Optical properties of nanostructured SRO

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2006.Includes bibliographical references (p. 190-195).We have conducted a study of the optical properties of sputtered silicon-rich silicon dioxide (SRO) thin films with specific application for the fabrication of erbium-doped waveguide amplifiers and lasers, polarization sensitive devices and devices to modify the polarization state of light. The SRO thin films were prepared through a reactive RF magnetron sputtering from a Si target in an O2/Ar gas mixture. The film stoichiometry was controlled by varying the power applied to the Si target or changing the percentage of 02 in the gas mixture. A deposition model is presented which incorporates the physical and chemical aspects of the sputtering process to predict the film stoichiometry and deposition rate for variable deposition conditions. The as-deposited films are optically anisotropic with a positive birefringence (nTM > nTE) that increases with increasing silicon content for as-deposited films. The dependence of the birefringence on annealing temperature is also influenced by the silicon content. After annealing, samples with high silicon content (>45 at%) showed birefringence enhancement while samples with low silicon content (<45 at%) showed birefringence reduction. A birefringence of more than 3% can be generated in films with high silicon content (50 at% Si) annealed at 11000C.(cont.) We attribute the birefringence to the columnar film morphology achieved through our sputtering conditions. Er was incorporated through reactive co-sputtering from Er and Si targets in the same O2/Ar atmosphere in order to investigate the energy-transfer process between SRO and Er for low annealing temperatures. By studying the photoluminescence (PL) intensity of Er:SRO samples annealed in a wide range of temperatures, we demonstrated that the Er sensitization efficiency is maximized between 600°C and 700°C. Temperature-resolved PL spectroscopy on SRO and Er:SRO samples has demonstrated the presence of two different emission sensitizers for samples annealed at 6000C and 1 100°C. This comparative study of temperature-resolved PL spectroscopy along with energy Filtered Transmission Electron Microscopy (EFTEM) has confirmed that the more efficient emission sensitization for samples annealed at 6000C occurs through localized centers within the SRO matrix without the nucleation of Si nanocrystals. Er-doped SRO slab waveguides were fabricated to investigate optical gain and loss for samples annealed at low temperatures.(cont.) Variable stripe length gain measurements show pump dependent waveguide loss saturation due to stimulated emission with a maximum modal gain of 3 ± 1.4 cm-1 without the observation of carrier induced losses. Pump and probe measurements on ridge waveguides also confirms the presence of SRO sensitized signal enhancement for samples annealed at 6000C. Transmission loss measurements demonstrate a significant loss reduction of 1.5 cm-1or samples annealed at 600°C compared to those annealed at 1000°C. These results suggest a possible route for the fabrication of compact, high-gain planar light sources and amplifiers with a low thermal budget for integration with standard Si CMOS processes.by Michael Anthony Stolfi.Ph.D

Size, Shape, and Spatial Distribution Analysis of Sub-Micron Hip Implant Wear Particles at Sub-Optical Resolution Using Deconvolution Methods

Total joint replacement (TJR) has long been a common and effective treatment option for individuals suffering from osteoarthritis. However, the bearing surfaces for TJR implants, generally a metal femoral head inserted into an ultra-high molecular weight polyethylene (UHMWPE) acetabular cup, are prone to wear. UHMWPE particles generated through articulating wear can contribute to the failure of implants, and have been shown to have health risks for patients. Understanding the generation and characteristics of wear particles is crucial for learning how to reduce these health risks and assess different implant materials and designs. Using a novel elliptically polarized light imaging system we employ new techniques for image acquisition, with subsequent manipulation to enhance particle analysis. Microscopy slides containing UHMWPE wear debris were prepared and imaged using a custom designed polarizing microscope. A calibration methodology was developed to model the point spread function (PSF) artifact introduced by the optical system. Deconvolution methods, based on a PSF model developed by Gibson et al. [33], were used to remove the PSF from images captured by the optical system. Optimization of the theoretical PSF produced a model that consistently correlated above 0.85, which is a threshold determined to result in reasonable improvement in resolution of image data. Particle size, shape, and spatial distribution were quantified and used to characterize the imaged particles. Statistical comparison of particle characterization before and after deconvolution, and compared against scanning electron microscopy images of the same particles, revealed a significant improvement in particle characterization. Further refinement and work could improve the packages presented in this work dramatically, offering a robust alternative to SEM analysis of wear debris. The main advantage of this new method is the ability to image UHMWPE wear particles in-situ from histology slides of relevant tissues, allowing for distribution and location data to be collected in addition to size and shape information.M.S., Biomedical Engineering -- Drexel University, 201

Molecular Signposts of the Physics and Chemistry of Planet Formation.

Observations of molecules in planet-forming circumstellar disks are powerful diagnostic tools, enabling characterization of both gas composition and underlying physical conditions using molecular excitation. My thesis has primarily focused on the role of disk structure and ionization for the chemistry of disks and the corresponding submillimeter emission. Changes in the overall morphology of disks, including inner holes or gaps, significantly alters the stellar irradiation of the disk, which will affect the disk heating, especially at the walls of an inner hole (Chapter 2). I have modeled the 3D chemistry of gapped disks, carved out by planets, including for the first time heating by a luminous protoplanet. The planet sublimates ices beyond expected disk "snow-lines" leading to observable signatures detectable with ALMA (Chapter 3). Regarding ionization, I have studied disk ionization by cosmic rays (Chapter 4), short-lived radionuclides (Chapter 5), and X-rays from the central star (Chapter 6). In Chapter 6, I investigated the molecular dependence on each of these processes and made testable predictions for sensitive submillimeter observations to map out disk ionization, which I applied to the TW Hya disk, finding a substantially lower than interstellar cosmic ray rate (Chapter 7). One of the major implications of this work is related to the formation chemistry of water, which requires ionization to proceed. In the absence of water-formation in the solar nebula protoplanetary disk, this work demonstrates that there must be a substantial inheritance of water from earlier evolutionary stages, pre-dating the Sun's formation (Chapter 8). Together, these projects have also enabled the development of a comprehensive 2D and 3D disk modeling framework, useful for parameter space studies and source-targeted modeling.PhDAstronomy and AstrophysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113307/1/cleeves_1.pd

Pozitron emisyon tomografide görüntü oluşturma yöntemlerinin incelenmesi ve iyileştirilmesi

06.03.2018 tarihli ve 30352 sayılı Resmi Gazetede yayımlanan “Yükseköğretim Kanunu İle Bazı Kanun Ve Kanun Hükmünde Kararnamelerde Değişiklik Yapılması Hakkında Kanun” ile 18.06.2018 tarihli “Lisansüstü Tezlerin Elektronik Ortamda Toplanması, Düzenlenmesi ve Erişime Açılmasına İlişkin Yönerge” gereğince tam metin erişime açılmıştır.POZİTRON EMİSYON TOMOGRAFİDE GÖRÜNTÜOLUŞTURMA YÖNTEMLERİNİN İNCELENMESİ VEİYİLEŞTİRİLMESİHalil EROLÖZETAnahtar Kelimeler : Tomografi, Pozitron Emisyon Tomografisi(PET), GeriOluşturma, Filtrelenmiş Geri Oluşum, Cebirsel Geri OluşumBu doktora çalışmasında tomografik görüntüleme yöntemleri incelenmiştir. Buyöntemler iki bölüme ayrılır. Bunların birincisi Direk geri oluşturma yöntemleridir,ki bunlar Fourier dönüşüm yöntemleri, filtrelenmiş geri projeksiyon, geriprojeksiyondan sonra filtreleme olmak üzere üç ana başlık atında toplanmıştır. Buyöntemlerin teorik altyapısı detayları ile anlatılmıştır. Yine bu yöntemlerinayrık(sayısal) gerçeklenimi de anlatılmış, Matlab ortamında çeşitli fontomlar üzerineuygulaması gerçeklenmiştir.Bunlardan ikincisi ise ötelemeli geri oluşturma algoritmalarıdır. Bunlar cebirsel gerioluşum(ART), çarpımsal cebirsel geri oluşum(MART), eşlenik gradyan(CG),beklenti maksimizasyonu(EM), maksimum olabilirlik beklentimaksimizasyonu(MLEM) yöntemleridir. Bu çalışmada, Matlab ortamında buyöntemlerle ilgili algoritmalar geliştirilmiş ve değişik fontomlara uygulamasıyapılmıştır.Yine bu çalışmada direk ve ötelemeli yöntemlerle elde edilen görüntüler, görüntükalitesi ve geri oluşturma zamanları bakımından karşılaştırılmıştır. Ötelemeliyöntemlerin zorluklarından en önemlisi ise büyük sistem matrislerinin hesaplanmasıve kullanımından dolayı ortaya çıkan karmaşadır. Sistem matrisi genelde oldukçaseyrektir. Matlab 7'de yüz milyondan fazla elemanı olan matrislerle işlem yapılamazve kaydedilemezler. Cebirsel yöntemlerde çözünürlüğü artırabilmek için sistemmatrisinin bu değerlerden büyük olması kaçınılmazdır. Bu problemi çözümlemekiçin bu çalışmada, yeni bir matris depolama yöntemi geliştirilmiş, yöntem görüntülerüzerine uygulanmıştır. Yöntemin avantaj ve dezavantajları değerlendirilmiştir.iiIMAGE ENHANCEMENT AND INVESTİGATION OFRECONSTRUCTION METHODS IN POSİTRON EMISSIONTOMOGRAPHYHalil EROLSUMMARYKey words: Tomography, Positron Emission Tomography(PET), Backprojection,Filtered Backprojection, Algebraic Reconstruction.Tomographic imaging and reconstruction methods are investigated in this PhDthesis. Reconstruction is implemented by using two methods. The first one is directreconstruction method. This method has three sub-methods which are Fourier Slice,Filtered Back Projection, Filtering After Backprojection methods. Theoreticalbackground of these methods are explained in detail, also implementation of thesemethods in Matlab environment is obtained. These methods are applied to differentprimitive figures and some fontoms. The second one is Algebraic reconstructionmethod. This method consists of five sub-methods. These are ART, multiplicativeART, Expectation Maximization(EM), Conjugate Garadient(CG) and MaximumLikelihood Expectation Maximization methods. In this thesis algorithms for thesemethods are obtained in Matlab environment. By using these algorithms somefontoms are reconstructed.Reconstruction time and image quality by using Direct reconstruction methods andAlgebraic reconstruction methods are compared in this thesis. The great advantage ofiterative methods is that correction to attenuation and depth-dependent detectorresponse can be incorporated to the reconstruction process. One of the drawbacks ofthe iterative reconstruction methods is the huge computation, due to large systemmatrices. This system matrix is very sparse. In Matlab 7, matrices having elementsmore than 100 million can not be executed or stored due to its size restriction. Toovercome this problem we have implemented a new storage technique. By thistechnique, large system matrices can be manipulated in Matlab7. Advantages anddisadvantages of this method is discussed.i

Molecular recognition using nanotube-adsorbed polymer complexes

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013.Cataloged from PDF version of thesis. "December 2012."Includes bibliographical references (p. 234-249).We first reported the selective detection of single nitric oxide (NO) molecules using a specific DNA sequence of d(AT) 15 oligonucleotides, adsorbed to an array of near infrared fluorescent semiconducting single-walled carbon nanotubes (AT₁₅-SWCNT). While SWNT suspended with eight other variant DNA sequences show fluorescence quenching or enhancement from analytes such as dopamine, NADH, L-ascorbic acid, and riboflavin, d(AT)₁₅ imparts SWNT with a distinct selectivity toward NO. In contrast, the electrostatically neutral polyvinyl alcohol, enables no response to nitric oxide, but exhibits fluorescent enhancement to other molecules in the tested library. For AT₁₅ - SWCNT, a stepwise fluorescence decrease is observed when the nanotubes are exposed to NO, reporting the dynamics of single-molecule NO adsorption via SWCNT exciton quenching. We describe these quenching traces using a birth-and-death Markov model, and the maximum likelihood estimator of adsorption and desorption rates of NO is derived. Applying the method to simulated traces indicates that the resulting error in estimation is less than 5% under our experimental conditions, allowing for calibration using a series of NO concentrations. As expected, the adsorption rate is found to be linearly proportional to NO concentration, and the intrinsic single-SWCNT-site NO adsorption rate constant is 0.001 s-¹ [mu]M NO-¹. The ability to detect nitric oxide quantitatively at the single-molecule level may find applications in new cellular assays for the study of nitric oxide carcinogenesis and chemical signaling, as well as medical diagnostics for inflammation. Further, we also explored the concept of creating molecular recognition sites using polymer-SWCNT complexes. Molecular recognition is central to the design of therapeutics, chemical catalysis and sensor platforms, with the most common mechanisms involving biological structures such as antibodies[l] and aptamers[2, 3]. The key to this molecular recognition is a folded and constrained heteropolymer pinned, via intra-molecular forces, into a unique three-dimensional orientation that creates a binding pocket or interface to recognize a specific molecule. An alternate approach to constraining a polymer in three-dimensional space involves adsorbing it onto a cylindrical nanotube surface[4-7]. To date, however, the molecular recognition potential of these structured, nanotube-associated complexes has been unexplored. In this work, we demonstrate three distinct examples in which synthetic polymers create unique and highly selective molecular recognition sites once adsorbed onto a single-walled carbon nanotube (SWCNT) surface. The phenomenon is shown to be generic, with new recognition complexes demonstrated for riboflavin, L-thyroxine, and estradiol, predicted using a 2D thermodynamic model of surface interactions. The dissociation constants are continuously tunable by perturbing the chemical structure of the heteropolymer. The complexes can be used as new types of sensors based on modulation of SWCNT photoemission, as demonstrated using a complex for real time spatio-temporal detection of riboflavin in murine macrophages. Cardiac biomarkers troponin I and T are recognized as standard indicators for acute myocardial infarction (AMI, or heart attack), a condition that comprises 10% of U.S. emergency room visits [8]. There is significant interest in a rapid, point-of-cae (POC) device for troponin detection[9]. In this work we demonstrate a rapid, quantitative, and label-free assay specific for cardiac troponin T detection, using fluorescent single-walled carbon nanotubes (SWCNTs). Chitosan-wrapped carbon nanotubes are crosslinked to form a thin gel that is further functionalized with nitrilotriacetic acid (NTA) moieties. Upon chelation of Ni²+, the Ni²+ -NTA group binds to a hexa-histidine-modified troponin antibody, which specifically recognizes the target protein, troponin T. As the troponin T binds to the antibody, the local environment of the sensor changes, allowing for the detection through changes in SWCNT bandgap fluorescence intensity. In this work, we have developed the first near-infrared SWCNT sensor array for specific cTnT detection. Detection can be completed within 3 minutes, and the sensor responds linearly to the cTnT concentrations, with the experimental detection limit of 100 ng/ml (2.5 nM). This platform may provide a promising new tool for POC AMI detection in the future. Moreover, the work presented two useful methods of characterizing two commonly used functional groups, amines and carboxylic acids in soft gels, and this will be useful for other researchers studying hydrogel chemistry. In addition, we synthesized and characterized chitosan-gels both with and without NTA groups, and we compared fluorescence responses upon the addition of four different divalent cations, including Ni²+ , CO², Mg²+, and Mn²+. We proposed a model based Flory-Huggins theory, without any fitted parameters, that is able to describe the fluorescence increase as the Ni²+ concentration increases. The model suggests that the strong binding of Ni²+ onto NTA groups decreases the number of mobile ions in the gel, resulting in a reduction in the ionic chemical potential inside the gel. As a result, the gel de-swells, leading to a local SWCNT concentration increase and an increase in the SWCNT fluorescence signal.by Jingqing Zhang.Ph.D

New Foundation in the Sciences: Physics without sweeping infinities under the rug

It is widely known among the Frontiers of physics, that “sweeping under the rug” practice has been quite the norm rather than exception. In other words, the leading paradigms have strong tendency to be hailed as the only game in town. For example, renormalization group theory was hailed as cure in order to solve infinity problem in QED theory. For instance, a quote from Richard Feynman goes as follows: “What the three Nobel Prize winners did, in the words of Feynman, was to get rid of the infinities in the calculations. The infinities are still there, but now they can be skirted around . . . We have designed a method for sweeping them under the rug. [1] And Paul Dirac himself also wrote with similar tune: “Hence most physicists are very satisfied with the situation. They say: Quantum electrodynamics is a good theory, and we do not have to worry about it any more. I must say that I am very dissatisfied with the situation, because this so-called good theory does involve neglecting infinities which appear in its equations, neglecting them in an arbitrary way. This is just not sensible mathematics. Sensible mathematics involves neglecting a quantity when it turns out to be small—not neglecting it just because it is infinitely great and you do not want it!”[2] Similarly, dark matter and dark energy were elevated as plausible way to solve the crisis in prevalent Big Bang cosmology. That is why we choose a theme here: New Foundations in the Sciences, in order to emphasize the necessity to introduce a new set of approaches in the Sciences, be it Physics, Cosmology, Consciousness etc

SEMIFLUORINATED POLYMERS VIA CYCLOADDITION AND NUCLEOPHILIC ADDITION REACTIONS OF AROMATIC TRIFLUOROVINYLETHERS

This dissertation encompasses the synthesis, characterization, and properties of semifluorinated polymers derived from thermal polymerization of aryl trifluorovinyl ether (TFVE) monomers. This work is divided into two parts based on the methodology of thermal polymerization using aryl TFVE monomers. The first part of this work involves the thermal [2 + 2]cyclodimerization of aryl TFVE monomers affording perfluorocyclobutyl (PFCB) aryl ether polymers. Chapter 1 provides an overview of PFCB aryl ether polymers as a next-generation class of high performance fluoropolymers that have been successfully employed for a myriad of technologies. PFCB aryl ether polymers are highly desired because of their high thermal stability, processability, and tailorability for specific material applications. Chapter 2 introduces a general perspective of polyhedral oligomeric silsesquioxanes (POSS) that were modified with PFCB aryl ether polymer for property enhancement, specifically for low surface energy materials. Chapter 3 and 4 show the synthesis, characterization, and properties of POSS modified PFCB aryl ether polymers as blends and a variety of copolymer architectures, respectively. The second portion of this dissertation focuses on the development of a new, facile step-growth polymerization of diols/bisphenols and aryl TFVEs to afford fluoroethylene/vinylene alkyl/aryl ether (FAE) polymers. Chapter 5 is a prelude to the development of FAE polymers which entails optimizing the methodology and mechanistic rationale of nucleophile addition to aryl TFVEs. Chapter 6 details the FAE polymerization kinetics, physical properties, and strategy for functionalization. Chapter 7 illustrates the modular modification of FAE polymers for the development of tunable light emissive materials for potential use as transport layer material for organic light emitting diodes (OLEDs) and also chemical sensors. Chapter 8 introduces postfunctionaliztion of FAE polymers resulting with sulfonated biaryl segments for the development of proton exchange membranes (PEMs) for fuel cells. Chapter 9 involves the development of bis-ortho-diynylarene (BODA) monomers for the development of high yielding and moldable glassy-carbon microstructures. The adhesion, wettability, density, and coefficient of thermal expansion of BODA-derived glassy carbon are discussed

Predictive modelling of organic crystallization processes.

This thesis is concerned with the development of a predictive model for batch cooling suspension pharmaceutical crystallizations, with a focus on product performance. A major challenge involved in the design of industrial pilot plant pharmaceutical crystallizers, is to predict the influence of crystallizer geometry, scale and operating conditions on the process behaviour and crystal size distribution (CSD). The design of industrial crystallizers is hindered by the lack of scale-up rules due to the absence of reliable predictive process models. Currently no reliable predictive or 'dial up a particle size' tool exists for scale-up predictions. The research involves the development of a novel predictive compartmental modelling framework for the scale-up of an organic fine chemical. A new approach of using compartments is developed in order to facilitate scale-up design and process modelling by separating crystallization kinetic and hydrodynamic phenomena. Application of this technique involves determining key process engineering information on a laboratory scale, which is critical for technology transfer, and combining this data with hydrodynamic information on transfer to large scale for predictive scale-up purposes. The key process engineering information required for predictive modelling includes the determination of solubility characteristics, thermodynamic properties and crystallization kinetics of the organic fine chemical. Attenuated Total Reflectance Ultra-Violet (ATR-UV) spectroscopy is used as an 'in-situ' measurement technique to measure solute concentration. A modified continuous Mixed Suspension Mixed Product Removal (MSMPR) crystallizer is designed specifically for innovative drug candidates available in limited quantities to derive steady state crystallization kinetics with minimal influence from hydrodynamic phenomena. Batch attrition experiments were carried out to determine the effects of specific power input on the CSD using Lasentec Focussed Beam Reflectance Monitoring (FBRM) to monitor the process on-line and to develop an attrition rate model. Computational Fluid Dynamics (CFD) is a simulation tool that is also introduced to provide valuable insight into mixing, heat transfer and hydrodynamic phenomena within agitated batch cooling suspension crystallization vessels including investigating the effects of scale-up. CFD is used to aid the development of the compartmental modelling framework. The design of the compartmental structure is based on high spatial resolution CFD simulations of internal flow, mixing and heat transfer within crystallizers upon scale-up. The great advantage of using a compartmental modelling framework is that the spatial resolution is reduced and the full population balance with kinetic models can be implemented. The detailed compartmental framework is based on the overall flow pattern, local energy dissipation rate, solids concentration and temperature distribution obtained from CFD. The number, location, cross-sectional area and volume of compartments are determined from CFD results based on the physical crystallizer dimensions. The compartments are selected such that they have approximately uniform temperature, local energy dissipation and solids concentration. Each dynamic compartment has a mass, concentration, enthalpy and population balance combined with MSMPR crystallization kinetic models. The compartments are therefore well mixed and physically connected via interconnecting flows determined from CFD. A general process modelling tool, gPROMS (Process Systems Enterprises) that supports both steady state and dynamics simulations is used to solve sets of ordinary differential and algebraic equations in each compartment. A single compartmental modelling approach is used initially as a first approach without taking into account local variations in process conditions. Predictions on a laboratory scale for an MSMPR and batch cooling crystallizer were satisfactory but upon scale-up the effects of mixing and hydrodynamics is not taken into account and therefore the predictions become less reliable. A compartmentalization approach can be introduced into gPROMS whereby the compartments are modelled as individual units with input and output streams using CFD hydrodynamic information

The biomechanics of human locomotion

Includes bibliographical references. The thesis on CD-ROM includes Animate, GaitBib, GaitBook and GaitLab, four quick time movies which focus on the functional understanding of human gait. The CD-ROM is available at the Health Sciences Library