This dissertation presents a discussion of blocky and randomly functionalized sulfonated syndiotactic polystyrene copolymers. These copolymers have been prepared over a range of functionalization (from 2% to 10%) in order to assess the effect of the incorporation of these polar side groups on both the thermal behavior and morphology of these polymer systems. The two different architectures are achieved by conducting the reaction in both the heterogeneous gel-state to obtain blocky copolymers and in the homogeneous solution state to obtain randomly functionalized copolymers. In order to compare both the thermal properties and morphology of these two systems several sets of samples were prepared at comparable levels of sulfonation. Thermal analysis of these two systems proved that the blocky functionalized copolymers provided superior properties with regard to the speed and total amount of the crystalline component of sulfonated syndiotactic polystyrene. Above 3% functionalizion the randomly functionalized copolymer was no longer able to crystallize, whereas, the blocky functionalized copolymer is able to crystallize even at a functionalization level of 10.5% sulfonate groups. When considering the morphology of these systems even at low percentages of sulfonation it is clear that the distribution of these groups is different based on the amplitude of the signal measured by small angle x-ray scattering. Additionally, methods were developed to describe both the distribution of ionic multiplets, which varies between blocky and randomly functionalized systems, but also the distribution of crystals. At a larger scale ultra-small angle x-ray scattering was employed to attempt to understand the clustering of ionic multiplets in these systems. Randomly functionalized polymers should a peak that is attributed to ion clusters, whereas blocky polymers show no such peak. Additional studies have also been done to look at the analysis of crystallite sizes in these systems when there are multiplet polymorphs present, it was observed the polymorphic composition is drastically different. All of these studies support that these systems bear vastly different thermal behavior and possess significantly different morphologies. This supports the hypothesis that this gel-state heterogeneous functionalization procedure produces a much different chain architecture compared to homogeneous functionalization in the solution-state. / Doctor of Philosophy / Polymers are a class of chemicals that are defined by having a very large set of molecules that are chemically linked together where each unit (monomer) is repeated within the chemical structure. In particular, this dissertation focuses on the construction what are termed as "blocky" copolymers, which are defined by having two chemically different monomers that are incorporated in the polymer chain. The "blocky" characteristic of these polymers means that these two different monomers are physically segregated from each other on the polymer chain, where long portions of the chain that are of one type, followed by another section of the polymer that has the other type of monomer. The goal of creating this type of structure is to try to take advantage of the properties of both types of monomers, which can create materials with superior synergistic properties. In this case a hydrophobic (water hating) monomer is combined with a hydrophilic (water loving) chain. This hydrophobic component in the polymer is able to crystallize, which provides mechanical and thermal stability in the material by acting as a physical tether to hold neighboring chains together. With the other set of hydrophilic monomers, which in this case have an ionic component incorporated, we can now take advantage of this chemical components ability to aide in the transportation of ions. Transportation of ions is useful in a variety of commercially relevant applications, two of the most important applications of these ionic materials is in membranes that can be used to purify water or membrane materials in fuel cell technologies, specifically for proton exchange membranes. The focus of this research in particular was to create a simple synthesis technique that can create these blocky polymer chain architectures, which is done by performing the reaction while the polymer is made into a gel. The key to this is that the crystals within the gel act as a barrier to chemical reactions, creating conditions where we have substantial portions of the material that are able to be functionalized and the crystals within the material that are protected from being functionalized. By looking at the thermal characteristics, such as melting temperatures and amount of crystals within these systems we have seen that functionalizing these polymers in the heterogeneous gel state gives substantially better properties than functionalizing these materials randomly. Much like oil and water, incompatible polymer chains will phase separate from each other. In this case the hydrophobic and ionic components will phase separate from each other. The shape and distribution of these phase separated structure will dictate many of the material properties, which can be described by modeling the data collected from x-ray scattering experiments. All of this information will tell us based on the initial conditions that these polymers were created in, what properties should be expected based on the morphology and thermal behavior. This gives a better understanding of how to fine tune these properties based on the structure of the gel and chemical reaction conditions.

Self-assembly of nanoparticles is a promising route to form complex, nanostructured materials with functional properties. Nanoparticle assemblies characterized by a crystallographic alignment of the nanoparticles on the atomic scale, i.e. mesocrystals, are commonly found in nature with outstanding functional and mechanical properties. This thesis aims to investigate and understand the formation mechanisms of mesocrystals formed by self-assembling iron oxide nanocubes. We have used the thermal decomposition method to synthesize monodisperse, oleate-capped iron oxide nanocubes with average edge lengths between 7 nm and 12 nm and studied the evaporation-induced self-assembly in dilute toluene-based nanocube dispersions. The influence of packing constraints on the alignment of the nanocubes in nanofluidic containers has been investigated with small and wide angle X-ray scattering (SAXS and WAXS, respectively). We found that the nanocubes preferentially orient one of their {100} faces with the confining channel wall and display mesocrystalline alignment irrespective of the channel widths.  We manipulated the solvent evaporation rate of drop-cast dispersions on fluorosilane-functionalized silica substrates in a custom-designed cell. The growth stages of the assembly process were investigated using light microscopy and quartz crystal microbalance with dissipation monitoring (QCM-D). We found that particle transport phenomena, e.g. the coffee ring effect and Marangoni flow, result in complex-shaped arrays near the three-phase contact line of a drying colloidal drop when the nitrogen flow rate is high. Diffusion-driven nanoparticle assembly into large mesocrystals with a well-defined morphology dominates at much lower nitrogen flow rates. Analysis of the time-resolved video microscopy data was used to quantify the mesocrystal growth and establish a particle diffusion-based, three-dimensional growth model. The dissipation obtained from the QCM-D signal reached its maximum value when the microscopy-observed lateral growth of the mesocrystals ceased, which we address to the fluid-like behavior of the mesocrystals and their weak binding to the substrate. Analysis of electron microscopy images and diffraction patterns showed that the formed arrays display significant nanoparticle ordering, regardless of the distinctive formation process.  We followed the two-stage formation mechanism of mesocrystals in levitating colloidal drops with real-time SAXS. Modelling of the SAXS data with the square-well potential together with calculations of van der Waals interactions suggests that the nanocubes initially form disordered clusters, which quickly transform into an ordered phase. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Manuscript. Paper 5: Manuscript.</p>

京都大学 / 0048 / 新制・課程博士 / 博士(薬科学) / 甲第22397号 / 薬科博第119号 / 新制||薬科||13(附属図書館) / 京都大学大学院薬学研究科薬科学専攻 / (主査)教授 髙倉 喜信, 教授 山下 富義, 教授 小野 正博 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

As hidrolases de glicosídeos (GHs) exercem papéis fundamentais em vários processos biomédicos e aplicações industriais. A maioria destas enzimas possui vários domínios funcionais ligados entre si por peptídeos conhecidos como linkers. Informações sobre organização estrutural destas enzimas e sua mobilidade, posições e orientações mútuas de domínios individuais, bem como mudanças conformacionais introduzidas por ligantes ou por mudanças de condições bioquímicas (pH e T) podem ser muito informativas. Por esse motivo, é muito importante determinar a organização estrutural de GHs em termos de posição e orientação de seus domínios individuais e compreender a interação entre estes domínios em condições próximas às fisiológicas. Entretanto, atualmente, a conformação, dinâmica e função dos GHs com múltiplos domínios ainda não são totalmente compreendidas. Assim, o principal objetivo deste projeto foi conduzir estudos de hidrolases de glicosídeos em solução, usando SAS. Um grande número de GHs foi clonado e expresso em laboratório sob a direção do Prof. Dr. Igor Polikarpov (Grupo de Biotecnologia Molecular, IFSC / USP), seguindo protocolos já estabelecidos na literatura, para sua expressão e purificação. Experimentos SAXS foram realizados em colaboração com o Dr. Evandro Ares de Araújo (USP, São Carlos) e com o Prof. Dr. Mário de Oliveira Neto (UNESP, Botucatu). Para estudar as hidrolases de glicosídeos, foi utilizado o método de espalhamento a baixo ângulo, e em adição ao trabalho experimental, foi desenvolvido um novo pacote de software SAXSMoW2 para processar os dados do SAXS. Este pacote permite obter rapidamente os principais parâmetros estruturais de moléculas de proteínas, calcular o peso molecular e o estado oligomérico. Também foi aperfeiçoado e aplicado o método de acoplamento estatístico (statistical coupling analysis) , para complementar os dados estruturais experimentais, em especial para xiloses isomerases. Este método pode permitir uma melhor compreensão da relação entre as características estruturais evolutivas e sua funcionalidade biológica. Além disso, métodos de bioinformática foram desenvolvidos para complementar e compreender melhor as informações estruturais obtidas nos experimentos de SAXS. O primeiro foi um método para separar sequências de GH7 em duas categorias, exo e endogluconases. É útil analisar cada tipo de proteína dentro da família separadamente e estudar o papel dos loops funcionais - características estruturais que influenciam significativamente a atividade biológica. Outro método foi desenvolvido para encontrar o centro de atividade na nova enzima Xilose Isomerase obtida, usando uma estrutura relacionada, bem conhecida, da mesma família. Este método foi aplicado a enzimas cujas estruturas foram estudadas pela técnica de cristalografia em nosso laboratório no IFSC / USP. Inspirado pelo SCA, um método de detecção de comunidades difusas de aminoácidos em proteínas foi desenvolvido. Essa informação também pode complementar os resultados do SCA, indicando conjuntos fortemente correlacionados de aminoácidos na enzima. Outro novo método desenvolvido é uma estimativa de afinidade nas famílias de enzimas ativas em carboidratos utilizando similaridade dos modelos escondidos de Markov e bancos de dados open access de sequências de proteínas. / The Glycoside Hydrolases (GHs) play a key role in a number of biomedical processes and industrial applications. Most of these enzymes are multidomain proteins composed of different functional domains connected by linker peptides. Thus, it is very important to determine structural organization of glycoside hydrolases in terms of positions and orientations of their individual domains and comprehend the interplay between their multiple domains under close-to physiological conditions. To study the glycoside hydrolases, in this work a small-angle scattering method has been used. Currently, the conformation, dynamics and function of GHs with multiple domains are not fully understood. This is why the information on their structural organization and mobility; mutual position and orientation of the individual domains and conformational changes induced by interaction with the substrates or difference in biochemical conditions might be very informative. A large number of GHs have been cloned and expressed in the lab under direction of Prof. Dr. Igor Polikarpov (Molecular Biotechnology group, IFSC/USP) and we follow already established protocols for their expression and purification. SAXS experiments have been carried out in collaboration with Dr. Evandro Ares de Araujo (USP, São Carlos) and Prof. Dr. Mario de Oliveira Neto (UNESP, Botucatu). Additionally to experimental work, a new software package SAXSMoW2 for SAXS data processing has been developed. The software allows to obtain rapidly main structural parameters of the protein molecule, calculate molecular weight and oligomeric state. To supplement an structural data, the method of statistical coupling analysis (SCA) has been significantly improved and applied. The method allows a better understanding of interconnection between evolutionary caused structural features and their biological functionality. Also, various bioinformatic methods were developed to complete and understand better structural information obtained in SAXS experiments. The first one is a method for separating sequences from GH7 into the two bins of exo- and endogluconases. It is helpful to analyze each type of proteins inside the family separately and study the role of functional loops -- structural features that significantly influence on biological activity. Other developed method is for finding of activity center in the new obtained Xylose Isomerase enzyme using related well-known structure from the same family. This method was applied to the enzyme whose structure was studied using crystallography technique in our laboratory at IFSC/USP. Inspired by SCA, a method of aminoacid fuzzy communities detection in proteins has been developed as well. This information also can complete SCA results showing strong correlated sets of aminoacids in the enzyme. Another one new developed method is an estimation of carbohydrate-active family affiliation of unknown proteins using Markov hidden model similarities and open access databanks of protein sequences.

No description available.

Esta tese apresenta uma abordagem para a criação rápida de modelos em diferentes geometrias (complexas ou de alta simetria) com objetivo de calcular a correspondente intensidade espalhada, podendo esta ser utilizada na descrição de experimentos de es- palhamento à baixos ângulos. A modelagem pode ser realizada com mais de 100 geome- trias catalogadas em um Banco de Dados, além da possibilidade de construir estruturas a partir de posições aleatórias distribuídas na superfície de uma esfera. Em todos os casos os modelos são gerados por meio do método de elementos finitos compondo uma única geometria, ou ainda, compondo diferentes geometrias, combinadas entre si a partir de um número baixo de parâmetros. Para realizar essa tarefa foi desenvolvido um programa em Fortran, chamado de Polygen, que permite modelar geometrias convexas em diferentes formas, como sólidos, cascas, ou ainda com esferas ou estruturas do tipo DNA nas arestas, além de usar esses modelos para simular a curva de intensidade espalhada para sistemas orientados e aleatoriamente orientados. A curva de intensidade de espalhamento é calculada por meio da equação de Debye e os parâmetros que compõe cada um dos modelos, podem ser otimizados pelo ajuste contra dados experimentais, por meio de métodos de minimização baseados em simulated annealing, Levenberg-Marquardt e algorítmicos genéticos. A minimização permite ajustar os parâmetros do modelo (ou composição de modelos) como tamanho, densidade eletrônica, raio das subunidades, entre outros, contribuindo para fornecer uma nova ferramenta para modelagem e análise de dados de espalhamento. Em outra etapa desta tese, é apresentado o design de modelos atomísticos e a sua respectiva simulação por Dinâmica Molecular. A geometria de dois sistemas auto-organizado de DNA na forma de octaedro truncado, um com linkers de 7 Adeninas e outro com linkers de ATATATA, foram escolhidas para realizar a modelagem atomística e a simulação por Dinâmica Molecular. Para este sistema são apresentados os resultados de Root Mean Square Deviations (RMSD), Root Mean Square Fluctuations (RMSF), raio de giro, torção das hélices duplas de DNA além da avaliação das ligações de Hidrogênio, todos obtidos por meio da análise de uma trajetória de 50 ns. / This thesis presents an approach to the fast creation of models in different geometries (complex or high symmetry) in order to calculate the scattering intensity, which can be used for the description of small angles scattering experiments. The modeling can be performed using more than 100 geometries cataloged in a database, besides the possibility to build structures from random positions distributed on the surface of a sphere. In all cases the models are generated using the finite element method composing a single geometry, or composing different geometries combined with each other, using a small number of parameters. To accomplish this task it was developed a program called Polygen, written in Fortran language, which allows the modeling of convex polyhedrons in different geometries, as solids, shells, with aligned beads or DNA-like structures at the edges. To simulate the scattering intensity curve, these models are used and is possible simulate oriented and randomly oriented systems. The scattering intensity curve is calculated using the Debye equation and the main parameters describing the models, can be optimized by the fitting of the calculated curves against experimental data. The optimization is performed by the use minimization methods based on simulated annealing, Levenberg-Marquardt and genetic algorithmic. The minimization procedures allows the optimization of themodel parameters (or models of composition) as size, electron density, gyration radius, among others, contributing to provide a new tool for modeling and scattering data analysis. In a further step of this thesis, the design of atomistic models is presented and therespective simulation by Molecular Dynamics. Two geometries for DNA self-assembly

The effect of shear on the evolution of floc properties was investigated to analyse the flocculation mechanisms. Little fundamental attention has been given to the shear influence that often creates compact aggregates, while the floc characteristics might differ in other aggregating conditions. It is thus crucial to understand how flocs evolve to steady state, if their properties are to be 'tailored' to suit subsequent solids-liquid separation processes. In this work, flocculation of monodisperse latex particles of various sizes (60, 380, and 810 nm diameter) via electrolyte addition was carried out in a couette-flow and also in shear fields generated by an axial-flow impeller (Fluid foil A310) and a radial-flow impeller (Rushton R100) in standard mixing tanks. A small-angle light scattering technique was used to acquire information regarding the time variation of floc properties in a non-intrusive manner. The structure was quantified by a measure of fractal dimension, signifying the degree of floc compactness. Estimates of the average floc mass were also obtained from the aggregate scattering patterns. By monitoring the changes in floc structure and mass, corresponding to the size evolution; mechanisms of floc formation, fragmentation, and restructuring were identified. Aggregates of 60 and 380 nm particles were observed to grew larger initially, before decreasing to their equilibrium sizes at moderate shear rates (32 - 100 s-1) in a homogeneous shear environment. Floc restructuring at large length scales occurred extensively, and was responsible for the drop in size, particularly at the early stage of the process. Aggregates of 810 nm particles did not, however, display this behaviour. Flocs of larger primary particles were presumably susceptible to breakage rather than deformation, as they were weaker under comparable conditions. Denser aggregates were found when restructuring transpired, while comparatively tenuous flocs were observed when formation and breakage kinetics were the governing mechanisms. The disparity in floc behaviour at higher shear rates (246 s-1 - 330 s-1) was less apparent. The intense hydrodynamic stresses in those instances inevitably caused fragmentation, regardless of the intrinsic particle properties; hence the observed floc compaction was the product of break-up and re-aggregation. A population balance model, incorporating variation in floc structure, displayed comparable trends in size evolution; verifying that restructuring indeed took an important role under certain flocculation conditions. Similar phenomena were likewise observed with the flocculation in stirred tanks. The results reinforced findings in literature; that while circulation time controlled the process kinetics; the floc size was determined by the turbulent stresses. In addition, the maximum shear levels also influenced the floc structures, with denser aggregates produced in a shear field generated using the radial-flow impeller at equivalent energy dissipation per-unit mass. A correlation between non-dimensional floc factor that embodied the aggregate size and structure, and aggregation factor comprising the significant parameters from flocculation conditions, was proposed. The proposed relationship takes into account aspects such as the aggregate structure, interparticle forces, and particle concentration that are often overlooked in existing relationships, which usually only relate the maximum floc size to the applied energy dissipation rate. It thus provides an improved manner of presenting general flocculation data, as well as a means to predict floc properties produced under a specific aggregation condition. Future studies with increasingly complex systems that resemble real conditions are recommended in order to establish a practical understanding of the flocculation mechanisms, for the purpose of optimising the aggregate properties.

This dissertation describes a structural investigation of hyaluronan (HA) with neutron scattering techniques. HA is a natural biopolymer and one of the major components of the extracellular matrix, synovial fluid, and vitreous humor.  It is used in several biomedical applications like tissue engineering, drug delivery, and treatment of osteoarthritis. Although HA is extensively studied, very little is known about its three-dimensional conformation and how it interacts with ions and other molecules. The study aims to understand the bulk structure of a cross-linked HA hydrogel, as well as the conformational arrangement of HA at solid-liquid interfaces. In addition, the structural changes of HA are investigated by simulation of physiological environments, such as changes in ions, interactions with nanoparticles, and proteins etc. Small-angle neutron scattering and neutron reflectivity are the two main techniques applied to investigate the nanostructure of hyaluronan in its original, hydrated state. The present study on hydrogels shows that they possess inhomogeneous structures best described with two correlation lengths, one of the order of a few nanometers and the other in the order of few hundred nanometers. These gels are made up of dense polymer-rich clusters linked to each other. The polymer concentration and mixing governs the connectivity between these clusters, which in turn determines the viscoelastic properties of the gels. Surface-tethered HA at a solid-liquid interface is best described with a smooth varying density profile. The shape of this profile depends on the immobilization chemistry, the deposition protocol, and the ionic interactions. HA could be suitably modified to enhance adherence to metal surfaces, as well as incorporation of proteins like growth factors with tunable release properties. This could be exploited for surface coating of implants with bioactive molecules. The knowledge gained from this work would significantly help to develop future biomaterials and surface coatings of implants and biomedical devices.

Nickel-base superalloys obtain high temperature mechanical properties through formation of precipitate phases formed via heat treatment. The precipitate microstructure evolves with heat treatment or thermal exposure, which can lead to degrading mechanical properties. This project focuses on the use of electrical resistivity as a non-destructive testing method to monitor the precipitate phase in Waspaloy (a polycrystalline nickel-base superalloy). The evolution of the precipitate microstructure is characterized throughout the volume of the specimens using both small angle neutron scattering (SANS) and ultra small angle X-ray scattering (USAXS) measurements. These measurements are also aided by microscopy and X-ray diffraction measurements.

The present thesis concerns with a few investigations on sensing/measurement of small angle rotation/tilt using Pattern Imaging Method. The methodology involves looking at the tailored-objects located adjacent to the observer (CCD camera) through a mirror and extracts the angular position of the mirror from their images by processing the latter through object specific algorithm. Its principal advantage stems from the fact that small-angle measurement can be done using ambient light which is neither collimated nor filtered for single wavelength. This makes the associated optical configuration not only simple but also robust for the said application, in comparison to currently competing technologies based on Autocollimation and Interferometry. The present thesis elaborates specifically four new Pattern-Designs proposed for tailoring the spatial-brightness of the objects. Introducing for the first time, processing algorithms based on ‘Modified Fringe-Processing Strategy’ and ‘Phase-Only-Correlation’, the investigations demonstrate enhanced performance for small angle measurement with all the proposed pattern designs. The first three designs for the pattern are evaluated for 1-D measurement through fringe processing approach while the fourth pattern design is evaluated for 2-D measurement through Phase-only-Correlation. The results of the investigations are utilized to propose, design and develop a novel optical inclinometer which can work with any of the proposed pattern designs as the object. The first three pattern-designs rely upon sinusoidal modulation of the object surface and utilize three custom developed algorithms -Algorithm-A, Algorithm-B and Algorithm-C -to extract two quantities namely wrapped phase Δαw and unwrapped phase Δαuw , from the captured images. Each of these quantities will have an associated measurement range and accuracy corresponding to any of the three pattern designs. All measurements are carried out keeping the object/camera to mirror distance constant at 250 mm. From wrapped phase measurement, all the three designs, each with pitch of 2mm for sinusoidal modulation and held at a distance of 250 mm from the mirror, have been found to facilitate reliable angle measurement over a range of 850 arc seconds with accuracy better than 1 arc second after curve fitting the experimentally obtained data. From unwrapped phase measurement, the color coded as well as BCD coded composite patterns, when tested using five bands of sinusoidal modulation (with a pitch of 2mm) and held at a distance of 250 mm from the mirror, facilitated reliable angle measurement over a larger range of nearly 10 . The 2-D angle measurement using fourth pattern-design and the Algorithm-D, facilitated measurement over a range of 10 with an accuracy of 9 arc seconds when the distance between the mirror and the pattern is held at 250 mm. A comparison of the results from the present investigation with the best performance from other investigators reveals the following. The proposed modifications in the processing algorithms as well as the pattern designs help to achieve a measurement range of 750 arc seconds with accuracy better than 1 arc second from this method, with an object pattern whose lateral size is smaller by a factor of nearly 15. Such a size reduction in the object as well as the associated mirror would help to construct angle measuring instruments that work on this method more compactly. The results of the investigation have been utilized to propose and demonstrate a novel prototype optical inclinometer which has been experimentally found to work in a range of 0.40 with accuracy nearly 6 arc seconds.