Full and Model-Reduced Structure-Preserving Simulation of Incompressible Fluids

This thesis outlines the construction of several types of structured integrators for incompressible fluids. We first present a vorticity integrator, which is the Hamiltonian counterpart of the existing Lagrangian-based fluid integrator. We next present a model-reduced variational Eulerian integrator for incompressible fluids, which combines the efficiency gains of dimension reduction, the qualitative robustness to coarse spatial and temporal resolutions of geometric integrators, and the simplicity of homogenized boundary conditions on regular grids to deal with arbitrarily-shaped domains with sub-grid accuracy.

Both these numerical methods involve approximating the Lie group of volume-preserving diffeomorphisms by a finite-dimensional Lie-group and then restricting the resulting variational principle by means of a non-holonomic constraint. Advantages and limitations of this discretization method will be outlined. It will be seen that these derivation techniques are unable to yield symplectic integrators, but that energy conservation is easily obtained, as is a discretized version of Kelvin's circulation theorem.

Finally, we outline the basis of a spectral discrete exterior calculus, which may be a useful element in producing structured numerical methods for fluids in the future.

Biochemical and Biophysical Characterization of Huntingtin

Huntington’s disease (HD) is a fatal autosomal dominant neurodegenerative disease. HD has no cure, and patients pass away 10-20 years after the onset of symptoms. The causal mutation for HD is a trinucleotide repeat expansion in exon 1 of the huntingtin gene that leads to a polyglutamine (polyQ) repeat expansion in the N-terminal region of the huntingtin protein. Interestingly, there is a threshold of 37 polyQ repeats under which little or no disease exists; and above which, patients invariably show symptoms of HD. The huntingtin protein is a 350 kDa protein with unclear function. As the polyQ stretch expands, its propensity to aggregate increases with polyQ length. Models for polyQ toxicity include formation of aggregates that recruit and sequester essential cellular proteins, or altered function producing improper interactions between mutant huntingtin and other proteins. In both models, soluble expanded polyQ may be an intermediate state that can be targeted by potential therapeutics.

In the first study described herein, the conformation of soluble, expanded polyQ was determined to be linear and extended using equilibrium gel filtration and small-angle X-ray scattering. While attempts to purify and crystallize domains of the huntingtin protein were unsuccessful, the aggregation of huntingtin exon 1 was investigated using other biochemical techniques including dynamic light scattering, turbidity analysis, Congo red staining, and thioflavin T fluorescence. Chapter 4 describes crystallization experiments sent to the International Space Station and determination of the X-ray crystal structure of the anti-polyQ Fab MW1. In the final study, multimeric fibronectin type III (FN3) domain proteins were engineered to bind with high avidity to expanded polyQ tracts in mutant huntingtin exon 1. Surface plasmon resonance was used to observe binding of monomeric and multimeric FN3 proteins with huntingtin.

Studies on rabbit reticulocyte ribosomes and polyribosomes and their relation to hemoglobin synthesis

This dissertation is divided into three parts.

The first section is concerned with protein synthesis in cellfree systems from reticulocytes. The sub-cellular reticulocyte fractions, reagents, etc. have been examined for the presence of traces of ribonuclease, using. an assay based upon the loss of infectivity of RNA fran bacteriophage MS2. This assay is sensitive to 5 x 10^-7 γ RNase/ml. In addition, the loss of synthetic capacity of an 80S ribosome on dissociation has been studied, and can be attributed to loss of messenger RNA when the monomer is separated into subunits. The presence of ribonuclease has been shown to be a major cause of polyribosome disintegration during cell-free protein synthesis.

The second section concerns the changes in ribosomes and polyribosomes which occur during the maturation of a reticulocyte into an erythrocyte. With increasing age, the cells lose a large proportion of the ribonucleoprotein, but the percentage of ribosomes present as polyribosomes is only slightly altered. The loss of hemoglobin synthesis on maturation is probably due to both the loss of total ribosomes and to the lessened specific activity of the polyribosomes.

The third section contains analytical ultracentrifugation data on 80S ribosomes, polyribosomes, and ribosomal RNA from reticulocytes. The 60s and 40s subunits, obtained by dissociation of the 80s particle with inorganic pyrophosphate, were also studied. The RNA from reticulocyte ribosomes has been examined under a variety of denaturing conditions, including dimethyl sulfoxide treatment, formaldehyde reaction and thermal denaturation. From these studies we can conclude that the 28S and 16S RNA's are single polynucleotide chains and are not made up of smaller RNA subunits hydrogen-bonded together.

I. Proton magnetic resonance of polynucleotides and transfer RNA. II. Electron spin relaxation studies of manganese (II) complexes in acetonitrile

Part I. Proton Magnetic Resonance of Polynucleotides and Transfer RNA.

Proton magnetic resonance was used to follow the temperature dependent intramolecular stacking of the bases in the polynucleotides of adenine and cytosine. Analysis of the results on the basis of a two state stacked-unstacked model yielded values of -4.5 kcal/mole and -9.5 kcal/mole for the enthalpies of stacking in polyadenylic and polycytidylic acid, respectively.

The interaction of purine with these molecules was also studied by pmr. Analysis of these results and the comparison of the thermal unstacking of polynucleotides and short chain nucleotides indicates that the bases contained in stacks within the long chain poly nucleotides are, on the average, closer together than the bases contained in stacks in the short chain nucleotides.

Temperature and purine studies were also carried out with an aqueous solution of formylmethionine transfer ribonucleic acid. Comparison of these results with the results of similar experiments with the homopolynucleotides of adenine, cytosine and uracil indicate that the purine is probably intercalating into loop regions of the molecule.

The solvent denaturation of phenylalanine transfer ribonucleic acid was followed by pmr. In a solvent mixture containing 83 volume per cent dimethylsulf oxide and 17 per cent deuterium oxide, the tRNA molecule is rendered quite flexible. It is possible to resolve resonances of protons on the common bases and on certain modified bases.

Part II. Electron Spin Relaxation Studies of Manganese (II) Complexes in Acetonitrile.

The electron paramagnetic resonance spectra of three Mn⁺² complexes, [Mn(CH₃CN)₆]⁺², [MnCl₄]^-2, and [MnBr₄]^-2, in acetonitrile were studied in detail. The objective of this study was to relate changes in the effective spin Hamiltonian parameters and the resonance line widths to the structure of these molecular complexes as well as to dynamical processes in solution.

Of the three systems studied, the results obtained from the [Mn(CH₃CN)₆]⁺² system were the most straight-forward to interpret. Resonance broadening attributable to manganese spin-spin dipolar interactions was observed as the manganese concentration was increased.

In the [MnCl₄]^-2 system, solvent fluctuations and dynamical ion-pairing appear to be significant in determining electron spin relaxation.

In the [MnBr₄]^-2 system, solvent fluctuations, ion-pairing, and Br- ligand exchange provide the principal means of electron spin relaxation. It was also found that the spin relaxation in this system is dependent upon the field strength and is directly related to the manganese concentration. A relaxation theory based on a two state collisional model was developed to account for the observed behavior.

Efeito da superalimentação neonatal sobre a função adrenal e o desenvolvimento da microesteatose hepática em ratos adultos

O estado nutricional e hormonal em fases iniciais de desenvolvimento (gestação e lactação) está relacionado a alterações epigenéticas, que podem levar ao desenvolvimento de doenças. A obesidade infantil está relacionada com a ocorrência da obesidade na idade adulta, resistência à insulina e maior risco cardiometabólico. Em estudos experimentais, a superalimentação neonatal causa obesidade e aumenta o risco de doenças cardiovasculares. Estes animais apresentam obesidade visceral, hiperfagia, hiperleptinemia e hipertensão na idade adulta. Previamente, demonstramos que a hiperleptinemia neonatal causa hiperfunção da medula adrenal e microesteatose na idade adulta. No presente estudo avaliamos a função adrenal de ratos adultos obesos no modelo de superalimentação neonatal por redução do tamanho da ninhada e a sensibilidade as catecolaminas no tecido adiposo visceral (TAV) e no fígado. Ao nascimento todas as ninhadas tiveram seu número de filhotes ajustados para 10. Para induzir a superalimentação neonatal, o tamanho da ninhada foi reduzido de dez para três filhotes machos no terceiro dia de lactação até o desmame (SA), enquanto que o grupo controle permaneceu com 10 filhotes durante toda a lactação. Após o desmame, os ratos tiveram livre acesso à dieta padrão e água até 180 dias (1 animal de cada ninhada, n = 7). O TAV e as glândulas adrenais foram pesadas. As contrações hormonais séricas, o conteúdo hepático de glicogênio e triglicerídeos foram avaliados por kits comerciais. O conteúdo e a secreção de catecolaminas adrenais foram avaliados utilizando o método do trihidroxindol. O conteúdo dos hormônios eixo hipotálamo-hipófise-córtex adrenal, das enzimas da via de síntese das catecolaminas na glândula adrenal, ADRB2 no fígado e ADRB3 no TAV foram determinados por Western blotting ou imunohistoquímica. As diferenças foram consideradas significativas quando p <0,05. Aos 180 dias de vida, o grupo SA apresentou maior massa corporal (+15%), maior consumo alimentar (+15%) e maior adiposidade visceral (+79%). Os hormônios do eixo hipotálamo-hipófise-córtex-adrenal não foram alterados. O grupo SA apresentou maior expressão de tirosina hidroxilase e de DOPA descarboxilase (+31% e 90%, respectivamente); conteúdo de catecolaminas adrenais (absoluta: 35% e relativa: 40%), e secreção de catecolaminas, tanto basal quanto estimulada por cafeína (+35% e 43%, respectivamente). O conteúdo ADRB3 no TAV não foi alterado nos grupo SA, entretanto o ADRB2 no fígado apresentou-se menor (-45%). O grupo SA apresentou maior conteúdo de glicogênio e triglicerídeos no fígado (+79% e +49%, respectivamente), além de microesteatose. A superalimentação neonatal resulta em hiperativação adrenomedular e aparentemente está associada a preservação da sensibilidade às catecolaminas no VAT. Adicionalmente sugerimos que o maior conteúdo de glicogênio e triglicerídeos hepático seja devido a menor sensibilidade as catecolaminas. Tal perfil pode contribuir para a disfunção metabólica hepática e hipertensão arterial que são características deste modelo de obesidade programada.

Preparação e caracterização de microesferas poliméricas à base de poli(ácido metacrílico-co-divinilbenzeno) obtidas por polimerização por precipitação

Neste trabalho foi feito um estudo sobre a preparação e caracterização de microesferas poliméricas à base de poli(ácido metacrílico-co-divinilbenzeno) por polimerização por precipitação. As partículas foram sintetizadas e analisadas em diferentes condições de reação. Partículas esféricas políméricas foram sintetizadas na faixa de 1,66 - 8,41 m, assim como partículas no estado de microgel. As partículas foram caracterizadas pelas técnicas de espalhamento de luz dinâmica (DLS), análise termogravimétrica (TGA), espectroscopia na região do infravermelho (FTIR), adsorção de nitrogênio pelos métodos BET (Brunauer, Emmett e Teller) e BJH (Barret, Joyner e Halenda), microscopia ótica, microscopia eletrônica de varredura, e testes de razão de inchamento. A análise das partículas foi feita para verificar a influência da mudança na composição de comonômeros, grau de reticulação, relação de monômeros totais/diluentes em massa/volume (g/100 mL), e quanto à relação volumétrica de diluentes. Verificou-se que houve um aumento no tamanho das partículas e da resistência térmica com a diminuição da fração molar de MAA (ácido metacrílico). Na preparação de partículas com fração molar de 50% de MAA, e relação volumétrica acetonitrila/tolueno de 75/25, quanto maior a relação de monômeros totais/diluentes (g/100 mL), maior o tamanho e o rendimento das partículas. Com a mudança da relação volumétrica de diluentes, houve mudança nas características de porosidade, tamanho das partículas, e grau de inchamento das partículas, sendo que na relação volumétrica acetonitrila/tolueno de 50/50, houve formação de microgel

Frances E. W. Harper and Pauline E. Hopkins: the uplifting of black women through literature

A presente dissertação tem como objetivo apresentar duas influentes autoras afro-americanas do século XIX, Frances E. W. Harper e Pauline E. Hopkins. Ambas as autoras, através de seus romances Iola Leroy, or, Shadows Uplifted (1892) e Contending Forces: a Romance Illustrative of Negro Life North and South (1900) respectivamente, entrelaçam ficção e história com o propósito de criar novas alternativas de discurso, afastando-se, portanto, do oficial. Ademais, o presente trabalho propõe demonstrar como Frances Harper e Pauline Hopkins fazem uso do espaço literário com a finalidade de escrever a história do oprimido, permitindo, principalmente, que as mulheres afro-americanas dessem voz as suas experiências e as suas próprias histórias. Assim sendo, a literatura produzida por Frances e Harper e Pauline Hopkins será analisada como forma de empoderamento da comunidade afro-americana, principalmente como forma de aquisição de poder para as Mulheres Afro-Americanas.

Democracia, política externa e integração regional: um estudo comparativo das trejetórias de Argentina e Brasil

Este trabalho focaliza os fenômenos da politização da política externa e da luta pela democratização do seu processo decisório no que se refere às políticas deintegração regional de Argentina e Brasil, nos âmbitos do MERCOSUL e da ALCA. O objetivo principal é analisar, por um lado, os processos de liberalização política edemocratização do regime ocorridos nestes dois países entre os anos 1970 e 1980,e, por outro, as relações entre a incorporação do regionalismo às respectivas estratégias de inserção internacional e a politização da política externa, desde o finalda Guerra Fria. Considerando as controvérsias em torno do conceito de democracia,são discutidas as principais estratégias de análise encontradas na políticacomparada e as três principais perspectivas teóricas contemporâneas (realismo,pluralismo e deliberativismo). A análise empírica concentra-se em dois processos: a criação do MERCOSUL, desde suas origens até o final da fase de transição (1991-1994), e as negociações para a criação da ALCA, desde o seu lançamento até a suspensão (1994 2005). Argumenta-se que apesar da incorporação do regionalismo haver gerado um aumento da politização doméstica em torno da política externa, isto não significou, no entanto, qualquer avanço no sentido da democratização das decisões nestes âmbitos específicos

Growth and survival of sockeye salmon (Oncorhynchus nerka) from Karluk Lake and River, Alaska, in relation to climatic and oceanic regimes and indices, 1922–2000

We examined whether the relationship between climate and salmon production was linked through the effect of climate on the growth of sockeye salmon (Oncorhynchus nerka) at sea. Smolt length and juvenile, immature, and maturing growth rates were estimated from increments on scales of adult sockeye salmon that returned to the Karluk River and Lake system on Kodiak Island, Alaska, over 77 years, 1924–2000. Survival was higher during the warm climate regimes and lower during the cool regime. Growth was not correlated with survival, as estimated from the residuals of the Ricker stock-recruitment model. Juvenile growth was correlated with an atmospheric forcing index and immature growth was correlated with the amount of coastal precipitation, but the magnitude of winter and spring coastal downwelling in the Gulf of Alaska and the Pacific Northwest atmospheric patterns that influence the directional bifurcation of the Pacific Current were not related to the growth of Karluk sockeye salmon. However, indices of sea surface temperature, coastal precipitation, and atmospheric circulation in the eastern North Pacific were correlated with the survival of Karluk sockeye salmon. Winter and spring precipitation and atmospheric circulation are possible processes linking survival to climate variation in Karluk sockeye salmon.

Ecotypic variation and predatory behavior among killer whales (Orcinus orca) off the eastern Aleutian Islands, Alaska

From 2001 to 2004 in the eastern Aleutian Islands, Alaska, killer whales (Orcinus orca) were encountered 250 times during 421 days of surveys that covered a total of 22,491 miles. Three killer whale groups (resident, transient, and offshore) were identified acoustically and genetically. Resident killer whales were found 12 times more frequently than transient killer whales, and offshore killer whales were encountered only once. A minimum of 901 photographically identified resident whales used the region during our study. A total of 165 mammal-eating transient killer whales were identified, and the majority (70%) were encountered during spring (May and June). The diet of transient killer whales in spring was primarily gray whales (Eschrichtius robustus), and in summer primarily northern fur seals (Callorhinus ursinus). Steller sea lions (Eumetopias jubatus) did not appear to be a preferred prey or major prey item during spring and summer. The majority of killer whales in the eastern Aleutian Islands are the resident ecotype, which does not consume marine mammals.

First Annual Report for the year ended 31st March, 1966

This is the first Annual report of the Cumberland River Authority on information of its activities and responsibilities on river management in its area between the beginning of April 1965, to the end of March 1966. The report contains 5 main sections on water resources, land drainage, fisheries, pollution, and finally the expenditure and income for the 12 month period. The first area that the report deals with is water resources, which includes periodical surveys, hydrometric schemes, acceptable flows, conservation works and a review of rainfall and river flow. The section on land drainage looks at work on improvement schemes, floods, charges and information on maintenance work carried out on rivers including Wampool, Waver, Marron, Irt, Esk, Eden, Caldew, Petteril, Eamont and Annas. The fisheries section covers 5 districts of the River Eden, Esk, Ellen, Derwent, and South West Cumberland. It includes angling information and a general report for salmon and sea trout, brown trout and freshwater fish. It also looks at fish hatchery, fisheries protection and byelaws including licence numbers issued for the different districts. The fourth section on pollution deals with water quality of the rivers and their tributaries from the same 5 areas mentioned above. It also covers information on sewage and trade effluents. The River Authorities preceded the Environment Agency which came into existence in 1996.

Second Annual Report for the year ended 31st March, 1967

This is the second Annual report of the Cumberland River Authority on information of its activities and responsibilities on river management in its area between the beginning of April 1966, to the end of March 1967. The report contains 5 main sections on water resources, land drainage, fisheries, pollution, and finally the expenditure and income for the 12 month period. The first area that the report deals with is water resources, which includes periodical surveys, hydrometric schemes, acceptable flows, conservation works and a review of rainfall and river flow. The section on land drainage looks at work on improvement schemes, floods, charges and information on maintenance work carried out on rivers including Wampool, Waver, Marron, Ellen, Derwent, Esk, Eden, Caldew, Petteril, Eamont, Gelt and Annas. The fisheries section covers 5 districts of the River Eden, Esk, Ellen, Derwent and South West Cumberland. It includes angling information and a general report for salmon and sea trout, Brown trout and freshwater fish. Fish disease and fish hatchery are also included as well as fisheries protection and byelaws. The fourth section on pollution deals with water quality and the results of samples taken from rivers Eden, Eamont, Caldew, Calder, Derwent, Ehen, Ellen, Wampool and Waver are also given. It also covers information on sewage and trade effluents. The River Authorities preceded the Environment Agency which came into existence in 1996.

Third Annual Report for the year ended 31st March, 1968

This is the third Annual report of the Cumberland River Authority on information of its activities and responsibilities on river management in its area between the beginning of April 1967, to the end of March 1968. The report contains 5 main sections on water resources, land drainage, fisheries, pollution, and finally the expenditure and income for the 12 month period. The first area that the report deals with is water resources, which includes periodical surveys, hydrometric schemes, acceptable flows, conservation works and a review of rainfall and river flow. The section on land drainage looks at work on improvement schemes, floods, charges and information on maintenance work carried out on rivers including Wampool, Waver, Glenderamackin, Marron, Eden, Caldew, and Lyvennet. The fisheries section covers 5 districts of the River Eden, Esk, Ellen, Derwent and South West Cumberland. It includes angling information and a general report for salmon and sea trout, brown trout and freshwater fish. Fish disease and fish hatchery are also covered as well as fisheries protection and licence duties. The fourth section on pollution deals with water quality, and the results of samples taken from rivers Eden, Eamont, Petteril, Caldew, Calder, Derwent, Ehen, Ellen, Wampool and Waver are also given. It also covers information on sewage and trade effluents. The River Authorities preceded the Environment Agency which came into existence in 1996.