Current models of cosmology and galaxy formation are possibly at odds with observations of small-scale galaxies. Such is the case for the dwarf spheroidal (dSph) galaxies of the Milky Way (MW), where tension exists in explaining their observed abundance, mass, and internal structure. Here we present an analysis of the substructure surrounding MW-sized haloes in a Lambda Cold Dark Matter (LCDM) simulation suite. Combined with a semi-analytic model of galaxy formation and evolution, we identify substructures that are expected to host dSph galaxies similar to the satellites of the MW. We subsequently use these simulations to investigate the orbital properties of dSph satellite galaxies to make contact with those orbiting the MW. After accretion into the main halo, the higher mass ``luminous'' substructure remains on highly radial orbits while the orbits of lower mass substructure, which are not expected to host stars, tend to scatter off of the luminous substructure, and thus circularize over time. The orbital ellipticity distribution of the luminous substructure shows little dependence on the mass or formation history of the main halo, making this distribution a robust prediction of LCDM. Through comparison with the ellipticity distribution computed from the positions and velocities of the nine MW dSph galaxies that currently have proper motion estimates as a function of the assumed MW mass, we present a novel means of estimating the virial mass of the Milky Way. The best match is obtained assuming a mass of 1.1 x 10^12 M_sun with 95 per cent confidence limits of (0.6 - 3.1) x 10^12 M_sun. The uncertainty in this estimate is dominated by the large uncertainties in the proper motions and small number of MW satellites used, and will improve significantly with better proper motion measurements from Gaia. We also measure the shape of the gravitational potential of subhaloes likely to host dSphs, down to radii comparable to the half-light radii of MW dSphs. Field haloes are triaxial in general, while satellite haloes become more spherical over time due to tidal interactions with the host. Thus through the determination of the shape of a MW dSph's gravitational potential via line of sight velocity measurements, one could in principle deduce the impact of past tidal interactions with the MW, and thus determine its dynamical history. Additionally, luminous subhaloes experience a radial alignment of their major axes with the direction to the host halo over time, caused by tidal torquing with the host's gravitational potential during close pericentric passages. This effect is seen at all radii, even down to the half-light radii of the satellites. Radial alignment must be taken into account when calibrating weak-lensing surveys which often assume isotropic orientations of satellite galaxies surrounding host galaxies and clusters. / Graduate / 0606

Inorganic scintillators are playing an ever increasing role in the search for rare events. Progress in the use of cryogenic phonon-scintillation detectors (CPSD) has allowed for a rapid increase in sensitivity and resolution of experiments using this technique. It is likely that CPSD will be used in future dark matter searches with multiple scintillator materials. Further improvements in the performance of CPSD can be expected if the amount of light collected is increased. In this thesis, two approaches are used to look at ways of maximising the amount of light collected in CPSD modules. The first approach is to obtain a detailed understanding of the spectroscopic properties in the crystal to identify ways of increasing their scintillation intensity. The second is to simulate the light collection properties using a Monte-Carlo simulation program. This requires a detailed understanding of the optical properties of inorganic scintillators and obtaining this information is the focus of the current work. Two new methods have been developed to evaluate the scintillation decay time and the intrinsic light yield of scintillators. These methods are tested on CRESST CaWO₄ crystals so that all the input parameters necessary for the simulation of CRESST modules is available. These input parameters are used to successfully explain features of the light collection in CRESST CPSD modules and to suggest possible improvements to the design of the modules. In summary, the current work has contributed to the development of a standardised method to maximise the light yield that can be obtained from CPSD for application to rare event searches.

Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

Single-molecule fluorescence spectroscopy techniques such as Fluorescence Correlation Spectroscopy (FCS) and single-molecule Förster Resonance Energy Transfer (smFRET) not only possess an unprecedented high sensitivity but also have high temporal and spatial resolution. Therefore, they have an immense potential both in investigation of fundamental biological principles and in clinical applications. FCS analyses are based on both theoretical approximations of the beam geometry and assumptions of the underlying molecular processes. To address the accuracy of analysis, firstly the experimental conditions that should be fulfilled in order to obtain reliable physical parameters are discussed and the input parameters are carefully controlled accordingly to demonstrate the performance of FCS measurements on our home-built confocal multiparameter photon-counting microscope in several in vitro and in-vivo applications. Secondly, we performed a comprehensive FCS analysis of rhodamine family of dyes to evaluate the validity of assigning the correlation relaxation times to the time constant of conformational dynamics of biomolecules. While it is the common approach in literature our data suggests that conformational dynamics mainly appear in the correlation curve via modulation of the dark states of the fluorophores. The size and shape of the folded, unfolded and chemically-denatured states of the N-terminal Src-homology-3 of downstream of receptor kinases (DrkN SH3) were investigated by FCS and smFRET burst experiments. Based on the data, we conclude that a considerable sub-population of the denatured protein is in a closed loop state which is most likely formed by cooperative hydrogen bonds, salt bridges and nonpolar contacts. As a clinical application, we developed and characterized an ultrasensitive capillary electrophoresis method on our multiparameter confocal microscope. This allowed us to perform Direct Quantitative Analysis of Multiple microRNAs (DQAMmiR) with about 500 times better sensivity than a commercial instrument. Quite remarkably, we were able to analyze samples of cell lysate down to the contents of a single cell.

The aim of this project was to explore the shapes of dark matter halos using high resolution N-body simulations. One of the main aspects explored was how well the shape can be measured through weak lensing. To explore this, simulations were run using the GADGET-2 code \cite{SPRING05} and a method used to measure ellipticities was tested \cite{oguri1}. It was found that Large Scale Structure along the line of sight diluted the measurements and made halos appear more spherical. On the other hand, substructure close to the halo introduced a bias where intrinsically elliptical halos appeared to be slightly more spherical and intrinsically spherical halos appeared to be slightly more elliptical. The effects of projection on concentration were also explored, it was concluded that halos which are most elliptical in 3D tend to appear the most concentrated in projection. Finally, we tested the possibility of using shape or concentration measurements to help break the degeneracy in $\Omega_M$ and $\sigma_8$. We found that this may be possible with $\sim$ 3000-4000 shape measurements or $\sim$ 400-500 concentration measurements.

A variety of precision observations suggest that the present universe is dominated by some unknown components, the so-called dark matter and dark energy. The distribution and properties of these components are the focus of modern cosmology and we are only beginning to understand them. Gravitational lensing, the bending of light in the gravitational field of a massive object, is one of the predictions of the general theory of relativity. It has become an ever more important tool for investigating the dark universe, especially with recent and coming advances in observational data. This thesis studies gravitational lensing effects on scales ranging over ten orders of magnitude to probe very different aspects of the dark universe. Implementing a matter distribution following the predictions of recent simulations, we show that microlensing by a large population of massive compact halo objects (MACHOs) is unlikely to be the source of the observed long-term variability in quasars. We study the feasibility of detecting the so far elusive galactic dark matter substructures, the so-called “missing satellites”, via millilensing in galaxies close to the line-of-sight to distant light sources. Finally, we utilise massive galaxy clusters, some of the largest structures known in the universe, as gravitational telescopes in order to detect distant supernovae, thereby gaining insight into the expansion history of the universe. We also show, how such observations can be used to put constraints on the dark matter component of these galaxy clusters. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 6: Submitted.

Thesis (Ph. D.)--Ohio State University, 2008. / Title from first page of PDF file. Includes bibliographical references (p. 160-175).

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 93-98).

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 103-111).

Hard diffraction in proton collisions, where the initial state proton emerges from the interaction rather undisturbed despite a hard interaction scale, has been studied for a few decades. First observed in proton-proton collisions, the phenomenon is seen as well in deep inelastic electron-proton scattering (DIS) as a leading final state proton and a rapidity gap-region without final state particles. Although a rather successful description in terms of the exchange of a hadronic color singlet pomeron with a parameterized gluon content exists, it is still an open question whether a theoretically more well-founded description can be obtained based on quantum chromodynamics. The soft color interaction model (SCI) attempts this through additional gluon exchanges at momentum scales below the conventional scale of perturbative QCD and the hadronization scale. Such gluons can lead to an effective color singlet exchange and therefore to diffraction. This thesis explores the phenomenology of the SCI model in diffractive W and photon+jet production. For diffractive deep inelastic scattering, a dynamic color screening model is developed based on a summed amplitude for soft gluon exchanges. The studies of the model within Monte Carlo event simulation show that the additional dynamics improve the description of electron-positron scattering data from HERA. Dijet events in proton-proton collisions with an upper limit on the energy flow between the jets is sensitive to large angle gluon emissions. This thesis applies a resummation method which takes into account also secondary emissions to describe this observable and shows that a good description of data from ATLAS can be achieved. Supersymmetric extensions to the Standard Model provide a possible explanation for dark matter in the universe. The next-to-minimal supersymmetric extension (NMSSM) can contain a dark matter candidate in form of the lightest neutralino with a substantial singlino component. This thesis studies the prospects for indirect detection of dark matter for such viable NMSSM model points via the observation of neutrinos from neutralino annihilation in the sun with IceCube and the future extension PINGU. It is shown that with a few years of data taking large parts of the parameter space can be excluded or a discovery be made.