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.

Essays in optimal resource allocation under uncertainty with capacity constraints

This thesis brings together four papers on optimal resource allocation under uncertainty with capacity constraints. The first is an extension of the Arrow-Debreu contingent claim model to a good subject to supply uncertainty for which delivery capacity has to be chosen before the uncertainty is resolved. The second compares an ex-ante contingent claims market to a dynamic market in which capacity is chosen ex-ante and output and consumption decisions are made ex-post. The third extends the analysis to a storable good subject to random supply. Finally, the fourth examines optimal allocation of water under an appropriative rights system.

The heat capacity of superfluid ^4He in the presence of a constant heat flux near Tλ

We present the first experimental evidence that the heat capacity of superfluid ⁴He, at temperatures very close to the lambda transition temperature, T_λ,is enhanced by a constant heat flux, Q. The heat capacity at constant Q, C_Q,is predicted to diverge at a temperature T_c(Q) < T_λ at which superflow becomes unstable. In agreement with previous measurements, we find that dissipation enters our cell at a temperature, T_DAS(Q),below the theoretical value, T_c(Q). Our measurements of C_Q were taken using the discrete pulse method at fourteen different heat flux values in the range 1µW/cm² ≤ Q≤ 4µW /cm². The excess heat capacity ∆C_Q we measure has the predicted scaling behavior as a function of T and Q:∆C_Q • t^α ∝ (Q/Q_c)², where Q_cT) ~ t^2ν is the critical heat current that results from the inversion of the equation for T_c(Q). We find that if the theoretical value of T_c( Q) is correct, then ∆C_Q is considerably larger than anticipated. On the other hand,if T_c(Q)≈ T_DAS(Q),then ∆C_Q is the same magnitude as the theoretically predicted enhancement.

High pressure states in condensed matter: I. High pressure behavior of the iron-sulphur system with applications to the earth's core. II. Empirical equation of state for organic compounds at high pressures

Part I:

The earth's core is generally accepted to be composed primarily of iron, with an admixture of other elements. Because the outer core is observed not to transmit shear waves at seismic frequencies, it is known to be liquid or primarily liquid. A new equation of state is presented for liquid iron, in the form of parameters for the 4th order Birch-Murnaghan and Mie-Grüneisen equations of state. The parameters were constrained by a set of values for numerous properties compiled from the literature. A detailed theoretical model is used to constrain the P-T behavior of the heat capacity, based on recent advances in the understanding of the interatomic potentials for transition metals. At the reference pressure of 10⁵ Pa and temperature of 1811 K (the normal melting point of Fe), the parameters are: ρ = 7037 kg/m³, K_S0 = 110 GPa, K_S' = 4.53, K_S" = -.0337 GPa-1, and γ = 2.8, with γ α ρ^-1.17. Comparison of the properties predicted by this model with the earth model PREM indicates that the outer core is 8 to 10 % less dense than pure liquid Fe at the same conditions. The inner core is also found to be 3 to 5% less dense than pure liquid Fe, supporting the idea of a partially molten inner core. The density deficit of the outer core implies that the elements dissolved in the liquid Fe are predominantly of lower atomic weight than Fe. Of the candidate light elements favored by researchers, only sulfur readily dissolves into Fe at low pressure, which means that this element was almost certainly concentrated in the core at early times. New melting data are presented for FeS and FeS₂ which indicate that the FeS₂ is the S-hearing liquidus solid phase at inner core pressures. Consideration of the requirement that the inner core boundary be observable by seismological means and the freezing behavior of solutions leads to the possibility that the outer core may contain a significant fraction of solid material. It is found that convection in the outer core is not hindered if the solid particles are entrained in the fluid flow. This model for a core of Fe and S admits temperatures in the range 3450K to 4200K at the top of the core. An all liquid Fe-S outer core would require a temperature of about 4900 K at the top of the core.

Part II.

The abundance of uses for organic compounds in the modern world results in many applications in which these materials are subjected to high pressures. This leads to the desire to be able to describe the behavior of these materials under such conditions. Unfortunately, the number of compounds is much greater than the number of experimental data available for many of the important properties. In the past, one approach that has worked well is the calculation of appropriate properties by summing the contributions from the organic functional groups making up molecules of the compounds in question. A new set of group contributions for the molar volume, volume thermal expansivity, heat capacity, and the Rao function is presented for functional groups containing C, H, and O. This set is, in most cases, limited in application to low molecular liquids. A new technique for the calculation of the pressure derivative of the bulk modulus is also presented. Comparison with data indicates that the presented technique works very well for most low molecular hydrocarbon liquids and somewhat less well for oxygen-bearing compounds. A similar comparison of previous results for polymers indicates that the existing tabulations of group contributions for this class of materials is in need of revision. There is also evidence that the Rao function contributions for polymers and low molecular compounds are somewhat different.

Information-theoretic Studies and Capacity Bounds: Group Network Codes and Energy Harvesting Communication Systems

Network information theory and channels with memory are two important but difficult frontiers of information theory. In this two-parted dissertation, we study these two areas, each comprising one part. For the first area we study the so-called entropy vectors via finite group theory, and the network codes constructed from finite groups. In particular, we identify the smallest finite group that violates the Ingleton inequality, an inequality respected by all linear network codes, but not satisfied by all entropy vectors. Based on the analysis of this group we generalize it to several families of Ingleton-violating groups, which may be used to design good network codes. Regarding that aspect, we study the network codes constructed with finite groups, and especially show that linear network codes are embedded in the group network codes constructed with these Ingleton-violating families. Furthermore, such codes are strictly more powerful than linear network codes, as they are able to violate the Ingleton inequality while linear network codes cannot. For the second area, we study the impact of memory to the channel capacity through a novel communication system: the energy harvesting channel. Different from traditional communication systems, the transmitter of an energy harvesting channel is powered by an exogenous energy harvesting device and a finite-sized battery. As a consequence, each time the system can only transmit a symbol whose energy consumption is no more than the energy currently available. This new type of power supply introduces an unprecedented input constraint for the channel, which is random, instantaneous, and has memory. Furthermore, naturally, the energy harvesting process is observed causally at the transmitter, but no such information is provided to the receiver. Both of these features pose great challenges for the analysis of the channel capacity. In this work we use techniques from channels with side information, and finite state channels, to obtain lower and upper bounds of the energy harvesting channel. In particular, we study the stationarity and ergodicity conditions of a surrogate channel to compute and optimize the achievable rates for the original channel. In addition, for practical code design of the system we study the pairwise error probabilities of the input sequences.

The life capacity of copepod's eggs passed through the gut of Ladoga lake Coregonus [Translation from: Zool.Journal.Moscow 29-5, 476-477, 1950]

This short paper summarises findings of experiments that were carried out using copepod eggs taken from guts of Coregonus which breeds in various Ural lakes. The study showed that copepod eggs can pass through the gut of Coregonus unharmed.

Late Transition Metals Supported by Aryl Ethers and Phenoxides Bearing Pendant Phosphines: Mechanistic Insights Relevant to Ether C-O Bond Cleavage

Terphenyl diphosphines bearing pendant ethers were prepared to provide mechanistic insight into the mechanism of activation of aryl C–O bonds with Group 9 and Group 10 transition metals. Chapters 2 and 3 of this dissertation describe the reactivity of compounds supported by the model phosphine and extension of this chemistry to heterogenous C–O bond activation.

Chapter 2 describes the synthesis and reactivity of aryl-methyl and aryl-aryl model systems. The metallation of these compounds with Ni, Pd, Pt, Co, Rh, and Ir is described. Intramolecular bond activation pathways are described. In the case of the aryl-methyl ether, aryl C–O bond activation was observed only for Ni, Rh, and Ir.

Chapter 3 outlines the reactivity of heterogenous Rh and Ir catalysts for aryl ether C–O bond cleavage. Using Rh/C and an organometallic Ir precursor, aryl ethers were treated with H2 and heat to afford products of hydrogenolysis and hydrogenation. Conditions were modified to optimize the yield of hydrogenolysis product. Hydrogenation could not be fully suppressed in these systems.

Appendix A describes initial investigations of bisphenoxyiminoquinoline dichromium compounds for selective C2H4 oligomerization to afford α-olefins. The synthesis of monometallic and bimetallic Cr complexes is described. These compounds are compared to literature examples and found to be less active and non-selective for production of α-olefins.

Appendix B describes the coordination chemistry of terphenyl diphosphines, terphenyl bisphosphinophenols, and biphenyl phosphinophenols proligands with molybdenum, cobalt, and nickel. Since their synthesis, terphenyl diphosphine molybdenum compounds have been reported to be good catalysts for the dehydrogenation of ammonia borane. Biphenyl phosphinophenols are demonstrated provide both phosphine and arene donors to transition metals while maintaining a sterically accessible coordination sphere. Such ligands may be promising in the context of the activation of other small molecules.

Appendix C contains relevant NMR spectra for the compounds presented in the preceding sections.

On a fiber grating sensor system with the capacity of cross-sensitivity discrimination

A novel fiber Bragg grating (FBG) sensor system based on an interrogating technique by two parallel matched gratings was designed and theoretically discussed. With an interrogation grating playing the role of temperature compensation grating simultaneously, the wavelength drifts induced by temperature and strain were discriminated. Additionally, the expressions of temperature and strain were deduced for our solution, and dual-value problem and cross sensitivity were solved synchronously through data processing. The influence of the FBG's parameters on the dynamic range and precision was discussed. Besides, the change of environment temperature cannot influence the dynamic range of the sensor system through temperature tuning. The system proposed in this paper will be of great significance to accelerate the real engineering applications of FBG sensing techniques. (c) 2007 Elsevier GmbH. All rights reserved.

Caracterização das estratégias ecofisiológicas de samambaias em resposta à inundação na restinga de Maricá, Rio de Janeiro, Brasil

As matas inundáveis e brejos presentes nas restingas desencadeiam uma série de processos que influenciam as características físico-químicas e biológicas do solo, levando as plantas a apresentarem mecanismos de aclimatação ou adaptação ao estresse da inundação, como alterações morfológicas e fisiológicas de forma a minimizar os efeitos da falta de oxigênio. Dentre as espécies vegetais de samambaias ocorrentes em ambientes inundáveis nas restingas, se destacam três espécies: Acrostichum danaeifolium Langsd. & Fisch., Blechnum serrulatum Rich. e Thelypteris interrupta (Willd.) K.Iwats. O objetivo deste trabalho é caracterizar os aspectos ecofisiológicos que os esporófitos dessas samambaias apresentam para sobreviver em ambientes de inundação na restinga de Maricá, estado do Rio de Janeiro. Neste sentido, foi determinada a caracterização física e química dos sítios de ocorrências destas samambaias, as variações foliares entre elas, espessura, densidade, massa por unidade de folha, teor de clorofilas e atributos quantitativos das células epidérmicas, além da quantificação e determinação à distribuição dos carboidratos. Para as variáveis dos vegetais foram feitas coletas na estação chuvosa e seca e para variáveis do solo na estação seca. Os sítios analisados se mostraram extremamente ácidos, de baixa fertilidade e com toxidez por macro e micro nutrientes, indicando que as samambaias apresentam tolerância a estes fatores. Na época chuvosa (inundação), as samambaias apresentaram queda na densidade foliar, acompanhada de um aumento de massa por unidade de folha. Esta habilidade de conseguir ganhar massa seca por área classifica todas as samambaias analisadas como tolerantes à inundação. Os altos valores de carboidratos solúveis nas folhas indicam aumento da degradação do amido foliar e o menor teor de carboidrato solúvel encontrado nos caules explicita a redução na respiração das raízes destas plantas sob anoxia/ hipoxia, para evitar a oxidação e o incremento do estoque de amido de reserva, elucidando estratégia de tolerância à inundação. A menor disponibilidade de água na estação seca afeta diretamente os atributos foliares diminuindo o índice estomático, a suculência e a massa por unidade de folha, no qual reflete na queda das concentrações de clorofilas. Os menores valores nas concentrações de clorofila têm influencia direta na presença de amidos foliar que são estocado e, alterando toda a dinâmica dos carboidratos nestas espécies. A análise do sítio onde cresce Acrostichum danaeifolium indica níveis críticos de Na no solo e provavelmente, a produção de mucilagem no caule e no pecíolo é uma estratégia de tolerância ao ambiente salino e inundado. O elevado índice de cobertura de Blechnum serrulatum em ambientes inundados indica que esta espécie possui adaptações a solos hidromórficos, entre elas, grande capacidade de estocagem de amido no caule. A maior sinuosidade das células epidérmicas em T. interrupta permite uma alta suculência mantendo o status hidrológico da folha em ambas as estações. Os resultados apresentados, além de agregar informações sobre a biologia das samambaias nos neotrópicos, irão contribuir para a compreensão da dinâmica de ocupação de espécies herbáceas em ambientes alagáveis nas restingas brasileiras

Plastidic Phosphoglucose Isomerase Is an Important Determinant of Starch Accumulation in Mesophyll Cells, Growth, Photosynthetic Capacity, and Biosynthesis of Plastidic Cytokinins in Arabidopsis

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization of glucose-6-phosphate and fructose-6-phosphate. It is involved in glycolysis and in the regeneration of glucose-6-P molecules in the oxidative pentose phosphate pathway (OPPP). In chloroplasts of illuminated mesophyll cells PGI also connects the Calvin-Benson cycle with the starch biosynthetic pathway. In this work we isolated pgi1-3, a mutant totally lacking pPGI activity as a consequence of aberrant intron splicing of the pPGI encoding gene, PGI1. Starch content in pgi1-3 source leaves was ca. 10-15% of that of wild type (WT) leaves, which was similar to that of leaves of pgi1-2, a T-DNA insertion pPGI null mutant. Starch deficiency of pgi1 leaves could be reverted by the introduction of a sex1 null mutation impeding beta-amylolytic starch breakdown. Although previous studies showed that starch granules of pgi1-2 leaves are restricted to both bundle sheath cells adjacent to the mesophyll and stomata guard cells, microscopy analyses carried out in this work revealed the presence of starch granules in the chloroplasts of pgi1-2 and pgi1-3 mesophyll cells. RT-PCR analyses showed high expression levels of plastidic and extra-plastidic beta-amylase encoding genes in pgi1 leaves, which was accompanied by increased beta-amylase activity. Both pgi1-2 and pgi1-3 mutants displayed slow growth and reduced photosynthetic capacity phenotypes even under continuous light conditions. Metabolic analyses revealed that the adenylate energy charge and the NAD(P) H/NAD(P) ratios in pgi1 leaves were lower than those of WT leaves. These analyses also revealed that the content of plastidic 2-C-methyl-D-erythritol 4-phosphate (MEP)-pathway derived cytokinins (CKs) in pgi1 leaves were exceedingly lower than in WT leaves. Noteworthy, exogenous application of CKs largely reverted the low starch content phenotype of pgi1 leaves. The overall data show that pPGI is an important determinant of photosynthesis, energy status, growth and starch accumulation in mesophyll cells likely as a consequence of its involvement in the production of OPPP/glycolysis intermediates necessary for the synthesis of plastidic MEP-pathway derived hormones such as CKs.