A protocol was developed to measure ammonia emission concentrations from dairies using an isolation flux chamber. A hybrid dairy in Comanche county, Texas, was measured for one week each during August 2002 and January 2003. Sixty total ammonia samples were taken from the free stall barn, open lot, mixing tank, separated solids, compost, and two lagoons using the developed protocol. The ammonia concentration measurements were made using a chemiluminescence analyzer located inside a mobile laboratory. From the emission concentrations recorded, it was estimated that 9.68 metric tons of ammonia were produced from this dairy per year. An emission factor of 13.34 ± 28.80 kilograms per day per thousand head of cattle (kg/day/1000 head) was estimated for this dairy (±95% confidence intervals) during summer conditions. For winter conditions the emission factor was 12.05 ± 12.89 kg/day/1000 head. The 11% difference of the emission factors from summer to winter conditions was predominantly from the change in ambient and control volume temperatures (a mean difference of approximately 25 degrees Celsius), differences in source temperatures, and seasonal variability in husbandry. The adsorption of ammonia onto different polymer tubing used in pollutant stream conveyance was researched for possible systematic losses. Teflon and low density polyethylene (LDPE) were tested for ammonia losses with treatments of: temperature, length, and inlet concentration. Inlet concentration and temperature were significant factors used to describe ammonia adsorption for Teflon, whereas LDPE was also affected by tubing length. These factors were used to create a model to correct the summer dairy measurements for ammonia losses, resulting in an emission factor increase of 8.3% over the original value obtained from the flux chamber. A nitrogen mass balance was performed to estimate the amount of nitrogen available for ammonia formation as excreted - 177.5 kilograms per year per animal (wet basis). The amount of ammonia excreted per year was also estimated to be 26.63 kilograms per year. The measured ammonia emitted from the dairy was five times less than the ammonia excreted and thirty-six times less than the total nitrogen excreted.

La caldera du volcan Rinjani contient un lac d’un volume de 1 km³ qui est probablement le plus grand lac volcanique au monde présentant une anomalie thermique nette. Ce lac présente une composition neutre chlorure sulfate bicarbonate inhabituelle pour les lacs volcaniques. Sa TDS (2600 mg/l) et conductivité (3500µs/cm) élevées indiquent un apport de fluides hydrothermaux très important. Enfin, son alcalinité élevée (520 mg/l), indique un apport important de dioxyde de carbone dans le lac. Les sources thermales situées autour du Gunung Baru (cône volcanique situé dans la caldera) ont une composition chimique en éléments majeurs et une composition isotopique proche de celles du lac volcanique indiquant qu’elles sont essentiellement le résultat du recyclage du lac par le système hydrothermal. Les variations de compositions entre les différentes sources ont permis de montrer que leurs compositions est le résultat du mélange entre un fluide hydrothermal profond de composition neutre chlorure, dont la température a été estimée à 270°C, et d’un fluide plus superficiel riche en magnésium et en sulfate. Le flux de dioxyde de carbone à la surface du lac a été estimé à l’aide de la méthode de la chambre d’accumulation et par calcul à environ 2300 t/j, ce qui représente un apport significatif de gaz. Cependant, comme le lac présente une structure polymictique, le risque d’accumulation de dioxyde de carbone en profondeur et donc d’éruption limnique peut être exclus. Pour la première fois dans cette thèse, le modèle d’estimation des flux thermiques émis par les lacs volcaniques mis au point par Stevenson (1992) a été contraint par des mesures des paramètres météorologiques mesurés en continu, ce qui a permis de valider le modèle. De plus, nous avons pu montrer que l’essentiel des variations de températures des lacs volcaniques est dû à des variations météorologiques. En utilisant le flux thermique plutôt que la température, il est dès lors possible d’avoir accès à des variations de l’activité volcanique. Le flux thermique estimé pour le lac du Rinjani est de 1700 MW, ce qui représente le flux le plus élevé jamais mesuré sur un lac volcanique aérien. Ce flux thermique est aussi plus élevé que le flux thermique mesuré sur des lacs de lave à 800°C. Ce paradoxe apparent s’explique par la plus grande dimension des lacs volcaniques, la capacité calorifique de l’eau quatre fois plus importante que celle du magma et la viscosité de l’eau 1 million de fois inférieure, ce qui fait de l’eau un excellent fluide caloporteur pour transporter les calories vers la surface.

Studying the acceleration and propagation mechanisms of Galactic cosmic rays can provide information regarding astrophysical sources, the properties of our Galaxy, and possible exotic sources such as dark matter. To understand cosmic ray acceleration and propagation mechanisms, accurate measurements of different cosmic ray elements over a wide energy range are needed. The PAMELA experiment is a satellite-borne apparatus which allows different cosmic ray species to be identified over background. Measurements of the cosmic ray antiproton flux and the antiproton-to-proton flux ratio from 1.5 GeV to 180 GeV are presented in this thesis, employing the data collected between June 2006 and December 2008. Compared to previous experiments, PAMELA extends the energy range of antiproton measurements and provides significantly higher statistics. During about 800 days of data collection, PAMELA identified approximately 1300 antiprotons including 61 above 31.7 GeV. A dramatic improvement of statistics is evident since only 2 events above 30 GeV are reported by previous experiments. The derived antiproton flux and antiproton-to-proton flux ratio are consistent with previous measurements and generally considered to be produced as secondary products when cosmic ray protons and helium nuclei interact with the interstellar medium. To constrain cosmic ray acceleration and propagation models, the antiproton data measured by PAMELA were further used together with the proton spectrum reported by PAMELA, as well as the B/C data provided by other experiments. Statistical tools were interfaced with the cosmic ray propagation package GALPROP to perform the constraining analyses. Different diffusion models were studied. It was shown in this work that only current PAMELA data, i.e. the antiproton-to-proton ratio and the proton flux, are not able to place strong constraints on propagation parameters. Diffusion models with a linear diffusion coefficient and modified diffusion models with a low energy dependence of the diffusion coefficient were studied in the $\chi^{2}$ study. Uncertainties on the parameters and the goodness of fit of each model were given. Some models are further studied using the Bayesian inference. Posterior means and errors of the parameters base on our prior knowledge on them were obtained in the Bayesian framework. This method also allowed us to understand the correlation between parameters and compare models. Since the B/C ratio used in this analysis is from experiments other than PAMELA, future PAMELA secondary-to-primary ratios (B/C, $^{2}$H/$^{4}$He and $^{3}$He/$^{4}$He) can be used to avoid the data sets inconsistencies between different experiments and to minimize uncertainties on the solar modulation parameters. More robust and tighter constraints are expected. The statistical techniques have been demonstrated useful to constrain models and can be extended to other observations, e.g. electrons, positrons, gamma rays etc. Using these channels, exotic contributions from, for example, dark matter will be further investigated in future. / QC 20120523

The development of genome scale metabolic models have been aided by the increasing availability of genome sequences of microorganisms such as Geobacter sulfurreducens, involved in environmentally relevant processes such as the in-situ bioremediation of U(VI). Since microbial activities are the major driving forces for geochemical changes in the sub-surface, understanding of microbial behavior under a given set of conditions can help predict the likely outcome of potential subsurface bioremediation strategies. Hence, a model based lookup table was created to capture the variation in physiology of G. sulfurreducens in response to environmental perturbations. Thermodynamically feasible flux distributions were generated by incorporating thermodynamic constraints in the model. These constraints together with the mass balance constraints formed the thermodynamics based metabolic flux analysis model (TMFA). Metabolomics experiments were performed to determine the concentration of intracellular metabolites. These concentrations were posed as constraints in the TMFA model to improve the model accuracy.

Plasmodium falciparum is the causative agent of malaria, one of the world‟s most prevalent infectious diseases. The emergence of strains resistant to current therapeutics creates the urgent need to identify new classes of antimalarials. Here we present and analyse a constraints-based model (iMPMP427) of P. falciparum metabolism. Consisting of 427 genes, 513 reactions, 457 metabolites, and 5 intracellular compartments, iMPMP427 is relatively streamlined and contains an abundance of transport reactions consistent with P. falciparum’s observed reliance on host nutrients. Flux Balance Analysis simulations reveal the model to be predictive in regards to nutrient transport requirements, amino acid efflux characteristics, and glycolytic flux calculation, which are validated by a wealth of experimental data. Furthermore, enzymes deemed to be essential for parasitic growth by iMPMP427 lend support to several previously computationally hypothesized metabolic drug targets, while discrepancies between essential enzymes and experimentally annotated drug targets highlight areas of malarial metabolism that could benefit from further research.

Plasmodium falciparum is the causative agent of malaria, one of the world‟s most prevalent infectious diseases. The emergence of strains resistant to current therapeutics creates the urgent need to identify new classes of antimalarials. Here we present and analyse a constraints-based model (iMPMP427) of P. falciparum metabolism. Consisting of 427 genes, 513 reactions, 457 metabolites, and 5 intracellular compartments, iMPMP427 is relatively streamlined and contains an abundance of transport reactions consistent with P. falciparum’s observed reliance on host nutrients. Flux Balance Analysis simulations reveal the model to be predictive in regards to nutrient transport requirements, amino acid efflux characteristics, and glycolytic flux calculation, which are validated by a wealth of experimental data. Furthermore, enzymes deemed to be essential for parasitic growth by iMPMP427 lend support to several previously computationally hypothesized metabolic drug targets, while discrepancies between essential enzymes and experimentally annotated drug targets highlight areas of malarial metabolism that could benefit from further research.

The development of genome scale metabolic models have been aided by the increasing availability of genome sequences of microorganisms such as Geobacter sulfurreducens, involved in environmentally relevant processes such as the in-situ bioremediation of U(VI). Since microbial activities are the major driving forces for geochemical changes in the sub-surface, understanding of microbial behavior under a given set of conditions can help predict the likely outcome of potential subsurface bioremediation strategies. Hence, a model based lookup table was created to capture the variation in physiology of G. sulfurreducens in response to environmental perturbations. Thermodynamically feasible flux distributions were generated by incorporating thermodynamic constraints in the model. These constraints together with the mass balance constraints formed the thermodynamics based metabolic flux analysis model (TMFA). Metabolomics experiments were performed to determine the concentration of intracellular metabolites. These concentrations were posed as constraints in the TMFA model to improve the model accuracy.

En la present tesi s'exposa una síntesi de la hidrogeologia del massís de les Gavarres i zones adjacents amb l'objectiu final d'identificar i descriure'n la dinàmica, ampliant el coneixement hidrogeològic d'aquesta zona sotmesa a una creixent demanda i avaluant la disponibilitat de recursos hídrics. Concretament, l'estudi hidrogeològic defineix i descriu les formacions hidrogeològiques locals, les seves àrees de recàrrega i els sistemes de flux que es produeixen acompanyant-ho de diverses cartografies piezomètriques. Addicionalment, es caracteritza la dinàmica del sistema mitjançant l'estudi de les fàcies hidroquímiques i de les dotacions en isòtops estables i radiogènics (d18O, dD, 3H, d13C, 87Sr/86Sr) que permeten integrar-les en un sistema hidrogeològic regional. Els resultats es corroboren amb una anàlisi multivariable, consistent en l'anàlisi de components principals, i amb un estudi de mescla de membres extrems. També, s'estudien les fonts riques en CO2 o "picants" mitjançant un seguiment de cabal i hidroquímic, amb la finalitat d'afinar el model conceptual hidrològic derivat de les dades anteriors integrant-hi aquests elements singulars del sistema.El desenvolupament de la tesi ha permès identificar dos sistemes principals de flux com a origen de la recàrrega del sistema. Es descriu un sistema de caràcter local representat per la recàrrega procedent del massís de les Gavarres, que s'estableix en sentit divergent de d'aquest, el qual es fa present a la zona del Baix Ter i a la Vall d'Aro, així com a algunes captacions del marge oriental de la depressió de la Selva. Es de tipus pistó governat per fractures locals i adopta un sentit vertical ascendent a la zona nord a través de les formacions paleògenes. S'estimen els temps de residència en base al contingut en triti segons un model de desintegració i s'obtenen temps de trànsit d'entre 20-30 anys. En base als isòtops estables es determina l'estacionalitat de la recàrrega i s'avalua el percentatge de la precipitació infiltrant (10-15%) mitjançant mètodes hidroquímics. El segon sistema de flux que es constata és d'àmbit regional. Aquest es manifesta en les captacions més profundes de la depressió de la Selva, s'indueix antròpicament a les formacions sedimentàries soprajacents i ve governat per fractures regionals que delimiten les unitats morfoestructurals. Presenta característiques hidroquímiques diferenciades com a conseqüència de la interacció amb la roca sota elevats temps de residència, majors a 50 anys, segons indica el contingut en triti. La dotació en isótops estables suggereix una àrea de recàrrega que se situa a la serralada Transversal i/o en el massís de les Guilleries.En les fonts riques en CO2 es constata la presència d'ambdós sistemes de flux els quals s'hi mesclen en diferents proporcions. Es considera que el sistema de flux local s'incorpora al cabal de les fonts amb posterioritat a l'addició del gas diluint les elevades mineralitzacions de l'aigua que s'atribueixen a la presència del gas. Al sistema regional es constata amb una major constància quantitativa i qualitativa.L'anàlisi de components principals i l'estudi de la mescla de membres extrems corroboren la dinàmica hidrogeològica descrita mitjançant l'estudi multisotòpic. En concret, senyalen el domini de les reaccions silicatades i les influencies menors d'altres processos relacionats amb heterogeneïtats locals del medi, inducció antròpica de fluxos i mescla amb sistemes superficials. Concretament, a la zona del Baix Ter es caracteritza el sistema de flux dominant procedent de les gavarres que s'estableix en sentit vertical ascendent a la depressió i localment s'estimen les aportacions d'un flux influenciat per elevats cabals d'extracció procedent del riu Ter i intrusió salina. Els resultats manifesten l'aplicabilitat d'ambdós mètodes així com les seves limitacions.Finalment l'estudi manifesta el paper de les fractures en el control dels sistemes de flux i de la recàrrega que afavoreixen l'aportació d'aigües amb temps de residència molt elevats i l'establiment de fluxos de sentit vertical ascendent. També, planteja la dinàmica del sistema a una escala regional considerant que les aportacions subterrànies procedents de les formacions hidrogeològiques profundes contribueixen notablement a les aportacions i als recursos disponibles. / This dissertation is focused on the hydrogeology of the Gavarres range and the surrounding basins of Selva and Baix Empordà. Its main objective consists on describing the hydrodynamics of the system based on geological field work, potentiometric data, hydrochemistry as well as isotopic data ((d18O, dD, 3H, d13C, 87Sr/86Sr). The purpose is to determine a conceptual model that describes the main flow systems of the area as a useful tool to define future exploitation criteria for those related aquifers. The occurrence of rich-CO2 cold springs in the area provides an opportunity to investigate a specific hydrological behavior and are studied as a singular points of the hydrogeological system.This research has pointed out the existence of two main flow systems: a local system flow with recharge area in the Gavarres range and a regional system flow with longer flow paths from the Transversal and/or Guilleries range. The data results are summarized as follows.The study identifies and characterizes different hydrogeological formations and potentiometric data show a divergent flux from the Gavarres range towards the sourronding basins. Hydraulic head data also indicates the influence of fractures in the local flow system and a vertical ascending recharge is suggested in the north basin. Furthermore, hydrochemical data supports potentiometric observations and also suggests different residence times depending on flow path. The local meteoric line obtained from rainfall stable isotopes indicates seasonal recharge and its positions respect groundwater samples suggests different dynamics and recharge area in Empordà and Selva basins. Gavarres is the main recharge area but in deepest points of south basin a different and higher recharge areas are considered. CO2-rich springs also agree with these observations despite a modification of its d18O contents because of CO2 exsolution. According to the geological setting, those recharge areas would be located at the Transversal and Guilleries range, which bound the Selva basin in its northern and western boundaries. Tritium content points out different residence times of water samples. Two different groups of tritium data are distinguished, which correlates with the observed differences using stable isotopes, one infiltrated before 1952 occurs at the deepest wells of the Selva basin and at the CO2-rich springs, and is related to a regional flow system. The high exploitation rate in this basin induces flow from this deep regional system to arkosic basin materials. A second, modern set of data which would enter the system 20 years ago is described in Empordà and Aro basin as well as in shallow aquifers in Selva basin. Strontium content and 87Sr/86Sr ratios are used to tracer the flow path and the isotopic content. In particular, Empordà aquifers show a radiogenic signature acquired in the local metamorphic recharge area supporting the existence of vertical upwelling flow.Principal component analysis (PCA) allows statistical grouping that reflects bedrock lithology and supports some of the identified chemical reactions. Subsequently, end-member mixing analysis has been applied to the Baix Empordà samples to verify mixing rates between the Gavarres recharge through the paleogene aquifers, the Ter river capture and salt water intrusion. Despite that the method needs to be carefully checked for consistency, its application to water samples from the alluvial aquifer demonstrates the major recharge from the underlying paleogene formations, a Ter river participation of about 20%, and a maximum percentage of 10% of salt water in specific wells.In conclusion, the study of the hydrogeology of the Gavarres-Selva-Baix Empordà system has pictured two distinct flow systems with different chemical and isotopic content and characterized by different dynamics. Furthermore, it shows that the Gavarres range only acts as a local recharge area, and that groundwater from the Selva basin also gets its inflow from distant areas, namely the Transversal and Guilleries ranges.

Building a quantum computer is a formidable challenge. In this thesis, we focus on two projects, which tackle very different aspects of quantum computation, and yet still share a common goal in hopefully getting us closer to implementing a quantum computer on a large scale. The first project involves a numerical error threshold calculation of a quantum error correcting code called a surface code. These are local check codes, which means that only nearest neighbour interaction is required to determine where errors occurred. This is an important advantage over other approaches, as in many physical systems, doing operations on arbitrarily spaced qubits is often very difficult. An error threshold is a measure of how well a given error correcting scheme performs. It gives the experimentalists an idea of which approaches to error correction hold greater promise. We simulate both toric and planar variations of a surface code, and numerically calculate a threshold value of approximately $6.0 \times 10^{-3}$, which is comparable to similar calculations done by others \cite{Raussendorf2006,Raussendorf2007,Wang2009}. The second project deals with coupling superconducting flux qubits together. It expands the scheme presented in \cite{Plourde2004} to a three qubit, two coupler scenario. We study L-shaped and line-shaped coupler geometries, and show how the coupling strength changes in terms of the dimensions of the couplers. We explore two cases, the first where the interaction energy between two nearest neighbour qubits is high, while the coupling to the third qubit is as negligible as possible, as well as a case where all the coupling energies are as small as possible. Although only an initial step, a similar scheme can in principle be extended further to implement a lattice required for computation on a surface code.

Building a quantum computer is a formidable challenge. In this thesis, we focus on two projects, which tackle very different aspects of quantum computation, and yet still share a common goal in hopefully getting us closer to implementing a quantum computer on a large scale. The first project involves a numerical error threshold calculation of a quantum error correcting code called a surface code. These are local check codes, which means that only nearest neighbour interaction is required to determine where errors occurred. This is an important advantage over other approaches, as in many physical systems, doing operations on arbitrarily spaced qubits is often very difficult. An error threshold is a measure of how well a given error correcting scheme performs. It gives the experimentalists an idea of which approaches to error correction hold greater promise. We simulate both toric and planar variations of a surface code, and numerically calculate a threshold value of approximately $6.0 \times 10^{-3}$, which is comparable to similar calculations done by others \cite{Raussendorf2006,Raussendorf2007,Wang2009}. The second project deals with coupling superconducting flux qubits together. It expands the scheme presented in \cite{Plourde2004} to a three qubit, two coupler scenario. We study L-shaped and line-shaped coupler geometries, and show how the coupling strength changes in terms of the dimensions of the couplers. We explore two cases, the first where the interaction energy between two nearest neighbour qubits is high, while the coupling to the third qubit is as negligible as possible, as well as a case where all the coupling energies are as small as possible. Although only an initial step, a similar scheme can in principle be extended further to implement a lattice required for computation on a surface code.