Dissertations / Theses on the topic 'Experimental Surface Physics'

This thesis describes research into infrared (IR) laser irradiation and damage of four commercially significant polymers: polyimide (PI), polyether ether ketone (PEEK), polyethylene terephthalate (PET) and polypropylene (PP). Many research groups have studied the laser ablation and irradiation of polymers, but they have focussed mainly on ultraviolet and pulsed infrared sources. There appears to be little published data for laser irradiation of polymers with IR lasers operating with pulse durations in the range 50µs to 1ms. Laser coupling to polymers is strongly dependent on the absorption coefficient at the emission wavelength. These properties are widely known and used to inform experimental practice but the absorption coefficient used in the literature is usually that measured at room temperature and low power. In this way it does not truly represent typical experimental conditions. It is also commonly assumed that the laser wavelength is constant. In this work the laser wavelength has been determined as a function of time during a typical pulse for a radio frequency (RF) excited CO2 laser. It was found that the emission wavelength could move from as short as 10.53µm to as long as 10.63µm during a 200µs duration pulse. This alone was seen to affect the absorption cofficient of the polymers studied. The absorption coefficient as a function of polymer temperature was measured over all wavelengths. This allowed any changes in the optical coupling during laser heating to be inferred. The change in absorption coefficient as a function of temperature was determined as being -0.40cm-1K-1, 0.86cm-1K-1, 0.48cm-1K-1and 0.04cm-1K-1 for PI, PEEK, PET and PP respectively at a wavelength of 10.59µm. The threshold fluence for damage was determined as a function of the laser pulse duration. Damage included any permanent change to the polymer surface and in this way took into account decomposition and melting, as well as ablation. Together with the absorption coefficient data, this allowed the energy densities to be calculated. For PI and PEEK these were found to be 2.4kJ/cm3 and 1.9kJ/cm3 respectively and agreed with existing data. The threshold energy density was 0.1kJ/cm3 for PET and 0.2kJ/cm3 for PP. These results were smaller than those expected from the literature due to melting rather than ablation taking place. The threshold fluence for each polymer was found to be mostly independent of laser pulse duration over the range investigated. The small thermal diffusivity of the materials was thought to be the reason for this. Calculations using solutions to the heat diffusion equation and a rate limited thermal decomposition model were found to be consistent with the experimental results. Some initial calculations of the effect of including the temperature dependent absorption coefficient indicated that this does indeed affect the temperature profile during and after the laser pulse. It has been shown that the RF CO2 laser is suitable for polymer processing, particularly for applications where spot size and high resolution etching are not an issue. Laser marking, cutting and hole-drilling would be acceptable applications for this laser which offers more choice in terms of duty-cycle and pulse duration than the pulsed TEA CO2 alternatives. Quantification of the thermal and optical properties and the interaction between these two parameters could be extended to other polymers and it is expected that similar behaviours would be observed.

Ions trapped in Paul traps provide a system which has been shown to exhibit most of the properties required to implement quantum information processing. In particular, a two-dimensional array of ions has been shown to be a candidate for the implementation of quantum simulations. Microfabricated surface geometries provide a widely used technology with which to create structures capable of trapping the required two-dimensional array of ions. To provide a system which can utilise the properties of trapped ions a greater understanding of the surface geometries which can trap ions in two-dimensional arrays would be advantageous, and allow quantum simulators to be fabricated and tested. In this thesis I will present the design, set-up and implementation of an experimental apparatus which can be used to trap ions in a variety of different traps. Particular focus will be put on the ability to apply radio-frequency voltages to these traps via helical resonators with high quality factors. A detailed design guide will be presented for the construction and operation of such a device at a desired resonant frequency whilst maximising the quality factor for a set of experimental constraints. Devices of this nature will provide greater filtering of noise on the rf voltages used to create the electric field which traps the ions which could lead to reduced heating in trapped ions. The ability to apply higher voltages with these devices could also provide deeper traps, longer ion lifetimes and more efficient cooling of trapped ions. In order to efficiently cool trapped ions certain transitions must be known to a required accuracy. In this thesis the 2S1/2 → 2P1/2 Doppler cooling and 2D3/2 → 2D[3/2]1/2 repumping transition wavelengths are presented with a greater accuracy then previous work. These transitions are given for the 170, 171, 172, 174 and 176 isotopes of Yb+. Two-dimensional arrays of ions trapped above a microfabricated surface geometry provide a technology which could enable quantum simulations to be performed allowing solutions to problems currently unobtainable with classical simulation. However, the spin-spin interactions used in the simulations between neighbouring ions are required to occur on a faster time-scale than any decoherence in the system. The time-scales of both the ion-ion interactions and decoherence are determined by the properties of the electric field formed by the surface geometry. This thesis will show how geometry variables can be used to optimise the ratio between the decoherence time and the interaction time whilst simultaneously maximising the homogeneity of the array properties. In particular, it will be shown how the edges of the geometry can be varied to provide the maximum homogeneity in the array and how the radii and separation of polygons comprising the surface geometry vary as a function of array size for optimised arrays. Estimates of the power dissipation in these geometries will be given based on a simple microfabrication.

When azobenzene-modified photosensitive polymer films are irradiated with light interference patterns, topographic variations in the film develop that follow the electric field vector distribution resulting in the formation of surface relief grating (SRG). The exact correspondence of the electric field vector orientation in interference pattern in relation to the presence of local topographic minima or maxima of SRG is in general difficult to determine. In my thesis, we have established a systematic procedure to accomplish the correlation between different interference patterns and the topography of SRG. For this, we devise a new setup combining an atomic force microscope and a two-beam interferometer (IIAFM). With this set-up, it is possible to track the topography change in-situ, while at the same time changing polarization and phase of the impinging interference pattern. To validate our results, we have compared two photosensitive materials named in short as PAZO and trimer. This is the first time that an absolute correspondence between the local distribution of electric field vectors of interference pattern and the local topography of the relief grating could be established exhaustively. In addition, using our IIAFM we found that for a certain polarization combination of two orthogonally polarized interfering beams namely SP (↕, ↔) interference pattern, the topography forms SRG with only half the period of the interference patterns. Exploiting this phenomenon we are able to fabricate surface relief structures below diffraction limit with characteristic features measuring only 140 nm, by using far field optics with a wavelength of 491 nm. We have also probed for the stresses induced during the polymer mass transport by placing an ultra-thin gold film on top (5–30 nm). During irradiation, the metal film not only deforms along with the SRG formation, but ruptures in regular and complex manner. The morphology of the cracks differs strongly depending on the electric field distribution in the interference pattern even when the magnitude and the kinetic of the strain are kept constant. This implies a complex local distribution of the opto-mechanical stress along the topography grating. The neutron reflectivity measurements of the metal/polymer interface indicate the penetration of metal layer within the polymer resulting in the formation of bonding layer that confirms the transduction of light induced stresses in the polymer layer to a metal film.
Azobenzolhaltige Polymere gehören zu einer Klasse funktionaler Materialien, bei denen durch ein äußeres Strahlungsfeld eine starke mechanische Reaktion ausgelöst werden kann. Durch die Bindung an das Polymerrückgrat können die Azobenzole, die unter UV-Belichtung eine Photoisomerisierung ausführen, was zum Teil drastische Effekte zur Folge hat. Unter Belichtung mit Intensitätsmustern, d.h. mit räumlich variierender Verteilung der Polarisation oder der Intensität des einfallenden Lichts verändert sich die Topographie der azobenzolhaltigen Filme, was zur Bildung von Oberflächengittern (engl. Surface Relief Gratings, SRG) führt. In dieser Arbeit wurde eine neue Methode vorgeschlagen, bei der das Verhalten elastischer/morphologischer Eigenschaften unter verschiedenen Belichtungsbedingungen, d.h. mit unterschiedlicher Verteilung der Polarisation und der Intensität in situ lokal als Funktion der Position entlang der SRG aufgenommen werden kann. Außerdem wurde hier vorgeschlagen, opto-mechanische Spannungen, die innerhalb der photosensitiven Polymerfilme während der Belichtung entstehen, mit Hilfe dünner aufgebrachter metallischen Schichten abzubilden und zu analysieren.

Nous présentons une étude expérimentale et théorique sur la nucléation et l'évolution de la supraconductivité au voisinage d'un microtrou dans une couche mince. Sous champ magnétique la température critique d'une couche perforée est plus élevée que celle d'une couche sans trou et montre deux types d'oscillations quan tiques.

Cette thèse vise à une meilleure compréhension de la dynamique du voilier et à la validation des outils numériques de prédiction de performances et d'optimisation par l'étude expérimentale in situ du problème aéro-élastique d'un gréement. Une instrumentation est développée sur un voilier de 8m de type J80 pour la mesure dynamique des efforts dans le gréement, de la forme des voiles en navigation, du vent et des attitudes du bateau. Un effort particulier est apporté à la mesure des caractéristiques géométriques et mécaniques des éléments du gréement, la calibration des capteurs et au système d'acquisition des données. Les principaux résultats montrent que le voilier instrumenté est un outil adapté pour les mesures instationnaires et soulignent l'amplitude de variation d'effort rencontrée en mer (20 à 50% de l'effort moyen dans une houle modérée). En outre, les variations du signal d'effort sont déphasées avec l'angle d'assiette, créant un phénomène d'hystérésis. Le comportement dynamique d'un voilier en mouvement diffère ainsi de l'approche quasi-statique. Les simulations numériques proviennent du code ARAVANTI, couplage implicite d'un code structure éléments finis ARA et d'un code fluide parfait, limitant son domaine de validité aux allures de près Les résultats de simulation sont très proches des cas stationnaires et concordent bien avec les mesures en instationnaire dans une houle de face. L'expérimentation numérique d'un gréement soumis à des oscillations harmoniques en tangage souligne l'importance de l'approche Interaction Fluide Structure (IFS) et montre que l'énergie échangée par le système avec la houle est reliée à la fréquence réduite et l'amplitude du mouvement. Certaines informations n'étant pas disponibles sur le voilier instrumenté, une expérience contrôlée en laboratoire est développée. Elle consiste en un carré de tissu tenu par deux lattes en oscillation forcée. Les mesures sur cette " voile oscillante " permettent d'étudier les phénomènes IFS avec décollement et sont utilisées pour la validation du couplage ARA-ISIS entre un code fluide Navier-Stokes (RANS) et le même code structure.

Ces travaux s'inscrivent dans le cadre du programme R et D PARRNe (Production d'atomes radioactifs riches en neutrons ). Ce programme vise d'une façon générale à déterminer les conditions optimales pour produire d'intenses faisceaux d'isotopes riches en neutrons. Cette thèse traite des multiples aspects techniques liés à la production d'isotopes radioactifs séparés en ligne (ISOL). Elle porte principalement sur le développement de l'ensemble cible-source qui est l'élément clé pour les projets comme SPIRAL-2 ou EURISOL. La première partie présente les différentes méthodes utilisant la fission comme réaction exploitée en ligne ainsi que leur comparaison : fission thermique, fission induite par des neutrons rapides et photofission. L'expérience faite au CERN a permis de valider la photofission comme mode prometteur pour la production d'ions radioactifs, c'est pour cela que l'IPN d'Orsay a décidé de construire un accélérateur linéaire d'électrons auprès du Tandem d'Orsay (ALTO). La deuxième partie de cette thèse a porté sur le développement de cibles d'uranium. Des techniques d'analyse comme la diffraction X et la microscopie électronique à balayage ont été utilisées. Elles ont permis de déterminer les caractéristiques chimiques et structurales de cibles de carbure d'uranium portées à différentes températures de chauffage. Après la production le processus d'ionisation est étudié. Deux types de sources ont été mises en oeuvre : la première est une source à ionisation de surface et la deuxième est une source basée sur l'ionisation résonante par laser. Ces deux types de sources seront utilisées pour le projet ALTO.

The high energy lasers are emerging as an innovative material processing tool to effectively fabricate complex shapes on the hard and brittle structural ceramics, which previously had been near impossible to be machined effectively using various conventional machining techniques. In addition, the in-situ measurement of the thermo-physical properties in the severe laser machining conditions (high temperature, short time duration, and small interaction volume) is an extremely difficult task. As a consequence, it is extremely challenging to investigate the evolution of surface topography through experimental analyses. To address this issue, an integrated experimental and computational (multistep and multiphysics based finite-element modeling) approach was employed to understand the influence of laser processing parameters to effectively control the various thermo-physical effects (recoil pressure, Marangoni convection, and surface tension) during transient physical processes (melting, vaporization) for controlled surface topography (surface finish). The results indicated that the material lost due to evaporation causes an increase in crater depth of machined cavity, whereas liquid expulsion created by the recoil pressure increases the material pileup height around the lip of machined cavity, the major attributes of surface topography (roughness). Also, it was found that the surface roughness increased with increase in laser energy density and pulse rate (from 10 to 50Hz), and with the decrease in distance between two pulses (from 0.6 to 0.1mm) or the increase in lateral and transverse overlap (0, 17, 33, 50, 67, and 83%). The results of the computational model are also validated by experimental observations with reasonably close agreement.

Utilitzant una tecnologia implementada prèviament en el grup, en aquesta Tesi s'ha optimitzat el procés de formació de plantilles d'Alumini / Alúmina mitjançant anoditzat d'aliatges AA 1050 i 1080. L'estructura i geometria de les plantilles s'ha optimitzat mitjançant tècniques de reducció de la capa barrera (procés BLT) i d'obertura de porus (procés OBL i atac amb àcid fosfòric). Amb aquestes plantilles s'han obtingut electroquímicament nanoestructures 1D de Ni, Au i Co. En tots els casos s'ha comprovat que les úniques tècniques que permeten obtenir nanodipòsits de qualitat són les polsants, amb polsos complexos que combinen polsos de reducció, d'oxidació i a circuit obert. Amb tots els metalls s'ha estudiat el procés de creixement i s'ha constatat que hi ha importants diferències entre el creixement del níquel i el dels altres dos metalls: mentre el creixement dels nanofils de Ni es produeix uniformement en tots els porus de la plantilla, els de Au i Co es produeixen en feixos distribuïts aleatòriament per tota la superfície. En un estudi paral•lel de les primeres etapes de l'anoditzat, s'ha caracteritzat l'estructura i composició de les protuberàncies que apareixen en l'anomenat procés de cremat (burning) de l’alumini; s'ha comprovat que en tots els casos en què apareixen aquestes protuberàncies l'EDX detecta Fe en el vèrtex. Es tracta, doncs, de les restes d'una partícula inter-metàl•lica AI Fe Si , dissolta en el pretractament de I 'alumini .
Using a technology previously implemented in the group, in this PhD thesis the process of obtaining aluminium/alumina templates has been optimized by anodizing AA1050 and 1080 aluminium alloys. The structure and geometry of the template has been optimized using techniques such as barrier layer reduction (BLT process) and opening of pores (OBL process and attack with phosphoric acid). With these templates 1D nanostructures of Ni, Au and Co have been obtained electrochemically. Pulse techniques have demonstrated to be the most suitable to obtain the nanowires. The growth process has been studied for all metals and it has been verified that, while the growth of Ni nanowires occurs uniformly in all the pores of the template, those of Au and Co do occur randomly distributed across the surface. In a parallel study of the early stages of anodization, the structure and composition of the bumps that appear in the process called burning of aluminium have been characterized. In all cases Fe has been detected at the apex of the bumps. It is, therefore, the remains of an intermetallic particle of A1FeSi dissolved in the pretreatment of aluminium.

Water aerosols affect the climate because they have an impact on the radiation balance and cloud formation. Water is present in all forms in the atmosphere (water, ice and steam), for example as rain and hail. Water aerosols play an important role in many biological and chemical processes in the atmosphere. The most common form of water in the atmosphere is water droplets or vapor which often come from oceans and lakes and these aerosols often contain organic compounds. It is therefore interesting to study if organic compounds, in this case glycerol, will reside on the surface or inside the water droplets. The investigations were performed by using theoretical studies, molecular dynamic simulations in GROMACS, and experimental investigations; X-ray photoelectron spectroscopy with a liquid jet. The experiments were performed at BESSY II, Berlin. The concentrations of glycerol were varied from 75:1; 8:1 to 4:1 (water: glycerol molecules). The results were that the experiments and simulations indicated that when theconcentration of glycerol increased the glycerol concentration at the surface of the waterdroplet increases until a monolayer of glycerol molecules was formed at the surface. When the monolayer was formed (or close to) less and less glycerol molecules were placed at thewater surface and more and more glycerol molecules were placed in the bulk of the waterdroplet.
Vattenaerosoler påverkar klimatet eftersom de har en inverkan på strålningsbalansen och molnbildningen. Vatten finns i alla former i atmosfären (vatten, is och ånga) som bland annat regn och hagel. Vatten aerosolerna spelar en viktig roll i många kemiska och biologiska processer i atmosfären. Den vanligaste formen av vatten i atmosfären är små vattendroppar eller ånga som ofta kommer från hav och sjöar och som ofta innehar organiska föreningar. Då vattenaerosoler påverkar klimatet och organiska föreningar är vanligt förekommande i vattendroppar är det intressant att undersöka om organiska föreningar, i detta fall glycerol, hamnar på ytan eller inuti vattnet. Undersökningarna har gjorts genom att använda teoretiska perspektiv, molekylärdynamiska simuleringar i GROMACS, samt experimentella undersökningar i form av röntgen fotoelektronspektroskopi med en vätskejet. Dessa experiment utfördes i BESSY II, Berlin. Koncentrationerna av glycerol varierades från75:1; 8:1 till 4:1 (vatten: glycerolmolekyler). Resultaten från experimenten och simuleringarna indikerade att när koncentrationen av glycerol ökade så ökade glycerolkoncentrationen på ytan av vattendroppen tills det bildades ett monolager av glycerolmolekyler på vattenytan. När monolagret hade bildats så placerades mindre och mindre glycerolmolekyler på vattenytan och fler och fler glycerolmolekyler placerades inne i vattendroppen.

La surface d'une polyolefine traitee par plasma micro-ondes ou par faible dose d'implantation ionique d'azote devient mouillable. Pour obtenir des peroxydes polarisables sur une polyolefine, un traitement par plasma d'argon de courte duree est suffisant. Les analyses xps couplees avec les resultats obtenus en resonance paramagnetique electronique, par decomposition des peroxydes, par mesures de mouillabilite et par l'exploitation des spectres actifs en infrarouge ont montre que les structures oxydees, formees par differentes techniques de traitement, jouent un role important pour interpreter la variation des proprietes chimiques a la surface du polymere. Compare a l'implantation ionique, le traitement par plasma micro-ondes, en particulier par plasma argon, produit plus de groupes polarisables. Il est interessant pour les applications de greffage. La durete et le module d'elasticite, mesures par nanoindentation sur une polyolefine augmentent avec une dose appropriee d'implantation ionique. Une dose de 1,4 x 10#1#7 ions. Cm#-#2 permet de multiplier par 15 la durete du polyethylene a tres haut poids moleculaire et par 7 son module d'elasticite a une profondeur de 30 nm. Le passage du comportement visco-plastique a quasi-elastique est mis en evidence. L'epaisseur de la couche modifiee depasse 300 nm. L'etude du couple de frottement entre sphere metallique et cupule en polyethylene montre que l'implantation ionique du polymere permet de reduire la vitesse d'usure du polyethylene, par amelioration de ses proprietes mecaniques liees a la formation d'une couche reticulee, dure et elastique. Les effets des traitements de surface sur les polymeres utilises comme biomateriaux permettent d'adapter les proprietes en surface des applications specifiques

Cheng and Wu (2001) introduced a method for response surface exploration using only one design by using a 3-level design to first screen a large number of factors and then project onto the significant factors to perform response surface exploration. Previous work generally involved selecting designs based on projection properties first and aliasing structure second. However, having good projection properties is of little concern if the correct factors cannot be identified. We apply Jones and Nachtsheim’s (2009) method for finding optimal designs with minimal aliasing to find 18, 27, and 30-run designs to use for single-step screening and optimization. Our designs have better factor screening capabilities than the designs of Cheng and Wu (2001) and Xu et al. (2004), while maintaining similar D-efficiencies and allowing all projections to fit a full second order model.

Dans une expérience destinée à la détection directe des WIMPS (un candidat plausible pour la matière noire) les détecteurs jouent un rôle essentiel. L'expérience EDELWEISS a choisi des détecteurs semiconducteurs (Ge) avec lesquels on peut mesurer simultanément la chaleur (mesure bolométrique) et la charge issues de l'impact d'une particule. On discrimine ainsi les événements de type "recul noyau" (WIMPS) des événements de type "recul électron" (bruit de fond hormis les neutrons). Cependant, pour un événement ayant lieu très près de la surface des électrodes de collecte de charge, un déficit de collecte peut dégrader d'une manière importante l'efficacité de cette discrimination. Ce travail propose une nouvelle méthode d'identification des événements de surface basée sur le régime transitoire "chaleur" obtenu au moyen de couches minces NbxSi1-x , isolant d'Anderson, déposées directement sur l'absorbeur (saphir ou Ge). Un événement ayant lieu à une profondeur inférieure à une valeur critique dc (de l'ordre du millimètre dans le Ge) donne un signal transitoire (athermique) amplifié et de forme différente comparée à un événement de volume de même énergie. Nous avons paramétré cette amplification en fonction de la profondeur d

Solar energy is increasingly being considered a promising solution to reduce the emissions of CO2 and green house gas. The performance of solar collectors largely depends on the ability to absorb incoming solar radiation with minimal thermal radiation losses. To weigh the potential absorbed energy to thermal losses, the performance criterion (PC) can be used, calculated as PC =α−xε, where α is absorptance, ε is emittance and x is a scaling factor < 1. It has been shown by G. Vargas et al. that Co-Cr alloys excibit great potential (α = 0.98 and ε = 0.03) for use in solar concentrators. The main goal of this project is to quantify the impact of key factors (controlled input variables) on an electroplating process of Co-Cr alloys, using the design of experiment (DOE) methodology. It is part of an ongoing collaboration between Absolicon and the physics department at Umeå university. Six factors were investigated using a fractional factorial (FrF) design. Data was collected through a series of experiments where stainless steel substrates were electroplated with Co-Cr alloys. The resulting samples were analyzed in terms of α and ε as well as the quality of deposition (QD). Using the experimental results, three models were made in a DOE-software called MODDE. Models are used to correlate the factors with each response, i.e. α, ε and QD. Ideally the predictive power of the models (Q2) should be as high as possible, and at least > 0.5. The analysis of variance (ANOVA) test was used to determine the significance of the models. Based on the models, the ’Optimizer’ tool in MODDE was used to predict two set of optimum factor settings, producing two samples, S1 and S2. S1 and S2 were evaluated in terms of α, ε and QD as well as chemical composition and structural properties of the coatings. The predictive power of the models was 0.49 for α, 0.38 for ε and 0.53 for QD. The predictive power of the models were therefore limited. ANOVA-test showed that the models for α and QD were statistically significant. For all three responses the significant effects were mostly two factor interactions. All three models showed significant lack of fit (model error) as a result of high reproducibility. S1 had the best PCAbsolicon (performance criterion for Absolicons solar collectors) of all samples with 0.858. S2 was not as good, even though it was predicted to have a higher value of PCAbsolicon by MODDE. EDS, XPS and SEM measurements of samples S1 and S2 showed that the two samples were very similar in terms of chemical composition. The main difference was that the coating of S1 was more porous, and also thicker than S2, 0.81 μm compared to 0.26 μm. Even though the models showed some predictive capabilities, the impact of the factors could not be fully determined. That is due to the nature of the FrF-design, which cannot accurately determine two-factor interactions.

Metal surface cleaning is highly required in different fields of modern industry. Nuclear industry seeks for new methods for oxidized surface decontamination, and thermonuclear installations require the cleaning of plasma facing components from tritium-containing deposited layer. The laser ablation is proposed as an effective and safe method for metal surface cleaning and decontamination. The important factor influencing the laser heating and ablation is the in-depth distribution of laser radiation. The model of light propagation in a scattering layer on a metal substrate is developed and applied to analyse the features of light distribution. To simulate the contaminated surfaces, the stainless steel AISI 304L was oxidized by laser and in a furnace. Radioactive contamination of the oxide layer was simulated by introducing europium and/or sodium. The decontamination factor of more than 300 was demonstrated with found optimal cleaning regime. The decreasing of the corrosion resistance was found after laser cleaning. The ablation thresholds of ITER-like surfaces were measured. The cleaning productivity of 0.07 m2/hour∙W was found. For mirror surfaces, the damage thresholds were determined to avoid damage during laser cleaning. The possibility to restore reflectivity after thin carbon layer deposition was demonstrated. The perspectives of further development of laser cleaning are discussed.

Développement de diagnostics expérimentaux permettant d'étudier les masses éjectées obtenues a partir de défauts de surface reparties ou localises. Evaluation de la masse éjectée en fonction de la vitesse des particules moyennant l'hypothèse du transfert inélastique de la quantité de mouvement entre l'éjecta et une cible mince placée initialement devant la surface libre et dont on suit la vitesse par interférométrie doppler laser. Etude de la structure spatiale des éjecta au moyen d'un générateur de rayons-x pulse et de l'évolution des contours a l'aide d'une camera ultrarapide a images intégrales. Elaboration d'un modèle.

Etude de la solubilisation du pentanol-1 dans des micelles mixtes d'agents de surface anioniques, cationiques, non ioniques, hydrogenes et perfluores, et de la perturbation de la condensation ionique a la surface micellaire

Cette these a pour cadre l'optimisation de films minces (1-10 microns) polymeres hybrides pour la realisation de composants passifs et actifs de l'optique integree. Nous avons plus precisement etudie la mobilite de molecules d'azobenzene soumises a des excitations electriques et photoniques dans deux types de matrices sol-gel : - dans une matrice faiblement reticulee, le processus de photo-isomerisation conduit a des phenomenes de migration moleculaire pouvant provoquer des deformations de surface spectaculaires (> 1 micron). Notre etude a porte plus particulierement sur la reponse du materiau vis-a-vis du de l'intensite, de la polarisation et des frequences spatiales de la figure d'illumination (franges d'interferences). On decrit aussi la realisation d'un coupleur a reseau, qui constitue l'un des composants passifs de l'optique integree. - dans une matrice fortement reticulee, l'orientation thermo-assistee des molecules d'azobenzene par un champ electrostatique applique au film permet de briser la centrosymetrie du materiau et de lui conferer des proprietes non-lineaires quadratiques. Les mecanismes d'orientation ont ete plus finement etudies en analysant l'influence de la concentration moleculaire sur l'efficacite du doublage de frequence par le materiau. On montre qu'un moyen d'ecranter les interactions dipolaires et ainsi d'augmenter notablement la mobilite des molecules actives est d'incorporer dans le materiau des groupements steriques passifs. Appliquee a des molecules optimisees par l'ingenierie moleculaire, cette strategie supramoleculaire a permis d'obtenir de forts coefficients electro-optiques stables a temperature ambiante et depassant ceux des meilleurs materiaux inorganiques (> 50 pm/v a 832 nm). Si de plus, les groupements steriques presentent des proprietes de photoconduction, on realise un materiau photorefractif. Nous avons analyse les proprietes originales d'un systeme presentant un effet photorefractif sans champ applique. .

Des couches minces de nitrure de bore ont ete synthetisees a partir de melanges bcl#3/n#2/h#2/ar dans un reacteur plasma r. F. A couplage capacitif. L'etude a porte dans un premier temps sur la caracterisation de la phase gazeuse par spectrometrie de masse et par spectroscopie optique d'emission. En particulier, l'effet de la teneur de la phase gazeuse en hydrogene sur la nature et la concentration relative des especes a ete etudie: tout d'abord dans un plasma argon-hydrogene, dans lequel ont ensuite ete ajoutes les deux precurseurs bcl#3 et n#2, separement puis simultanement. Le debit d'hydrogene moleculaire determine le taux de dissociation de bcl#3 et donc la nature et la quantite des especes chlorees. De meme, lorsque la teneur en hydrogene des plasmas n#2/h#2/ar augmente, il apparait successivement les especes suivantes: n, nh, nh#2 puis nh#3. Deux reactions chimiques pouvant aboutir a la formation du nitrure de bore ont ete mises en evidence: bcl#3 + nh bn#s + hcl + cl#2 bcl + nh bn#s + hcl dans une seconde partie, des couches minces de nitrure de bore ont ete deposees dans differentes conditions experimentales de bombardement ionique (effet de la puissance r. F. Et de la taille des electrodes) et de composition de la phase gazeuse. Ces parametres jouent un role determinant sur la structure des couches de nitrure de bore: il existe un optimum d'energie des ions et de teneur de la phase gazeuse en hydrogene qui permet la croissance de couches a forte teneur en bn-cubique. A partir des experiences de traitements des couches par des plasmas d'argon, argon-hydrogene et argon-chlore, nous avons mis en evidence l'existence d'une part d'un mecanisme de pulverisation preferentielle du bn-hexagonal et, d'autre part, d'un mecanisme de gravure chimique selective de la phase hexagonale par l'hydrogene atomique et par le chlore qui permettent l'obtention de couches a forte teneur en bn-cubique

Le CO₂ est l’un des principaux gaz à effet de serre qui participe activement au réchauffement du système climatique. La capture et le stockage géologique du carbone permettent de limiter les impacts des augmentations de concentration en CO₂ dans l’atmosphère. La principale qualité d’un site de stockage est de présenter une probabilité de fuite minimale. Il est donc essentiel de développer des outils de surveillance afin d’évaluer leur importance et de prévoir des actions correctives. Ce travail de thèse a pour objectif d’étudier les processus physicochimiques et les impacts d’une fuite de CO₂ sur les hydrosystèmes proches surface (zone vadose (ZV) et nappe) dans un système carbonaté réservoir d’âge Oligocène situé au sein du bassin aquitain. Cette étude a suivi : i) une approche expérimentale sur le site pilote de Saint-Emilion (Gironde, France) où une injection de CO₂ a eu lieu dans l’aquifère à partir d’un puits de forage ; ii) une approche en laboratoire à l’échelle de la carotte afin d’étudier les interactions du système CO₂-H₂O-CaCO₃. Ce travail apporte une démarche expérimentale nouvelle en couplant des méthodes géochimiques et géophysiques sur les deux échelles d’investigation. La ligne de base, réalisée à travers la ZV l’année précédant l’expérience d’injection, a étudié l’évolution naturelle du CO₂ lors d’un cycle hydrogéologique. Après l’injection dans la nappe et au regard de nos résultats, la conductivité électrique (σ), le pH, les concentrations en Ca²⁺, HCO₃- et CO₂ se sont avérés être de bons indicateurs, suffisamment sensibles et réactifs, pouvant être utilisés sur un site de stockage de CO₂ afin de suivre toutes perturbations physicochimiques. Des simulations numériques ont permis de mieux appréhender les processus de réaction et de transport. Les expériences à l’échelle de la carotte ont quantifié l’influence des effets du CO₂ sur le comportement électrique de la roche carbonatée. Une meilleure définition de la relation entre les concentrations en CO₂, la σ et le pH permet de passer de l’échelle de la carotte à l’échelle du site pilote et vice versa. L’ensemble des résultats de ce travail de thèse met en avant l’importance de la caractérisation de l’hétérogénéité pétrophysique du réservoir. Il est également essentiel d’établir une ligne de base, permettant de distinguer les variations naturelles en CO₂ de celles induites par une fuite. Le couplage des observations sur le terrain et des démonstrations en laboratoire permet d’augmenter les chances de détection d’une fuite de CO₂ sur un site de stockage géologique
CO₂ is one of the main greenhouse gases that actively contributes to the global warming. The carbon capture and geological storage can limit the impacts of increases in CO₂ concentration in the atmosphere. The main quality of a storage site is to present a minimum probability of leakage. Therefore, it is essential to develop monitoring tools in order to assess their importance and plan corrective actions. The objective of this thesis is to study the physicochemical processes and the impacts of a CO₂ leak on near-surface hydrosystems (vadose zone (VZ) and aquifer) in a carbonate reservoir system of Oligocene age located within the Aquitaine basin. This study followed: i) an experimental approach at the Saint-Emilion pilot site (Gironde, France) where CO₂ injection took place into the aquifer from a borehole; ii) a core-scale laboratory approach to study the interactions of the CO₂-H₂O-CaCO₃ system. This work brings a new experimental approach by coupling geochemical and geophysical methods on the two scales of investigation. The baseline, carried out through the VZ the year before the injection experiment, studied the natural evolution of CO₂ during a hydrogeological cycle. After injection into the aquifer and according to our results, the electrical conductivity (σ), the pH, the concentrations of Ca²⁺, HCO₃- and CO₂ turned out to be good indicators, sufficiently sensitive and reactive, which can be used on a CO₂ storage site to monitor any physicochemical disturbances. Numerical simulations have made it possible to better understand the reaction and transport processes. Core-scale experiments quantified the influence of CO₂ effects on the electrical behavior of carbonate rock. Better definition of the relationship between the concentrations of CO₂, σ and pH makes it possible to pass from the core scale to the pilot site scale and vice versa. All the results of this thesis work highlight the importance of characterizing the petrophysical heterogeneity of the reservoir. It is also essential to establish a baseline, making it possible to distinguish natural variations in CO₂ from those induced by a leak. Coupling field observations and laboratory demonstrations increases the chances of detecting a CO₂ leak at a geological storage site

Dans l'etude des assemblages colles, les caracteristiques des subjectiles (surfaces elaborees par un procede reproductible sur lesquelles on applique l'adhesif) jouent un role preponderant dans le developpement des mecanismes complexes qui assurent l'adhesion. Nous etudions l'influence de l'etat de surface (en particulier la rugosite) des subjectiles sur le comportement mecanique fin de l'assemblage colle, du type escalier simple, sollicite en traction uniaxiale. L'optimisation de la longueur de recouvrement est egalement realisee. La methodologie scientifique experimentale mise en uvre est basee sur l'utilisation en simultane de l'extensometrie et de l'emission acoustique. L'analyse des donnees experimentales conduira a la determination des differentes phases du comportement mecanique fin (domaine elastique global, amorcage et croissance des microfissures au sein du joint en regime stable, propagation rapide des criques en regime instable et rupture ultime). L'existence d'une rugosite optimale conferant a l'assemblage ses performances mecaniques les plus elevees est mise en evidence dans le cas de traitement par sablage. Ces dernieres sont ameliorees sous l'effet d'un decapage sulfochromique. La repartition des contraintes dans le joint est analysee par la methode des elements finis mais egalement a l'aide de solutions issues d'etudes theoriques etablies anterieurement. Le degre d'adequation theorie-experience montre les limites des modelisations analytiques au-dela des premiers dommages observes experimentalement.

Dans cette thèse, nous avons étudié les mécanismes de diffusion Raman induite par les collisions dans le cas du CO2 comprimé et en mélange avec de 'argon, ceci pour les bandes v2 et v3. Nous avons analysé des mélanges de concentrations relatives différentes, dans l'intervalle de pressions 10-100 atm, et déterminé les sections efficaces, qui caractérisent les interactions CO2-CO2 et CO2-Ar, en unités absolues. Nous avons optimisé le seuil de détection du signal, ce qui nous a permis, pour la première fois, d'acquérir les deux moments principaux qui caractérisent les diffusions isotrope et anisotrope. Nous avons découvert un nouvel effet : une diffusion Raman qui change la parité de la molécule libre et qui est liée à l'émission dipolaire magnétique. Pour interpréter quantitativement les moments mesurés, nous avons élaboré une technique diagrammatique pour calculer les caractéristiques électro-optiques des couples déterminés par les interactions à longues distances. L'analyse diagrammatique de la polarisabilité induite a permis de révéler le nouveau mécanisme d'induction qui est lié à la polarisation non linéaire du partenaire de collision par le champ extérieur et par le champ du moment dipolaire transitoire de la molécule qui effectue la transition ( mécanisme NLD). Nous avons défini les formules des moments des bandes Raman induites par les interactions anisotropes des couples de molécules linéaires. Notre calcul a montré le rôle substantiel du mécanisme NLD dont la prise en compte permet d'obtenir un bon accord avec les résultats expérimentaux.

In this PhD thesis I have studied through state-of-the-art quantum simulations (mainly within the density functional theory approach, DFT) triarylmethyl (TAM) based systems with potential for future nano-devices and designed a series of TAM-based 2D covalent organic frameworks (from now on TAM 2D-COFs). TAMs are organic radicals (i.e. open-shell molecules) which have been used for numerous applications during the last 20 years. In the first part of this PhD thesis I have studied a series of TAM-based systems in collaboration with the experimental groups led by Profs. Jaume Veciana and Concepció Rovira and Dr. Marta Mas-Torrent, respectively, both from the Institute of Materials Science of Barcelona (ICMAB). In such collaborative studies we have evaluated the potential of TAMs for different potential applications. In the first two works we assess the possibility of using closed-shell quinoidal TAMs which, upon being chemisorbed in metal substrates give rise to an open-shell (i.e. radical) monolayer. This is demonstrated by means of on-surface techniques such as X-ray photo-electron spectroscopy (XPS) and angle-resolved ultra-violet photo-electron spectroscopy (ARUPS) and our periodic density functional theory calculations. Complementing to this work I also present a second where a similar radical SAM is formed using, in this case, a TAM-based bi-radical compound. In a third collaborative study we study the E – Z isomerisation in a hydrogenated closed-shell TAM (the so-called H-PTM) bonded with an ethylene unit. An irreversible E to Z transformation is experimentally measured with no evident explanation. Based in DFT and ab initio molecular dynamics simulations (AIMD), I was able to provide a sensible hypothesis for such results based in a sterical blocking effect in the Z conformer. The last two chapters of this PhD thesis collect the computational works focused in making theoretical predictions of yet un-synthesized systems. In Chapter 4, I present a work were we studied how to control the unpaired electron in TAMs, finding out that in these molecules there exists a linear correlation between the aryl ring twist angles and the localization of their unpaired electron. Based on this study we then looked for TAM-based systems where the aryl rings’ twist angles could be externally manipulated. In such direction, I present TAM 2D-COFs (see above) as the only possible platform where aryl ring twist angles may be externally manipulated. As reported in the second publication of Chapter 4, uniaxially stretching the structure of our designed TAM 2D-COFs allows for a fine and reversible (i.e. elastic) twisting of all aryl rings within the 2D material. This allows controlling the localization of all unpaired electron in the network, as well as the band of the material and magnetic interactions. In the last work of this chapter we assess the possibility of having chemical persistence of TAM monomers and structural flexibility through a screening procedure based in force-field calculations. In the last chapter of this PhD thesis I present two studies where it is demonstrated that TAMs, upon being covalently bonded in para- one respect each other, present electrical conductive characteristics. In the first work, in collaboration with the experimental groups from ICMAB, this is demonstrated for a PTM dimer where one of the PTM units is reduced to the anion. The resulting negative charge is found to conduct between both PTM units at room temperature. Finally, in the last predictive work of this thesis, I present a work where we demonstrate based in hybrid DFT calculations that para-connected TAM 2D-COFs behave as semimetals with energetically close-lying semiconductor solutions.
En esta tesis doctoral presentada por artículos he estudiado mediante cálculos DFT (density functional theory, del inglés) sistemas basados en moléculas triaril-metil (TAM) para potenciales aplicaciones futuras. Las moléculas TAM son compuestos orgánicos radicales (es decir, con un electrón desapareado) que se han utilizado para construir diversos materiales durante los últimos 20 años. En la primera parte de la tesis presento los estudios llevados a cabo en colaboración con grupos experimentales del Instituto de Ciencia de los Materiales de Barcelona (ICMAB) expertos en la síntesis de tales compuestos. En los primeros estudios de esta parte se ha llevado a cabo la formación de una mono-capa auto-ensamblada de TAMs en diferentes superficies metálicas. Mediante técnicas de superficie i cálculos DFT periódicos hemos demostrado que utilizando moléculas TAM de capa cerrada (es decir, diamagnéticas) se puede generar una mono-capa radical, o de capa abierta (es decir, paramagnética). En un tercer estudio en colaboración con los mismos grupos experimentales estudiamos la isomerización E – Z (o cis- trans-) irreversible en un sistema TAM-etileno (de capa cerrada). Los cálculos computacionales han sido claves en este estudio para entender el bloqueo cinético que se da en el isómero Z (cis-), lo cual impide su isomerización al isómero E (trans-), a pesar de ser éste último más estable termodinámicamente. En la segunda parte de esta tesis doctoral presento una serie de estudios en los cuales hemos diseñado materiales 2D basados en moléculas TAM, aún no preparados en el laboratorio. En estos estudios se demuestra el gran potencial de dichas redes basadas en moléculas TAM y su gran versatilidad electrónica a la nano-escala. Nuestros resultados demuestran que dichos materiales 2D se puede comportar tanto como aislantes eléctricos, como semiconductores o como semimetales (tales como el grafeno) según su diseño molecular. Además, en dicho materiales es posible controlar sus propiedades electrónicas mediante la manipulación del ángulo de giro de los anillos aril en cada unidad TAM.

L'évolution du spectre infrarouge du benzène adsorbe sur des faujasites est suivie en fonction de la composition chimique des adsorbants (zéolites désaluminées, zéolite y ou x, zéolites modifiées par des ions Na, Rb, etc) et de la quantité de benzène adsorbé. On note que 4 formes de benzène ont été mises en évidence, dont l'une est faiblement fixée sur les solides.

This thesis details work performed in the Distributed Array Shower Head (DASH) and Pocket Rocket systems over the past three years, and is targeted at use in surface processing applications. The DASH source produces plasma in an array of hollow cathodes. Pocket Rocket is a geometrically similar analogue to a single hollow cathode in the DASH source, used for its superior optical access. The work aims to investigate the physics that underpins the operation of such a plasma source. To characterise the expansion plumes from the hollow cathodes, two dimensional maps of ion densities in argon are measured using a Langmuir probe. A peak density of 1E18 per cubic metre is measured at the interface between hollow cathode and expansion chamber. Downstream of the plasma plume, densities are as low as 1E14 per cubic metre. Plasma density in the plume has a 1/z squared dependence, as plasma freely diffuses into the expansion chamber. Further downstream, there is an abrupt change in behaviour as the plasma density becomes nearly constant with increasing distance from the hollow cathode. A compensated Langmuir probe is used in conjunction with an emissive probe to make spatially resolved measurements of the plasma potential, floating potential, and electron energy probability function (EEPF). Inside the hollow cathode a Maxwellian distribution is observed with an electron temperature of 2 eV. The EEPFs measured in the plume show bi-Maxwellian behaviour, before becoming a single Maxwellian with temperatures as high as 11 eV far from the source. To investigate its etching capabilities, the DASH source is also operated using SF6 to produce atomic fluorine and to chemically etch unbiased silicon. Etch rates of up to 3.2 micrometres per minute are measured using a profilometer. Scanning Electron Microscopy of some processed wafers demonstrates the isotropic profile expected of the chemical etching process. It is shown that scaling of the DASH source to process a 300 mm wafer with uniformity of plus-minus 5% uniformity of etch rate is possible. To investigate the possible use of DASH in deposition processes, optical experiments on hydrogen plasma with a pressure on the order of 1 Torr are performed in Pocket Rocket. Two operational modes are observed, named the diffuse and the bright modes after their respective appearances. Fulcher alpha spectroscopy yields gas temperatures of approximately 350 K for the diffuse mode and 500 K in the bright mode. Temperature is observed to be independent of pressure but strongly dependent on power. Pocket Rocket is also investigated using an intensified CCD (ICCD) camera for spatially resolved, sub-rf cycle imaging of Balmer alpha emission. The diffuse mode is found to be operating as a typical gamma capacitive discharge, while the bright mode displays evidence of some degree of inductive coupling. The bright mode has high enough gas temperatures to precipitate the formation of a supersonic shock as gas expands from the hollow cathode. The shock is stationary, but is only apparent once per rf cycle as a burst of energetic electrons passes through it.

Electrons on the surface of liquid helium form a nearly ideal 2-dimensional electron system (2DES). An electron density up to 2 × 10^9 cm-2, known as the critical electron density, can be achieved on the liquid helium surface, above which an electro-hydrodynamic (EHD) instability sets in, which results in the formation of MEBs. Due to this limitation in maximum possible density, only the classical liquid and solid phases of the 2DES can be accessed in this system. But at the same time, on the surface of thin liquid helium film and with the multi-electron bubbles (MEBs), it may be possible to achieve high electron density than that of the critical electron density. This can allow the observation of quantum melting, i.e., the phase transition between the quantum solid to the liquid phase of the 2DES. Although extensive theoretical and experimental studies have already been done, the quantum melting transition has not been achieved experimentally on these systems yet. In this thesis, we have used multiple new experimental approaches to obtain electron densities higher than what has been achieved before and to study the MEBs effectively. First, we studied the temporal dynamics of the EHD instability and the effect of the applied electric field and charge density on the instability. The unstable wave vectors were determined experimentally, and their temporal growth was studied carefully. The determined unstable wave vectors were found to be a good match with the theoretically expected values obtained from the dispersion relation. At the same time, the analysis of the growth rate of unstable vectors were found to be limited by the kinematic viscosity of the liquid helium. Next, we investigated the lifetime of MEBs trapped on a dielectric surface and compared the result with previous results on free bubbles in bulk liquid helium. The reduced lifetime of trapped bubbles suggested an impact of convective heat flow around the bubbles on their lifetimes. Then we performed an experimental investigation that confirmed the effect of convective heat flow direction inside the experimental cell on the lifetime of such trapped MEBs. Determination of the electronic phase inside an MEB is one of the biggest challenges of the time. Unfortunately, there is no direct way or technique for such investigation. We discussed how the MEB surface fluctuation with an external oscillating electric field could be observed, which may allow a possible way of studying the phase of the 2DES. We studied the surface fluctuations of electrically excited MEBs and observed different normal mechanical modes of the bubble wall. Then we extended our discussion on why liquid helium-4 is not a suitable medium to study the MEBs at low temperatures (below λ), where interesting phenomena occur, and how liquid helium-3, based on its physical property, can be a suitable replacement for this purpose. We generated MEBs inside liquid helium for the first time. The generated MEBs at 1.1 K were found to be stable with long lifetimes. This result opens the possibility of studying the MEBs at much lower temperatures where quantum properties dominate over classical for the 2DES. Finally, we discussed the problem associated with achieving high electron density on the thin helium film and how integrating an NEA material as a substrate can help us overcome the problem. We fabricated NEA materials, i.e., cBN pellet, and optimized the rf sputtering deposition of cBN film. We performed a preliminary pick-up measurement on the charged thin helium with these materials as substrates, which showed some positive indications that need to be confirmed with further advanced experimental investigations.
INSPIRE, DST India

Xylanases (EC 3.2.1.8) are glycosyl hydrolases that catalyze the hydrolysis of internal β-1,4 glycosidic bonds of xylan backbones, and have potential economical and environment friendly applications in the paper pulp, food, animal feed, detergent industries, bio-ethanol and bio-energy production systems. A xylanase from Bacillus sp. NG-27 (BSX), which is an extracellular endoxylanase, belonging to glycosyl hydrolase family 10 (GH10), shows optimum activity at a temperature of 70 °C and at a pH 8.5. It has a (β/α)8-triosephosphate isomerase (TIM) barrel fold, which has been studied concerning its function, structural properties, design and evolution. BSX, apart from thermo-alkalophilic features, shows resistance to SDS denaturation and protease K degradation. Hence, BSX serves as an important model system for fundamental understanding of the structure-stability-evolution relations of the ubiquitous TIM barrel fold. While the factors responsible for the thermal stability of GH10 xylanases have been analyzed, the improvement of thermostability of already thermostable enzymes is an important challenge. In general, there are large differences in optimal temperature (Tm) between hyperthermostable proteins with respect to their mesophilic homologs, indicating considerable scope available for introducing novel protein engineering approaches to improve protein stability. Thermostability and thermotolerance are of particular importance for industrial enzymes, because higher operating temperatures allow higher reactivity, higher bioavailability, higher process yield, lower viscosity, and reducing the risk of contamination. Thus, finding enzymes that can function at high temperatures has immense industrial importance and constitutes an active area of research. Earlier studies on enzymatic activity and thermostability of a recombinant BSX (RBSX) with different extreme N-terminus mutants by biochemical/biophysical methods showed that a single amino acid substitution (Val1→Leu) markedly enhanced the thermostability of recombinant xylanase from 70 °C to 75 °C without compromising its catalytic activity and showed higher cooperativity in the thermal unfolding transition. Conversely, substitution of Val1→Ala (V1A) at the same position decreased the stability of the protein from 70 °C to 68 °C. Furthermore, it was observed that substitution of Phe4 by Ala decreased the stability by ~4 °C whereas substitution of Trp6→Ala and Tyr343→Ala decreased the stability by ~10 °C with respect to RBSX. On the other hand, substitution of Phe4 by another aromatic residue Trp (F4W) did not change the stability and activity of RBSX. However, structural details were not available at that time, precluding any structure-based rationalization of stability changes resulting from a single amino acid substitution. The thesis reports the crystal structures of a recombinant xylanase from Bacillus sp. NG-27 (RBSX) and its various N-terminal and C-terminal mutants namely V1A, V1L, F4A, F4W, W6A, and Y343A. The crystal structure of RBSX (PDB ID: 4QCE) was solved at a resolution of 2.35 Å whereas those of V1A mutant (PDB ID: 4QCF) and V1L mutant (PDB ID: 4QDM) were solved at a resolution of 2.26 Å and 1.99 Å respectively. On the other hand, the crystal structure of F4A was solved at a resolution of 2.23 Å whereas F4W, W6A, and Y343A mutants were solved at a resolution of 2.22 Å, 1.67 Å, and 2.30 Å respectively. The availability of experimentally determined RBSX structure and its various mutant structures has enabled a critical examination including from a network perspective, of factors influencing thermal stability. The crystal structures in combination with computational analysis have provided valuable insights into the structural features that govern protein thermostability. The thesis candidate established a link between N-terminal to C-terminal contacts and RBSX thermostability. The study reveals that augmenting N-terminal to C-terminal noncovalent interactions is associated with enhancement of the stability of the enzyme. Perhaps, for the first time, the study provides a network perspective of N-terminal to C-terminal interactions and shows that the stabilizing interactions are not restricted to terminal regions but propagate to different parts of the protein structure. Furthermore, analysis of structures of different aromatic mutants of RBSX and structural bioinformatics studies were combined to understand the role of long-range aromatic cluster in the form of 'aromatic-clique' in the thermal stabilization of proteins. The results highlight an additional source of stability in thermophilic proteins, which could arise due to the prevalence of aromatic-cliques. In addition, the work exemplifies the experimental evidence specifically through long-range aromatic clique, in reiterating the role of interactions between N- and C-termini in protein stabilization. The thesis candidate demonstrated the experimental evidence depicting the role of partially solvent exposed tryptophan residues in shielding a surface pocket, which influenced the solvation of backbone atoms and stability of the RBSX enzyme. The candidate carried out a comprehensive database analysis of available crystal structures to look into the possible role of partially exposed tryptophan in hyperthermophilic proteins. The study provides strong evidence that partially exposed tryptophan side-chain is recruited in hyperthermophilic proteins for occluding potential surface pockets, to provide backbone solvent shielding and local stabilization. The overall structure of this thesis is further explained through a chapter wise description below: Chapter 1 | An introduction and outline of the thesis This chapter starts with a general introduction about the diversity of microorganisms and their ability to thrive in extreme environments such as high temperature. The research on these enterprising organisms offers not just the insights into the resilience of life on earth or possibilities of life elsewhere in the universe but also can provide exciting opportunities for a variety of industrial, environmental, biomedical, and pharmaceutical applications. While the adaptation of the cell inventory is important, it is a challenge for proteins to overcome high temperature in order to remain folded in the correct three-dimensional structure while maintaining adequate flexibility for their desired function. Hence, elucidation of the molecular basis of protein stability at extreme temperature continues to attract researcher over a board range of disciplines. The various structural features responsible for protein stability are outlined and the basic structural and molecular strategies for the adaptation to high temperatures revealed by structure analysis are delineated. Of all potentially deactivating factors of protein stability, temperature is the best studied. A brief outline of the strategies and approaches for the design of proteins to meet the desirable properties such as increased thermal stability are presented whereas the structural features responsible for stability of triosephosphate isomerase (TIM)-barrel fold is outlined under a separate section. Subsequently a short introduction of family 10 (GH10) xylanases, which has the ubiquitous TIM-barrel fold and their classifications are presented. A section is dedicated to describe various thermostable GH10 xylanases, their structural features responsible for stability, and current and potential biotechnological applications. At the end, the scope of the present work is detailed. Chapter 2| Crystallization, Data Collection and Data processing of recombinant BSX (RBSX) and its different variants: Chapter 2 presents the purification of recombinant xylanase from Bacillus sp. NG-27 (RBSX), its N-terminal variants (V1A, V1L), and aromatic variants (F4W, F4A, W6A, and Y343A). The expression and purification of RBSX and its variants were carried out at the laboratory of our collaborator Prof. V. S. Reddy, Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India. Initial crystallization trials were screened by hanging drop vapor diffusion method and micro-batch diffusion method using crystallization-screening kits (Crystal Screen and Crystal Screen 2) from Hampton Research, USA and a laboratory made screen, which was based on reported crystallization condition of native BSX. After a few rounds of trials and optimization of the crystallization condition, diffraction quality rod shaped crystals of recombinant BSX (RBSX) were obtained within ten days, when 2-µl protein solution (10 g/ml) was mixed with 2-µl reservoir solution composed of 0.12 M MgCl2, 0.1 M NaCl, 0.1M Tris-HCl pH 8.5 and 15% PEG 8000. Subsequently, crystal was used for X-ray data collection and it diffracted X-rays to better than 2.2 Å at the home source at cryo-temperature (100 K). RBSX crystals belong to orthorhombic space group P212121 with unit cell parameters a = 54.77 Å, b = 75.65 Å, c = 179.91 Å and α = β = γ =90°. A three-dimensional screening grid was prepared based on crystallization condition of RBSX by carefully varying salt concentration (NaCl and MgCl2 from 10mM to 300mM in the interval of 10mM), different PEG variants (PEG 1000, PEG 3350, PEG 4000, PEG 8000, and PEG 10000) in the range of 5% to 20%. Tris-HCl buffer of pH 8.0 and of pH 8.5 was used in the concentration range of 0.05M and 0.1M respectively. Rod shaped crystals were obtained using hanging drop vapor diffusion method from the condition of 0.1M NaCl, 80mM MgCl2, 0.05M Tris-HCl pH 8.5 and 18 % PEG 8000 and 0.1M NaCl, 60mM MgCl2, 0.1M Tris-HCl pH 8.5 and 16 % PEG 8000 for V1L mutant and V1A mutant respectively. The diffracting crystals of F4A mutant were obtained from the condition of 0.1M NaCl, 140mM MgCl2, 0.05M Tris-HCl pH 8.5 and 15% PEG 8000 by using hanging drop vapor diffusion method. On the other hand, F4W and Y343A, crystals were grown by micro-batch diffusion method containing 1.1-μ1 ratio of protein and crystallization solution of 0.1M NaCl, 120mM MgCl2, 0.1M Tris-HCl pH 8.5 and 18% PEG 8000 and 0.1M NaCl, 150mM MgCl2, 0.1M Tris-HCl pH 8.5 and 15 % PEG 6000 respectively . W6A mutant crystals were grown by hanging drop vapor diffusion method of 0.1M NaCl, 160mM MgCl2, 0.05M Tris-HCl pH 8.5 and 20% PEG 8000. All the crystals were obtained at 20 °C-22 °C in 5-10 days, and were used for diffraction experiments (details in the table below). Table 1 Protein Space a b c α β γ X-ray source PDB group (Å) (Å) (Å) (°) (°) (°) ID RBSX P212121 54.77 75.65 176.91 90 90 90 Home-source 4QCE V1A C2 73.57 80.12 69.90 90 110.81 90 Home-source 4QCF V1L P212121 54.88 76.58 176.73 90 90 90 Synchrotron 4QDM F4W P212121 55.27 77.32 176.75 90 90 90 Home- source 5EB8 F4A P212121 52.62 67.71 181.54 90 90 90 Home- source 5EFF W6A P212121 54.99 76.60 181.54 90 90 90 Synchrotron 5EFD Y343A C2 73.86 80.11 69.21 90 111.19 90 Home- source 5EBA The quality of all dataset was assessed by SFCHECK. The data sets were found appropriate and useful for structure determination as discussed in Chapter 3. Chapter 3 | Molecular Replacement, Model Building, Refinement, validation of recombinant xylanase (RBSX), and different mutant structures: Chapter 3 details the application of molecular replacement method to the structure solution of RBSX structure, N-terminal and aromatic mutants of RBSX, the course of iterative model building and the refinement carried out and the quality of the final protein structure models. The structure solution for all the structures was obtained by the molecular replacement (MR) method with the program PHASER-MR in the PHENIX package using a search model of native-enzyme (2F8Q). The asymmetric unit of RBSX, V1L, F4A, F4W, W6A crystals was expected to contain two molecules whereas V1A and Y343A crystal was expected to contain one molecule as indicated by Matthews’s coefficient calculation. The final round of refinement was carried out with restrained refinement with TLS parameters for all the structures. The most essential refinement statistics of the final model of RBSX, V1A, and V1L mutant structures are given in Table 2 whereas the same for aromatic mutant structures, F4A, F4W, W6A, and Y343A are given in Table 3. Table 2 Refinement Statistics RBSX V1A V1L Resolution (Å) 27.7-2.32 26.8-2.26 40.2-1.96 Rwork / Rfree (%) 17.9/22.7 17.4/22.5 15.2/19.0 Average B-factors (Å2) Protein 21.6 26.3 13.9 Ligand/ion 15.6 26.4 18.74 Water 20.6 27.2 23.2 RMSD Bond distance (Å) 0.007 0.005 0.019 Bond angles (◦) 1.123 0.955 1.802 Luzzati coordinate 0.279 0.269 0.175 error (Å) Working set Table 3 Refinement Statistics F4A F4W W6A Y343A Resolution (Å) 18.15-2.23 18.97-2.22 32.1-1.67 34.03-2.30 Rwork / Rfree (%) 17.8/24.0 16.8/21.0 15.68/18.58 17.8/23.0 Average B-factors (Å2) Protein 13.1 19.5 16.7 26.8 Ligand/ion 14.2 20.0 21.4 26.1 Water 11.5 28.9 25.9 30.7 RMSD Bond distance (Å) 0.0144 0.0088 0.0139 0.0063 Bond angles (◦) 1.593 1.228 1.5995 1.0951 Luzzati coordinate 0.261 0.252 0.176 0.293 error (Å) Working set Chapter 4 | Mutations at the extreme N-terminus modulate thermostability of RBSX: Implications of interactions between termini for stability This chapter details the structural analysis of RBSX and its various extreme N-terminus mutations in relation to their different thermostability scale. Although several factors have been attributed to thermostability, the stabilization strategies used by proteins are still enigmatic. Studies on a RBSX, which has the ubiquitous (β/α)8-TIM (Triosephosphate isomerase) barrel fold showed that just a single mutation, Valine1→Leucine (V1L), though not part of any secondary structural element, markedly enhanced the stability from 70 °C to 75 °C without loss of catalytic activity. Conversely, substitution of Valine1→Alanine (V1A) at the same position decreased the stability of the enzyme from 70 °C to 68 °C. To gain structural insights as to how a single extreme N-terminus mutation can markedly influence the thermostability of the enzyme, the candidate has determined the crystal structure of RBSX and two mutants. Based on computational analysis of their crystal structures including residue interaction network, a link was established between N- to C-terminal contacts and RBSX thermostability. The study reveals that augmenting N- to C-terminal non-covalent interactions is associated with the enhancement of the stability of the enzyme. Perhaps, for the first time, the study provides a network perspective of N-terminal to C-terminal interactions and shows that the stabilizing interactions are not restricted to terminal regions but propagate to different parts of the protein structure. In addition, several lines of evidence were discussed that point to support the structural coupling between the chain termini and implications of stability changes in different proteins. It is proposed that the strategy of mutations at the termini could be exploited with a view to modulate stability without compromising on enzymatic activity, or in general, protein function, in diverse folds where N- and C-termini are in close proximity. Chapter 5 | Role of long-range aromatic cluster in the structural stability of RBSX Chapter 5 describes the different aromatic mutant crystal structures of RBSX namely F4W, F4A, W6A, and Y343A and the structural comparison with the RBSX crystal structure. Systematic studies of different alanine mutations (F4A, W6A, and Y343A) to disrupt this aromatic cluster showed that substitution of Phe4, Trp6, and Y343 by alanine drastically decreased the stability of recombinant BSX (RBSX). It was observed that substitution of Phe4 by Ala (F4A) decreased the RBSX stability by ~5 °C whereas substitutions of Trp6 by Ala (W6A) and Tyr343 by Ala (Y343A) markedly decreased the stability of the enzyme by ~10 °C. On the other hand, substitution of Phe4 by Trp (F4W) did not result any change in its thermal unfolding pattern of the enzyme. We observed that the mutated amino acid residues (Phe4, Trp6, and Tyr343) in the RBSX structure are part of an ‘aromatic-clique’. An aromatic-clique is defined as a cluster of aromatic residues in which each residue interacts with all other residues within the cluster through aromatic interactions. The study reveals that the decreased stability shown by F4A, W6A, and Y343A mutants resulted from cumulative effects in the loss of aromatic interactions and disruption of aromatic-clique, and reduced van der Waal interactions. In addition, the work exemplifies the importance of interactions between N-terminal and C-terminal through aromatic contacts or packing in folding and stability of the TIM-barrel fold protein. The structure based multiple sequence alignment of RBSX with other GH10 xylanase from Bacillus organisms revealed that aromatic-clique of interest is fully conserved in B. halodurans (BHX) and Bacillus firmus (BFX) xylanases, which are thermostable in nature, like RBSX. On the other hand, this aromatic-clique is not conserved in the GH10 xylanases from Bacillus N137, Bacillus alcalophilus, which are reported as thermo-labile in nature. Furthermore, analysis of available crystal structures of different thermostable xylanases from GH10 family showed the prevalence of aromatic-clique that may be playing a critical role in their structure-stability and folding. Lastly, a comprehensive analysis of homologous pairs of proteins from (hyper)thermophilic and mesophilic organisms was carried out and observed the high occurrence of aromatic-cliques in the thermophilic proteins in comparison to their mesophilic homologs. These results highlight an additional source of stability in thermophilic proteins, which can arise due to the prevalence of aromatic-cliques. The findings reported in the thesis provide important lessons for engineering xylanases for industrial applications. The strategy of mutations based on clustering of aromatic pairs in the form of ‘aromatic-clique’ may be effectively applied to other enzymes and provides new insights for engineers to design proteins for biotechnological applications. Chapter 6 | Tryptophan occludes surface pocket: Implications for protein stability Chapter 6 describes the structural feature of a partially exposed tryptophan residue, which effectively occludes a surface pocket and plays a critical role in RBSX thermo-stabilization. As a part our long-standing interest in the structural analysis of thermostable proteins, it was observed that just a single mutation, W6A of a recombinant xylanase (RBSX) from Bacillus sp. NG-27 decreased the stability from 70 °C to 60 °C. To gain structural insights into how a single mutation W6A can remarkably influence the thermostability of the enzyme, we determined the crystal structure of W6A mutant and compared the same with the crystal structure of RBSX. We serendipitously observed that substitution of Trp6 by alanine (W6A) in the protein results a small surface pocket, which was shielded by the bulky side-chain of Trp6 in the native structure. Inspection of the molecular structure of native protein structure revealed that side chain of Trp6 occludes the surface pocket, sterically impeding entry of solvent molecules including water. We demonstrated the experimental evidence depicting how a partially exposed tryptophan, which was shielding a surface pocket (tryptophan-shield), can directly influence the backbone solvation, and modulate the stability of the enzyme. Furthermore, computational analysis of high-resolution structures of hyperthermophilic proteins reveals that bulky and aromatic indole side-chain of tryptophan effectively occludes surface pockets in several hyperthermophilic proteins. The study provides a strong evidence that partially exposed tryptophan side-chain is recruited in hyperthermophilic proteins for occluding potential surface pockets to provide backbone solvent shielding and local stabilization. Chapter 7 | Summary and future direction Chapter 7 summaries the important findings of the present study from the crystal structure and computational analysis of a recombinant xylanase (RBSX) and its various N-terminal and C-terminal mutants and also outlines the future direction of the work. Appendix A details SFCHECK output for the processed data for all the structures reported in the thesis. Appendix B Reprints of the publications

abstract: The role of environmental factors that influence atmospheric propagation of sound originating from freeway noise sources is studied with a combination of field experiments and numerical simulations. Acoustic propagation models are developed and adapted for refractive index depending upon meteorological conditions. A high-resolution multi-nested environmental forecasting model forced by coarse global analysis is applied to predict real meteorological profiles at fine scales. These profiles are then used as input for the acoustic models. Numerical methods for producing higher resolution acoustic refractive index fields are proposed. These include spatial and temporal nested meteorological simulations with vertical grid refinement. It is shown that vertical nesting can improve the prediction of finer structures in near-ground temperature and velocity profiles, such as morning temperature inversions and low level jet-like features. Accurate representation of these features is shown to be important for modeling sound refraction phenomena and for enabling accurate noise assessment. Comparisons are made using the acoustic model for predictions with profiles derived from meteorological simulations and from field experiment observations in Phoenix, Arizona. The challenges faced in simulating accurate meteorological profiles at high resolution for sound propagation applications are highlighted and areas for possible improvement are discussed. A detailed evaluation of the environmental forecast is conducted by investigating the Surface Energy Balance (SEB) obtained from observations made with an eddy-covariance flux tower compared with SEB from simulations using several physical parameterizations of urban effects and planetary boundary layer schemes. Diurnal variation in SEB constituent fluxes are examined in relation to surface layer stability and modeled diagnostic variables. Improvement is found when adapting parameterizations for Phoenix with reduced errors in the SEB components. Finer model resolution (to 333 m) is seen to have insignificant ($<1\sigma$) influence on mean absolute percent difference of 30-minute diurnal mean SEB terms. A new method of representing inhomogeneous urban development density derived from observations of impervious surfaces with sub-grid scale resolution is then proposed for mesoscale applications. This method was implemented and evaluated within the environmental modeling framework. Finally, a new semi-implicit scheme based on Leapfrog and a fourth-order implicit time-filter is developed.
Dissertation/Thesis
Doctoral Dissertation Mechanical Engineering 2014