Within turbulence there are many phenomena which are currently unsolved. In the solar wind temperature anisotropies and low growth rates instability have a dominant role in defining the turbulent behaviour of plasma. Due to the non- linearity of the equations involved in the description of the physics of plasmas numerical simulations are a fundamental tool to study the dynamics of turbulent phenomena. In particular, hybrid codes are widely used in space plasma applications due to their ability to simulate large regions of volume maintaining some kinetic effects. However, due to the sensitivity to the initial level of noise in the simulation, low growth rate instabilities are particularly difficult to simulate. Particle in Cell-hybrid simulations require too many particles to reduce the initial noise, while Vlasov-hybrid simulations require too many grid points to fully discretize spatial and velocity phase spaces. We present here a Vlasov-hybrid algorithm and code implementation where the distribution function is expanded in series of Hermite functions. Thanks to the properties of these it is possible to project the Vlasov equation to find an equation for each coefficient of the expansion. These coefficients are advanced in time using a Current Advance Method algorithm with splitting method for the Vlasov operator. The former is treated explicitly, while the latter is treated implicitly with a GMRES solver. The current is advanced with a temporal ODE derived taking moments of the Vlasov equation. A 1D3V code is implemented, tested and used to study low growth rate instabilities such as a proton cyclotron instability and a ion/ion right hand resonant instability with small relative velocity drift between beam and core populations. The results are compared with existing hybrid algorithms that we implemented. A 2D3V parallelized version of the code is implemented and described here. Initial results are presented and future improvements are discussed.

The as-produced isomer mixture of the organic photovoltaic device acceptor material bisPC62BM has been purified into its constituents by peak-recycling HPLC, and those individual isomers were characterised by UV-Vis absorption spectroscopy and cyclic voltammetry. A total of 18 isomers were purified from the mixture to a standard exceeding 99.5% with respect to other isomers. The HOMOs, LUMOs, and HOMO-LUMO gaps of the purified isomers vary from (-5.673 to -5.402 eV), (-3.901 to -3.729 eV), and (1.664 to 1.883 eV), respectively. We also find a correlation between HPLC retention time and the relative positions of the addends; in that generally the closer the addends are to each other the longer the retention time of the isomer, and vice versa. The OPV acceptor molecule PC71BM was also purified into its constituent isomers to a standard of at least 99%. The total three purified isomers were each characterized by 13C NMR and UV-vis spectroscopy, and cyclic voltammetry. These characterizations were supported by HF/DFT ab-initio calculations. All three isomers are methano-fullerenes. The most abundant isomer (85% of the mixture) exists as a racemate involving the 8-25 bond of C70. The other two isomers both involved the 9-10 bond of C70, but are distinguished by opposing orientations of the addend with r and s pseudo-asymmetry about carbon atom 71. The r and s isomers comprised 9% and 6% of the as-produced of the mixture, respectively. In order of decreasing abundance, the LUMO levels of the isomers were -3.9316, -3.9194 and -3.9197 eV and the HOMO-LUMO gaps were 1,772, 1.754 and 1.748 eV.

In this thesis the author reports his collaborative efforts on two distinct areas of research that has been conducted. The first part of the thesis pertains to the author and his collaborators research on a particular class of organic magnets called the bimetallic oxalates. The main theme of this research was to predict magnetic compensation (magnetization reversal) in unsynthesized bimetallic oxalate structures, motivated by experiments which showed that Fe(II)Fe(III) exhibited magnetic compensation. In addition it was known that a large amount of anisotropy was present in the bimetallic oxalate structure which resulted from the intermediate oxalate molecules between the transition metal ions which would drastically change the angular momentum of the transition metals. Consequently, because of the large anisotropy, we predicted that, if neutron diffraction measurements were performed on these materials, a spin-wave gap would exist of the order of 7.8 meV. The second half of this thesis is devoted to the author's and his collaborators' research on the cerium volume collapse. Until 2004 the collapse was largely believed to be understood as the result of Kondo screening of the local moment in cerium. However in 2004 it was realized that, in addition to a large Kondo effect driving the cerium volume collapse, the phonon frequency was very different between the large and small volume phases, and consequently the change in phonon frequency was the direct result of large electron-phonon correlations. This upset the apple cart of Kondo correlation being solely responsible for the volume collapse in cerium, and the change in phonon frequency must be accounted for to accurately describe the cerium volume collapse. To this end the author and his collaborators' developed a model which would include both of the correlations (Kondo and phononic) in the volume collapse. To analyze this model we used Dynamical Mean Field Theory in conjunction with Continuous Time Quantum Monte Carlo. What we found in our simulations was that the small volume Kondo phase was drastically influenced by the presence of the electron-phonon correlations.

Complex Materials, such as transition-metal oxides (TMOs) with exotic properties provide immense opportunities in condensed matter and materials science. The signature and challenge of these materials is the multitude of competing ground states that can be tuned or manipulated by doping, structural modification, strain induction, or the application of external stimulus. In the past few years, it is becoming increasingly clear that surfaces/interfaces, thin films, and heterostructures of TMOs, display a rich diversity of fascinating properties that are related to, but not identical to, the bulk phenomena. The fundamental issues for the understanding of these emergent phenomena include the structure and chemical composition in the proximity of surface/interface. In the thesis, I have developed a method using angle resolved X-ray photoelectron spectroscopy (ARXPS) to characterize the surface structure and chemical composition. In particular, I have considered the photoelectron diffraction effects on the relative intensities of different core electron levels which are essential to reveal the variation of chemical composition. I developed the basic methodology for the data analysis of the ARXPS spectra and used the well-known crystal surface of Sr2RuO4 (100) to verify our methodology. Using the angle-dependence of Sr 3d/ Ru 3p core level intensity ratio, our method clearly confirms that the termination layer of the surface is SrO-layer with minor amount of oxygen vacancies. The diffraction pattern matches very well with the theoretical calculation of forward scattering peaks. Then I have used the developed ARXPS method coupled with low energy electron diffraction (LEED) and scanning tunneling microscopy (STM) to investigate the surface structure and chemical composition of a widely used crystal surface: SrTiO3(100). I found that, although maintaining in-plane unreconstructed: primary p(1×1), the surface exhibits out-of-the-plane bulking relaxation. More importantly, the systematic analysis of ARXPS spectra show that the surface is TiO2-layer terminated and has significant oxygen vacancies. These results confirm the conjecture from LEED-I(V) refinement on structure. The existence of surface oxygen-vacancies may explain the observed surface metallicity of SrTiO3. Finally, I have studied the chemical composition of the ultrathin crystalline films of La2/3Sr1/3MnO3 on SrTiO3 (100), especially focusing on the Sr surface segregation. I found that Sr concentration at the surface is appreciably higher than the corresponding bulk value. Such an off-stoichiometric behavior should link to the different physical properties such as nonmetallic/nonmagnetic dead layer behavior in the ultrathin films compared with the bulk crystal. To conclude, by considering the photoelectron diffraction effects, I have developed a method of ARXPES to characterize the surface chemical composition, which is essential for the understanding of emergent phenomena at surface, interface and thin film of complex materials.

Understanding and controlling the complexity that develops in complex transition metal compounds such as high-Tc superconductivity, "colossal" magnetoresistance in manganites, and heavy-fermion compounds, is one of the grand challenges of the 21st century. The exotic properties displayed by these compounds are closely related to the coexistence of nearly degenerate states, coupling simultaneously several active degrees of freedom such as the charge, lattice, orbital, and spin. In this work, we have focused on two systems, one is the newly discovered Fe-based superconducting compounds ((Ba, Ca)(Fe1-xCox)2As2, FeTe1-xSex) and the other one is the doped Ruddleden-Popper (RP) ruthenates (Sr3(Ru1-xMnx)2O7). The materials community was astonished by the discovery of superconductivity with a critical temperature exceeding 55 K in the iron-based superconductors in 2008. This new family of high Tc superconductors with layered structure without Cu has opened up a completely new venue for understanding not only high Tc superconductors but in general the coupling between lattice, charge, orbital and spin. While ruthenates is a prototype of strong correlated electron materials (CEMs) and Mn-doping in Sr3(Ru1-xMnx)2O7 have induced a rich coupled phase diagrams. We approach from the surface to study their geometric and electronic structure because the symmetry breaking offers great opportunities to tune the balance of the coupling. We applied Low energy electron diffraction (LEED) and its Intensity-voltage (I-V) analysis to quantitatively characterize the detail surface structure from momentum space. Then we used low and variable temperature scanning tunneling microscopy/spectroscopy (STM/S) to study surface electronic structure from real space. At last, spin-polarized density functional theory (DFT) calculations were utilized to enhance our understanding of the experimental data, thus providing a new prospective of our discovery. Our results on the domain surface of BaFe2As2 show that the strong spin-lattice coupling at the surface results in the coexistence of structure and spin antiphase domain boundaries with C2 symmetry. For the stripe surface of (Ba, Ca)(Fe1-xCox)2As2, we determined the surface structure which is proved to be stabilized by bulk spin ordering through spin-lattice-charge coupling. Superconductivity has also been observed on stripe surface indicating a spatial-resolved coexisting of anti-ferromagnetic and superconducting order. On FeTe1-xSex system, we observed a nano-scale chemical phase separation of Te and Se atoms thus the optimally doped superconductor is chemically inhomogeneous but electronically homogeneous, in contrast to many CEMs. However, using STM on a different system, Mn-dopants in Sr3(Ru1-xMnx)2O7 were shown to homogeneously (random) distribute on the surface in micro-scale but maybe phase separated in macro-scale.We also discovered a left- and right- chirality of the structural rotation of MnO6, thus to understand the correlation between the magnetic dopants. Our approach of using state-of-the-art surface techniques to study the manifestation of broken symmetry in these complex transition metal compounds, especially the iron pnictides and ruthernate offered the community a fresh look at the underlying physics.

The Kerr rotation and Kerr ellipticity of thin films can be measured using an AC magneto-optic Kerr effect (AC-MOKE) system. The longitudinal MOKE measurements were taken for a series of Co2MnSixAl1-x thin films with values of x= 0.00, 0.25, 0.50, 0.75, 1.00. The films were fabricated using ultra high vacuum, pulsed laser deposition (PLD) techniques. The PLD targets were made using conventional arc-melting techniques. Using a Jones matrix analysis, it was shown that the Kerr rotation and Kerr ellipticity can be measured separately using two optical setups by taking advantage of a photoelastic modulator and lock-in techniques. Co2MnAl and Co2MnSi are both in a class of materials known as Heusler alloys and are predicted to have a high degree of spin polarization. The crystal structure was confirmed as the L21 using powder x-ray diffraction. The lattice constants were shown to be 5.61Å and 5.77 Å for Co2MnSi andCo2MnAl, respectively. For each film, the DC-MOKE, AC-Kerr rotation, and AC- Kerr ellipticity were measured. The DC-MOKE loops were used to estimate the total Kerr rotation. There was no noticeable trend in the values of the total Kerr rotation as calculated using a technique based on Malus law. The Kerr rotation showed a decreasing trend with concentration (x). The sample with x=0.50 was calculated to be the same as the one with x=0.00 value. The Kerr ellipticity also decreased as x was increased. There have been no reports in the literature on direct measurements of the Kerr rotation or ellipticity for Co2MnSixAl1-x for any values of x. The measurements gave values that were comparable to reported calculations and measured values of similar Heusler alloys.

Purpose: Adaptive filtration facilitates spectral breast CT by decreasing count rate and dynamic range requirements of photon counting detectors. This project investigated the effect of adaptive filtration on beam hardening, CT numbers, noise, and dose in dedicated breast CT. Methods: Adaptive filters were simulated to provide a flat fluence at the detector surface when used with a 14 cm breast phantom at 120 kVp. Beam hardening with each filter type was measured against increasing x-ray beam half-fan angle.. Breast CT images were simulated with and without an adaptive filter in the beam at multiple tube voltages. CT number, noise, and contrast to noise ratio (CNR) were measured for contrast elements inside the phantom. Finally, dose measurements were performed with and without an adaptive filter to determine its effect on breast dose. Results: Acrylic filters, while larger in size, provided a more uniform spectral distribution across the detector field of view compared to other filters tested. Without the adaptive filter in the beam, CT numbers, noise and CNR of the contrast elements were non-uniform across the CT images, and became uniform when the adaptive filter was used. When combining an adaptive filter and scaled x-ray exposure, the CNR increased and became comparable to or higher than the CNR without using an adaptive filter. Measurements showed breast dose distributions were more spatially uniform with an adaptive filter than without. Furthermore, the dose distribution across the phantom with the adaptive filter was more uniform at lower tube voltages than at higher tube voltages. Conclusion: We concluded the filter material should be similar to breast tissue with respect to the attenuation coefficients and density. Acrylic adaptive filters provided the flattest intensity with minimal beam hardening for the 14 cm breast phantom. Finally, breast dose uniformity with filter was comparable or better than without filter.

Purpose: To investigate the feasibility of volumetric modulated arc therapy (VMAT) for post-mastectomy radiotherapy (PMRT) and to compare dual-arc VMAT treatment plans to helical tomotherapy (HT) plans on the basis of dosimetric quality, radiobiological calculations and delivery efficiency. Methods: Dual-arc VMAT and HT treatment plans were created for fifteen patients previously treated at our clinic. Planning target volumes (PTV) included the chest wall and regional lymph nodes. The following metrics were used to compare treatment plans for each patient: dose homogeneity index (DHI) and conformity index (CI); coverage of the PTV; dose to organs at risk (OAR); tumor control probability (TCP), normal tissue complication probability (NTCP) and secondary cancer complication probability (SCCP); and treatment delivery time. Differences between treatment plans were tested for significance using the paired Students t-test. Results: Both modalities produced clinically acceptable PMRT plans. VMAT plans showed better CI (p < 0.01) and better OAR sparing at low doses than HT plans. For example, VMAT plans showed a 26% (p < 0.01) and 9% (p < 0.01) decrease in V5Gy in the lungs and heart respectively. On the other hand, HT plans showed better DHI (p < 0.01) and PTV coverage (p < 0.01). HT plans also showed better sparing at higher doses for some OARs, including 8% (p < 0.01) and 9% (p < 0.01) lower maximum doses to the lungs and heart, respectively. Both modalities achieved nearly 100% tumor control and approximately 1% NTCP in the lungs and heart, with VMAT showing lower SCCP (p < 0.01). VMAT plans also required 66.2% less time to deliver. Conclusion: Both VMAT and HT provide acceptable treatment plans for PMRT. Our study showed that VMAT in addition to being significantly faster achieved better CI and low-dose OAR sparing while HT achieved better DHI.

In this study, a proton pencil beam dose calculation algorithm was developed for a parallel, monoenergetic beam incident on a homogeneous water phantom. Fermi-Eyges theory (Eyges 1948) was used to transport pencil beams, and the characteristic width of elastic scatter events was modeled using the differential Moliere scattering power (Gottschalk 2010). The incorporation of this scattering power formalism allowed our model to account for multiple Coulomb scattering, single scattering, plural scattering, and rigorously accounted for material effects on scatter. Nonelastic nuclear interactions were incorporated into an additional pencil beam model. The attenuation of primary fluence due to nuclear events was accounted for using a weighted sum of primary and nuclear pencil beam components (Pedroni et al. 2005, Soukup et al. 2005). Free parameters of the nuclear pencil beam model were determined by a non-linear least squares fit to narrow field Monte Carlo data. Our dose calculation model was commissioned using central-axis depth dose data extracted from Monte Carlo simulations. Analytical corrections were incorporated to ensure that all input central-axis data satisfied side scatter equilibrium. <p> The dose calculation model was evaluated against Monte Carlo simulations of dose in a simplified beamline. Proton beam energies of 50, 100, 150, 200, and 250 MeV and field sizes of 4x4 cm² and 10x10 cm² were evaluated in three geometries: (1) flat phantom; (2) step phantoms (step heights of 1 and 4 cm); and (3) oblique phantom (rotation angle of 45°). All geometries evaluated with Monte Carlo dose calculations yielded 100% of points passing distance-to-agreement (DTA) ≤ 1 mm or Percent Dose Difference ≤ 3%. At least 99% of points passed with a DTA ≤ 1 mm or Percent Dose Difference ≤ 2%. The pencil beam dose calculation model provided excellent results when compared with Monte Carlo data.

In this thesis we describe data quality considerations for the Side Muon Rang Detector (SMRD), one of the six sub-detectors of the ND280 near detector of the Tokai to Kamiokande (T2K) long baseline neutrino oscillation experiment. Herein we show that the data quality of the SMRD has taken good data 99.9584% of the time it has been recording data. Also, 99.676% of SMRD data channels are shown to be operating optimally. In addition we discuss the stability of the SMRD. We find that based on a subset of data unbiased cosmic triggers have light yield of 112.8 +/- 0.3 p.e. vs. 100.7 +/- 0.5 p.e. for vertical and horizontal counters respectively. For a more stringent data set cosmic light yield for tracks with a nearly vertical path is determined to be 79:6 +/- 0.5 p.e. Detector stability is found to be related to the applied cosmic trigger mask, and this is evidenced in the increased stability of Run II over that of Run I. Also included is a basic introduction to neutrino physics and an overview of the T2K experiment.