particles under steady and spatially uniform turbulent flow above a flat sediment bed of uniform grain size. Using a high‐speed video imaging system, we recorded the trajectories of the moving particles and measured their velocity and the length and duration of their flights, as well as the surface density of the moving particles. Our observations show that entrained particles exhibit intermittent motion composed of the succession of periods of “flight” and periods of rest. During one flight, a particle may go through phases of reptation, during which it moves in nearly persistent contact with the rough bed, and phases of saltation, during which it travels sufficiently high above the bed to reach high velocities. The distributions of longitudinal and transverse particle velocities obey a decreasing exponential and a Gaussian law, respectively. Interestingly, these observations are similar to those previously reported for viscous flows. The experimental results presented here support the erosion‐deposition model of Charru (2006) and allow the calibration of the involved coefficients. In particular, noting τ *, the Shields number, and τ * c , the threshold Shields number, we find that (1) the surface density of moving particles increases linearly with τ * − τ * c ; (2) the average particle velocity increases linearly with τ * 1/2 − τ * c 1/2 , with a finite nonzero value at the threshold; (3) the flight duration scales with a characteristic settling time with no significant dependence on either τ * or the settling Reynolds number; and (4) the flight length increases linearly with τ * 1/2 − τ * c 1/2 . The results presented in this paper should provide a valuable physical framework to describe bed form development in turbulent flows.

Abstract A series of laboratory experiments demonstrates that riparian vegetation can cause a braided channel to self‐organize to, and maintain, a dynamic, single‐thread channel. The initial condition for the experiments was steady‐state braiding in non‐cohesive sand under uniform discharge. From here, an experiment consisted of repeated cycles alternating a short duration high flow with a long duration low flow, and uniform dispersal of alfalfa seeds over the bed at the end of each high flow. Plants established on freshly deposited bars and areas of braidplain that were unoccupied during low flow. The presence of the plants had the effect of progressively focusing the high flow so that a single dominant channel developed. The single‐thread channel self‐adjusted to carry the high flow. Vegetation also slowed the rate of bank erosion. Matching of deposition along the point bar with erosion along the outer bend enabled the channel to develop sinuosity and migrate laterally while suppressing channel splitting and the creation of new channel width. The experimental channels spontaneously reproduced many of the mechanisms by which natural meandering channels migrate and maintain a single dominant channel, in particular bend growth and channel cutoff. In contrast with the braided system, where channel switching is a nearly continuous process, vegetation maintained a coherent channel until wholesale diversion of flow via cutoff and/or avulsion occurred, by which point the previous channel tended to be highly unfavorable for flow. Thus vegetation discouraged the coexistence of multiple channels. Varying discharge was key to allowing expression of feedbacks between the plants and the flow and promoting the transition from braiding to a single‐thread channel that was then dynamically maintained. Copyright © 2010 John Wiley & Sons, Ltd.

A considerable fraction of life develops in the sea at temperatures lower than 15 degrees C. Little is known about the adaptive features selected under those conditions. We present the analysis of the genome sequence of the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. We find that it copes with the increased solubility of oxygen at low temperature by multiplying dioxygen scavenging while deleting whole pathways producing reactive oxygen species. Dioxygen-consuming lipid desaturases achieve both protection against oxygen and synthesis of lipids making the membrane fluid. A remarkable strategy for avoidance of reactive oxygen species generation is developed by P. haloplanktis, with elimination of the ubiquitous molybdopterin-dependent metabolism. The P. haloplanktis proteome reveals a concerted amino acid usage bias specific to psychrophiles, consistently appearing apt to accommodate asparagine, a residue prone to make proteins age. Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome.

The turbulence generated by a vertically oscillating grid in a water tank and the entrainment across a salinity interface caused by this turbulence have been investigated experimentally. Measurements were carried out in a homogeneous layer of fluid as well as a two-layered fluid, which permitted us to determine the decay law of this turbulence and the way in which the structure of the turbulence depends on the mesh size and on the frequency and amplitude of the grid oscillation. It was found that the turbulent kinetic energy decays with distance from the grid according to a power law $\overline{q^2}\propto z^{-n}$ , with n close to 2, and that the turbulent Reynolds number remains approximately constant during decay. The linear dependence of the r.m.s. turbulent velocity on the grid oscillation frequency found by Thompson & Turner (1975) in the case of a square-bar grid has been confirmed. It is shown here that this linear relation remains valid when an interface is present and consequently the dependence of the entrainment velocity on the local Richardson number is of the form $u_e/u \propto Ri^{-\frac{3}{2}}$ , the Péclet number being high. While the bearing of these results on the problem of the thermocline or an inversion is clear we wish to emphasize that the spatial decay of turbulence is interesting in itself.

Highly luminescent CuI complexes with one phenanthroline and one (bis[2-(diphenylphosphino)phenyl]ether) ligand show an emission quantum yield of up to 28 % upon deactivation of the metal-to-ligand charge-transfer excited states; their X-ray crystal structure shows a distorted tetrahedral geometry (see figure and inside cover). One of these compounds is used as an active material in a light-emitting electrochemical cell; it exhibits an efficiency similar to that of RuII-type complexes.

As many as 1200 solvent molecules can be entrapped by one molecule of the cationic dimeric surfactants 1 to form a gel in CHCl3. These new gelators contain chiral counterions and form gels with both organic solvents and water upon their assembly into helical aggregates, which have similar structures in both media.

The sparse identification of nonlinear dynamics (SINDy) is a recently proposed data-driven modelling framework that uses sparse regression techniques to identify nonlinear low-order models. With the goal of low-order models of a fluid flow, we combine this approach with dimensionality reduction techniques (e.g. proper orthogonal decomposition) and extend it to enforce physical constraints in the regression, e.g. energy-preserving quadratic nonlinearities. The resulting models, hereafter referred to as Galerkin regression models, incorporate many beneficial aspects of Galerkin projection, but without the need for a high-fidelity solver to project the Navier–Stokes equations. Instead, the most parsimonious nonlinear model is determined that is consistent with observed measurement data and satisfies necessary constraints. Galerkin regression models also readily generalize to include higher-order nonlinear terms that model the effect of truncated modes. The effectiveness of such an approach is demonstrated on two canonical flow configurations: the two-dimensional flow past a circular cylinder and the shear-driven cavity flow. For both cases, the accuracy of the identified models compare favourably against reduced-order models obtained from a standard Galerkin projection procedure. Finally, the entire code base for our constrained sparse Galerkin regression algorithm is freely available online.

Abstract. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) U–Pb geochronology of carbonate minerals, calcite in particular, is rapidly gaining popularity as an absolute dating method. The high spatial resolution of LA-ICP-MS U–Pb carbonate geochronology has benefits over traditional isotope dilution methods, particularly for diagenetic and hydrothermal calcite, because uranium and lead are heterogeneously distributed on the sub-millimetre scale. At the same time, this can provide limitations to the method, as locating zones of radiogenic lead can be time-consuming and “hit or miss”. Here, we present strategies for dating carbonates with in situ techniques, through imaging and petrographic techniques to data interpretation; our examples are drawn from the dating of fracture-filling calcite, but our discussion is relevant to all carbonate applications. We review several limitations to the method, including open-system behaviour, variable initial-lead compositions, and U–daughter disequilibrium. We also discuss two approaches to data collection: traditional spot analyses guided by petrographic and elemental imaging and image-based dating that utilises LA-ICP-MS elemental and isotopic map data.

The turbulent boundary layer along a compression ramp with a deflection angle of 18° at a free-stream Mach number of M = 3 and a Reynolds number of Re θ = 1685 with respect to free-stream quantities and mean momentum thickness at inflow is studied by direct numerical simulation. The conservation equations for mass, momentum, and energy are solved in generalized coordinates using a 5th-order hybrid compact- finite-difference-ENO scheme for the spatial discretization of the convective fluxes and 6th-order central compact finite differences for the diffusive fluxes. For time advancement a 3rd-order Runge–Kutta scheme is used. The computational domain is discretized with about 15 × 10 6 grid points. Turbulent inflow data are provided by a separate zero-pressure-gradient boundary-layer simulation. For statistical analysis, the flow is sampled 600 times over about 385 characteristic timescales δ 0 / U ∞, defined by the mean boundary-layer thickness at inflow and the free-stream velocity. Diagnostics show that the numerical representation of the flow field is sufficiently well resolved. Near the corner, a small area of separated flow develops. The shock motion is limited to less than about 10% of the mean boundary-layer thickness. The shock oscillates slightly around its mean location with a frequency of similar magnitude to the bursting frequency of the incoming boundary layer. Turbulent fluctuations are significantly amplified owing to the shock–boundary-layer interaction. Reynolds-stress maxima are amplified by a factor of about 4. Turbulent normal and shear stresses are amplified differently, resulting in a change of the structure parameter. Compressibility affects the turbulence structure in the interaction area around the corner and during the relaxation after reattachment downstream of the corner. Correlations involving pressure fluctuations are significantly enhanced in these regions. The strong Reynolds analogy which suggests a perfect correlation between velocity and temperature fluctuations is found to be invalid in the interaction area.

Despite claims, based largely on molecular dynamics simulations, that the surface of water at the air/water interface is acidic, with a positive charge, there is compelling experimental evidence that it is in fact basic, with a negative charge due to the specific adsorption of hydroxide ions. The oil/water interface behaves similarly. The pH dependence of the zeta potentials of oil drops has been measured by two very different techniques: on a single drop in a rotating electrophoresis cell and on about 10(14) submicrometer drops in a 2 vol % emulsion by an electroacoustic method to give similar results with a sigmoidal pH dependence characterized by an isoelectric point at pH 2-3 and a half adsorption point about pH 5.5, or at 10(-8.5) M hydroxide ion. This indicates that hydroxide ion is absorbed much more strongly than other anions. The pH dependence of a single N(2) bubble has also been measured and has the same pH dependence, independently of whether HCl or HI is used to adjust the pH. These similarities between the pH dependences of the zeta potentials of air bubbles and oil drops, as well as those reported from streaming potentials on solid inert surfaces such as Teflon, indicate that water behaves similarly, with only subtle differences, at each of these low dielectric hydrophobic surfaces, with an isoelectric point of pH 2-4. In acidic solutions at pH's below the isoelectric point, the surface is indeed positive, consistent with spectroscopic observations of the adsorption of hydrogen ions.

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically 'entangled' helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at http://kinefold.curie.fr/.

A statistical theory is developed for the structure and propagation velocity of premixed flames in turbulent flows with scales large compared with the laminar flame thickness. The analysis, free of usual closure assumptions, involves a regular perturbation for small values of the ratio of laminar flame thickness to turbulence scale, termed the scale ratio ε, and a singular perturbation for large values of the non-dimensional activation temperature β. Any effects of the flame on the flow are considered to be given. In this initial study, molecular coefficients for diffusion of heat and reactants are set equal. The results identify convective-diffusive and reactive-diffusive zones in the flame and predict thickening of the flame by turbulence through streamwise displacement of the reactive-diffusive zone. Profiles for intensities of temperature fluctuations and for streamwise turbulent transport are obtained. A fundamental quantity occurring in the analysis is the longitudinal displacement of the reactive-diffusive zone in an Eulerian frame by turbulent fluctuations, and to first order in the scale ratio this equals the longitudinal displacement of fluid elements in an Eulerian frame by turbulent fluctuations, herein termed simply the Eulerian displacement. To first order in the scale ratio it is found that, if the Eulerian displacement experiences the same type of statistical non-stationarity as the corresponding Lagrangian displacement, then the diffusion approximation is valid for streamwise turbulent transport but the turbulent flame thickens as time increases, while if the Eulerian displacement is statistically stationary then the diffusion approximation necessitates a negative coefficient of diffusion in part of the flame but the flame thickness remains constant. By carrying the analysis to second order in the scale ratio it is shown that the turbulent-flame speed exceeds the laminar-flame speed by an amount proportional to the mean square of the transverse gradient of the Eulerian displacement. This result can be understood from the mechanistic viewpoint of a wrinkled laminar flame in terms of the increase in flame area produced by turbulence. Thus the theory provides a precise statistical quantification of the model of the wrinkled laminar flame for describing structures of turbulent flames.

The scenario of transition to chaos for a sphere falling or ascending under the action of gravity in a Newtonian fluid is investigated by numerical simulation. The mathematical formulation is parameterized using two non-dimensional parameters: the solid/fluid density ratio and the generalized Galileo number expressing the ratio between the gravity–buoyancy and viscosity effects. The study is carried out fully in this two-parameter space. The results show that for all density ratios the vertical fall or ascension becomes unstable via a regular axisymmetry breaking bifurcation. This bifurcation sets in slightly earlier for light spheres than for dense ones. A steady oblique fall or ascension follows before losing stability and giving way to an oscillating oblique movement. The secondary Hopf bifurcation is shown not to correspond to that of a fixed sphere wake for density ratios lower than 2.5, for which the oscillations have a significantly lower frequency. Trajectories of falling spheres become chaotic directly from the oblique oscillating regime. Ascending spheres present a specific behaviour before reaching a chaotic regime. The periodically oscillating oblique regime undergoes a subharmonic transition yielding a low-frequency oscillating ascension which is vertical in the mean (zigzagging regime). In all these stages of transition, the trajectories are planar with a plane selected randomly during the axisymmetry breaking. The chaotic regime appears to result from an interplay of a regular and of an additional Hopf bifurcation and the onset of the chaotic regime is accompanied by the loss of the remaining planar symmetry. The asymptotic chaotic states present an intermittent character, the relaminarization phases letting the subcritical plane and periodic trajectories reappear.

Abstract A novel deterministic symbolic regression method SpaRTA (Sparse Regression of Turbulent Stress Anisotropy) is introduced to infer algebraic stress models for the closure of RANS equations directly from high-fidelity LES or DNS data. The models are written as tensor polynomials and are built from a library of candidate functions. The machine-learning method is based on elastic net regularisation which promotes sparsity of the inferred models. By being data-driven the method relaxes assumptions commonly made in the process of model development. Model-discovery and cross-validation is performed for three cases of separating flows, i.e. periodic hills ( R e =10595), converging-diverging channel ( R e =12600) and curved backward-facing step ( R e =13700). The predictions of the discovered models are significantly improved over the k - ω SST also for a true prediction of the flow over periodic hills at R e =37000. This study shows a systematic assessment of SpaRTA for rapid machine-learning of robust corrections for standard RANS turbulence models.

The beta-proteobacterial strain ULPAs1, isolated from an arsenic-contaminated environment, is able to efficiently oxidize arsenite [As(III)] to arsenate [As(V)]. Mutagenesis with a lacZ-based reporter transposon yielded two knockout derivatives deficient in arsenite oxidation. Sequence analysis of the DNA flanking the transposon insertions in the two mutants identified two adjacent open reading frames, named aoxA and aoxB, as well as a putative promoter upstream of the aoxA gene. Reverse transcription-PCR data indicated that these genes are organized in an operonic structure. The proteins encoded by aoxA and aoxB share 64 and 72% identity with the small Rieske subunit and the large subunit of the purified and crystallized arsenite oxidase of Alcaligenes faecalis, respectively (P. J. Ellis, T. Conrads, R. Hille, and P. Kuhn, Structure [Cambridge] 9:125-132, 2001). Importantly, almost all amino acids involved in cofactor interactions in both subunits of the A. faecalis enzyme were conserved in the corresponding sequences of strain ULPAs1. An additional Tat (twin-arginine translocation) signal peptide sequence was detected at the N terminus of the protein encoded by aoxA, strongly suggesting that the Tat pathway is involved in the translocation of the arsenite oxidase to its known periplasmic location.