A measurement of the proton elastic form factors for 1 ≤ Q^2 ≤ 3 (GeV/c)^2

We report measurements of the proton form factors, G^p_E and G^p_M, extracted from elastic electron scattering in the range 1 ≤ Q^2 ≤ 3 (GeV/c)^2 with uncertainties of <15% in G^p_E and <3% in G^p_M. The results for G^p_E are somewhat larger than indicated by most theoretical parameterizations. The ratio of Pauli and Dirac form factors, Q^2(F^p_2/F^p_1), is lower in value and demonstrates less Q^2 dependence than these parameterizations have indicated. Comparisons are made to theoretical models, including those based on perturbative QCD, vector-meson dominance, QCD sum rules, and diquark constituents to the proton. A global extraction of the form factors, including previous elastic scattering measurements, is also presented.

Competing Ecosystem services: an Assessment of Carbon and timber in the Tropical forests of Central America

4 p.

Competing Ecosystem Services: an Assessment of Carbon and Timber in the Tropical Forests of Central America

29 p.

New insights into the formation and modification of carbonate-bearing minerals and methane gas in geological systems using multiply substituted isotopologues

This thesis describes the use of multiply-substituted stable isotopologues of carbonate minerals and methane gas to better understand how these environmentally significant minerals and gases form and are modified throughout their geological histories. Stable isotopes have a long tradition in earth science as a tool for providing quantitative constraints on how molecules, in or on the earth, formed in both the present and past. Nearly all studies, until recently, have only measured the bulk concentrations of stable isotopes in a phase or species. However, the abundance of various isotopologues within a phase, for example the concentration of isotopologues with multiple rare isotopes (multiply substituted or 'clumped' isotopologues) also carries potentially useful information. Specifically, the abundances of clumped isotopologues in an equilibrated system are a function of temperature and thus knowledge of their abundances can be used to calculate a sample’s formation temperature. In this thesis, measurements of clumped isotopologues are made on both carbonate-bearing minerals and methane gas in order to better constrain the environmental and geological histories of various samples.

Clumped-isotope-based measurements of ancient carbonate-bearing minerals, including apatites, have opened up paleotemperature reconstructions to a variety of systems and time periods. However, a critical issue when using clumped-isotope based measurements to reconstruct ancient mineral formation temperatures is whether the samples being measured have faithfully recorded their original internal isotopic distributions. These original distributions can be altered, for example, by diffusion of atoms in the mineral lattice or through diagenetic reactions. Understanding these processes quantitatively is critical for the use of clumped isotopes to reconstruct past temperatures, quantify diagenesis, and calculate time-temperature burial histories of carbonate minerals. In order to help orient this part of the thesis, Chapter 2 provides a broad overview and history of clumped-isotope based measurements in carbonate minerals.

In Chapter 3, the effects of elevated temperatures on a sample’s clumped-isotope composition are probed in both natural and experimental apatites (which contain structural carbonate groups) and calcites. A quantitative model is created that is calibrated by the experiments and consistent with the natural samples. The model allows for calculations of the change in a sample’s clumped isotope abundances as a function of any time-temperature history.

In Chapter 4, the effects of diagenesis on the stable isotopic compositions of apatites are explored on samples from a variety of sedimentary phosphorite deposits. Clumped isotope temperatures and bulk isotopic measurements from carbonate and phosphate groups are compared for all samples. These results demonstrate that samples have experienced isotopic exchange of oxygen atoms in both the carbonate and phosphate groups. A kinetic model is developed that allows for the calculation of the amount of diagenesis each sample has experienced and yields insight into the physical and chemical processes of diagenesis.

The thesis then switches gear and turns its attention to clumped isotope measurements of methane. Methane is critical greenhouse gas, energy resource, and microbial metabolic product and substrate. Despite its importance both environmentally and economically, much about methane’s formational mechanisms and the relative sources of methane to various environments remains poorly constrained. In order to add new constraints to our understanding of the formation of methane in nature, I describe the development and application of methane clumped isotope measurements to environmental deposits of methane. To help orient the reader, a brief overview of the formation of methane in both high and low temperature settings is given in Chapter 5.

In Chapter 6, a method for the measurement of methane clumped isotopologues via mass spectrometry is described. This chapter demonstrates that the measurement is precise and accurate. Additionally, the measurement is calibrated experimentally such that measurements of methane clumped isotope abundances can be converted into equivalent formational temperatures. This study represents the first time that methane clumped isotope abundances have been measured at useful precisions.

In Chapter 7, the methane clumped isotope method is applied to natural samples from a variety of settings. These settings include thermogenic gases formed and reservoired in shales, migrated thermogenic gases, biogenic gases, mixed biogenic and thermogenic gas deposits, and experimentally generated gases. In all cases, calculated clumped isotope temperatures make geological sense as formation temperatures or mixtures of high and low temperature gases. Based on these observations, we propose that the clumped isotope temperature of an unmixed gas represents its formation temperature — this was neither an obvious nor expected result and has important implications for how methane forms in nature. Additionally, these results demonstrate that methane-clumped isotope compositions provided valuable additional constraints to studying natural methane deposits.

A note on the shallow ponds on the gravel ridge of Epping Forest, Essex

In a recent study in Freshwater Forum on Speakman's Pond (also known as Nursery Pond) the impression was given that it had been a permanent water-filled pond which had recently dried out due to exceptionally low rainfall. In fact, Nursery Pond was created by the extraction of gravel and was never more than 50 cm deep, until the creation of trenches in 1989 to provide a refuge for aquatic life. The Nursery Pond followed a seasonal pattern of filling with winter rain and slowly drying out between 1940 to 1970. It had no established aquatic vegetation, no fish, and only rarely amphibians. Permanent water was present only from about 1979 until 1995 due to leakage from a Thames water storage reservoir.

Caracterização físico-química e avaliação dos níveis de elementos-traço em sedimentos de manguezais das baías da Ilha Grande e de Sepetiba, RJ, por metodologias de digestão ácida assistidas por micro-ondas

O presente trabalho teve como objetivo principal comparar dois métodos de extração de elementos-traço em sedimentos que são assistidos por radiação micro-ondas. Foram coletadas amostras de sedimentos superficiais em um manguezal localizado na baía da Ilha Grande e em três manguezais localizados na baía de Sepetiba, RJ. As amostras de sedimentos coletadas foram secas, destorroadas e peneiradas. Sub-amostras foram submetidas a análises de caracterização física e química. Os métodos de extração de elementos-traço comparados foram o EPA-3051A e o método água régia assistido por micro-ondas. Os elementos-traço analisados foram: Cd, Cr, Cu, Ni, Pb e Zn. As concentrações dos elementos-traço nos extratos produzidos foram determinadas por FAAS (Espectrometria de absorção atômica com chama). Foram encontradas nos sedimentos dos manguezais estudados concentrações acima dos níveis estabelecidos pela Resolução CONAMA 344/2004 para os elementos-traço: Cd, Ni, Pb e Zn. Os resultados mostraram que as capacidades de extração de elementos-traço dos métodos EPA-3051A e água régia assistido por micro-ondas variam em função das características físico-químicas dos sedimentos. A análise estatística pela técnica de regressão linear simples mostrou que as duas metodologias são estatisticamente similares apenas para o Cr e os valores dos coeficientes de determinação (R2) obtidos obedeceram à seqüência: Cu > Pb > Zn > Ni > Cr > Cd. Na análise pela técnica estatística de regressão linear múltipla ocorreram melhorias estatisticamente significativas nos coeficientes de determinação quando foram incluídas as seguintes variáveis independentes: potencial redox e fósforo total para o Cd, argila para o Cr, areia para o Ni e fósforo total para o Pb e para o Zn

The astrophysics of strongly interacting systems

This thesis presents investigations in four areas of theoretical astrophysics: the production of sterile neutrino dark matter in the early Universe, the evolution of small-scale baryon perturbations during the epoch of cosmological recombination, the effect of primordial magnetic fields on the redshifted 21-cm emission from the pre-reionization era, and the nonlinear stability of tidally deformed neutron stars.

In the first part of the thesis, we study the asymmetry-driven resonant production of 7 keV-scale sterile neutrino dark matter in the primordial Universe at temperatures T >~ 100 MeV. We report final DM phase space densities that are robust to uncertainties in the nature of the quark-hadron transition. We give transfer functions for cosmological density fluctuations that are useful for N-body simulations. We also provide a public code for the production calculation.

In the second part of the thesis, we study the instability of small-scale baryon pressure sound waves during cosmological recombination. We show that for relevant wavenumbers, inhomogenous recombination is driven by the transport of ionizing continuum and Lyman-alpha photons. We find a maximum growth factor less than ≈ 1.2 in 10⁷ random realizations of initial conditions. The low growth factors are due to the relatively short duration of the recombination epoch.

In the third part of the thesis, we propose a method of measuring weak magnetic fields, of order 10^-19 G (or 10^-21 G if scaled to the present day), with large coherence lengths in the inter galactic medium prior to and during the epoch of cosmic reionization. The method utilizes the Larmor precession of spin-polarized neutral hydrogen in the triplet state of the hyperfine transition. We perform detailed calculations of the microphysics behind this effect, and take into account all the processes that affect the hyperfine transition, including radiative decays, collisions, and optical pumping by Lyman-alpha photons.

In the final part of the thesis, we study the non-linear effects of tidal deformations of neutron stars (NS) in a compact binary. We compute the largest three- and four-mode couplings among the tidal mode and high-order p- and g-modes of similar radial wavenumber. We demonstrate the near-exact cancellation of their effects, and resolve the question of the stability of the tidally deformed NS to leading order. This result is significant for the extraction of binary parameters from gravitational wave observations.

Experiments using an artificial stream to investigate the seasonal growth of chalk-stream algae

Research into the production ecology of chalk streams using a large artificial recirculating stream is described. Physical chemical processes including calcium and inorganic phosphate levels, and exchange of gaseous carbon dioxide in both a simple closed system and a circulating system with gravel substrate have been monitored in both light and dark conditions. Further experiments were concerned with the seasonal changes in algal growth over the gravel substrate with constant water velocities and replenishment. The algal population, composed mainly of the diatoms Achnanthes minutissima, Meridion circulare, Nitzschia fonticola and Synedra ulna reached a peak in mid May and declined rapidly during June. Concentrations of phosphate phosphorus fell as the diatoms grew but was not thought to limit growth. Silicate concentrations followed the diatom cycle closely but never fell below 0.8 mg/l Si. It is possible that one of the nutrients may have been limiting the rate of growth due to steep diffusion gradients through the algal mat. In the last summer and autumn a hard calcareous crust composed of the green alga Gongrosira incrustans and the blue green alga Homeothrix varians , developed. The channel stream is compared with the natural conditions found in chalk streams.

Eutrophication and the management of planktonic algae: What Vollenweider couldn't tell us

The ”Vollenweider model” is a sophisticated mathematical statement about the long-range behaviour of (mainly temperate) lakes and their ability to support phytoplankton chlorophyll. Misapplication of the model, against which Vollenweider himself warned, has led to many misconceptions about the dynamics of plankton in lakes and reservoirs and about how best to manage systems subject to eutrophication. This contribution intends to frame the most important issues in context of the phosphorus- loading and phosphorus-limitation concepts. Emphasis is placed on the need to distinguish rate-limitation from capacity-limitation, to understand which is more manageable and why, to discern the mechanisms of internal recycling and their importance, and to appreciate the respective roles of physical and biotic components in local control of algal dynamics. Some general approaches to the management of water quality in lakes and reservoirs to eutrophication are outlined.

TRANSFER OF ANALYTICAL METHODS FOR THE CHARACTERISATION OF NATURAL PRODUCTS TO R&D PROCESSES OF IDOKI

IDOKI SCF Technologies S.L. is a technology-based company, set up on September 2006 in Derio (Biscay) with the main scope of developing extraction and purification processes based on the use of supercritical fluid extraction technology (SFE) in food processing, extraction of natural products and the production of personal care products. IDOKI¿s researchers have been working on many different R&D projects so far, most of them using this technology. However, the optimization of a SFE method for the different matrices cannot be performed unless we have an analytical method for the characterisation of the extracts obtained in each experiment. The analytical methods are also essential for the quality control of the raw materials that are going to be used and also for the final product. This PhD thesis was born to tackle this problem and therefore, it is based on the development of different analytical methods for the characterisation of the extracts and products. The projects that we could include in this thesis were the following: the extraction propolis, the recovery of agroindustrial residues (soy and wine) and the dealcoholisation of wine.On the one hand, for the extraction of propolis, several UV-Vis spectroscopic methods were used in order to measure the antioxidant capacity and the total polyphenol and flavonoid content of the extracts. A SFC method was also developed in order to measure more specific phenolic compounds. On the other hand, for the recovery of agroindustrial residues UV-Vis spectroscopy was used to determine the total polyphenol content and two SFC methods were developed to analyse different phenolic compounds. Extraction methods such as MAE, FUSE and rotary agitation were also evaluated for the characterisation of the raw materials.Finally, for the dealcoholisation of wine, the development of a SBSE-TD-GC-MS and DHS-TD-GC-MS methods for the analysis of aromas and a NIR spectroscopic method for the determination of ethanol content with the help of chemometrics was necessary. Most of these methods are typically used in IDOKI¿s lab as routine analyses apart from others not included in this PhD thesis.

Quantificação e avaliação da biodisponibilidade de metais em sedimentos na Baía da Ribeira RJ

A toxicidade dos metais em ambientes aquáticos está relacionada à sua biodisponibilidade e esta, por sua vez, pode ser influenciada por diversos fatores. As características do sedimento fazem dele um importante compartimento para avaliação do nível de contaminação no ambiente aquático. A presente pesquisa teve por objetivo quantificar e avaliar a biodisponibilidade de metais em sedimentos da baía da Ribeira. Nessa região, encontram-se os bairros mais populosos de Angra dos Reis RJ. Essa baía está localizada na parte nordeste da baía da Ilha Grande, que consiste de um espaço pesqueiro, turístico e de importante valor econômico e industrial. Foram coletados 12 sedimentos na baía da Ribeira e determinados os teores dos metais Al, Cu, Cd , Cr, Fe, Mn, Ni, Pb e Zn, através da extração com água régia (protocolo BCR-701), e o potencial de toxicidade dos metais Cd, Cu, Ni, Pb e Zn pelo método de extração dos sulfetos voláteis em meio ácido e quantificação dos metais extraídos simultaneamente (em inglês Acid Volatile Sulfide and Simultaneously Extracted Metal, AVS/SEM). Também foram efetuadas medidas de pH, potencial redox (Eh), carbono orgânico, fósforo total e granulometria. Através desses dados, foi possível estudar correlações entre essas variáveis. As concentrações de cada metal são similares nas diferentes localizações dos sedimentos e não apresentam significativas diferenças com relação a estudos reportados para a área, com exceção do Pb que apresentou a mais alta concentração já reportada. Os valores de SEM/AVS (entre 0,02 e 0,2) menores que 1, indicam que há quantidade de sulfetos suficiente para o aprisionamento dos metais investigados. As correlações obtidas através da Análise dos Componentes Principais demonstram relação direta entre as concentrações da maioria dos metais extraídos por água-régia (Ni, Fe, Cr, Cu, Zn); entre os metais Mn, Pb, Al e o fósforo total; entre os teores de matéria orgânica, carbono orgânico total, fósforo total com as frações finas de silte e argila com o Eh. Os resultados sugerem que a região não sofre influência significativa de fontes antrópicas em relação a metais e que, segundo o AVS/SEM, esses se encontram pouco disponíveis para o ambiente e, portanto, apresentam baixo potencial tóxico

DNA extraction from formalin-fixed Franciscana tissues

The present paper reports the extraction of DNA from formalin-fixed Pontoporia blainvillei tissues. Following the Vachot and Monerot (1996) protocol, fragmented DNA (300-700bp) was extracted from more than 95% of liver and muscle samples. DNA yield in liver samples was significantly higher than in muscle samples (4.574 ± 1.169mg DNA/mg versus 0.808 ± 0.297mg DNA/mg). Similar results were obtained from nine other species of cetaceans and five species of pinnipeds. It is of special interest to have a method that allows the utilisation of museum specimens not originally preserved for genetic studies, which may include rarely available, declining or extinct species. SPANISH: El presente trabajo reporta la extracción de ADN a partir de tejidos formolizados de Pontoporia blainvillei. Siguiendo el protocolo de Vachot y Monerot (1996) se pudo extraer ADN degradado (300-700pb) en más del 95% de las muestras de hígado y músculo analizadas. El rendimiento en ADN fue significativamente mayor en muestras de hígado que en muestras de músculo (4.574 ± 1.169mg DNA/mg tejido húmedo versus 0.808 ± 0.297mg DNA/mg tejido húmedo). Resultados similares se obtuvieron en otras nueve especies de Cetáceos y cinco de Pinnípedos. Resulta de gran interés contar con un método que permita la utilización de especímenes depositados en museos y que no hayan sido originalmente colectados para estudios genéticos, incluyendo especies de difícil obtención, en franca declinación o extintas.

Integração de dados geofísicos de poços e geoquímicos na avaliação do potencial gerador dos folhelhos betuminosos da Formação Tremembé, Bacia de Taubaté

Nos depósitos cenozóicos da Bacia de Taubaté são encontrados depósitos de folhelhos betuminosos (oleígenos) pertencentes à Formação Tremembé, de idade oligocênica, que durante alguns anos na década de 50 foram investigados com relação ao seu aproveitamento econômico através da extração industrial do óleo nele contido. Entretanto, em face de aspectos tecnológicos e conjunturais da época, esse aproveitamento industrial foi considerado inviável do ponto de vista econômico. Nesta dissertação é proposta uma aplicação da perfilagem geofísica para a caracterização da faciologia dos folhelhos betuminosos da Formação Tremembé, tendo como objetivo principal a identificação das eletrofácies nos perfis elétricos, através de uma metodologia robusta e consistente. A identificação de eletrofácies é importante para ajudar na determinação da caracterização de uma reserva não convencional e na análise da viabilidade econômica. Neste estudo foram utilizados os perfis convencionais de poço: Raio gama, resitividade, potencial espontâneo e sônico. Os dados de perfis de poços foram integrados com os testemunhos e dados geoquímicos, mais precisamente os dados de COT, S, IH, S2 para uma caracterização realística das eletrofácies. Os dados foram obtidos a partir de três sondagens rotativas realizadas na Bacia de Taubaté, resultantes de testemunhagem contínua e perfilagem a cabo ao longo do intervalo de folhelhos da Formação Tremembé. A partir disto, obtém-se como resposta um modelo específico para cada litologia, onde cada pico corresponde a uma eletrofácies, permitindo o estabelecimento de alguns padrões ou assinaturas geofísicas para as principais fácies ocorrentes. Como resultado deste trabalho, foi possível correlacionar as eletrofácies entre os poços numa seção modelo, a partir de similaridade lateral das eletrofácies entre os marcos estratigráficos representado, foi possível observar a continuidade de duas sequências de folhelhos betuminoso com alto teores de COT, S, IH, S2, considerados os mais importantes do ponto de vista econômico e gerado um modelo faciológico 2D e 3D dessas camadas. Os resultados obtidos neste trabalho são bastante promissores, apontando para a possibilidade de aplicação desta técnica a outros poços da Bacia de Taubaté, fornecendo subsídios relevantes à determinação da evolução sedimentar.

Calculation of the electronic structure of carbon films using electron energy loss spectroscopy.

The detailed understanding of the electronic properties of carbon-based materials requires the determination of their electronic structure and more precisely the calculation of their joint density of states (JDOS) and dielectric constant. Low electron energy loss spectroscopy (EELS) provides a continuous spectrum which represents all the excitations of the electrons within the material with energies ranging between zero and about 100 eV. Therefore, EELS is potentially more powerful than conventional optical spectroscopy which has an intrinsic upper information limit of about 6 eV due to absorption of light from the optical components of the system or the ambient. However, when analysing EELS data, the extraction of the single scattered data needed for Kramers Kronig calculations is subject to the deconvolution of the zero loss peak from the raw data. This procedure is particularly critical when attempting to study the near-bandgap region of materials with a bandgap below 1.5 eV. In this paper, we have calculated the electronic properties of three widely studied carbon materials; namely amorphous carbon (a-C), tetrahedral amorphous carbon (ta-C) and C60 fullerite crystal. The JDOS curve starts from zero for energy values below the bandgap and then starts to rise with a rate depending on whether the material has a direct or an indirect bandgap. Extrapolating a fit to the data immediately above the bandgap in the stronger energy loss region was used to get an accurate value for the bandgap energy and to determine whether the bandgap is direct or indirect in character. Particular problems relating to the extraction of the single scattered data for these materials are also addressed. The ta-C and C60 fullerite materials are found to be direct bandgap-like semiconductors having a bandgaps of 2.63 and 1.59eV, respectively. On the other hand, the electronic structure of a-C was unobtainable because it had such a small bandgap that most of the information is contained in the first 1.2 eV of the spectrum, which is a region removed during the zero loss deconvolution.

Observations on changes in the major protein nitrogen fraction of prawns and sardines during ice storage

Changes in the major protein nitrogen fractions (sarcoplasmic, myofibrillar, stroma) have been studied in two species of prawns and in oil sardine held in ice storage. Myofibrillar proteins were observed to get denatured at a rapid rate as determined by salt extractability method. The sarcoplasmic proteins were not denatured to any considerable extent. With sardine however, the extraction of myofibrillar proteins was inhibited rather in the uniced condition itself presumably owing to the presence of free fatty acids.