This research uses a Bayesian approach to study the biases that may occur when kinematic data is used to estimate the mass of a galaxy. Data is simulated from the Hernquist (1990) distribution functions (DFs) for velocity dispersions of the isotropic, constant anisotropic, and anisotropic Osipkov (1979) and Merritt (1985) type, and then analysed using the isotropic Hernquist model. Biases are explored when i) the model and data come from the same DF, ii) the model and data come from the same DF but tangential velocities are unknown, iii) the model and data come from different DFs, and iv) the model and data come from different DFs and the tangential velocities are unknown. Mock observations are also created from the Gauthier (2006) simulations and analysed with the isotropic Hernquist model. No bias was found in situation (i), a slight positive bias was found in (ii), a negative bias was found in (iii), and a large positive bias was found in (iv). The mass estimate of the Gauthier system when tangential velocities were unknown was nearly correct, but the mass profile was not described well by the isotropic Hernquist model. When the Gauthier data was analysed with the tangential velocities, the mass of the system was overestimated. The code created for the research runs three parallel Markov Chains for each data set, uses the Gelman-Rubin statistic to assess convergence, and combines the converged chains into a single sample of the posterior distribution for each data set. The code also includes two ways to deal with nuisance parameters. One is to marginalize over the nuisance parameter at every step in the chain, and the other is to sample the nuisance parameters using a hybrid-Gibbs sampler. When tangential velocities, v(t), are unobserved in the analyses above, they are sampled as nuisance parameters in the Markov Chain. The v(t) estimates from the Markov chains did a poor job of estimating the true tangential velocities. However, the posterior samples of v(t) proved to be useful, as the estimates of the tangential velocities helped explain the biases discovered in situations (i)-(iv) above. / Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2013-03-26 17:23:14.643

Identifying the relic particles that constitute the cold dark matter in our Universe is an outstanding problem in astro-particle physics. Direct detection experiments are among the most promising methods of detecting particle dark matter through non-gravitational interactions. In this thesis, the usual assumptions made when calculating the event rate at direct detection experiments are examined. Varying astrophysical parameters and the dark matter velocity distribution leads to significant changes in acceptance regions and exclusion curves for scenarios in which the tail of the velocity distribution is sampled; this includes 'light dark matter' (mass less than 10 GeV) and 'inelastic dark matter'. The DAMA and CoGeNT collaborations both report an annual modulation in their event rate that they attribute to dark matter. Two analyses of these experiments are performed. In the first, it is shown that these experiments can be compatible with each other and with the constraints from other direct detection experiments. This requires some isospin violation in the couplings of dark matter to protons and neutrons and a small inelastic splitting to boost the modulation fraction. The second analysis provides a comparison of the modulation signals free from all astrophysical parameters, under the assumption that dark matter scatters elastically. Again it is found that some isospin violation and a boosted modulation fraction is required in order that DAMA and CoGeNT are consistent with all experiments. A boosted modulation fraction may arise from a velocity distribution different from the Maxwell-Boltzmann distribution, which is usually assumed. Finally, a supersymmetric theory in which the dark matter candidate is a mixture of left- and right-handed sneutrino is considered. This theory has many novel signatures at colliders, indirect detection and direct detection experiments.

The identification of the relic particles which presumably constitute cold dark matter is a key challenge for astroparticle physics. Indirect methods for their detection using high energy astro- physical probes such as cosmic rays have been much discussed. In particular, recent ‘excesses’ in cosmic ray electron and positron fluxes, as well as in microwave sky maps, have been claimed to be due to the annihilation or decay of dark matter. In this thesis, we argue however that these signals are plagued by irreducible astrophysical backgrounds and show how plausible con- ventional physics can mimic the alleged dark matter signals. In chapter 1, we review evidence of, and possible particle candidates for, cold dark matter, as well as our current understanding of galactic cosmic rays and the state-of-the-art in indirect detection. All other chapters contain original work, mainly based on the author’s journal publications. In particular, in chapter 2, we consider the possibility that the rise in the positron fraction observed by the PAMELA satellite is due to the production through (hadronic) cosmic ray spallation and subsequent acceleration of positrons, in the same sources as the primary cosmic rays. We present a new (unpublished) analytical estimate of the range of possible fluctuations in the high energy electron flux due to the discreteness of plausible cosmic ray sources such as supernova remnants. Fitting our result for the total electron-positron flux measured by the Fermi satellite allows us to fix the only free parameter of the model and make an independent prediction for the positron fraction. Our explanation relies on a large number of supernova remnants nearby which are accelerating hadronic cosmic rays. Turning the argument around, we find encouraging prospects for the observation of neutrinos from such sources in km^3-scale detectors such as IceCube. Chapter 3 presents a test of this model by considering similar effects expected for nuclear secondary-to-primary ratios such as B/C. A rise predicted above O(100)GeV/n would be an unique confirmation of our explanation for a rising positron fraction and rule out the dark matter explanation. In chapter 4, we review the assumptions made in the extraction of the `WMAP haze' which has also been claimed to be due to electrons and positrons from dark matter annihilation in the Galactic centre region. We argue that the energy-dependence of their diffusion means that the extraction of the haze through fitting to templates of low frequency diffuse galactic radio emission is unreliable. The systematic effects introduced by this can, under specific circumstances, reproduce the residual, suggesting that the ‘haze’ may be just an artefact of the template subtraction. We present a summary and thoughts about further work in the epilogue.

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.

We show that the projected number density profiles of Sloan Digital Sky Survey photometric galaxies around galaxy clusters display strong evidence for the splashback radius, a sharp halo edge corresponding to the location of the first orbital apocenter of satellite galaxies after their infall. We split the clusters into two subsamples with different mean projected radial distances of their members, < R-mem >, at fixed richness and redshift. The sample with smaller < R-mem > has a smaller ratio of the splashback radius to the traditional halo boundary R-200m than the subsample with larger < R-mem >, indicative of different mass accretion rates for these subsamples. The same subsamples were recently used by Miyatake et al. to show that their large-scale clustering differs despite their similar weak lensing masses, demonstrating strong evidence for halo assembly bias. We expand on this result by presenting a 6.6 sigma difference in the clustering amplitudes of these samples using cluster-photometric galaxy cross-correlations. This measurement is a clear indication that halo clustering depends on parameters other than halo mass. If < R-mem > is related to the mass assembly history of halos, the measurement is a manifestation of the halo assembly bias. However, our measured splashback radii are smaller, while the strength of the assembly bias signal is stronger, than the predictions of collisionless. cold dark matter simulations. We show that dynamical friction, cluster mis-centering, or projection effects are not likely to be the sole source of these discrepancies. However, further investigations regarding unknown catastrophic weak lensing or cluster identification systematics are warranted.

We study the sensitivity of fixed target neutrino experiments (LSND, T2K, CENNS, and COHERENT) and proton beam dumps (MiniBooNE off-target, and SHiP) to sub-GeV dark matter. In order to reproduce the observed thermal relic abundance, these states are coupled to the Standard Model via new, low mass mediators in the form of a kinetically mixed U(1)0 vector mediator or a vector mediator gauging baryon number. We present a model for the production of low mass dark matter from proton-nucleon collisions in fixed targets. Sensitivity projections are made using signals from elastic electron- and nucleon-dark matter scattering, as well as coherent nuclear-dark matter scattering and dark matter induced inelastic π 0 production. A fixed target Monte Carlo code has been developed for this analysis, and documentation is included. We find that analyses using current and future proton fixed target experiments are capable of placing new limits on the hidden sector dark matter parameter space for dark matter masses of up to 500\,MeV and mediator masses as large as a few GeV. / Graduate

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.

Many astronomical observations, including rotational curve measurements of stars and the analysis of the cosmic microwave background, suggest the existence of an invisible matter density content in the Universe, commonly called Dark Matter (DM). Possibly, DM could be of particle nature, where Weakly Interacting Massive Particles (WIMPs) could be a viable DM candidate. The cubic-kilometer sized IceCube neutrino observatory located at the Earth’s South Pole can search indirectly for the existence of DM by detecting neutrino signals from WIMP self-annihilation in the Galactic center (GC) and the Galactic halo (GH). Two main physics analyses were developed and conducted to search indirectly for WIMP self-annihilation in the Milky Way’s GC and GH. Signal hypotheses for different WIMP annihilation channels, WIMP masses and DM halo profiles were tested. The results of both analyses were compatible with the background-only hypothesis for all tested signal hypotheses. Thus, upper limits at the 90% confidence level (C.L.) on the thermally averaged DM self-annihilation cross-section, &lt;σΑv&gt;, were set. Dedicated atmospheric muon veto techniques have been developed for the GC search making such an IceCube analysis possible for the first time. The GC analysis utilized data from 319.7 days of live-time of the IceCube detector running in its 79-string configuration during 2010 and 2011, whereas the GH analysis utilized pre-existing data samples developed for point-like neutrino sources with a live-time of 1701.9 days between 2008 and 2013. The most stringent upper limits on &lt;σΑv&gt; were obtained for WIMP annihilation directly into a pair of neutrinos assuming a Navarro-Frenk-White (NFW) DM halo profile. Conducting the GC and GH analyses for this annihilation channel an upper limit on &lt;σΑv&gt; as low as 4.0 · 10-24 cm3 s-1 and 4.5 · 10-24 cm3 s-1 is set for a 65 GeV and 500 GeV massive WIMP, respectively. These galactic indirect neutrino searches for DM are complementary to the indirect gamma-ray DM searches usually performed on extra-galactic targets like spheroidal dwarf galaxies. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.</p>

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.