Protein adsorption at the solid/liquid interface is of wide ranging importance in many different areas of science such as biomaterial design, the fate of nanoparticles and in the food industry. As a result, many studies have been undertaken with varying foci but there still remains a lack of agreement between many working in this field and fundamental questions regarding the adsorption of proteins at the solid/liquid interface. Neutron reflectivity is a powerful technique for probing the properties of adsorbed layers at interfaces due to its high structural resolution and the possibility of using isotopic substitution to distinguish between components of a mixture. In this work, neutron reflectivity has been used as the primary technique for the investigation of proteins adsorbed sequentially or from a binary mixture. Initially, the adsorption of four proteins (carbonic anhydrase II, lysozyme, human serum albumin and maltose binding protein) onto a clean silica surface was investigated which revealed the importance of electrostatic interactions and entropic contributions to the driving forces for adsorption. Most of the adsorbed layers were described by a 2-layer model with a thinner, denser layer adjacent to the surface and a thick, diffuse layer extending into the bulk solution. The presence of impurities is also shown to have a significant impact on the adsorption of HSA. A study of the HSA/myristic acid system shows that the presence of small amphiphiles can inhibit HSA adsorption and also remove a pre-adsorbed layer. A comparison was made between the protonated and deuterated forms of two proteins, HSA & MBP, showing the deuterated proteins to have a higher affinity for the surface with adsorption occurring in a 3:1 ratio when from a 1:1 mixture. Likewise, d-MBP displaced h-MBP more readily than vice versa in an investigation into the effect of incubation time on the properties of the protein layer. The extent of desorption into protein free buffer is not affected by incubation time but the extent to which d-MBP was displaced by h-MBP showed a clear trend of decreased exchange with increasing incubation time indicating an active exchange process was occurring. This was also observed to a lesser extent for the sequential adsorption of binary protein systems, HSA & LYS and HSA & MBP. When investigating binary protein mixtures the higher propensity for deuterated proteins to adsorb is observed. LYS dominates when adsorbed from a mixture with h-HSA but from a d-HSA & LYS mix both proteins were adsorbed. The marked difference between the adsorption characteristics of perdeuterated proteins and their protonated counterparts provides a good case study for testing the neutron reflectivity technique when investigating systems with more than one component. This thesis assesses the limitations of the methodology of contrast variation for investigating mixtures as well as using different solvent contrasts. A comparison of neutron reflectivity and dual polarisation interferometry (DPI) shows that the two techniques are similar and any small differences can be attributed to the small change in surface chemistry. This comparison also highlights the advantages of DPI; high throughput of samples and detailed information but the restriction to using a 1-layer model limits its use.

Sommaire L’oxygène fait partie intégrante de l’environnement et ceci jusqu’au fonctionnement même des structures cellulaires qui composent le corps humain. Deux systèmes sont intimement liés à la distribution de l’oxygène, ce sont les systèmes cardiovasculaire et respiratoire. La transparence du système optique de l’œil peut être exploitée afin de mesurer de façon non invasive la concentration en oxyhémoglobine du sang qui alimente le système nerveux central. L’oxygénation capillaire de l’œil a été mesurée par spectro-réflectométrie dans deux régions de l’œil: d’une part les capillaires de la zone du nerf optique qui représentent principalement la circulation rétinienne; d’autre part, les capillaires du limbe cornéen. Cinq sujets volontaires, non fumeurs, sains, âgés de 20 à 45 ans et cinq sujets volontaires, fumeurs, sains, âgés de 20 à 40 ans ont participé à cette étude. Tous ces sujets ont été exposés à des conditions d’hyper et d’hypo oxygénation. Une séance d’expérimentations était composée d’un enregistrement continu de 360 secondes. Durant la première étape de 60 secondes, le sujet respirait de l’air ambiant. Durant une deuxième étape de 180 secondes, le sujet était exposé soit à une condition d’hyper (60% O2) soit, à une condition d’hypo oxygénation (15% O2), tandis que les 120 dernières secondes de la séance de mesure permettait d’exposer le sujet, une fois de plus à l’air ambiant. Le rythme cardiaque et les changements d’oxygénation artérielle au niveau du doigt étaient mesurés pendant ce temps vec le sphygmo-oxymètre. Les variations du taux d’oxyhémoglobine du sang au niveau capillaire de l’œil (nerf optique ou sclérotique) étaient toujours en corrélation directe avec les variations du taux d’oxyhémoglobine artériel. Toutefois, les capillaires du nerf optique offrent plus de précision pour les mesures d’oxygénation, relativement aux mesures d’oxygénation du sang contenu dans les capillaires de la sclérotique. La précision de la mesure de la concentration d’oxyhémoglobine obtenue dans cette étude par spectro-réflectométrie de l’œil, en fait un instrument utile au diagnostic d’une grande partie des pathologies pulmonaires ou oculaires. / Abstract Oxygen is an integral part of the environment. It has a major role to play in the cellular structures of the human body. The two systems, which are closely related to the distribution of oxygen within the body are the cardiovascular and the respiratory systems. The transparency of the eye can be used as a way to non-invasively measure the concentration of oxyhemoglobin in the blood which feeds the central nervous system. The capillary oxygenation of the eye was measured using multichannel spectro-reflectometry technology. Two areas of the eye were studied: the capillaries of the optical nerve which represent retinal circulation as well as the capillaries of the eye at the corneal limbus. Five healthy non-smoking volunteers aged 20-45 years and five healthy smoking volunteers aged 20-40 years took part in this study. All subjects were exposed to hypo and hyper oxygenation conditions. The experimental session was composed of a continuous recording of 360 seconds. In the first 60 seconds, volunteers breathed ambient air, followed by a second phase of 180 seconds during which the subjects were either exposed to a condition of hyper (60% O2) or hypo oxygenation (15% O2). The final phase of the experimental session was an exposure to ambient air. Cardiac rhythm and arterial oxygenation were measured at the tip of the finger with a sphygmo-oxymeter. Clearly, variations in the oxyhemoglobin blood concentration in the capillaries of the optic nerve or the sclerotic are always directly correlated with variations in the arterial oxyhemoglobin levels. However, the optic nerve capillaries offer more precision for measurements of oxygenation as compared to the sclerotic capillaries. In this study, accurate information has been provided on the oxyhemoglobin concentration using spectro-reflectometry of the eye. This technology could become a tool in the diagnosis of various pulmonary or ocular pathologies.

La turbulence plasma engendre un transport anormal de la chaleur et des particules qui dégrade l’efficacité d’un réacteur de fusion. La mesure de la turbulence plasma dans un tokamak est donc essentielle à la compréhension et au contrôle de ce phénomène. Parmi les instruments de mesure à disposition, le réflectomètre à balayage installé sur le tokamak Tore Supra a accès à la densité du plasma et ses fluctuations depuis le bord jusqu’au centre des décharges, avec une excellente résolution spatiale (mm) et temporelle (µs), de l’ordre des échelles de la turbulence. Cette thèse est dédiée à la caractérisation de la turbulence plasma dans Tore Supra à partir de mesures de réflectométrie à balayage ultrarapide. Des analyses de corrélations ont permis d’évaluer les échelles spatiales et temporelles de la turbulence ainsi que sa vitesse radiale. Dans la première partie, la caractérisation des propriétés de la turbulence à partir des profils de densité reconstruits est discutée, notamment au travers d’une comparaison avec les données des sondes de Langmuir. Ensuite une étude paramétrique est présentée mettant en relief l’effet de la collisionalité sur la turbulence, dont une interprétation est proposée en termes de stabilisation d’une turbulence électronique due aux électrons piégés. Finalement, on illustre comment le chauffage additionnel produit une modification locale de la turbulence dans le plasma proche des parois, se traduisant par une augmentation de la vitesse des structures et une diminution de leur temps de corrélation. L’effet supposé des potentiels rectifiés générés par l’antenne est étudié à l’aide de simulations. / The performance of a fusion reactor is closely related to the turbulence present in the plasma. The latter is responsible for anomalous transport of heat and particles that degrades the confinement. The measure and characterization of turbulence in tokamak plasma is therefore essential to the understanding and control of this phenomenon. Among the available diagnostics, the sweeping reflectometer installed on Tore Supra allows to access the plasma density fluctuations from the edge to the centre of the plasma discharge with a fine spatial (mm) and temporal resolution (µs ) , that is of the order of the characteristic turbulence scales.This thesis consisted in the characterization of plasma turbulence in Tore Supra by ultrafast sweeping reflectometry measurements. Correlation analyses are used to quantify the spatial and temporal scales of turbulence as well as their radial velocity. In the first part, the characterization of turbulence properties from the reconstructed plasma density profiles is discussed, in particular through a comparative study with Langmuir probe data. Then, a parametric study is presented, highlighting the effect of collisionality on turbulence, an interpretation of which is proposed in terms of the stabilization of trapped electron turbulence in the confined plasma. Finally, it is shown how additional heating at ion cyclotron frequency produces a significant though local modification of the turbulence in the plasma near the walls, resulting in a strong increase of the structure velocity and a decrease of the correlation time. The supposed effect of rectified potentials generated by the antenna is investigated via numerical simulations.

La turbulence est supposée être la source principale du transport anormal dans les tokamaks, qui conduit à la perte de chaleur beaucoup plus rapidement que celui prédit par la théorie néoclassique. Développement de diagnostics dédiés à la caractérisation de la turbulence du plasma est l'un des principaux enjeux de la fusion nucléaire pour contrôler les flux de particules et de transport d'énergie de la centrale électrique de fusion avenir. Les diagnostics basés sur la diffusion des micro-ondes induite par le plasma ont focalisé l'attention des chercheurs comme outils non perturbants, et nécessitant seulement un accès unique de faible encombrement au plasma. Le principe de base est lié à la phase de l'onde réfléchie qui contient des informations sur la position de la couche de coupure et les fluctuations de densité. La réflectométrie corrélation considérée ici, maintenant couramment utilisée dans les expériences, est la technique fournissant de l'information sur le plasma microturbulence. Bien que le diagnostic soit largement répandu l'interprétation des données reste une tâche assez compliquée. Ainsi, il a été supposé que la distance à laquelle la corrélation des deux signaux reçus à partir du plasma est supprimée est égale à la longueur de corrélation de turbulence. Toutefois, cette approche est erronée et introduit des erreurs énormes sur l'évaluation des paramètres de la microturbulence du plasma. L'objectif de cette thèse fut d'abord le développement d'une théorie analytique, puis de fournir une interprétation correcte des données de la réflectométrie de corrélation radiale (RCR) et enfin d'offrir aux chercheurs des formules simples pour extraire des informations sur les paramètres de turbulence à partir d'expériences utilisant la RCR. Des simulations numériques basées sur la théorie ont été utilisées pour prouver l'applicabilité de la méthode théorique, pour donner un aperçu aux expérimentateurs sur ses capacités et pour optimiser les paramètres du diagnostic lors de son utilisation en fonction des conditions de plasma. De plus, les résultats obtenus sur trois machines différentes sont soigneusement analysés et comparés avec les prédictions théoriques et des simulations numériques / Turbulence is supposed to be the main source of anomalous transport in tokamaks which leads to loss of heat much faster than as it is predicted by neoclassical theory. Development of plasma turbulence diagnostics is one of the key issues of nuclear fusion to control turbulent particles and energy transport in a future fusion power station. Diagnostics based on microwaves scattered from plasma attract attention of researchers as non-disturbing and requiring just a single access to plasma. The phase of the reflected wave contains information on the position of the cut-off layer and density fluctuations. Correlation reflectometry is now a routinely used technique providing information on plasma microturbulence. Although the diagnostics is widely spread data interpretation remains quite a complicated task. Thus, it was supposed that the distance at which the correlation of two signals received from plasma is suppressed is equal to the turbulence correlation length. However this approach is incorrect and introduces huge errors to determined plasma microturbulence parameters. The aim of this thesis is to develop an analytical theory, to give a correct interpretation of radial correlation reflectometry (RCR) data and to provide researchers with simple formulae for extracting information on microturbulence parameters from RCR experiments. Numerical simulations based on the theory prove applicability of this theoretical method and give an insight for experimentalists on its capability and on optimized diagnostic parameters to use. Furthermore the results obtained on three different machines are carefully analyzed and compared with theoretical predictions and numerical simulations as well

La supraconductivité s’établit par une organisation collective des électrons, décrite dans le cadre de la théorie BCS par une même fonction d’onde macroscopique. En présence de fort désordre, la situation est plus complexe : le désordre induit un renforcement des interactions coulombiennes et une localisation des électrons, s’opposant à l’établissement de la supraconductivité. Pour un désordre critique, la supraconductivité est détruite et le système devient métallique ou isolant. A 2D, en l’absence de fortes interactions coulombiennes, la théorie de la localisation d’Anderson interdit l’existence d’un état métallique : le désordre induit une Transition Supraconducteur-Isolant (TSI). Durant cette thèse, nous avons étudié les propriétés de transport à très basse température de films minces amorphes de NbxSi1-x. Nous avons effectué des mesures de résistance à basse fréquence à travers la TSI et initié des mesures d’impédance complexe à hautes fréquences (quelques GHz), afin de sonder la dynamique du système à travers la TSI. L’étude du transport statique s’est focalisée sur l’évolution du NbxSi1-x avec le recuit. Ce paramètre induit une variation progressive du désordre microscopique de notre système, ce qui nous a permis d’étudier finement la TSI. Nous avons ainsi mis en évidence deux états dissipatifs, séparant les états supraconducteurs et isolants, et non-prédits par les théories actuelles. Par ailleurs, nous avons mis au point un dispositif de mesure de réflectométrie micro-onde large bande. Nous avons en particulier développé une méthode de calibration, utilisant non pas la mesure de références externes comme il est usuel, mais un ensemble d’hypothèses sur la réponse électrodynamique des échantillons. Cette méthode permet de s’affranchir de l’environnement micro-onde de ceux-ci. Les résultats obtenus permettent une première validation de cette démarche et constituent donc un premier pas vers la détermination de la réponse dynamique absolue du système à travers la TSI. / Superconductivity is established by the collective organization of electrons, then described within the BCS theory through a single macroscopic wave function. In the presence of strong disorder, the situation becomes more complex: disorder enhances Coulomb interactions and induces the localization of electrons. These two phenomena act against superconductivity. For a critical disorder, the superconducting state is destroyed and the system becomes either metallic or insulating. In 2D, in the absence of strong Coulomb interactions, the theory of Anderson localization prevents the existence of a metallic state. Disorder thus induces a Superconductor-Insulator Transition (SIT). We have studied the transport properties of amorphous NbxSi1-x thin films at very low temperature. We have performed resistance measurements at low frequencies through the SIT and initiated measurements of the complex impedance at higher frequencies (a few GHz) in order to probe the dynamics of the system through this quantum phase transition. The study of the static properties of NbxSi1-x films have focused on the effect of annealing. This parameter induces a gradual variation of the microscopic disorder of this system, which allowed us a very fine tuning of the SIT. We have thus evidenced two dissipative states, non-predicted by the current theories of the SIT, which separate the superconducting and insulating ground states. In parallel, we have set up a broadband microwave reflectometry experiment. In particular, we have developed a calibration procedure based on hypotheses on the electrodynamic response of the samples and not on the measure of external references as it is usual. This method allows us to measure the sample’s response independently from the experimental setup. The results we have obtained provide a first validation of this approach and therefore constitute a first step towards the determination of the absolute dynamical response of the system through the SIT.

L’étude systématique de la turbulence plasma dans les tokamaks, via une méthode de paramétrisation des spectres de fréquence extraits de la base de données de réflectométrie de Tore Supra a été effectuée. Cette base de données est constituée de 350 000 acquisitions obtenues à partir de 6 000 chocs incluant différents scénarios de chauffage. La paramétrisation consiste en une décomposition de chaque spectre en quatre composantes : la composante dite continue, les fluctuations de basse fréquence (BF), la turbulence à large bande en fréquence (BB) et le niveau de bruit où chaque composante a été approchée par une fonction prédéfinie. Pour la composante de turbulence BB, trois fonctions différentes ont été testées et comparées. La fonction gaussienne généralisée et la fonction de Taylor ont montré d’excellentes performances dans la plupart des cas. Dans les plasmas ohmiques, EBB dans le régime de confinement ohmique saturé est systématiquement plus élevé que dans le régime de confinement ohmique linéaire. Dans les plasmas en mode bas confinement L, EBB dans les plasmas chauffés par une onde à la résonance. / To systematically study the plasma turbulence in tokamaks, a parametrization method of frequency spectra from the Tore Supra reflectometry database has been developed. The database includes 350,000 acquisitions obtained from 6,000 discharges with different heating scenarios. In the parametrization, each spectrum has been decomposed into four component: the direct current component, the low-frequency (LF) fluctuations, the broadband (BB) turbulence and the noise level, and each component has been fitted by a function. Specifically for the BB turbulence component, three different functions have been tested and compared. The generalized Gaussian function and the Taylor function have shown excellent fitting performance. In Ohmic plasmas, EBB in the saturated Ohmic confinement regime is observed to be systematically higher than in the linear Ohmic confinement regime. In L-mode plasmas, EBB in the ion cyclotron resonance heating plasmas is globally much higher than in the lower hybrid heating plasmas. The collisional effects on the modifications of the spectra have also been studied. With the previous kinetic simulation results, a change of the dominating micro-instabilities, i.e., between the trapped electron modes and the ion temperature gradients modes, has been proposed to explain the behaviors of EBB, supported by database analysis of the density peaking and the LF component.

The preparation of layered magnets needs the knowledge of growth techniques which are focused on the growth of Fe/V(001) superlattices. Such films have been structurally investigated by X-rays reflectivity and diffraction. The magnetic investigations have been carried out by magneto-optic Kerr effect (MOKE), Superconducting Quantum Interference Device (SQUID) magnetometry and polarized neutron reflectivity (PNR). This latter technique has been used in cooperation with the Institute Laue Langvin (Grenoble, France) and Ruhr Universität (Bochum, Germany). The cross-over in universality class is shown in a series of layered magnets where a δ-doping layer of Fe has been embedded between two layers of Pd showing that the magnetization depends on the effective magnetic thickness of the polarized Pd. A model for the cross-over has been developed in terms of magnetic excitations. The interlayer exchange coupling (IEC) mediated by a non-magnetic spacer has been reviewed focusing the attention on the recent theoretical and experimental works based on Fe/V(001) superlattices. The IEC can be tailored at will by reversibly alloying of the spacer with H: this has been proved in Fe/V(001) double layers showing that in the two dimensional limit, the universality class is not affected by the coupling. The magnetic order-disorder transitions in Fe/V(001) superlattices do not seem to belong to any universality class. A phenomenological model which accounts for the effective coupling at the boundaries has been developed. The influence of the inherent ordering temperatures of single magnetic layers has been investigated in Fe/V(001) superlattices proving that the weakest ferromagnetic layer affects the overall magnetic ordering. A new kind of layered magnet has been developed to increase the effect of the boundaries. PNR measurements show that the universality class depends on which length-scale is investigated.

A controlled column experiment was conducted to investigate the geophysical response of gasoline spills into the partially saturated sand column. The column was 0.61 diameter (ID) and 2 m high cylindrical polyvinyl chloride, which was packed with the Borden sand to a height of 1.95 m, flushed with CO2, saturated, and drained to a height of 0.73 m. The monitoring techniques used for this experiment was DC resistivity and time domain reflectometry (TDR) methods. The column was equipped with resistivity electrodes and TDR probes, which were placed on the column wall vertically with 3 cm intervals, on opposite sides, two monitoring wells, an injection well, a manometer, an outlet/inlet system, and a vent. A total amount of 5 liters of standard API 91-01 gasoline was added to the system in steps of 1, 2, and 2 liters to examine the geophysical response to different amounts of gasoline. Measurements were taken before and after each injection and also during subsequent fluctuation of the water table. Both monitoring techniques were able to record even the minor changes in the trend of conductivity and permittivity profiles due to the addition of the small amount of gasoline during the first spill. The conductivity and permittivity profiles obtained before lowering the water level below the original level and those obtained after the water level reached to the original level do not match, which is an indication of entrapped gasoline inside the pores. Two core samples was taken from the sand symmetrically after each water table fluctuation and analyzed for total petroleum hydrocarbon (TPH) analysis and the results were compared to the conductivity and permittivity results. The conductivity profile obtained using DC resistivity method was compared to that of obtained using TDR method. The profiles match in the saturated zone where all of the pores are connected with water and therefore electrolytic conduction is predominant. In the unsaturated zone, where there is low pore water connectivity, TDR measured conductivity values are higher than those measured using the resistivity method. Water saturation values were calculated using conductivity and permittivity values before and after each injection. Different values of saturation exponent (n) were tested for Archie’s law until an appropriate value was found which gave the best water saturation from conductivity data for clean Borden sand. Then, the water saturation obtained from permittivity values using Topp’s equations for different materials were compared to that of obtained from conductivity values using Archie’s equation. Topp’s equation for 30 µm glass beads provided the best match. Furthermore, other equations developed by other researchers were examined to obtain water saturation profiles from the permittivity values; all of them overestimate the water saturation for Borden sand. The water saturation profiles after the gasoline spills obtained using both Archie’s law and Topp’s equation do not match, perhaps because both equations were developed for three-phase (water-solid-air) systems.

A controlled column experiment was conducted to investigate the geophysical response of gasoline spills into the partially saturated sand column. The column was 0.61 diameter (ID) and 2 m high cylindrical polyvinyl chloride, which was packed with the Borden sand to a height of 1.95 m, flushed with CO2, saturated, and drained to a height of 0.73 m. The monitoring techniques used for this experiment was DC resistivity and time domain reflectometry (TDR) methods. The column was equipped with resistivity electrodes and TDR probes, which were placed on the column wall vertically with 3 cm intervals, on opposite sides, two monitoring wells, an injection well, a manometer, an outlet/inlet system, and a vent. A total amount of 5 liters of standard API 91-01 gasoline was added to the system in steps of 1, 2, and 2 liters to examine the geophysical response to different amounts of gasoline. Measurements were taken before and after each injection and also during subsequent fluctuation of the water table. Both monitoring techniques were able to record even the minor changes in the trend of conductivity and permittivity profiles due to the addition of the small amount of gasoline during the first spill. The conductivity and permittivity profiles obtained before lowering the water level below the original level and those obtained after the water level reached to the original level do not match, which is an indication of entrapped gasoline inside the pores. Two core samples was taken from the sand symmetrically after each water table fluctuation and analyzed for total petroleum hydrocarbon (TPH) analysis and the results were compared to the conductivity and permittivity results. The conductivity profile obtained using DC resistivity method was compared to that of obtained using TDR method. The profiles match in the saturated zone where all of the pores are connected with water and therefore electrolytic conduction is predominant. In the unsaturated zone, where there is low pore water connectivity, TDR measured conductivity values are higher than those measured using the resistivity method. Water saturation values were calculated using conductivity and permittivity values before and after each injection. Different values of saturation exponent (n) were tested for Archie’s law until an appropriate value was found which gave the best water saturation from conductivity data for clean Borden sand. Then, the water saturation obtained from permittivity values using Topp’s equations for different materials were compared to that of obtained from conductivity values using Archie’s equation. Topp’s equation for 30 µm glass beads provided the best match. Furthermore, other equations developed by other researchers were examined to obtain water saturation profiles from the permittivity values; all of them overestimate the water saturation for Borden sand. The water saturation profiles after the gasoline spills obtained using both Archie’s law and Topp’s equation do not match, perhaps because both equations were developed for three-phase (water-solid-air) systems.

Fluoride-containing solutions are widely used to etch silicon dioxide-based films. A critical issue in integrated circuit (IC) and microelectromechanical systems (MEMS) fabrication is achievement of adequate selectivity during the etching of different film materials when they are present in different areas on a device or in a stack. The use of organic fluoride-based salts in aqueous/organic solvent solutions can yield etch selectivities <1.9 for thermally-grown silicon dioxide relative to borophosphosilicate glass films, and thus may also obviate the need to add surfactants to the etch solutions to realize uniform etching. Etch studies with aqueous-organic fluoride salt-based solutions also offer insight into the etch mechanism of these materials. Specifically, the importance of water content in the solutions and of ion solvation in controlling the etch chemistry is described. With respect to fluoride-containing solutions, etching of SiO₂ films using aqueous HF-based chemistries is widely used in IC and MEMS industries. To precisely control film loss during cleaning or etching processes, good control over the contact time between the liquid (wet) chemistry and the substrate is necessary. An integrated wet etch and dry reactor system has been designed and fabricated by studying various geometrical configurations using computational fluid dynamics (CFD) simulations incorporating reaction kinetics from laboratory data and previously published information. The effect of various process parameters such as HF concentration, flow rate, and flow velocity on the etch rates and uniformity of thermally-grown silicon dioxide and borophosphosilicate glass films was studied. Simulations agree with experiments within experimental error. This reactor can also be used to wet etch/clean and dry other films in addition to SiO₂-based films using aggressive chemistries as well as aqueous HF under widely different process conditions. A spectroscopic reflectometry technique has been implemented in-situ in this custom fabricated reactor to monitor the thickness and etch rate in wet etching environments. The advantages of this technique over spectroscopic ellipsometry in specific situations are discussed. A first principles model has been developed to analyze the reflectometry data. The model has been validated on a large number of previously published studies. The match between experimental and simulated thickness is good, with the difference ~ 5 nm. In-situ thickness and etch rate have been estimated using Recursive Least Squares (RLS), Extended Kalman Filter (EKF) and modified Moving Horizon Estimator (mMHE) analyses applied to spectroscopic reflectometry using multiple wavelengths with ZnO employed as a model film. The initial guess for EKF and mMHE has been obtained from a CFD model. It has been shown that both EKF and mMHE are less oscillatory than RLS/LS in the prediction of thickness and ER and more robust when a smaller number of wavelengths are used, in addition, the computational time for EKF is less than that of mMHE/RLS. For no restrictions on computational requirements, LS should be the method of choice whereas in the case of faster etching systems, with the availability of a better process model, EKF should be starting point. The choice of algorithm is thus based on sampling rate for data collection, process model uncertainty and the number of wavelengths required.