PIV measurements combined with the motion tracking technique to analyze flow around a moving porous structure

To gain a better understanding of the fluid–structure interaction and especially when dealing with a flow around an arbitrarily moving body, it is essential to develop measurement tools enabling the instantaneous detection of moving deformable interface during the flow measurements. A particularly useful application is the determination of unsteady turbulent flow velocity field around a moving porous fishing net structure which is of great interest for selectivity and also for the numerical code validation which needs a realistic database. To do this, a representative piece of fishing net structure is used to investigate both the Turbulent Boundary Layer (TBL) developing over the horizontal porous moving fishing net structure and the turbulent flow passing through the moving porous structure. For such an investigation, Time Resolved PIV measurements are carried out and combined with a motion tracking technique allowing the measurement of the instantaneous motion of the deformable fishing net during PIV measurements. Once the two-dimensional motion of the porous structure is accessed, PIV velocity measurements are analyzed in connection with the detected motion. Finally, the TBL is characterized and the effect of the structure motion on the volumetric flow rate passing though the moving porous structure is clearly demonstrated.

Microfluidic platforms for the characterization of in meso membrane protein crystallization

Membrane proteins, which reside in the membranes of cells, play a critical role in many important biological processes including cellular signaling, immune response, and material and energy transduction. Because of their key role in maintaining the environment within cells and facilitating intercellular interactions, understanding the function of these proteins is of tremendous medical and biochemical significance. Indeed, the malfunction of membrane proteins has been linked to numerous diseases including diabetes, cirrhosis of the liver, cystic fibrosis, cancer, Alzheimer's disease, hypertension, epilepsy, cataracts, tubulopathy, leukodystrophy, Leigh syndrome, anemia, sensorineural deafness, and hypertrophic cardiomyopathy.1-3 However, the structure of many of these proteins and the changes in their structure that lead to disease-related malfunctions are not well understood. Additionally, at least 60% of the pharmaceuticals currently available are thought to target membrane proteins, despite the fact that their exact mode of operation is not known.4-6 Developing a detailed understanding of the function of a protein is achieved by coupling biochemical experiments with knowledge of the structure of the protein. Currently the most common method for obtaining three-dimensional structure information is X-ray crystallography. However, no a priori methods are currently available to predict crystallization conditions for a given protein.7-14 This limitation is currently overcome by screening a large number of possible combinations of precipitants, buffer, salt, and pH conditions to identify conditions that are conducive to crystal nucleation and growth.7,9,11,15-24 Unfortunately, these screening efforts are often limited by difficulties associated with quantity and purity of available protein samples. While the two most significant bottlenecks for protein structure determination in general are the (i) obtaining sufficient quantities of high quality protein samples and (ii) growing high quality protein crystals that are suitable for X-ray structure determination,7,20,21,23,25-47 membrane proteins present additional challenges. For crystallization it is necessary to extract the membrane proteins from the cellular membrane. However, this process often leads to denaturation. In fact, membrane proteins have proven to be so difficult to crystallize that of the more than 66,000 structures deposited in the Protein Data Bank,48 less than 1% are for membrane proteins, with even fewer present at high resolution (< 2Å)4,6,49 and only a handful are human membrane proteins.49 A variety of strategies including detergent solubilization50-53 and the use of artificial membrane-like environments have been developed to circumvent this challenge.43,53-55 In recent years, the use of a lipidic mesophase as a medium for crystallizing membrane proteins has been demonstrated to increase success for a wide range of membrane proteins, including human receptor proteins.54,56-62 This in meso method for membrane protein crystallization, however, is still by no means routine due to challenges related to sample preparation at sub-microliter volumes and to crystal harvesting and X-ray data collection. This dissertation presents various aspects of the development of a microfluidic platform to enable high throughput in meso membrane protein crystallization at a level beyond the capabilities of current technologies. Microfluidic platforms for protein crystallization and other lab-on-a-chip applications have been well demonstrated.9,63-66 These integrated chips provide fine control over transport phenomena and the ability to perform high throughput analyses via highly integrated fluid networks. However, the development of microfluidic platforms for in meso protein crystallization required the development of strategies to cope with extremely viscous and non-Newtonian fluids. A theoretical treatment of highly viscous fluids in microfluidic devices is presented in Chapter 3, followed by the application of these strategies for the development of a microfluidic mixer capable of preparing a mesophase sample for in meso crystallization at a scale of less than 20 nL in Chapter 4. This approach was validated with the successful on chip in meso crystallization of the membrane protein bacteriorhodopsin. In summary, this is the first report of a microfluidic platform capable of performing in meso crystallization on-chip, representing a 1000x reduction in the scale at which mesophase trials can be prepared. Once protein crystals have formed, they are typically harvested from the droplet they were grown in and mounted for crystallographic analysis. Despite the high throughput automation present in nearly all other aspects of protein structure determination, the harvesting and mounting of crystals is still largely a manual process. Furthermore, during mounting the fragile protein crystals can potentially be damaged, both from physical and environmental shock. To circumvent these challenges an X-ray transparent microfluidic device architecture was developed to couple the benefits of scale, integration, and precise fluid control with the ability to perform in situ X-ray analysis (Chapter 5). This approach was validated successfully by crystallization and subsequent on-chip analysis of the soluble proteins lysozyme, thaumatin, and ribonuclease A and will be extended to microfluidic platforms for in meso membrane protein crystallization. The ability to perform in situ X-ray analysis was shown to provide extremely high quality diffraction data, in part as a result of not being affected by damage due to physical handling of the crystals. As part of the work described in this thesis, a variety of data collection strategies for in situ data analysis were also tested, including merging of small slices of data from a large number of crystals grown on a single chip, to allow for diffraction analysis at biologically relevant temperatures. While such strategies have been applied previously,57,59,61,67 they are potentially challenging when applied via traditional methods due to the need to grow and then mount a large number of crystals with minimal crystal-to-crystal variability. The integrated nature of microfluidic platforms easily enables the generation of a large number of reproducible crystallization trials. This, coupled with in situ analysis capabilities has the potential of being able to acquire high resolution structural data of proteins at biologically relevant conditions for which only small crystals, or crystals which are adversely affected by standard cryocooling techniques, could be obtained (Chapters 5 and 6). While the main focus of protein crystallography is to obtain three-dimensional protein structures, the results of typical experiments provide only a static picture of the protein. The use of polychromatic or Laue X-ray diffraction methods enables the collection of time resolved structural information. These experiments are very sensitive to crystal quality, however, and often suffer from severe radiation damage due to the intense polychromatic X-ray beams. Here, as before, the ability to perform in situ X-ray analysis on many small protein crystals within a microfluidic crystallization platform has the potential to overcome these challenges. An automated method for collecting a "single-shot" of data from a large number of crystals was developed in collaboration with the BioCARS team at the Advanced Photon Source at Argonne National Laboratory (Chapter 6). The work described in this thesis shows that, even more so than for traditional structure determination efforts, the ability to grow and analyze a large number of high quality crystals is critical to enable time resolved structural studies of novel proteins. In addition to enabling X-ray crystallography experiments, the development of X-ray transparent microfluidic platforms also has tremendous potential to answer other scientific questions, such as unraveling the mechanism of in meso crystallization. For instance, the lipidic mesophases utilized during in meso membrane protein crystallization can be characterized by small angle X-ray diffraction analysis. Coupling in situ analysis with microfluidic platforms capable of preparing these difficult mesophase samples at very small volumes has tremendous potential to enable the high throughput analysis of these systems on a scale that is not reasonably achievable using conventional sample preparation strategies (Chapter 7). In collaboration with the LS-CAT team at the Advanced Photon Source, an experimental station for small angle X-ray analysis coupled with the high quality visualization capabilities needed to target specific microfluidic samples on a highly integrated chip is under development. Characterizing the phase behavior of these mesophase systems and the effects of various additives present in crystallization trials is key for developing an understanding of how in meso crystallization occurs. A long term goal of these studies is to enable the rational design of in meso crystallization experiments so as to avoid or limit the need for high throughput screening efforts. In summary, this thesis describes the development of microfluidic platforms for protein crystallization with in situ analysis capabilities. Coupling the ability to perform in situ analysis with the small scale, fine control, and the high throughput nature of microfluidic platforms has tremendous potential to enable a new generation of crystallographic studies and facilitate the structure determination of important biological targets. The development of platforms for in meso membrane protein crystallization is particularly significant because they enable the preparation of highly viscous mixtures at a previously unachievable scale. Work in these areas is ongoing and has tremendous potential to improve not only current the methods of protein crystallization and crystallography, but also to enhance our knowledge of the structure and function of proteins which could have a significant scientific and medical impact on society as a whole. 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Aerodynamic behavior of an airfoil with morphing trailing edge for wind turbine applications

The length of wind turbine rotor blades has been increased during the last decades. Higher stresses arise especially at the blade root because of the longer lever arm. One way to reduce unsteady blade-root stresses caused by turbulence, gusts, or wind shear is to actively control the lift in the blade tip region. One promising method involves airfoils with morphing trailing edges to control the lift and consequently the loads acting on the blade. In the present study, the steady and unsteady behavior of an airfoil with a morphing trailing edge is investigated. Two-dimensional Reynolds-Averaged Navier-Stokes (RANS) simulations are performed for a typical thin wind turbine airfoil with a morphing trailing edge. Steady-state simulations are used to design optimal geometry, size, and deflection angles of the morphing trailing edge. The resulting steady aerodynamic coefficients are then analyzed at different angles of attack in order to determine the effectiveness of the morphing trailing edge. In order to investigate the unsteady aerodynamic behavior of the optimal morphing trailing edge, time-resolved RANS-simulations are performed using a deformable grid. In order to analyze the phase shift between the variable trailing edge deflection and the dynamic lift coefficient, the trailing edge is deflected at four different reduced frequencies for each different angle of attack. As expected, a phase shift between the deflection and the lift occurs. While deflecting the trailing edge at angles of attack near stall, additionally an overshoot above and beyond the steady lift coefficient is observed and evaluated.

A comparative study of the photophysics and photochemistry of 4-chlorophenol adsorbed on silicalite and beta-cyclodextrin

The photochemistry and photophysics of 4-chlorophenol (4-CP) were studied onto two model solid supports, silicalite and beta-cyclodextrin (beta-Cl)), using time resolved diffuse reflectance techniques and product degradation analysis. The results have shown that the photochemistry and photophysics of 4-CP are different from solution and depend on the solid. Ground state diffuse reflectance and time resolved luminescence demonstrated the inclusion of the probe in both substrates. 4-CP exhibits room temperature luminescence in both hosts, being structured and much more intense in beta-CD. The emission was assigned to phosphorescence of the inclusion complex. Transient absorption demonstrated the formation of the unsubstituted phenoxyl radical and of 4-chlorophenoxyl radical in beta-CD. In silicalite only the later was detected. The studies of the photodegradation products indicate that phenol is the main photoproduct in beta-CD. In silicalite the chromatographic analysis indicates the presence of products that involve the ring cleavage. (C) 2002 Elsevier Science B.V. All rights reserved.

Surface photochemistry: photodegradation study of pyrene adsorbed onto microcrystalline cellulose and silica

Ground-state diffuse reflectance, time resolved laser-induced luminescence, diffuse reflectance laser flash-photolysis transient absorption and chromatographic techniques were used to elucidate the photodegradation processes of pyrene adsorbed onto microcrystalline cellulose and silica. Ground-state diffuse reflectance showed that on both substrates low concentrations display absorption of pyrene monomers. At high concentrations spectral changes attributed to aggregate formation were observed. Laser induced fluorescence showed that pyrene onto microcrystalline cellulose mainly presents fluorescence from monomers, while for silica, excimer-like emission was observed from low surface loadings (greater than or equal to 0.5 mumol g(-1)). Transient absorption and photodegradation studies were performed at concentrations where mainly monomers exist. On silica, pyrene presents transient absorption from its radical cation. On microcrystalline cellulose both radical cation, radical anion and pyrene triplet-triplet absorption were detected. Irradiation followed by chromatographic analysis showed that pyrene decomposes on both substrates. For pyrene on microcrystalline cellulose 1-hydroxypyrene was the main identified photoproduct since in the absence of oxygen further oxidation of 1-hydroxypyrene was very slow. For pyrene on silica photodegradation was very efficient. Almost no 1-hydroxypyrene was detected since in the presence of oxygen it is quickly oxidized to other photooxidation products. On both substrates, pyrene radical cation is the intermediate leading to photoproducts and oxygen it is not involved in its formation.

Photochemistry of 4-chlorophenol on cellulose and silica

The photochemistry of 4-chlorophenol (4-CP) was studied on silica and cellulose, using time-resolved diffuse reflectance techniques and product degradation analysis. The results have shown that the photochemistry of 4-CP depends on the support, on the concentration, and also on the sample preparation method. Transient absorption and photoproduct results can be understood by assuming the formation of the carbene 4-oxocyclohexa-2,5-dienylidene in both supports. On cellulose, at concentrations lower than 10 mumol g(-1), the carbene leads to the unsubstituted phenoxyl radical, and phenol is the main degradation product. At higher concentrations a new transient resulting from phenoxyl radicals coupling was also observed, and dihydroxybiphenyls are also formed. The reaction of the carbene with ground-state 4-CP was also detected through the formation of 5-chloro-2,4'-dihydroxybiphenyl. 4-Chlorophenoxyl radical and degradations products resulting from its coupling were also detected. Oxygen has little effect on the photochemistry of 4-CP on cellulose. On silica the transient benzoquinone O-oxide was formed in the presence of oxygen. Benzoquinone and hydroquinone are the main degradation products. In well-dried samples the formation of hydroquinone is reduced. At higher concentrations the same products as detected on cellulose were observed. 4-CP undergoes slow photochemical decomposition under solar radiation in both supports. The same main degradation products were observed in these conditions.

Vortex evolution in the wake of accelerating low-aspect-ratio plates and three-dimensional bodies of revolution

To find examples of effecient locomotion and manoeuvrability, one need only turn to the elegant solutions natural flyers and swimmers have converged upon. This dissertation is specifically motivated by processes of evolutionary convergence, which have led to the propulsors and body shapes in nature that exhibit strong geometric collapse over diverse scales. These body features are abstracted in the studies presented herein using low-aspect-ratio at plates and a three-dimensional body of revolution (a sphere). The highly-separated vortical wakes that develop during accelerations are systematically characterized as a function of planform shape, aspect ratio, Reynolds number, and initial boundary conditions. To this end, force measurements and time-resolved (planar) particle image velocimetry have been used throughout to quantify the instantaneous forces and vortex evolution in the wake of the bluff bodies. During rectilinear motions, the wake development for the flat plates is primarily dependent on plate aspect ratio, with edge discontinuities and curvature playing only a secondary role. Furthermore, the axisymmetric case, i.e. the circular plate, shows strong sensitivity to Reynolds number, while this sensitivity quickly diminishes with increasing aspect ratio. For rotational motions, global insensitivity to plate aspect ratio has been observed. For the sphere, it has been shown that accelerations play an important role in the mitigation of flow separation. These results - expounded upon in this dissertation - have begun to shed light on the specific vortex dynamics that may be coopted by flying and swimming species of all shapes and sizes towards efficient locomotion.

Procesos hopping a través del modelo difusional en materiales nanocristalinos usados para aplicaciones fotovoltaicas

Se presentan los modelos de hopping de rango variable (variable range hopping; VRH), vecinos cercanos (nearest neighbor hopping; NNH) y barreras de potencial presentes en las fronteras de grano; como mecanismos de transporte eléctrico predominantes en los materiales semiconductores para aplicaciones fotovoltaicas. Las medidas de conductividad a oscuras en función de temperatura fueron realizadas para región de bajas temperaturas entre 120 y 400 K con Si y compuestos Cu3BiS2 y Cu2ZnSnSe4. Siguiendo la teoría de percolación, se obtuvieron parámetros hopping y la densidad de estados cerca del nivel de Fermi, N(EF), para todas las muestras. A partir de los planteamientos dados por Mott para VRH, se presentó el modelo difusional, que permitió establecer la relación entre la conductividad y la densidad de estados de defecto o estados localizados en el gap del material. El análisis comparativo entre modelos, evidenció, que es posible obtener mejora hasta de un orden de magnitud en valores para cada uno de los parámetros hopping que caracterizan el material.

Fluorescence of nitrobenzoxadiazole (NBD)-labeled lipids in model membranes is connected not to lipid mobility but to probe location

Nitrobenzoxadiazole (NBD)-labeled lipids are popular fluorescent membrane probes. However, the understanding of important aspects of the photophysics of NBD remains incomplete, including the observed shift in the emission spectrum of NBD-lipids to longer wavelengths following excitation at the red edge of the absorption spectrum (red-edge excitation shift or REES). REES of NBD-lipids in membrane environments has been previously interpreted as reflecting restricted mobility of solvent surrounding the fluorophore. However, this requires a large change in the dipole moment (Dm) of NBD upon excitation. Previous calculations of the value of Dm of NBD in the literature have been carried out using outdated semi-empirical methods, leading to conflicting values. Using up-to-date density functional theory methods, we recalculated the value of Dm and verified that it is rather small (B2 D). Fluorescence measurements confirmed that the value of REES is B16 nm for 1,2-dioleoyl-sn-glycero-3- phospho-L-serine-N-(NBD) (NBD-PS) in dioleoylphosphatidylcholine vesicles. However, the observed shift is independent of both the temperature and the presence of cholesterol and is therefore insensitive to the mobility and hydration of the membrane. Moreover, red-edge excitation leads to an increased contribution of the decay component with a shorter lifetime, whereas time-resolved emission spectra of NBD-PS displayed an atypical blue shift following excitation. This excludes restrictions to solvent relaxation as the cause of the measured REES and TRES of NBD, pointing instead to the heterogeneous transverse location of probes as the origin of these effects. The latter hypothesis was confirmed by molecular dynamics simulations, from which the calculated heterogeneity of the hydration and location of NBD correlated with the measured fluorescence lifetimes/REES. Globally, our combination of theoretical and experiment-based techniques has led to a considerably improved understanding of the photophysics of NBD and a reinterpretation of its REES in particular.

Embedded representations of social interactions

Social interactions have been the focus of social science research for a century, but their study has recently been revolutionized by novel data sources and by methods from computer science, network science, and complex systems science. The study of social interactions is crucial for understanding complex societal behaviours. Social interactions are naturally represented as networks, which have emerged as a unifying mathematical language to understand structural and dynamical aspects of socio-technical systems. Networks are, however, highly dimensional objects, especially when considering the scales of real-world systems and the need to model the temporal dimension. Hence the study of empirical data from social systems is challenging both from a conceptual and a computational standpoint. A possible approach to tackling such a challenge is to use dimensionality reduction techniques that represent network entities in a low-dimensional feature space, preserving some desired properties of the original data. Low-dimensional vector space representations, also known as network embeddings, have been extensively studied, also as a way to feed network data to machine learning algorithms. Network embeddings were initially developed for static networks and then extended to incorporate temporal network data. We focus on dimensionality reduction techniques for time-resolved social interaction data modelled as temporal networks. We introduce a novel embedding technique that models the temporal and structural similarities of events rather than nodes. Using empirical data on social interactions, we show that this representation captures information relevant for the study of dynamical processes unfolding over the network, such as epidemic spreading. We then turn to another large-scale dataset on social interactions: a popular Web-based crowdfunding platform. We show that tensor-based representations of the data and dimensionality reduction techniques such as tensor factorization allow us to uncover the structural and temporal aspects of the system and to relate them to geographic and temporal activity patterns.

Dove il DNA antico tace: studio della 'life history' individuale nelle popolazioni umane del passato tramite analisi istologica e biogeochimica ad alta risoluzione di tessuti dentali mineralizzati da contesti archeologici e paleontologici umani

Questa tesi mira a presentare una panoramica, anche sperimentale con dati editi ed inediti, della ricostruzione delle life histories umane mediante metodi istologici e biogeochimici applicati allo smalto dentale delle dentizioni decidue. La tesi si concentra sulle metodologie biogeochimiche ad alta risoluzione spaziale che consentono di ottenere livelli temporali di dettaglio senza precedenti (da stagionali fino a sub-settimanali), quando combinate con l'analisi istomorfometrica dei tessuti dentali mineralizzati. La presente ricerca si concentra sulla creazione di modelli consistenti di variazione delle concentrazioni di elementi in traccia (con particolare riferimento a stronzio e bario) lungo la giunzione smalto dentinale, ottenuti tramite LA-ICPMS (Laser Ablation Inductively Coupled Mass Spectrometry), in funzione dei cambiamenti nella dieta (allattamento, svezzamento) nel primo anno di età di individui a storia nutrizionale nota (utilizzando denti decidui naturalmente esfoliati). In una prospettiva bioarcheologica, i risultati delle indagini sulla dieta altamente risolte nel tempo e interpretate con modelli come quelli proposti si correlano direttamente alle life histories individuali e consentono una analisi più sfumata e completa del comportamento umano nel passato, fornendo informazioni essenziali per la comprensione degli adattamenti bioculturali e aprendo finestre conoscitive su aspetti quali il rapporto madre-progenie, la gravidanza, l’allattamento, lo stress infantile, la dieta sia della progenie che della madre, la mobilità ad alta risoluzione e molti altri aspetti della vita delle popolazioni del passato che lo studio del DNA antico e della morfologia scheletrica non possono fornire. Dove il DNA antico tace, lo studio avanzato delle life histories parla.

Shot-noise spectroscopy of energy resolved ballistic currents

We investigate the shot noise of nonequilibrium carriers injected into a ballistic conductor and interacting via long-range Coulomb forces. Coulomb interactions are shown to act as an energy analyzer of the profile of injected electrons by means of the fluctuations of the potential barrier at the emitter contact. We show that the details in the energy profile can be extracted from shot-noise measurements in the Coulomb interaction regime, but cannot be obtained from time-averaged quantities or shot-noise measurements in the absence of interactions.

Shot-noise spectroscopy of energy resolved ballistic currents

We investigate the shot noise of nonequilibrium carriers injected into a ballistic conductor and interacting via long-range Coulomb forces. Coulomb interactions are shown to act as an energy analyzer of the profile of injected electrons by means of the fluctuations of the potential barrier at the emitter contact. We show that the details in the energy profile can be extracted from shot-noise measurements in the Coulomb interaction regime, but cannot be obtained from time-averaged quantities or shot-noise measurements in the absence of interactions.

Diffusion-weighted spectroscopy: a novel approach to determine macromolecule resonances in short-echo time 1H-MRS.

Quantification of short-echo time proton magnetic resonance spectroscopy results in >18 metabolite concentrations (neurochemical profile). Their quantification accuracy depends on the assessment of the contribution of macromolecule (MM) resonances, previously experimentally achieved by exploiting the several fold difference in T(1). To minimize effects of heterogeneities in metabolites T(1), the aim of the study was to assess MM signal contributions by combining inversion recovery (IR) and diffusion-weighted proton spectroscopy at high-magnetic field (14.1 T) and short echo time (= 8 msec) in the rat brain. IR combined with diffusion weighting experiments (with δ/Δ = 1.5/200 msec and b-value = 11.8 msec/μm(2)) showed that the metabolite nulled spectrum (inversion time = 740 msec) was affected by residuals attributed to creatine, inositol, taurine, choline, N-acetylaspartate as well as glutamine and glutamate. While the metabolite residuals were significantly attenuated by 50%, the MM signals were almost not affected (< 8%). The combination of metabolite-nulled IR spectra with diffusion weighting allows a specific characterization of MM resonances with minimal metabolite signal contributions and is expected to lead to a more precise quantification of the neurochemical profile.

Frequency resolved admittance spectroscopy measurements on In0.52Al0.48As/InxGa1¿xAs/In0.52Al0.48As single quantum well structures

In this work a new admittance spectroscopy technique is proposed to determine the conduction band offset in single quantum well structures (SQW). The proposed technique is based on the study of the capacitance derivative versus the frequency logarithm. This method is found to be less sensitive to parasitic effects, such as leakage current and series resistance, than the classical conductance analysis. Using this technique, we have determined the conduction band offset in In0.52Al0.48As/InxGa1¿xAs/In0.52Al0.48As SQW structures. Two different well compositions, x=0.53, which corresponds to the lattice¿matched case and x=0.60, which corresponds to a strained case, and two well widths (5 and 25 nm) have been considered. The average results are ¿Ec=0.49±0.04 eV for x=0.53 and ¿Ec =0.51±0.04 eV for x=0.6, which are in good agreement with previous reported data.