A code for direct numerical simulation of turbulent boundary layers at high Reynolds numbers in BG/P supercomputers

A new high-resolution code for the direct numerical simulation of a zero pressure gradient turbulent boundary layers over a flat plate has been developed. Its purpose is to simulate a wide range of Reynolds numbers from Reθ = 300 to 6800 while showing a linear weak scaling up to 32,768 cores in the BG/P architecture. Special attention has been paid to the generation of proper inflow boundary conditions. The results are in good agreement with existing numerical and experimental data sets.

Characteristics of the turbulent/nonturbulent interface in boundary layers, jets and shear-free turbulence

The characteristics of turbulent/nonturbulent interfaces (TNTI) from boundary layers, jets and shear-free turbulence are compared using direct numerical simulations. The TNTI location is detected by assessing the volume of turbulent flow as function of the vorticity magnitude and is shown to be equivalent to other procedures using a scalar field. Vorticity maps show that the boundary layer contains a larger range of scales at the interface than in jets and shear-free turbulence where the change in vorticity characteristics across the TNTI is much more dramatic. The intermittency parameter shows that the extent of the intermittency region for jets and boundary layers is similar and is much bigger than in shear-free turbulence, and can be used to compute the vorticity threshold defining the TNTI location. The statistics of the vorticity jump across the TNTI exhibit the imprint of a large range of scales, from the Kolmogorov micro-scale to scales much bigger than the Taylor scale. Finally, it is shown that contrary to the classical view, the low-vorticity spots inside the jet are statistically similar to isotropic turbulence, suggesting that engulfing pockets simply do not exist in jets

Entrainment Effects in Turbulent Boundary Layers

Esta tesis estudia el comportamiento de la región exterior de una capa límite turbulenta sin gradientes de presiones. Se ponen a prueba dos teorías relativamente bien establecidas. La teoría de semejanza para la pared supone que en el caso de haber una pared rugosa, el fluido sólo percibe el cambio en la fricción superficial que causa, y otros efectos secundarios quedarán confinados a una zona pegada a la pared. El consenso actual es que dicha teoría es aproximadamente cierta. En el extremo exterior de la capa límite existe una región producida por la interacción entre las estructuras turbulentas y el flujo irrotacional de la corriente libre llamada interfaz turbulenta/no turbulenta. La mayoría de los resultados al respecto sugieren la presencia de fuerzas de cortadura ligeramente más intensa, lo que la hace distinta al resto del flujo turbulento. Las propiedades de esa región probablemente cambien si la velocidad de crecimiento de la capa límite aumenta, algo que puede conseguirse aumentando la fricción en la pared. La rugosidad y la ingestión de masa están entonces relacionadas, y el comportamiento local de la interfaz turbulenta/no turbulenta puede explicar el motivo por el que las capas límite sobre paredes rugosas no se comportan como en el caso de tener paredes lisas precisamente en la zona exterior. Para estudiar las capas límite a números de Reynolds lo suficientemente elevados, se ha desarrollado un nuevo código de alta resolución para la simulación numérica directa de capas límite turbulentas sin gradiente de presión. Dicho código es capaz de simular capas límite en un intervalo de números de Reynolds entre ReT = 100 — 2000 manteniendo una buena escalabilidad hasta los dos millones de hilos en superordenadores de tipo Blue Gene/Q. Se ha guardado especial atención a la generación de condiciones de contorno a la entrada correctas. Los resultados obtenidos están en concordancia con los resultados previos, tanto en el caso de simulaciones como de experimentos. La interfaz turbulenta/no turbulenta de una capa límite se ha analizado usando un valor umbral del módulo de la vorticidad. Dicho umbral se considera un parámetro para analizar cada superficie obtenida de un contorno del módulo de la vorticidad. Se han encontrado dos regímenes distintos en función del umbral escogido con propiedades opuestas, separados por una transición topológica gradual. Las características geométricas de la zona escalan con o99 cuando u^/isdgg es la unidad de vorticidad. Las propiedades del íluido relativas a la posición del contorno de vorticidad han sido analizados para una serie de umbrales utilizando el campo de distancias esféricas, que puede obtenerse con independencia de la complejidad de la superficie de referencia. Las propiedades del fluido a una distancia dada del inerfaz también dependen del umbral de vorticidad, pero tienen características parecidas con independencia del número de Reynolds. La interacción entre la turbulencia y el flujo no turbulento se restringe a una zona muy fina con un espesor del orden de la escala de Kolmogorov local. Hacia el interior del flujo turbulento las propiedades son indistinguibles del resto de la capa límite. Se ha simulado una capa límite sin gradiente de presiones con una fuerza volumétrica cerca de la pared. La el forzado ha sido diseñado para aumentar la fricción en la pared sin introducir ningún efecto geométrico obvio. La simulación consta de dos dominios, un primer dominio más pequeño y a baja resolución que se encarga de generar condiciones de contorno correctas, y un segundo dominio mayor y a alta resolución donde se aplica el forzado. El estudio de los perfiles y los coeficientes de autocorrelación sugieren que los dos casos, el liso y el forzado, no colapsan más allá de la capa logarítmica por la complejidad geométrica de la zona intermitente, y por el hecho que la distancia a la pared no es una longitud característica. Los efectos causados por la geometría de la zona intermitente pueden evitarse utilizando el interfaz como referencia, y la distancia esférica para el análisis de sus propiedades. Las propiedades condicionadas del flujo escalan con 5QQ y u/uT, las dos únicas escalas contenidas en el modelo de semejanza de pared de Townsend, consistente con estos resultados. ABSTRACT This thesis studies the characteristics of the outer region of zero-pressure-gradient turbulent boundary layers at moderate Reynolds numbers. Two relatively established theories are put to test. The wall similarity theory states that with the presence of roughness, turbulent motion is mostly affected by the additional drag caused by the roughness, and that other secondary effects are restricted to a region very close to the wall. The consensus is that this theory is valid, but only as a first approximation. At the edge of the boundary layer there is a thin layer caused by the interaction between the turbulent eddies and the irroational fluid of the free stream, called turbulent/non-turbulent interface. The bulk of results about this layer suggest the presence of some localized shear, with properties that make it distinguishable from the rest of the turbulent flow. The properties of the interface are likely to change if the rate of spread of the turbulent boundary layer is amplified, an effect that is usually achieved by increasing the drag. Roughness and entrainment are therefore linked, and the local features of the turbulent/non-turbulent interface may explain the reason why rough-wall boundary layers deviate from the wall similarity theory precisely far from the wall. To study boundary layers at a higher Reynolds number, a new high-resolution code for the direct numerical simulation of a zero pressure gradient turbulent boundary layers over a flat plate has been developed. This code is able to simulate a wide range of Reynolds numbers from ReT =100 to 2000 while showing a linear weak scaling up to around two million threads in the BG/Q architecture. Special attention has been paid to the generation of proper inflow boundary conditions. The results are in good agreement with existing numerical and experimental data sets. The turbulent/non-turbulent interface of a boundary layer is analyzed by thresholding the vorticity magnitude field. The value of the threshold is considered a parameter in the analysis of the surfaces obtained from isocontours of the vorticity magnitude. Two different regimes for the surface can be distinguished depending on the threshold, with a gradual topological transition across which its geometrical properties change significantly. The width of the transition scales well with oQg when u^/udgg is used as a unit of vorticity. The properties of the flow relative to the position of the vorticity magnitude isocontour are analyzed within the same range of thresholds, using the ball distance field, which can be obtained regardless of the size of the domain and complexity of the interface. The properties of the flow at a given distance to the interface also depend on the threshold, but they are similar regardless of the Reynolds number. The interaction between the turbulent and the non-turbulent flow occurs in a thin layer with a thickness that scales with the Kolmogorov length. Deeper into the turbulent side, the properties are undistinguishable from the rest of the turbulent flow. A zero-pressure-gradient turbulent boundary layer with a volumetric near-wall forcing has been simulated. The forcing has been designed to increase the wall friction without introducing any obvious geometrical effect. The actual simulation is split in two domains, a smaller one in charge of the generation of correct inflow boundary conditions, and a second and larger one where the forcing is applied. The study of the one-point and twopoint statistics suggest that the forced and the smooth cases do not collapse beyond the logarithmic layer may be caused by the geometrical complexity of the intermittent region, and by the fact that the scaling with the wall-normal coordinate is no longer present. The geometrical effects can be avoided using the turbulent/non-turbulent interface as a reference frame, and the minimum distance respect to it. The conditional analysis of the vorticity field with the alternative reference frame recovers the scaling with 5QQ and v¡uT already present in the logarithmic layer, the only two length-scales allowed if Townsend’s wall similarity hypothesis is valid.

XRD analysis of InGaN uniform layers grown on Si (111) without any buffer layers and on Sapphire

The International Workshop on Nitride Semiconductors (IWN) is a biennial academic conference in the field of group III nitride research. The IWN and the International Conference on Nitride Semiconductors (ICNS) are held in alternating years and cover similar subject areas.

Design of broadband transmitarray unit cells with comparative study of different numbers of layers

A generalized methodology to design low-profile transmitarray (TA) antennas made of several stacked layers with nonresonant printed phasing elements is presented. A study of the unit cell bandwidth, phase-shift range and tolerances has been conducted considering different numbers of layers. A structure with three metalized layers with capacitive and inductive elements enabling a phase range of nearly 360° and low insertion loss is introduced. A study of the four-layer structure shows improvement in the performance of the unit cells in terms of bandwidth from 2% to more than 20% and a complete phase coverage. Implementations on a flexible substrate of TAs with progressive phase shift operating at 19 GHz are used for validation.

Fluctuations and stimulus-induced changes in blood flow observed in individual capillaries in layers 2 through 4 of rat neocortex

Cortical blood flow at the level of individual capillaries and the coupling of neuronal activity to flow in capillaries are fundamental aspects of homeostasis in the normal and the diseased brain. To probe the dynamics of blood flow at this level, we used two-photon laser scanning microscopy to image the motion of red blood cells (RBCs) in individual capillaries that lie as far as 600 μm below the pia mater of primary somatosensory cortex in rat; this depth encompassed the cortical layers with the highest density of neurons and capillaries. We observed that the flow was quite variable and exhibited temporal fluctuations around 0.1 Hz, as well as prolonged stalls and occasional reversals of direction. On average, the speed and flux (cells per unit time) of RBCs covaried linearly at low values of flux, with a linear density of ≈70 cells per mm, followed by a tendency for the speed to plateau at high values of flux. Thus, both the average velocity and density of RBCs are greater at high values of flux than at low values. Time-locked changes in flow, localized to the appropriate anatomical region of somatosensory cortex, were observed in response to stimulation of either multiple vibrissae or the hindlimb. Although we were able to detect stimulus-induced changes in the flux and speed of RBCs in some single trials, the amplitude of the stimulus-evoked changes in flow were largely masked by basal fluctuations. On average, the flux and the speed of RBCs increased transiently on stimulation, although the linear density of RBCs decreased slightly. These findings are consistent with a stimulus-induced decrease in capillary resistance to flow.

Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments

A general strategy is described for designing proteins that self assemble into large symmetrical nanomaterials, including molecular cages, filaments, layers, and porous materials. In this strategy, one molecule of protein A, which naturally forms a self-assembling oligomer, An, is fused rigidly to one molecule of protein B, which forms another self-assembling oligomer, Bm. The result is a fusion protein, A-B, which self assembles with other identical copies of itself into a designed nanohedral particle or material, (A-B)p. The strategy is demonstrated through the design, production, and characterization of two fusion proteins: a 49-kDa protein designed to assemble into a cage approximately 15 nm across, and a 44-kDa protein designed to assemble into long filaments approximately 4 nm wide. The strategy opens a way to create a wide variety of potentially useful protein-based materials, some of which share similar features with natural biological assemblies.

Antioxidant Defenses in the Peripheral Cell Layers of Legume Root Nodules1

Ascorbate peroxidase (AP) is a key enzyme that scavenges potentially harmful H2O2 and thus prevents oxidative damage in plants, especially in N2-fixing legume root nodules. The present study demonstrates that the nodule endodermis of alfalfa (Medicago sativa) root nodules contains elevated levels of AP protein, as well as the corresponding mRNA transcript and substrate (ascorbate). Enhanced AP protein levels were also found in cells immediately peripheral to the infected region of soybean (Glycine max), pea (Pisum sativum), clover (Trifolium pratense), and common bean (Phaseolus vulgaris) nodules. Regeneration of ascorbate was achieved by (homo)glutathione and associated enzymes of the ascorbate-glutathione pathway, which were present at high levels. The presence of high levels of antioxidants suggests that respiratory consumption of O2 in the endodermis or nodule parenchyma may be an essential component of the O2-diffusion barrier that regulates the entry of O2 into the central region of nodules and ensures optimal functioning of nitrogenase.

Retinal engineering: engrafted neural cell lines locate in appropriate layers.

A major question in central nervous system development, including the neuroretina, is whether migrating cells express cues to find their way and settle at specific locations. We have transplanted quail neuroretinal cell lines QNR/D, a putative amacrine or ganglion cell, and QNR/K2, a putative Müller cell into chicken embryo eyes. Implanted QNR/D cells migrate only to the retinal ganglion and amacrine cell layers and project neurites in the plane of retina; in contrast, QNR/K2 cells migrate through the ganglion and amacrine layers, locate in the inner nuclear layer, and project processes across the retina. These data show that QNR/D and QNR/K2 cell lines represent distinct neural cell types, suggesting that migrating neural cells express distinct address cues. Furthermore, our results raise the possibility that immortalized cell lines can be used for replacement of specific cell types and for the transport of genes to given locations in neuroretina.

Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution.

The x-ray crystal structures of the sulfide oxidase antibody 28B4 and of antibody 28B4 complexed with hapten have been solved at 2.2-angstrom and 1.9-angstrom resolution, respectively. To our knowledge, these structures are the highest resolution catalytic antibody structures to date and provide insight into the molecular mechanism of this antibody-catalyzed monooxygenation reaction. Specifically, the data suggest that entropic restriction plays a fundamental role in catalysis through the precise alignment of the thioether substrate and oxidant. The antibody active site also stabilizes developing charge on both sulfur and periodate in the transition state via cation-pi and electrostatic interactions, respectively. In addition to demonstrating that the active site of antibody 28B4 does indeed reflect the mechanistic information programmed in the aminophosphonic acid hapten, these high-resolution structures provide a basis for enhancing turnover rates through mutagenesis and improved hapten design.

Experimental evidence for hydrogen-bonded network proton transfer in bacteriorhodopsin shown by Fourier-transform infrared spectroscopy using azide as catalyst.

Experimental evidence for proton transfer via a hydrogen-bonded network in a membrane protein is presented. Bacteriorhodopsin's proton transfer mechanism on the proton uptake pathway between Asp-96 and the Schiff base in the M-to-N transition was determined. The slowdown of this transfer by removal of the proton donor in the Asp-96-->Asn mutant can be accelerated again by addition of small weak acid anions such as azide. Fourier-transform infrared experiments show in the Asp-96-->Asn mutant a transient protonation of azide bound to the protein in the M-to-N transition and, due to the addition of azide, restoration of the IR continuum band changes as seen in wild-type bR during proton pumping. The continuum band changes indicate fast proton transfer on the uptake pathway in a hydrogen-bonded network for wild-type bR and the Asp-96-->Asn mutant with azide. Since azide is able to catalyze proton transfer steps also in several kinetically defective bR mutants and in other membrane proteins, our finding might point to a general element of proton transfer mechanisms in proteins.

Tuning the functional properties of Silicon Carbide Thin Film and Nanowires

The present thesis has been devoted to the synthesis and investigation of functional properties of silicon carbide thin films and nanowires. The work took profit from the experience of the research group in the synthesis of 3C-SiC from vapour phase. 3C-SiC thin films Thin films heteroepitaxy on silicon substrates was carried out in a vapour phase epitaxy reactor. The initial efforts were committed to the process development in order to enhance the crystal quality of the epi-layer. The carbonization process and a buffer layer procedure were optimized in order to obtain good quality monocrystalline 3C-SiC layers. The films characterization was used not only to improve the entire process, but also to assess the crystalline quality and to identify the defects. Methyltrichlorosilane (MTS) was introduced during the synthesis to increase the growth rate and enhance crystalline quality. The effect of synthesis parameters such as MTS flow and process temperature was studied in order to promote defect density reduction and the release of the strain due to lattice mismatch between 3C-SiC and silicon substrate. In-growth n-type doping was implemented using a nitrogen gas line and the effect of different synthesis parameters on doping level was studied. Raman measurements allowed a contactless characterization and evaluation of electrically active dopant. The effect of MTS on nitrogen incorporation was investigated and a promotion of dopant concentration together with a higher growth rate were demonstrated. This result allows to obtain higher doping concentrations without deteriorating crystal quality in 3C-SiC and, to the best of our knowledge, it has never been demonstrated before. 3C-SiC nanowires Core-shell SiC-SiO2 nanowires were synthesized using a chemical vapour deposition technique in an open tube configuration reactor on silicon substrates. Metal catalyst were used to promote a uniaxial growth and a dense bundle of nanowires 100 µm long and 60 nm thick was obtained. Substrate preparation was found to be fundamental in order to obtain a uniform nanowire density. Morphological characterization was carried out using scanning electron microscopy and the analysis of structural, compositional, optical properties is reported.

Electrochemical analysis of the performance of carbon supported Pd nanoparticles for direct formic acid fuel cells: from gold supported electrodes to catalyst-coated membranes

In this work carbon supported Pd nanoparticles were prepared and used as electrocatalysts for formic acid electrooxidation fuel cells. The influence of some relevant parameters such as the nominal Pt loading, the Nafion/total solids ratio as well as the Pd loading towards formic acid electrooxidation was evaluated using gold supported catalytic layer electrodes which were prepared using a similar methodology to that employed in the preparation of conventional catalyst coated membranes (CCM). The results obtained show that, for constant Pd loading, the nominal Pd loading and the Nafion percentage on the catalytic layer do not play an important role on the resulting electrocatalytic properties. The main parameter affecting the electrocatalytic activity of the electrodes seems to be the Pd loading, although the resulting activity is not directly proportional to the increased Pd loading. Thus, whereas the Pd loading is multiplied by a factor of 10, the activity is only twice which evidences an important decrease in the Pd utilization. In fact, the results obtained suggest the active layer is the outer one being clearly independent of the catalytic layer thickness. Finally, catalyst coated membranes with Pd catalyst loadings of 0.1, 0.5 and 1.2 mg cm-2 were also tested in a breathing direct formic acid fuel cell.