Summertime winds and direct cyclonic circulation: observations from Lake Geneva

International audienceRecords of wind, air temperature and air pressure from nine stations, situated along the shoreline of Lake Geneva, Switzerland, were analyzed for the summer period May to September. At all stations the consistent appearance of significant spectral peaks and changes in wind direction at the diurnal frequency indicates the importance of lake-land breezes. It is shown that the surrounding topography has a strong modifying effect (temporal and spatial) on the lake-land breeze. Superimposed on this cyclic wind pattern, short episodes of strong winds with long fetch over parts of Lake Geneva are regularly observed. Both of these winds exert a spatially variable wind stress over the lake surface on the same time scale. Typical examples of the expected lake's response are presented, among them the seasonally persistent gyre in the central part of the lake. Evidence is provided that this dominant circulation is part of a direct cyclonic circulation, generated by the curl of the diurnal wind field. It is concluded that the mean circulation is caused by these winds and affected by the topography of the surrounding land

Internal waves and temperature fronts on slopes

International audienceTime series measurements from an array of temperature miniloggers in a line at constant depth along the sloping boundary of a lake are used to describe the `internal surf zone' where internal waves interact with the sloping boundary. More small positive temperature time derivatives are recorded than negative, but there are more large negative values than positive, giving the overall distribution of temperature time derivatives a small negative skewness. This is consistent with the internal wave dynamics; fronts form during the up-slope phase of the motion, bringing cold water up the slope, and the return flow may become unstable, leading to small advecting billows and weak warm fronts. The data are analysed to detect `events', periods in which the temperature derivatives exceed a set threshold. The speed and distance travelled by `events' are described. The motion along the slope may be a consequence of (a) instabilities advected by the flow (b) internal waves propagating along-slope or (c) internal waves approaching the slope from oblique directions. The propagation of several of the observed 'events' can only be explained by (c), evidence that the internal surf zone has some, but possibly not all, the characteristics of the conventional 'surface wave' surf zone, with waves steepening as they approach the slope at oblique angles

Aspects of turbulence and fine sediment resuspension in accelerating and decelerating open-channel flow

River hydrodynamicsTurbulent open channel flow and transport phenomen

Turbulent transport in the outer region of rough-wall open-channel flows: the contribution of large coherent shear stress structures (LC3S)

Acoustic Doppler velocity profiler (ADVP) measurements of instantaneous three-dimensional velocity profiles over the entire turbulent boundary layer height, δ, of rough-bed open-channel flows at moderate Reynolds numbers show the presence of large scale coherent shear stress structures (called LC3S herein) in the zones of uniformly retarded streamwise momentum. LC3S events over streamwise distances of several boundary layer thicknesses dominate the mean shear dynamics. Polymodal histograms of short streamwise velocity samples confirm the subdivision of uniform streamwise momentum into three zones also observed by Adrian et al. (J. Fluid Mech., vol. 422, 2000, p. 1). The mean streamwise dimension of the zones varies between 1δ and 2.5δ. In the intermediate region (0.2<z/δ<0.75), the contribution of conditionally sampled u'w' events to the mean vertical turbulent kinetic energy (TKE) flux as a function of threshold level H is found to be generated by LC3S events above a critical threshold level Hmax for which the ascendant net momentum flux between LC3S of ejection and sweep types is maximal. The vertical profile of Hmax is nearly constant over the intermediate region, with a value of 5 independent of the flow conditions. Very good agreement is found for all flow conditions including the free-stream shear flows studied in Adrian et al. (2000). If normalized by the squared bed friction velocity, the ascendant net momentum flux containing 90% of the mean TKE flux is equal to 20% of the shear stress due to bed friction. In the intermediate region this value is nearly constant for all flow conditions investigated herein. It can be deduced that free-surface turbulence in open-channel flows originates from processes driven by LC3S, associated with the zonal organization of streamwise momentum. The good agreement with mean quadrant distribution results in the literature implies that LC3S identified in this study are common features in the outer region of shear flow

Compressive Sensing Using Iterative Hard Thresholding with Low Precision Data Representation: Theory and Applications

Modern scientific instruments produce vast amounts of data, which can overwhelm the processing ability of computer systems. Lossy compression of data is an intriguing solution, but comes with its own drawbacks, such as potential signal loss, and the need for careful optimization of the compression ratio. In this work, we focus on a setting where this problem is especially acute: compressive sensing frameworks for interferometry and medical imaging. We ask the following question: can the precision of the data representation be lowered for all inputs, with recovery guarantees and practical performance? Our first contribution is a theoretical analysis of the normalized Iterative Hard Thresholding (IHT) algorithm when all input data, meaning both the measurement matrix and the observation vector are quantized aggressively. We present a variant of low precision normalized {IHT} that, under mild conditions, can still provide recovery guarantees. The second contribution is the application of our quantization framework to radio astronomy and magnetic resonance imaging. We show that lowering the precision of the data can significantly accelerate image recovery. We evaluate our approach on telescope data and samples of brain images using CPU and FPGA implementations achieving up to a 9x speed-up with negligible loss of recovery quality.Comment: 19 pages, 5 figures, 1 table, in IEEE Transactions on Signal Processin

Molecular Modeling of Membrane Embedded Proteins

Over the past years, molecular modeling and simulation techniques have had a major impact on experimental life sciences. They are capable of providing accurate insight into microscopic mechanisms, which are usually difficult to investigate experimentally. Moreover, the integration of experimental data with molecular modeling appears to be a promising strategy to better understand complex biological processes. In this thesis, molecular dynamics simulation has been used in combination with experimental data to investigate two transmembrane proteins: (i) the bacterial chemoreceptor PhoQ and (ii) the Amyloid Precursor Protein (APP). (i) Bacterial two-component system PhoQ and bacterial membranes. Two-component systems (TCSs) are signaling complexes essential for bacterial survival and virulence. PhoQ is the histidine kinase chemoreceptor of the PhoQ-PhoP tandem machine that detects the concentration of cationic species at the inner membrane of Gram-negative bacteria. A full understanding of the PhoQ signal transduction mechanism is currently hindered by the lack of a complete atomistic structure. In this thesis project, the first structural model of the transmembrane (TM) portion of PhoQ from Escherichia coli was assembled, by using molecular simulations integrated with cross-linking disulfide scanning data. Its structural and dynamic features induce a concerted displacement of the TM helices at the periplasmic side, which modulates a rotation at the cytoplasmic end. This supports the idea that signal transduction is promoted through a combination of scissoring and rotational movements of the TM helices. Knowledge of this complex mechanism is essential in order to understand how the chemical stimuli sensed by the periplasmic sensor domain trigger, via the relay of the HAMP domain, the histidine auto-phosphorylation and kinase/phosphatase activity at the cytoplasmic end. The PhoQ sensor domain lies in close proximity to the membrane. Interaction with anionic lipids, such as phosphophatidylglycerols (PG) and cardiolipins (CL), are thought to play a key role in PhoQ activity. Present in bacterial and mitochondrial membranes, cardiolipins have a unique dimeric structure, which carries up to two charges, i.e. one per phosphate group, and under physiological conditions, can be unprotonated or singly protonated. Exhaustive models and characterization of cardiolipins are to-date scarce; therefore an ab initio parameterization of cardiolipin species for molecular simulation consistent with commonly used force fields is proposed here. Molecular dynamics (MD) simulations based on these models indicate a protonation-dependent lipid packing. A noteworthy interaction with solvating mono- and divalent cations is also observed. The proposed models will contribute to the biophysical and biochemical characterizations of bacterial and mitochondrial membranes and membrane-embedded proteins. (ii) Structural and dynamic properties of the Amyloid Precursor Protein. The Amyloid Precursor Protein (APP) is a type I membrane glycoprotein present at the neuronal synapsis. The proteolytic cleavage of its C-terminal segment produces amyloid-β (Aβ) peptides of different lengths, the deposition of which is an early indicator of Alzheimer"s disease (AD). Recently, the backbone structure of the APP transmembrane (TM) domain in detergent micelles was determined by nuclear magnetic resonance (NMR, independently by two different experimental groups). The TM conformations of these two structures are however markedly different. One is characterized by a highly kinked α-helix, whereas the other is mainly straight. Molecular dynamics simulations showed that the APP TM region is highly flexible and its secondary structure is influenced by the surrounding lipid environment. The size of the embedding detergent micelles strongly affects the conformation of the APP α-helix, with solvation being the main driving force for the development of a helical curvature. Once embedded in a membrane bilayer, APP systematically prefers a straight helical conformation. This is also confirmed when analyzing in silico the atomistic APP population observed in double electron-electron resonance (DEER) spectroscopy. In summary, the APP transmembrane domain is highly flexible due to the presence of glycine residues and can readily respond to the lipid environment, a property that might be critical for proteolytic processing by γ-secretase enzymes. The presented thesis work clearly shows how molecular simulations and their interplay with available experimental input can help advance the understanding of the mechanism of complex biological systems and processes on a molecular scale. These results, in particular, go well beyond the current understanding of the functioning of two transmembrane proteins relevant for human health. Furthermore, the computational approaches and procedures developed in these projects will hopefully promote novel integrated strategies for investigating biological systems

Near-field flow structure of a confined wall jet on flat and concave rough walls

Experimental results are presented of the mean flow and turbulence characteristics in the near field of a plane wall jet issuing from a nozzle onto flat and concave walls consisting of fixed sand beds. This is a flow configuration of interest for sediment erosion, also referred to as scouring. The measurements were made with an acoustic profiler that gives access to the three components of the instantaneous velocities. For the flat-wall flow, it is shown that the outer-layer spatial growth rate and the maxima of the Reynolds stresses approach the values accepted for the far field of a wall jet at a downstream distance x/b0 ≈ 8. These maxima are only about half the values of a plane free jet. This reduction in Reynolds stresses is also observed in the shear-layer region, x/b0 11, the maximum Reynolds shear stress approaches the value of a plane free jet. This change in Reynolds stresses is related to the mean vertical velocity that is negative for x/b0 < 8 and positive further downstream. The evolution of the inner region of the wall jet is found to be in good agreement with a previous model that explicitly includes the roughness length. On the concave wall, the mean flow and the Reynolds stresses are drastically changed by the adverse pressure gradient and especially by the development of Görtler vortices. On the downslope side of the scour hole, the flow is nearly separating with the wall shear stress tending to zero, whereas on the upslope side, the wall-friction coefficient is increased by a factor of about two by Görtler vortices. These vortices extend well into the outer layer and, just above the wall, cause a substantial increase in Reynolds shear stres

Double-average methodology applied to turbulent gravel-bed river flows

River hydrodynamicsTurbulent open channel flow and transport phenomen

Large scale PIV-measurements on the water surface of turbulent open-channel flow

An experimental open-channel laboratory study of secondary currents and surface boils is presented. Surface velocity dynamics over a large measuring field were investigated using Large Scale Particle Image Velocimetry (LSPIV). Data were analyzed for the structures of the large streamwise vortices and surface boils. The results indicate a mean multi-cellular pattern of faster and slower primary longitudinal velocities. The mean transversal velocities show a corresponding pattern. The spacing of the surface pattern of upwelling and downwelling is related to the water depth. The instantaneous pattern of the secondary currents meanders around the mean pattern. Vortex boils occur near the upwelling regions. Details of the vortex structures, in particular the growth and spreading of individual vortices when moving along the flow, are detected from instantaneous velocity maps of the water surface using a moving-camera PIV which follows the flow at the mean surface current speed