Master of Science / Genetics Interdepartmental Program / Sanzhen Liu / The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, revealing differences in organization of highly repetitive sequences between the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.

The striking evidence for the existence of dark matter in the Universe implies that there is new physics to be discovered beyond the Standard Model. To identify the nature of this dark matter is a key task for modern astroparticle physics, and a large number of experiments pursuing a range of different search strategies have been developed to solve it. The topic of this thesis is the complementarity of these different experiments and the issue of how to combine the information from different searches independently of experimental and theoretical uncertainties. The first part focuses on the direct detection of dark matter scattering in nuclear recoil detectors, with a special emphasis on the impact of the assumed velocity distribution of Galactic dark matter particles. By converting experimental data to variables that make the astrophysical unknowns explicit, different experiments can be compared without implicit assumptions concerning the dark matter halo. We extend this framework to include annual modulation signals and apply it to recent experimental hints for dark matter, showing that the tension between these results and constraints from other experiments is independent of astrophysical uncertainties. We explore possible ways of ameliorating this tension by changing our assumptions on the properties of dark matter interactions. In this context, we propose a new approach for inferring the properties of the dark matter particle, which does not require any assumptions about the structure of the dark matter halo. A particularly interesting option is to study dark matter particles that couple differently to protons and neutrons (so-called isospin-violating dark matter). Such isospin-violation arises naturally in models where the vector mediator is the gauge boson of a new U(1) that mixes with the Standard Model gauge bosons. In the second part, we first discuss the case where both the Z' and the dark matter particle have a mass of a few GeV and then turn to the case where the Z' is significantly heavier. While the former case is most strongly constrained by precision measurements from LEP and B-factories, the latter scenario can be probed with great sensitivity at the LHC using monojet and monophoton searches, as well as searches for resonances in dijet, dilepton and diboson final states. Finally, we study models of dark matter where loop contributions are important for a comparison of LHC searches and direct detection experiments. This is the case for dark matter interactions with Yukawa-like couplings to quarks and for interactions that lead to spin-dependent or momentum suppressed scattering cross sections at tree level. We find that including the contribution from heavy-quark loops can significantly alter the conclusions obtained from a tree-level analysis.

The nature of dark matter and dark energy are currently two of the most important questions in cosmology. In this thesis, we consider studying the dark universe with the redshifts and peculiar velocities of galaxies. In the first half of the thesis, we analyse current peculiar velocity measurements of the bulk flow of our local volume to estimate the underlying dark matter power spectrum. In the second half of the thesis, we consider the prospects for measuring dark matter and dark energy with future galaxy redshift surveys, particularly via redshift space distortions. Fundamentally, bulk flow measurements and redshift space distortions are both sensitive probes of the power spectrum and growth rate of cosmic structure. In the final chapter, we directly compare power spectrum measurements with both methods.

The dark matter paradigm has been a great source of speculation in both the 20th and 21st Centuries. Since its proposed existence in 1933, the mounting evidence has led to this theoretical particle becoming one of the greatest mysteries of modern physics. However, despite its dominant presence in the Universe, little is known about its nature and how it behaves. In this thesis I critically analyse one particular property of dark matter: the self-coupling. The self-interacting dark matter paradigm hypothesises that dark matter is not collisionless as assumed in most cosmological simulations, and in-fact has some probability that it will scatter off itself. Such a self-coupling will resolve many discrepancies that exist between observations and theory, particularly on small, non-linear scales. Moreover, any detection of a self-interaction cross-section will place considerable limitations on the acceptable particle physics models of dark matter and hence has grown to become an important question. In this thesis I develop and implement a method to constrain the self-interaction cross-section of dark matter that exploits continually accreting and merging groups of galaxies as they fall into galaxy clusters. Utilising the ubiquitous nature of accreting substructure, I measure the offsets between dark matter and baryonic gas as they become separated due to their differing interaction properties. Studying this effect over a sample of events, I will be able to make the first ever statistical estimate of the cross-section of dark matter, while averaging over many different unknown merging scenarios. I begin my thesis by deriving an analytical description of sub-halo in-fall, allowing me to constrain dark matter self-interaction models directly from observations. In this study, I find that current archival data should be able to detect a difference in the dynamical behaviour of dark matter and standard model particles at 6σ, and measure the total interaction cross-section σDM/m with 68% confidence limits of ±1 cm2g-1. Having constructed a new method to derive constraints on the cross-section of dark matter I carry out a study into the potential systematics that may affect a measurement. I determine the accuracy of weak gravitational lensing, which is the distortion of light due to intervening mass, as a tool to estimate the positions of substructure in galaxy clusters. I find that the public Lenstool software can measure the position of individual 1:5 x 1013Mʘ peaks with ~ 0:3" systematic bias, as long as they are at least ~ 30" from the cluster centre. Finally, I develop a pipeline that can analyse a sample of inhomogeneous observations from The Hubble Space Telescope and the Chandra X-ray Observatory. By measuring the positions of dark matter, gas and galaxies for 68 individual merging events, from a total of 28 galaxy clusters, I detect a 7:4σ offset between gas and an unobserved dark mass. I make the first ever measurement of cross-section of dark matter from a sample of clusters finding σDM < 0:50cm2/g [95% CL], the best constraints to date. In addition to this I find that the brightest group galaxy in-fact tends to lead the dark matter halo during merging events. Although evidence for the existence of interacting dark matter, I conclude that the astrophysics of the BCG is complicated, and that this apparent directional bias should be considered in all galaxy cluster analyses. Moreover, I show that this technique is easily extendable for future surveys that have larger samples of galaxy clusters, with constraints of σDM < 0:001cm2/g potentially attainable.

Einstein’s equations are derived by following Jacobson’s thermodynamic method. It is seen that a family of possible field equations exist which satisfy the thermodynamic argument. Modified theories of gravity are addressed as possible candidates for replacing dark matter as an explanation for anomalous cosmological phenomena. Many of the proposed modified theories are not powerful enough to explain the currently observed phenomena and are rejected as viable theories of gravity. A surviving candidate, TeVeS, is further analyzed under the aforementioned thermodynamic argument to check for its consistency with thermodynamics.

L'un des problèmes les plus intéressants de la physique moderne est celui de la matière noire de l'Univers, qui reste de nature insaisissable. L'existence de la matière noire est inférée par des preuves indirectes telles que les mesures des courbes de rotation des galaxies, des dispersions de vitesse des galaxies dans les amas galactiques et les effets de lentille gravitationnelle. Ces observations fournissent des preuves sur l'existence d'une matière invisible dominant notre Univers. Il n'existe cependant aucune indication claire sur sa nature. Les observations actuelles en font le constituant dominant de l'Univers, par opposition à la matière baryonique "normale". Deux solutions sont proposées pour résoudre ce mystère. La première est basée sur une modification de la loi de la gravité comme dans la dynamique newtonienne modifiée qui pourrait expliquer les divergences entre prédictions et observations de la dynamique des masses dans l'Univers. L'autre idée consiste à proposer l'existence d'une nouvelle particule massive qui n'interagit pas avec la lumière (appelée WIMP pour "Weakly Interactive Massive Particle"), mais pouvant influencer la matière lumineuse par gravité. Plusieurs théories proposent l'existence de telles nouvelles particules. La plus célèbre de ces théories est la supersymétrie, qui est une extension du Modèle Standard de la Physique des Particules. Si l'un des partenaires supersymétriques des bosons neutres est une particule stable et le plus léger de tous les superpartenaires, il devient alors un candidat idéal pour la matière noire. La supersymétrie est en général le cadre le plus favorable pour l'existence de la matière noire. / The early history of modern physics have been full of problems fixed with un-orthodox yet brilliant solutions. From the Hydrogen electron orbit, black bodyradiation and the ultraviolet catastrophe, to the perihelion precession of Mercury.Quantum Mechanics and General Relativity not only solved these problems butthey opened the path to new observations and predictions about the Universe welive in and the introduction of new problems to be solved.One of the more modern problems we are facing today in physics is the largediscrepancy among measurements of the visible mass in the Universe and the pre-dictions of laws of gravity. An indisputable mass of evidence from different partsof observational cosmology is showing again and again that the observed lumi-nous mass in the Universe constitutes a tiny fraction of the matter that actuallyexists. The proposed solutions of this problem comes in two completely differentflavors. One proposed solution is that the laws of gravity are not the same in thelimit of tiny accelerations. Theories of modified gravitational dynamics proposea non-linear term in Newton law of gravity that becomes relevant at small accel-erations which in turn can explains the missing matter. The other solution to themissing matter is the introduction of new type of matter that does not interact withlight, making it invisible yet inferred to exist by its gravitational effect. The newmatter becomes a new elementary particle to be added to list of already knownelementary particles. While there are many candidates to this new elementaryparticle the favored one is called a WIMP or Weakly Interacting Massive Particle.

Les courants stellaires de marée sont des structures en étoile immaculées qui jouent un rôle central dans la résolution des mystères de longue date de l'archéologie galactique. Étant donné que les flux sont de nature orbitale, ils possèdent intrinsèquement les caractéristiques de résolution de la distribution de masse sous-jacente de la galaxie et peuvent être utilisés pour sonder la forme du halo de matière noire. En plus de tester le scénario de «fusion hiérarchique» de la formation de galaxies, les brèches de ruisseau peuvent également fournir une preuve indirecte de l’existence de sous-halos de matière noire (ce qui, en principe, limite la nature de la particule de matière noire elle-même). Pour toutes ces raisons, l'analyse dynamique des flux stellaires de la Voie Lactée devient naturellement l'un des problèmes les plus intéressants. Cependant, le principal défi consiste à détecter ces structures. Au cours de la thèse, l’algorithme STREAMFINDER (un algorithme à la pointe de la technologie) a été conçu pour traiter systématiquement le jeu de données Gaia (le nouveau catalogue astrophysique de l’ESA contenant des solutions astrométriques sans précédent de plus de 1,6 milliard d’étoiles) pour la détection des flux stellaires de la Voie lactée. Cette lourde entreprise a permis de détecter 10 structures de flux de confiance, dont 5 étaient considérées comme de nouvelles découvertes. Cette récolte de structures a également facilité, pour la première fois, la création d’une carte structurale et cinématique panoramique des flux stellaires de la rivière Milky. Halo, poussant notre communauté encore plus loin dans l’histoire complexe de la formation de notre galaxie. Ce projet a été immédiatement suivi de l'analyse orbitale de l'un des flux détectés (à savoir GD-1) pour explorer les améliorations des modèles de potentiel gravitationnel de notre galaxie. Les contraintes imposées à la masse de la Voie lactée et à la forme de son halo de matière noire, obtenues simplement en utilisant ce seul flux, ont révélé la puissance potentielle que l'analyse d'un ensemble de flux permettrait de sonder la distribution globale de la masse galactique de notre galaxie. Ainsi, la thèse a ouvert la voie à de nouvelles découvertes des sous-structures stellaires, soulignant également les perspectives d'avenir dans ce domaine. / Tidal stellar streams are pristine star structures that play central role in addressing long standing mysteries of the Galactic archaeology. Since streams are orbital in nature, they inherently possess the characteristics of unravelling the underlying mass distribution of the galaxy, and can be used to probe the shape of the dark matter halo. Besides testing the ‘hierarchical merging’ scenario of galaxy formation, stream gaps can also provide indirect evidence for the existence of dark matter sub-halos (thereby, in principle, constraining the nature of the dark matter particle itself). Due to all these reasons, the dynamical analysis of stellar streams of the Milky Way Galaxy naturally becomes one of the interesting problems. However, the foremost challenge is to detect these structures. During the thesis, STREAMFINDER algorithm (a state of the art algorithm) was designed to systematically process the Gaia dataset (ESA’s novel astrophysical catalogue containing unprecedented astrometric solutions of over 1.6 billion stars) for the detection of the stellar streams of the Milky Way. This hefty endeavour led to the detection of 10 high confidence stream structures, of which 5 were reported as new discoveries.This harvest of structures also facilitated, for the first time, creation of a panoramic structural and kinematic map of the stellar streams of the Milky Way halo, taking our community a step further in unravelling the complex formation history of our Galaxy. This project was instantly followed by the orbital analysis of one of the detected streams (namely GD-1) to explore the improvements in the gravitational potential models of our Galaxy. The constraints on the Milky Way’s mass and that on the shape of its dark matter halo, that were obtained by simply employing this single stream, revealed the potential power the analysis of an ensemble of streams would hold in in probing the overall galactic mass distribtuion of our Galaxy. Thereby, the thesis paved way for new discoveries of the stellar substructures, also highlighting the future prospects in this field.

Le 4 Juillet 2012, la découverte d'une nouvelle particule scalaire d'une masse de l’ordre de 125 GeV a été annoncée par les collaborations ATLAS et CMS.Une nouvelle ère s'annonce : celle au cours de laquelle il faudra déterminer précisément les propriétés de cette nouvelle particule.Cela est crucial afin d'établir si cette particule est bien la trace du mécanisme responsable de la brisure de la symétrie du secteur électro-faible. Cela permettrait aussi de repérer tout élément susceptible d'être associé à une « nouvelle physique » dans le cas où le mécanisme de brisure ferait intervenir des ingrédients autres que ceux prédits par le Modèle Standard.Dans cette thèse, nous avons essayé de comprendre et de caractériser jusqu’à quel point ce nouveau champ scalaire est le boson de Higgs prédit par le Modèle Standard. Nous avons établi les applications d'une telle découverte dans le contexte de théories supersymétriques et de modèles décrivant la matière noire.Dans une première partie consacrée au Modèle Standard de la physique des particules, nous étudions après une courte introduction au domaine, le processus de production d'une paire de bosons de Higgs au LHC. Un résultat majeur est que ce mode de production permettra de mesurer le couplage trilinéaire du Higgs qui est un paramètre essentiel à mesurer afin de reconstruire le potentiel du Higgs et donc représente la dernière vérification à effectuer pour confirmer l'origine de la brisure spontanée de la symétrie électro-faible.La deuxième partie traite des théories supersymétriques. Après une introduction au sujet, un de nos importants résultats est d'avoir fortement contraint un certain nombre de modèles supersymétriques après la découverte du boson de Higgs. Nous avons aussi introduit une nouvelle approche qui permet aux physiciens expérimentateurs de rechercher de manière efficace les bosons de Higgs supersymétriques dans les expériences actuelles et futures du LHC.La troisième partie concerne la matière noire. Nous présentons des résultats qui établis-sent d'importantes limitations sur des modèles où la matière noire interagirait avec le boson de Higgs. Nous discutons aussi de scénarios alternatifs qui font intervenir de la matière noire hors équilibre avec le bain thermique. Dans un premier temps nous dé-montrons qu'il existe un lien étroit entre la température de réchauffement de l'univers et le schéma de brisure du groupe de jauge du Modèle Standard et dans un deuxième temps nous étudions la genèse de matière noire par l'intermédiaire de nouveaux bosons Z’. / On the 4th of July 2012, the discovery of a new scalar particle with a mass of order 125 GeV was announced by the ATLAS and CMS collaborations. An important era is now opening: the precise determination of the properties of the produced particle. This is of extreme importance in order to establish that this particle is indeed the relic of the mechanism responsible for the electroweak symmetry breaking and to pin down effects of new physics if additional ingredients beyond those of the Standard Model are involved in the symmetry breaking mechanism. In this thesis we have tried to understand and characterize to which extent this new scalar field is the Standard Model Higgs Boson and set the implications of this discovery in the context of Supersymmetric theories and dark matter models.In a first part devoted to the Standard Model of particle physics, we discuss the Higgs pair production processes at the LHC and the main output of our results is that they al-low for the determination of the trilinear Higgs self-coupling which represents a first important step towards the reconstruction of the Higgs potential and thus the final verifica-tion of the Higgs mechanism as the origin of electroweak symmetry breaking.The second part is about Supersymmetric theories. After a review of the topics one of our result is to set strong restrictions on Supersymmetric models after the Higgs discov-ery. We also introduce a new approach which would allow experimentalists to efficiently look for supersymmetric heavy Higgs bosons at current and next LHC runs.The third part concerns dark matter. We present results which give strong constraints on Higgs-portal models. We finally discuss alternative non-thermal dark matter scenario. Firstly, we demonstrate that there exists a tight link between the reheating temperature and the scheme of the Standard Model gauge group breaking and secondly we study the genesis of dark matter by a Z’ portal.

In this work we test a cosmological model with an interaction between dark energy and dark matter, where a tachyon scalar field plays the role of dark energy. With that in mind, we developed a numerical code that solves the background equations and extracts the cosmological parameters and we compared the results of the interacting tachyon model with those of other dark energy candidates. Our results show that the model indeed explains the observational data and has interesting cosmological properties, but might face challenges when compared to other dark energy candidates. / Neste trabalho testamos um modelo cosmológico com uma interação entre energia escura e matéria escura, onde um campo escalar taquiônico desempenha o papel da energia escura. Para isso, desenvolvemos um código computacional que resolve as equações numericamente e vincula os parâmetros cosmológicos e, assim, comparamos os resultados do modelo taquiônico interagente com os de outros candidatos à energia escura. Nossas análises mostram que o modelo, de fato, consegue explicar os dados observacionais, além de possuir propriedades cosmológicas interessantes, mas apresenta dificuldades quando comparado a outros modelos de energia escura.

Modern Cosmology offers us a great understanding of the universe with striking precision, made possible by the modern technologies of the newest generations of telescopes. The standard cosmological model, however, is not absent of theoretical problems and open questions. One possibility that has been put forward is the existence of a coupling between dark sectors. The idea of an interaction between the dark components could help physicists understand why we live in an epoch of the universe where dark matter and dark energy are comparable in terms of energy density, which can be regarded as a strange coincidence given that their time evolutions are completely different. Dark matter and dark energy are generally treated as perfect fluids. Interaction is introduced when we allow for a non-zero term in the right-hand side of their individual energy-momentum tensor conservation equations. We proceed with a phenomenological approach to test models of interaction with observations of redshift-space distortions. In a flat universe composed only of these two fluids, we consider separately two forms of interaction, through terms proportional to the densities of both dark energy and dark matter. An analytic expression for the growth rate approximated as f = Omega^gamma, where Omega is the percentage contribution from the dark matter to the energy content of the universe and gamma is the growth index, is derived in terms of the interaction strength and of other parameters of the model in the first case, while for the second model we show that a non-zero interaction cannot be accommodated by the index growth approximation. The successful expressions obtained are then used to compare the predictions with growth of structure observational data in a Markov Chain Monte Carlo code and we find that the current growth data alone cannot impose constraints on the interaction strength due to their large uncertainties. We also employ observations of galaxy clusters to assess their virial state via the modified Layzer-Irvine equation in order to detect signs of an interaction. We obtain measurements of observed virial ratios, interaction strength, rest virial ratio and departure from equilibrium for a set of clusters. A compounded analysis indicates an interaction strength of 0.29^{+2.25}_{-0.40}, compatible with no interaction, but a compounded rest virial ratio of 0.82^{+0.13}_{-0.14}, which means a 2 sigma confidence level detection. Despite this tension, the method produces encouraging results while still leaves room for improvement, possibly by removing the assumption of small departure from equilibrium. / A cosmologia moderna oferece um ótimo entendimento do universo com uma precisão impressionante, possibilitada pelas tecnologias modernas das gerações mais novas de telescópios. O modelo cosmológico padrão, porém, não é livre de problemas do ponto de vista teórico, deixando perguntas ainda sem respostas. Uma possibilidade que tem sido proposta é a existência de um acoplamento entre setores escuros. A ideia de uma interação entre os componentes escuros poderia ajudar os físicos a entender por que vivemos em uma época do universo na qual a matéria escura e a energia escura são comparáveis em termos de densidades de energia, o que pode ser considerado uma estranha coincidência dado que suas evoluções com o tempo são completamente diferentes. Matéria escura e energia escura são geralmente tratadas como fluidos perfeitos. A interação é introduzida ao permitirmos um tensor não nulo no lado direito das equações de conservação dos tensores de energia-momento. Prosseguimos com uma abordagem fenomenológica para testar modelos de interação com observações de distorções no espaço de redshift. Em um universo plano composto apenas por esses dois fluidos, consideramos, separadamente, duas formas de interação, através de termos proporcionais às densidades de energia escura e de matéria escura. Uma expressão analítica para a taxa de crescimento aproximada por f = Omega^gamma, onde Omega é a contribuição percentual da matéria escura para o conteúdo do universo e gamma é o índice de crescimento, é deduzida em termos da interação e de outros parâmetros do modelo no primeiro caso, enquanto para o segundo caso mostramos que uma interação não nula não pode ser acomodada pela aproximação do índice de crescimento. As expressões obtidas são então utilizadas para comparar as previsões com dados observacionais de crescimento de estruturas em um programa para Monte Carlo via cadeias de Markov. Concluímos que tais dados atuais por si só não são capazes de restringir a interação devido às suas grandes incertezas. Utilizamos também observações de aglomerados de galáxias para analisar seus estados viriais através da equação de Layzer-Irvine modificada a fim de detectar sinais de interação. Obtemos medições de taxas viriais observadas, constante de interação, taxa virial de equilíbrio e desvio do equilíbrio para um conjunto de aglomerados. Uma análise combinada indica uma constante de interação 0.29^{+2.25}_{-0.40}, compatível com zero, mas uma taxa virial de equilíbrio combinada de 0.82^{+0.13}_{-0.14}, o que significa uma detecção em um intervalo de confiança de 2 sigma. Apesar desta tensão, o método produz resultados encorajadores enquanto ainda permite melhorias, possivelmente pela remoção da suposição de pequenos desvios do equilíbrio.