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Quasar outflows are a major candidate for Active Galactic Nuclei (AGN) feedback, and their capacity to influence the evolution of their host galaxy depends on the mass-flow rate (M) and kinetic luminosity (E) of the outflowing material. Both quantities require measurement of the distance (R) to the outflow from the central source as well as physical conditions of the outflow, which can be determined using spectral observations of the quasar. This thesis presents spectral analyses leading to measurements of R, M and E for three different quasar outflows. Analysis of LBQS J1206+1052 revealed multiple diagnostic spectral features that could each be used to independently determine R. These diagnostics yielded measurements that were in close agreement, resulting in a robust outflow distance of 840 pc from the central source. This measurement is much larger than predicted from radiative acceleration models (~0.01-0.1 pc), suggesting that outflows appear much farther from the central source than is generally assumed. The outflow in SDSS J0831+0354 was found to carry a kinetic luminosity of 1045.7 erg/s, which corresponds to 5.2 per cent of the Eddington luminosity of the quasar. This outflow is one of the most energetic outflows to date and satisfies the criteria required to produce AGN feedback effects. A variability study of NGC 5548 revealed an obscuring cloud of gas that shielded the outflow components, dramatically lowering their ionization state. This resulted in the appearance of absorption from the rare element Phosphorus, as well as from sparsely-populated energy levels of CIII and SiIII. These spectral features allowed for an accurate determination of R and for constraints on the ionization phase to be obtained. The latter constraints were used to develop a self-consistent model that explained the variability of all six outflow components during five observing epochs spanning 16 years. Ph. D.

We investigate the relaxation properties of two distinct systems: magnetic vortex lines in disordered type-II superconductors and charge carriers in the Coulomb glass in disordered semiconductors. We utilize an elastic line model to simulate magnetic flux lines in disordered type-II superconductors by performing Langevin molecular dynamics simulations. We study the non-equilibrium relaxation properties of flux lines in the presence of uncorrelated point-like disorder or extended linear defects analyzing the effects of rapid changes in the system's temperature or magnetic field on these properties. In a previously-equilibrated system, either the temperature is suddenly changed or the magnetic field is abruptly altered by adding or removing random flux lines to or from the system. One-time observables such as the radius of gyration are measured to characterize steady-state properties, and two-time correlation functions such as the vortex line height autocorrelations are computed to investigate the relaxation dynamics in the aging regime and therefore distinguish the complex relaxation features that result from the different types of disorder in the system. This study allows us to test the sensitivity of the system's non-equilibrium aging kinetics to the selection of initial states and to make closer contact to experimental setups. Furthermore, we employ Monte Carlo simulations to study the relaxation properties of the two-dimensional Coulomb glass in disordered semiconductors and the two-dimensional Bose glass in type-II superconductors in the presence of extended linear defects. We investigate the effects of adding non-zero random on-site energies from different distributions on the properties of the correlation-induced Coulomb gap in the density of states and on the non-equilibrium aging kinetics highlighted by the autocorrelation functions. We also probe the sensitivity of the system's equilibrium and non-equilibrium relaxation properties to instantaneous changes in the density of charge carriers in the Coulomb glass or flux lines in the Bose glass. Ph. D.

Decays of B mesons to three-body charmless final states probe the properties of the weak interaction through their dependence on the complex quark couplings in the CKM matrix. They also test dynamical models for hadronic B decays. Based on a sample of 772 million BB pairs collected by the Belle experiment, we present a study of direct CP violation in the decay of charged B to three charged pions. Ph. D.

In this work, the antineutrino spectrum as specifically generated by nuclear reactors is studied. The topics covered include corrections and higher-order effects in reactor antineutrino experiments, one of which is covered in Ref. [1] and another contributes to Ref. [2]. In addition, a practical application, antineutrino safeguards for nuclear reactors, as summarized in Ref. [3,4] and Ref. [5], is explored to determine its viability and limits. The work will focus heavily on theory, simulation, and statistical analyses to explain the corrections, their origins, and their sizes, as well as the applications of the antineutrino signal from nuclear reactors. Chapter [1] serves as an introduction to neutrinos. Their origin is briefly covered, along with neutrino properties and some experimental highlights. The next chapter, Chapter [2], will specifically cover antineutrinos as generated in nuclear reactors. In this chapter, the production and detection methods of reactor neutrinos are introduced as well as a discussion of the theories behind determining the antineutrino spectrum. The mathematical formulation of neutrino oscillation will also be introduced and explained. The first half of this work focuses on two corrections to the reactor antineutrino spectrum. These corrections are generated from two specific sources and are thus named the spent nuclear fuel contribution and the non-linear correction for their respective sources. Chapter [3] contains a discussion of the spent fuel contribution. This correction arises from spent nuclear fuel near the reactor site and involves a detailed application of spent fuel to current reactor antineutrino experiments. Chapter [4] will focus on the non-linear correction, which is caused by neutron-captures within the nuclear reactor environment. Its quantification and impact on future antineutrino experiments are discussed. The research projects presented in the second half, Chapter [5], focus on neutrino applications, specifically reactor monitoring. Chapter [5] is a comprehensive examination of the use of antineutrinos as a reactor safeguards mechanism. This chapter will include the theory behind safeguards, the statistical derivation of power and plutonium measurements, the details of reactor simulations, and the future outlook for non-proliferation through antineutrino monitoring. Ph. D.

The mean field analysis of stochastic dynamical system allows us to gain insight into the qualitative features of their complex behavior, as well as quantitative estimates of certain aspects of their coarse-grained properties. As such, it usually furnishes a first front in approaching new dynamical systems and informs us about their stability landscape in the absence of fluctuations among other things. A knowledge of this landscape can be a valuable tool in model building for describing real world systems and provides a guiding principle for a justifiable choice of form and model parameters. In this work, we contribute to this analysis for two generic classes of high-dimensional models that possess a cyclic symmetry in the network that specifies their stochastic dynamics at the microscopic level. Our analysis is carried out in a manner that can be readily adapted for the mean field analysis of further generalized models that possess this symmetry. Moreover, in the second class of these models, we propose a new basic process that can change the stability landscape of an existing model and, as such, endow us with potential alternatives to model systems with robust biodiverse regimes. Ph. D.

This thesis presents work done investigating methods for constructing patterns on the nanometer scale. Various methods of nanolithography using atomic force microscopes (AFMs) are investigated. The use of AFMs beyond their imaging capabilities is demonstrated in various experiments involving nanografting and surface electrochemical modification. The use of an AFM to manipulate a monolayer of thiols deposited on a gold substrate via nanografting is shown in our work to enable chemical modification of the surface of the substrate by varying the composition of the monolayer deposited on it. This leads to the selective deposition of various polymers on the patterned areas. Conditions for enhancing the selective deposition of the self-assembled polymers are studied. Such conditions include the types of polymers used and the pH of the polyelectrolyte solutions used for polymer deposition. Another method of nanolithography is investigated which involves the electrochemical modification of a monolayer of silanes deposited on a silicon substrate. By applying a potential difference and maintaining the humidity of the ambient environment at a certain level we manage to change the chemical properties of select areas of the silane monolayer and thus manage to establish selective deposition of polymers and gold nanoparticles on the patterned areas. Parameters involved in the patterning process using surface electrochemical modification, such as humidity levels, are investigated. The techniques established are then used to construct circuit elements such as wires. Ph. D.

The Daya Bay experiment has determined the last unknown mixing angle $theta_{13}$. This thesis describes the layout of the experiment and the detector design. The analysis presented in the thesis covered the water attenuation, spent fuel neutrino and electron anti-neutrino spectrum. Other physics analysis and impact to future experiments are also discussed. Ph. D.

Neutrino physics has entered a precision era in which understanding backgrounds and systematic uncertainties is particularly important. With a precise understanding of neutrino physics, we can better understand neutrino sources. In this work, we demonstrate dependency of single detector oscillation experiments on reactor neutrino flux model. We fit the largest reactor neutrino flux model error, weak magnetism, using data from experiments. We use reactor burn-up simulations in combination with a reactor neutrino flux model to demonstrate the capability of a neutrino detector to measure the power, burn-up, and plutonium content of a nuclear reactor. In particular, North Korean reactors are examined prior to the 1994 nuclear crisis and waste removal detection is examined at the Iranian reactor. The strength of a neutrino detector is that it can acquire data without the need to shut the reactor down. We also simulate tau neutrino interactions to determine backgrounds to muon neutrino and electron neutrino measurements in neutrino factory experiments. Ph. D.

Modeling the Cosmic Muon Flux is very important for quantifying the backgrounds present for underground experiments. We measure the flux at various locations in the Kimballton Underground Research Facility (KURF) and compare these measurements with our model. Ph. D.

This thesis is devoted to a discussion of various aspects of supersymmetric quantum field theories in four and two dimensions. In four dimensions, 𝒩 = 1 supersymmetric quantum gauge theories on various four-manifolds are constructed. Many of their properties, some of which are distinct to the theories on flat spacetime, are analyzed. In two dimensions, general 𝒩 = (2, 2) nonlinear sigma models on S² are constructed, both for chiral multiplets and twisted chiral multiplets. The explicit curvature coupling terms and their effects are discussed. Finally, 𝒩 = (0, 2) gauged linear sigma models with nonabelian gauge groups are analyzed. In particular, various dualities between these nonabelian gauge theories are discussed in a geometric content, based on their Higgs branch structure. Ph. D.

We investigate the properties of two distinct disordered systems: the two-species predator-prey Lotka-Volterra model with rate variability, and an elastic line model to simulate vortex lines in type-II superconductors. We study the effects of intrinsic demographic variability with inheritance in the reaction rates of the Lotka-Volterra model via zero-dimensional Monte Carlo simulations as well as two-dimensional lattice simulations. Individuals of each species are assigned inheritable predation efficiencies during their creation, leading to evolutionary dynamics and thus population-level optimization. We derive an effective subspecies mean-field theory and compare its results to our numerical data. Furthermore, we introduce environmental variability via quenched spatial reaction-rate randomness. We investigate the competing effects and relative importance of the two types of variability, and find that both lead to a remarkable enhancement of the species densities, while the aforementioned optimization effects are essentially neutral in the densities. Additionally, we collected extinction time histograms for small systems and find a marked increase in the stability of the populations against extinction due to the presence of variability. We employ an elastic line model to investigate the steady-state properties and non-equilibrium relaxation kinetics of magnetic vortex lines in disordered type-II superconductors. To this end, we developed a versatile and efficient Langevin molecular dynamics simulation code, allowing us to do a careful study of samples with or without vortex-vortex interactions or disorder allows us to disentangle the various complex relaxational features present in this system and investigate their origin. In particular, we compare disordered samples with randomly distributed point defects versus correlated columnar defects. We extract two-time quantities such as the mean-square displacement, the height and density correlations, to investigate the relaxation kinetics of the system of flux lines. Additionally, we compare the steady-state mean velocity and gyration radius as a function of an external driving current in the presence of point-like and columnar disorder. We validate our simulation algorithm by matching our results against a previously-used Monte Carlo algorithm, verifying that these microscopically quite distinct methods yield similar results even in out-of-equilibrium settings. Ph. D.

Stimulated Electromagnetic Emissions SEEs may provide important diagnostic information about space plasma composition, energetics, and dynamics during active experiments in which ground-based high powered radio waves are transmitted into the ionosphere. The nonlinear plasma processes producing this secondary radiation are not well understood particularly for some recent observations where the transmitter (pump) frequency is near the second harmonic of the electron gyro-frequency. New, more comprehensive, experimental observations of spectral features within 1kHz of the pump wave frequency are reported here in order to begin more careful comparisons of the experimental observations and a possible theoretical underpinning which is also provided. The experimental observations typically show two distinct types of secondary radiation spectra which are a) discrete narrowband harmonic spectral structures ordered by the ion gyro-frequency, so-called stimulated ion Bernstein Scatter (SIBS) and, b) broadband spectral structure with center frequency near 500 Hz and similar spectral bandwidth named ion acoustic parametric decay (IAPD). A theoretical model is provided that interprets these spectral features as resulting from parametric decay instabilities in which the pump field ultimately decays into high frequency upper hybrid/electron Bernstein and low frequency neutralized ion Bernstein and/or obliquely propagating ion acoustic waves at the upper hybrid interaction altitude. Detailed calculations of the threshold level, growth rate, unstable wavenumber and frequency bandwidth of the instabilities are provided for comparisons with experimental observations. An assessment of the effect of the critical instability parameters are provided including pump electric field strength, proximity of the pump frequency to the electron gyro-frequency and pump electric field geometry. The model shows quite reasonable agreement with the experimental observations. Next, a two dimensional Particle-In-Cell Monte-Carlo Collision computational model (PIC-MCC) is employed in order to consider nonlinear aspects such as 1) electron acceleration through wave-particle heating, 2) more complex nonlinear wave-wave processes and 3) temporal evolution of electron irregularities through nonlinear saturation. The simulation results show that the IB associated parametric decay is primarily associated with electron acceleration perpendicular to the geomagnetic field. More gyro-harmonic lines are typically associated with more intense heating. Heating is reduced when the pump frequency is sufficiently close to 2fce. The IA associated parametric decay instability is primarily associated with electron tail heating along the magnetic field and heating is reduced when the pump frequency is sufficiently close to 2fce. Characteristics of caviton collapse behavior become prevalent in this case. Results are discussed within the context of some recent experimental observations. Further discussions are provided of connections with past observed SEE spectral features and potential new diagnostic information provided by these newly categorized spectra. Ph. D.

The chemical reaction of the first excited electronic state of molecular nitrogen, N₂(A), with ground state atomic oxygen is an important contributor to thermospheric nitric oxide (NO). The importance is assessed by including this reaction in a one-dimensional photochemical model. The method is to scale the photoelectron impact ionization rate of molecular nitrogen by a Gaussian centered near 100 km. Large uncertainties remain in the temperature dependence and branching ratios of many reactions important to NO production and loss. Similarly large uncertainties are present in the solar soft x-ray irradiance, known to be the fundamental driver of the low-latitude NO. To illustrate, it is shown that the equatorial, midday NO density measured by the Student Nitric Oxide Explorer (SNOE) satellite near the Solar Cycle 23 maximum can be recovered by the model to within the 20% measurement uncertainties using two rather different but equally reasonable chemical schemes, each with their own solar soft-xray irradiance parameterizations. Including the N₂(A) changes the NO production rate by an average of 11%, but the NO density changes by a much larger 44%. This is explained by tracing the direct, indirect, and catalytic contributions of N₂(A) to NO, finding them to contribute 40%, 33%, and 27% respectively. The contribution of N₂(A) relative to the total NO production and loss is assessed by tracing both back to their origins in the primary photoabsorption and photoelectron impact processes. The photoelectron impact ionization of N₂ is shown to be the main driver of the midday NO production while the photoelectron impact dissociation of N₂ is the main NO destroyer. The net photoelectron impact excitation rate of N₂, which is responsible for the N₂(A) production, is larger than the ionization and dissociation rates and thus potentially very important. Although the conservative assumptions regarding the level-specific NO yield from the N₂(A)+O reaction results in N₂(A) being a somewhat minor contributor, N₂(A) production is found to be the most efficient producer of NO among the thermospheric energy deposition processes. Ph. D.

Recent years have seen remarkable progress in our understanding of physical aging in nondisordered systems with slow, i.e. glassy-like dynamics. In many systems a single dynamical length L(t), that grows as a power-law of time t or, in much more complicated cases, as a logarithmic function of t, governs the dynamics out of equilibrium. In the aging or dynamical scaling regime, these systems are best characterized by two-times quantities, like dynamical correlation and response functions, that transform in a specific way under a dynamical scale transformation. The resulting dynamical scaling functions and the associated non-equilibrium exponents are often found to be universal and to depend only on some global features of the system under investigation. We discuss three different types of systems with simple and complex aging properties, namely reaction diffusion systems with a power growth law, driven diffusive systems with a logarithmic growth law, and a non-equilibrium polymer network that is supposed to capture important properties of the cytoskeleton of living cells. For the reaction diffusion systems, our study focuses on systems with reversible reaction diffusion and we study two-times functions in systems with power law growth. For the driven diffusive systems, we focus on the ABC model and a related domain model and measure two- times quantities in systems undergoing logarithmic growth. For the polymer network model, we explain in some detail its relationship with the cytoskeleton, an organelle that is responsible for the shape and locomotion of cells. Our study of this system sheds new light on the non- equilibrium relaxation properties of the cytoskeleton by investigating through a power law growth of a coarse grained length in our system. Ph. D.

In this work, the consequences of several modifications to quantum mechanics are examined. These modifications, motivated by string theory, fall into two categories: ones in which the canonical commutation relations between position and momentum are deformed and ones in which the space of states used are vector spaces over Galois fields instead of complex Hilbert spaces. The particular deformation of the canonical commutation relations used leads to a minimum value of the uncertainty in position which is interpreted as a minimum length scale. Both harmonic and anharmonic oscillators are studied in this framework with normalizable, positive energy eigenstates found in both cases. The quantum uncertainty relations and classical counterparts to these states are discussed. Creating modified quantum theories by replacing the Hilbert spaces of canonical quantum mechanics with vector spaces defined over several finite, Galois fields is accomplished. Correlation functions are calculated in these theories and the maximum values are shown to not behave as would be expected by the standard, Bell-like, bounding inequality theorems. The interpretations and implications of these theories are discussed. Ph. D.

It is known that knot homologies admit a physical description as spaces of open BPS states. We study operators and algebras acting on these spaces. This leads to a very rich story, which involves wall crossing phenomena, algebras of closed BPS states acting on spaces of open BPS states, and deformations of Landau-Ginzburg models. One important application to knot homologies is the existence of "colored differentials" that relate homological invariants of knots colored by different representations. Based on this structure, we formulate a list of properties of the colored HOMFLY homology that categorifies the colored HOMFLY polynomial. By calculating the colored HOMFLY homology for symmetric and anti-symmetric representations, we find a remarkable "mirror symmetry" between these triply-graded theories., 42 pages, 5 figures, additional references and explanations concerning colored differentials and grading choices, enhanced analysis of examples

This work sets out to be a description of the initiatives utilizing the Borexino liquid scintillator neutrino observatory to perform the first direct, high-precision, wideband solar neutrino spectroscopy measurement of the the solar neutrino spectrum's main components, as well as its next-generation short-baseline source program (SOX). Its original scope revolved around the creation of a O(MCi) ⁵¹Cr source to be inserted under the detector, intended to explore the small region of the anomaly-favored sin²θ₁₄/Δm₁₄² phase space where sterile neutrinos may lie -or otherwise unambiguously measure or disprove signs of anomalous oscillatory behavior in low L/E electron-neutrinos and antineutrinos. Investigating the feasibility and optimization of producing such a large amount of ⁵¹Cr for the source, by irradiating chromium material in a high-flux reactor, required extensive simulative work with the MCNP-5 neutronics code. With the switch of pace toward a ¹⁴Ce-¹⁴⁴Pr electron-antineutrino source, this work was re-oriented toward the efforts to re-calibrate the detector after the 2009-10 campaign, improving and expanding upon it by the introduction of new source fabrication techniques, a source positioning LED device, and a re-evaluation of the objectives sought after, fitting the needs of Borexino's Phase 2 priorities. Indeed, the detector's unprecedented and record-setting background levels are tightening its requirement for background stability. Aiming to reduce fluctuations in 210Po levels that remain problematic in Borexino's quest to lower the upper limit of the solar CNO neutrino flux (or even measure it), among other components, a new Temperature Monitoring and Management System was deployed and associated tools necessary to fully utilize it were developed as part of the present work. Computational Fluid Dynamics (CFD) simulations in 2D and 3D, conductive and fully convective, were also developed in collaboration with Dr Riccardo Mereu of Milan's Polytechnic Institute in order to model, characterize and ultimately predict the subtle fluid currents (around 10⁻⁷) m/s) that may be of concern for the required background stability. A brief discussion of the recent >5sigma measurement of geo-neutrinos by Borexino, a complementary part of the work for this thesis, is presented as well. Ph. D.

In this thesis the close relationship between the topological $K$-homology group of the spacetime manifold $X$ of string theory and D-branes in string theory is examined. An element of the $K$-homology group is given by an equivalence class of $K$-cycles $[M,E,\phi]$, where $M$ is a closed spin$^c$ manifold, $E$ is a complex vector bundle over $M$, and $\phi: M\rightarrow X$ is a continuous map. It is proposed that a $K$-cycle $[M,E,\phi]$ represents a D-brane configuration wrapping the subspace $\phi(M)$. As a consequence, the $K$-homology element defined by $[M,E,\phi]$ represents a class of D-brane configurations that have the same physical charge. Furthermore, the $K$-cycle representation of D-branes resembles the modern way of characterizing fundamental strings, in which the strings are represented as two-dimensional surfaces with maps into the spacetime manifold. This classification of D-branes also suggests the possibility of physically interpreting D-branes wrapping singular subspaces of spacetime, enlarging the known types of singularities that string theory can cope with. Master of Science

In this work, we examine how neutrino and collider experiments can each and together put constraints on new physics more stringently than ever. Constraints arise in three ways. First, possible new theoretical frameworks are reviewed and analyzed for the compatibility with collider experiments. We study alternate theories such as the superconnection formalism and non-commutative geometry (NCG) and show how these can be put to test, if any collider excess were to show up. In this case, we use the previous diboson and diphoton statistical excess as examples to do the analysis. Second, we parametrize low energy new physics in the neutrino sector in terms of non-standard interactions (NSI), which are constrained by past and proposed future neutrino experiments. As an example, we show the capability of resolving such NSI with the OscSNS, a detector proposed for Oak Ridge National Lab and derive interesting new constraints on NSI at very low energy (≲ 50 MeV). Apart from this, in order to better understand the NSI matter effect in long baseline experiments such as the future DUNE experiment, we derive a new compact formula to describe the effect analytically, which provides a clear physical picture of our understanding of the NSI matter effect compared to numerical computations. Last, we discuss the possibility of combining neutrino and collider data to get a better understanding of where the new physics is hidden. In particular, we study a model that produces sizable NSI to show how they can be constrained by past collider data, which covers a distinct region of the model parameter space from the DUNE experiment. In combining the two, we show that neutrino experiments are complementary to collider searches in ruling out models such as the ones that utilize a light mediator particle. More general procedures in constructing such models relevant to neutrino experiments are also described. Ph. D.