In the manufacturing process of float glass often atmospheric pressure chemical vapour deposition (APCVD) reactors are integrated on-line for the deposition of functional thin solid films. Such functional films have applications in architectural glass, flat panel displays and solar cells. As glass moves downstream in the process, the thin film is deposited at temperatures between 500 to 700°C. The high temperatures make it difficult to monitor the deposition process and thin film quality control is commonly done at the end of the line or at lower temperatures. A time delay therefore exists between the point of thin film deposition and subsequent quality control, which can lead to large quantities of defective product being produced before faults are detected. It is therefore desirable to monitor in the APCVD reactor for rapid feedback of unexpected deviations from desired process conditions, reaction progress and fault detection. High uniformity of film properties across the substrate are important, but APCVD reactors are often empirically designed and the detailed chemical reaction mechanism is unknown. This leads to inefficient gas flow patterns and precursor utilization as well as difficulties in the design of new reactors. The APCVD deposition of tin oxide from the mono-butyl-tin tri-chloride (MBTC) is an example of such a process. Optical monitoring instruments in-situ and in-line on the APCVD reactor provided rapid feedback about process stability and progress non-invasively. Near infrared diode laser absorption spectroscopy (NIR-LAS) monitored the concentration of the reaction species hydrogen chloride (HCl) in-situ and spatially in the coating zone. A mid-infrared grating absorption spectrometer (IR-GAS) with novel pyro-electric array detector monitored the concentration of precursor entering the coating system simultaneously. In combination these instruments provide the means for rapid process feedback. Fourier transform infrared absorption spectroscopy (FTIR) was used to investigate the unknown decomposition pathway of the precursor to find the yet unknown key tin radical that initiates film growth. Stable species forming during MBTC decomposition over a temperature range of 170 to 760°C were investigated but the tin intermediate remains unknown. Computational fluid dynamics (CFD) is routinely employed in research and industry for the numerical simulation of CVD processes in order to predict reactor flow patterns, deposition rates, chemical species distribution or temperature profiles. Two and three dimensional models with complex geometries and detailed reaction models exist. A three dimensional computational fluid dynamics (CFD) model of the used APCVD reactor was built using the Fluent CFD software. The numerical simulation included a chemical model that predicted qualitatively the chemical species distribution of hydrogen chloride in the gas phase. This was confirmed through comparison with NIR-LAS results. Design shortcomings due to inefficient flow patterns were also identified. In combination the optical tools developed provide the means for safe and efficient manufacturing of thin films in APCVD reactors. CFD simulations can be used to increase precursor utilization and film uniformity in the development of new reactor designs.

This research presents the results on an experimental investigation to identify the effect of polyphosphoric acid (PPA) on aging characteristics of an asphalt binder. Addition of PPA to asphalt binders is said to improve performance of flexible pavements. Asphalt binder PG 64-22 in modified and unmodified conditions was subjected to aging in the laboratory using a regular oven and also simulated short term aging using rolling thin film oven (RTFO) test. Aging experiments were conducted to analyze the extent of oxidation in terms of changes in molecular structure of the asphalt binder. These changes were appraised using Fourier transform infrared (FTIR) spectroscopy, dynamic shear rheometer (DSR), and epifluorescence microscopy tests. FTIR was used to determine the changes in major bands with addition of PPA. Stiffness and viscoelastic behaviors of asphalts were determined from the DSR test. The stiffness is measured by calculating the shear modulus, G* and the viscoelastic behavior is measured by calculating the phase angle, sin δ. Epifluorescence microscopy is a tool used to study properties of organic or inorganic substances. The morphological characteristics of PPA modified asphalt samples were observed through epifluorescence microscopy. Epifluorescence microscopy reveals the polymer phase distribution in the asphalt binders. Results of this investigation show PPA addition to asphalt binders improve G*/sin δ characteristics of asphalt binders. In addition, presence of PPA in polymer containing asphalt did not adversely affect aging of the binders.

Modern three-dimensional integrated circuit design is rapidly evolving to more complex architecture. With continuous downscaling of devices, there is a pressing need for metrology tool development for rapid but efficient process and material characterization. In this dissertation work, application of a novel multiple internal reflection infrared spectroscopy metrology is discussed in various semiconductor fabrication process development. Firstly, chemical bonding structure of thin fluorocarbon polymer film deposited on patterned nanostructures was elucidated. Different functional groups were identified by specific derivatization reactions and model bonding configuration was proposed for the first time. In a continued effort, wet removal of these fluorocarbon polymer was investigated in presence of UV light. Mechanistic hypothesis for UV-assisted enhanced polymer cleaning efficiency was put forward supported by detailed theoretical consideration and experimental evidence. In another endeavor, plasma-induced damage to porous low-dielectric constant interlayer dielectric material was studied. Both qualitative and quantitative analyses of dielectric degradation in terms of increased silanol content and carbon depletion provided directions towards less aggressive plasma etch and strip process development. Infrared spectroscopy metrology was also utilized in surface functionalization evaluation of very thin organic films deposited by wet and dry chemistries. Palladium binding by surface amine groups was examined in plasma-polymerized amorphous hydrocarbon films and in self-assembled aminosilane thin films. Comparison of amine concentration under different deposition conditions guided effective process optimization. A time- and cost-effective method such as current FTIR metrology that provides in-depth chemical information about thin films, surfaces, interfaces and bulk layers can be increasingly valuable as critical dimensions continue to scale down and subtle process variances begin to have a significant impact on device performance.

El diagnóstico final de la mayoría de tipos de cáncer lo realiza un médico experto en anatomía patológica que examina muestras tisulares o celulares sospechosas extraídas del paciente. Actualmente, esta evaluación depende en gran medida de la experiencia del médico y se lleva a cabo de forma cualitativa mediante técnicas de imagen tradicionales como la microscopía óptica. Esta tarea tediosa está sujeta a altos grados de subjetividad y da lugar a niveles de discordancia inadecuados entre diferentes patólogos, especialmente en las primeras etapas de desarrollo del cáncer. La espectroscopía infrarroja por Transformada de Fourier (siglas FTIR en inglés) es una tecnología ampliamente utilizada en la industria que recientemente ha demostrado una capacidad creciente para mejorar el diagnóstico de diferentes tipos de cáncer. Esta técnica aprovecha las propiedades del infrarrojo medio para excitar los modos vibratorios de los enlaces químicos que forman las muestras biológicas. La principal señal generada consiste en un espectro de absorción que informa sobre la composición química de la muestra iluminada. Los microespectrómetros FTIR modernos, compuestos por complejos componentes ópticos y detectores matriciales de alta sensibilidad, permiten capturar en un laboratorio de investigación común imágenes hiperespectrales de alta calidad que aúnan información química y espacial. Las imágenes FTIR son estructuras de datos ricas en información que se pueden analizar individualmente o junto con otras modalidades de imagen para realizar diagnósticos patológicos objetivos. Por lo tanto, esta técnica de imagen emergente alberga un alto potencial para mejorar la detección y la graduación del riesgo del paciente en el cribado y vigilancia de cáncer. Esta tesis estudia e implementa diferentes metodologías y algoritmos de los campos interrelacionados de procesamiento de imagen, visión por ordenador, aprendizaje automático, reconocimiento de patrones, análisis multivariante y quimiometría para el procesamiento y análisis de imágenes hiperespectrales FTIR. Estas imágenes se capturaron con un moderno microscopio FTIR de laboratorio a partir de muestras de tejidos y células afectadas por cáncer colorrectal y de piel, las cuales se prepararon siguiendo protocolos alineados con la práctica clínica actual. Los conceptos más relevantes de la espectroscopía FTIR se investigan profundamente, ya que deben ser comprendidos y tenidos en cuenta para llevar a cabo una correcta interpretación y tratamiento de sus señales especiales. En particular, se revisan y analizan diferentes factores fisicoquímicos que influyen en las mediciones espectroscópicas en el caso particular de muestras biológicas y pueden afectar críticamente su análisis posterior. Todos estos conceptos y estudios preliminares entran en juego en dos aplicaciones principales. La primera aplicación aborda el problema del registro o alineación de imágenes hiperespectrales FTIR con imágenes en color adquiridas con microscopios tradicionales. El objetivo es fusionar la información espacial de distintas muestras de tejido medidas con esas dos modalidades de imagen y centrar la discriminación en las regiones seleccionadas por los patólogos, las cuales se consideran más relevantes para el diagnóstico de cáncer colorrectal. En la segunda aplicación, la espectroscopía FTIR se lleva a sus límites de detección para el estudio de las entidades biomédicas más pequeñas. El objetivo es evaluar las capacidades de las señales FTIR para discriminar de manera fiable diferentes tipos de células de piel que contienen fenotipos malignos. Los estudios desarrollados contribuyen a la mejora de métodos de decisión objetivos que ayuden al patólogo en el diagnóstico final del cáncer. Además, revelan las limitaciones de los protocolos actuales y los problemas intrínsecos de la tecnología FTIR moderna, que deberían abordarse para permit / The final diagnosis of most types of cancers is performed by an expert clinician in anatomical pathology who examines suspicious tissue or cell samples extracted from the patient. Currently, this assessment largely relies on the experience of the clinician and is accomplished in a qualitative manner by means of traditional imaging techniques, such as optical microscopy. This tedious task is subject to high degrees of subjectivity and gives rise to suboptimal levels of discordance between different pathologists, especially in early stages of cancer development. Fourier Transform infrared (FTIR) spectroscopy is a technology widely used in industry that has recently shown an increasing capability to improve the diagnosis of different types of cancer. This technique takes advantage of the ability of mid-infrared light to excite the vibrational modes of the chemical bonds that form the biological samples. The main generated signal consists of an absorption spectrum that informs of the chemical composition of the illuminated specimen. Modern FTIR microspectrometers, composed of complex optical components and high-sensitive array detectors, allow the acquisition of high-quality hyperspectral images with spatially-resolved chemical information in a common research laboratory. FTIR images are information-rich data structures that can be analysed alone or together with other imaging modalities to provide objective pathological diagnoses. Hence, this emerging imaging technique presents a high potential to improve the detection and risk stratification in cancer screening and surveillance. This thesis studies and implements different methodologies and algorithms from the related fields of image processing, computer vision, machine learning, pattern recognition, multivariate analysis and chemometrics for the processing and analysis of FTIR hyperspectral images. Those images were acquired with a modern benchtop FTIR microspectrometer from tissue and cell samples affected by colorectal and skin cancer, which were prepared by following protocols close to the current clinical practise. The most relevant concepts of FTIR spectroscopy are thoroughly investigated, which ought to be understood and considered to perform a correct interpretation and treatment of its special signals. In particular, different physicochemical factors are reviewed and analysed, which influence the spectroscopic measurements for the particular case of biological samples and can critically affect their later analysis. All these knowledge and preliminary studies come into play in two main applications. The first application tackles the problem of registration or alignment of FTIR hyperspectral images with colour images acquired with traditional microscopes. The aim is to fuse the spatial information of distinct tissue samples measured by those two imaging modalities and focus the discrimination on regions selected by the pathologists, which are meant to be the most relevant areas for the diagnosis of colorectal cancer. In the second application, FTIR spectroscopy is pushed to their limits of detection for the study of the smallest biomedical entities. The aim is to assess the capabilities of FTIR signals to reliably discriminate different types of skin cells containing malignant phenotypes. The developed studies contribute to the improvement of objective decision methods to support the pathologist in the final diagnosis of cancer. In addition, they reveal the limitations of current protocols and intrinsic problems of modern FTIR technology, which should be tackled in order to enable its transference to anatomical pathology laboratories in the future. / El diagnòstic final de la majoria de tipus de càncer ho realitza un metge expert en anatomia patològica que examina mostres tissulars o cel¿lulars sospitoses extretes del pacient. Actualment, aquesta avaluació depèn en gran part de l'experiència del metge i es porta a terme de forma qualitativa mitjançant tècniques d'imatge tradicionals com la microscòpia òptica. Aquesta tasca tediosa està subjecta a alts graus de subjectivitat i dóna lloc a nivells de discordança inadequats entre diferents patòlegs, especialment en les primeres etapes de desenvolupament del càncer. L'espectroscòpia infraroja per Transformada de Fourier (sigles FTIR en anglès) és una tecnologia àmpliament utilitzada en la indústria que recentment ha demostrat una capacitat creixent per millorar el diagnòstic de diferents tipus de càncer. Aquesta tècnica aprofita les propietats de l'infraroig mitjà per excitar els modes vibratoris dels enllaços químics que formen les mostres biològiques. El principal senyal generat consisteix en un espectre d'absorció que informa sobre la composició química de la mostra il¿luminada. Els microespectrómetres FTIR moderns, compostos per complexos components òptics i detectors matricials d'alta sensibilitat, permeten capturar en un laboratori d'investigació comú imatges hiperespectrals d'alta qualitat que uneixen informació química i espacial. Les imatges FTIR són estructures de dades riques en informació que es poden analitzar individualment o juntament amb altres modalitats d'imatge per a realitzar diagnòstics patològics objectius. Per tant, aquesta tècnica d'imatge emergent té un alt potencial per a millorar la detecció i la graduació del risc del pacient en el cribratge i vigilància de càncer. Aquesta tesi estudia i implementa diferents metodologies i algoritmes dels camps interrelacionats de processament d'imatge, visió per ordinador, aprenentatge automàtic, reconeixement de patrons, anàlisi multivariant i quimiometria per al processament i anàlisi d'imatges hiperespectrals FTIR. Aquestes imatges es van capturar amb un modern microscopi FTIR de laboratori a partir de mostres de teixits i cèl¿lules afectades per càncer colorectal i de pell, les quals es van preparar seguint protocols alineats amb la pràctica clínica actual. Els conceptes més rellevants de l'espectroscòpia FTIR s'investiguen profundament, ja que han de ser compresos i tinguts en compte per dur a terme una correcta interpretació i tractament dels seus senyals especials. En particular, es revisen i analitzen diferents factors fisicoquímics que influeixen en els mesuraments espectroscòpiques en el cas particular de mostres biològiques i poden afectar críticament la seua anàlisi posterior. Tots aquests conceptes i estudis preliminars entren en joc en dues aplicacions principals. La primera aplicació aborda el problema del registre o alineació d'imatges hiperespectrals FTIR amb imatges en color adquirides amb microscopis tradicionals. L'objectiu és fusionar la informació espacial de diferents mostres de teixit mesurades amb aquestes dues modalitats d'imatge i centrar la discriminació en les regions seleccionades pels patòlegs, les quals es consideren més rellevants per al diagnòstic de càncer colorectal. En la segona aplicació, l'espectroscòpia FTIR es porta als seus límits de detecció per a l'estudi de les entitats biomèdiques més xicotetes. L'objectiu és avaluar les capacitats dels senyals FTIR per discriminar de manera fiable diferents tipus de cèl¿lules de pell que contenen fenotips malignes. Els estudis desenvolupats contribueixen a la millora de mètodes de decisió objectius que ajuden el patòleg en el diagnòstic final del càncer. A més, revelen les limitacions dels protocols actuals i els problemes intrínsecs de la tecnologia FTIR moderna, que haurien d'abordar per permetre la seva transferència als laboratoris d'anatomia patològica en el futur. / Peñaranda Gómez, FJ. (2018). Application of artificial vision algorithms to images of microscopy and spectroscopy for the improvement of cancer diagnosis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/99748 / TESIS

Amyloids are self-assembled protein materials containing beta-sheets.  While most studies focus on amyloids as the pathogen in neurodegenerative disease, there are instances of "functional" amyloids used to preserve life.  Functional amyloids serve as an inspiration in materials design.  In this study, it is shown that wheat gluten (WG) and gliadin:myoglobin (Gd:My) amyloid morphology can be varied from predominantly fibrillar at low polypeptide concentration to predominantly globular at high polypeptide concentration as measured at the nanometer scale using atomic force microscopy (AFM).  The ability to control the morphology of a material allows control of its properties.  Fourier transform infrared (FTIR) spectroscopy shows that at low concentration, fibrils require interdigitation of methyl groups on alanine (A), isoleucine (I), leucine (L), and valine (V).  At higher concentration, globules do not have the same interdigitation of methyl groups but more random hydrophobic interactions.  The concentration dependence of the morphology is shown as a kinetic effect where many polypeptides aggregate very quickly through hydrophobic interactions to produce globules while smaller populations of polypeptides aggregate slowly through well-defined hydrophobic interactions to form fibrils. Functional amyloids also provide a means of creating a low energy process for composites. Poor fiber/matrix bonding and processing degradation have been observed in previous WG based composites.  This study aims to improve upon these flaws by implementing a self-assembly process to fabricate self-reinforced wheat gluten composites. These composites are processed in aqueous solution at neutral pH by allowing the fibers to form in a matrix of unassembled peptides.  The fiber and the matrix are formed from the same solution, thus the two components create a compatible system with ideal interfacial interaction for a composite.  The fibers in the composite are about 10 microns in diameter and can be several millimeters long.  It has been observed that the number of fibers present along the fracture surface influences the modulus of the composite. In this study, self-assembled wheat gluten composites are formed and then characterized with 3-point bend (3PB) mechanical testing, scanning electron microscopy (SEM), and Fourier transform infrared (FTIR) spectroscopy. / Master of Science

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Alzheimer’s Disease (AD) is a neurodegenerative disease marked by progressive neuronal cell death, leading to dementia. AD is the most common disease that results in dementia and largely affects the elderly, with five million people in the United States diagnosed with the disease as of 2015 and approximately 35 million people worldwide. Diseases resulting in dementia cost the US healthcare system an estimated $172 billion in 2010 and that cost is expected to increase as the population ages and as diagnostic techniques improve so that more people are treated (Holtzman, 2011). The disease was first reported by psychiatrist Alois Alzheimer at the onset of the 20th century, when one of his patients “suffered memory loss, disorientation, hallucinations and delusions and died at the age of 55,” then was found to have severe brain atrophy post-mortem (Cipriani, Dolciotti, Picchi, & Bonuccelli, 2011). There are palliative treatments available that marginally slow disease progression but there is currently no cure for the disease (Awasthi, Singh, Pandey, & Dwivedi, 2016). More research is needed to develop effective therapeutic strategies to combat the disease. Currently, AD cytotoxicity is believed to be caused by increased amyloid β (Aβ) peptide plaque deposition in the brain, as described by the amyloid cascade hypothesis (Barage & Sonawane, 2015). The current understanding is that oligomers of Aβ peptide lead to neuronal death through multiple mechanisms, most notably hyper-phosphorylation of the tau protein. Having a better understanding of the structural changes in the fibrillization process of Aβ will provide a broader insight into mechanisms of cell death and open new possibilities for pharmacological treatments, which is what this research intends to provide.