Optical and Spin Properties of Defect-Bound Excitons in Semiconductors

Thesis (Ph.D.)--University of Washington, 2016-08

Thermodynamics and Heat Transport of doped Spin-Ice Materials

In this thesis the low-temperature magnetism of the spin-ice systems Dy2Ti2O7 and Ho2Ti2O7 is investigated. In general, a clear experimental evidence for a sizable magnetic contribution kappa_{mag} to the low-temperature, zero-field heat transport of both spin-ice materials is observed. This kappa_{mag} can be attributed to the magnetic monopole excitations, which are highly mobile in zero field and are suppressed by a rather small external field resulting in a drop of kappa(H). Towards higher magnetic fields, significant field dependencies of the phononic heat conductivities kappa_{ph}(H) of Ho2Ti2O7 and Dy2Ti2O7 are found, which are, however, of opposite signs, as it is also found for the highly dilute reference materials (Ho0.5Y0.5)2Ti2O7 and (Dy0.5Y0.5)2Ti2O7. The dominant effect in the Ho-based materials is the scattering of phonons by spin flips which appears to be significantly stronger than in the Dy-based materials. Here, the thermal conductivity is suppressed due to enhanced lattice distortions observed in the magnetostriction. Furthermore, the thermal conductivity of Dy2Ti2O7 has been investigated concerning strong hysteresis effects and slow-relaxation processes towards equilibrium states in the low-temperature and low-field regime. The thermal conductivity in the hysteretic regions slowly relaxes towards larger values suggesting that there is an additional suppression of the heat transport by disorder in the non-equilibrium states. The equilibration can even be governed by the heat current for particular configurations. A special focus was put on the dilution series Dy2Ti2O7x. From specific heat measurements, it was found that the ultra-slow thermal equilibration in pure spin ice Dy2Ti2O7 is rapidly suppressed upon dilution with non-magnetic yttrium and vanishes completely for x>=0.2 down to the lowest accessible temperatures. In general, the low-temperature entropy of (Dy1-xYx)2Ti2O7, considerably decreases with increasing x, whereas its temperature-dependence drastically increases. Thus, it could be clarified that there is no experimental evidence for a finite zero-temperature entropy in (Dy1-xYx)2Ti2O7 above x>=0.2, in clear contrast to the finite residual entropy S_{P}(x) expected from a generalized Pauling approximation. A similar discrepancy is also present between S_{P}(x) and the low-temperature entropy obtained by Monte Carlo simulations, which reproduce the experimental data from 25 K down to 0.7 K, whereas the data at 0.4 K are overestimated. A straightforward description of the field-dependence kappa(H) of the dilution series with qualitative models justifies the extraction of kappa_{mag}. It was observed that kappa_{mag} systematically scales with the degree of dilution and its low-field decrease is related to the monopole excitation energy. The diffusion coefficient D_{mag} for the monopole excitations was calculated by means of c_{mag} and kappa_{mag}. It exhibits a broad maximum around 1.6 K and is suppressed for T<=0.5 K, indicating a non-degenerate ground state in the long-time limit, and in the high-temperature range for T>=4 K where spin-ice physics is eliminated. A mean-free path of 0.3 mum is obtained for Dy2Ti2O7 at about 1 K within the kinetic gas theory.

Integrability for Relativistic Spin Networks

The evaluation of relativistic spin networks plays a fundamental role in the Barrett-Crane state sum model of Lorentzian quantum gravity in 4 dimensions. A relativistic spin network is a graph labelled by unitary irreducible representations of the Lorentz group appearing in the direct integral decomposition of the space of L^2 functions on three-dimensional hyperbolic space. To `evaluate' such a spin network we must do an integral; if this integral converges we say the spin network is `integrable'. Here we show that a large class of relativistic spin networks are integrable, including any whose underlying graph is the 4-simplex (the complete graph on 5 vertices). This proves a conjecture of Barrett and Crane, whose validity is required for the convergence of their state sum model.

Research-based spin-offs as agents of knowledge dissemination: evidence from the analysis of innovation networks

The paper addresses the role played by research-based spin-offs (RBSOs) as knowledge dissemination mechanisms, through their position in knowledge networks. For this purpose the paper analyses the formal networks established by the Portuguese RBSOs in the context of publicly funded research, technology and pre-commercial product development projects, and investigates their configuration along two levels. At organisational level, in order to understand whether RBSOs extend their reach beyond the academic sphere; and if they do, whether they relate with similar firms or connect to organisations located downstream in the knowledge value chain, and which is their position in networks involving both research organisations and other firms. At spatial level, in order to understand whether RBSOs extend their reach beyond the region where they are created, thus potentially acting as connectors between diverse regions. The analysis starts from the population of RBSOs created in Portugal until 2007 (387) and identifies those that have established formal technological relationships as part of projects funded by all the programmes launched in the period 1993-2012. As a result, the analysis encompasses 192 collaborative projects and involves 82 spin-offs and 281 partners, of which only 20% are research organisations, the remaining being other firms and a variety of other user organisations. The results, although still preliminary, provide some insights into the knowledge networking behaviour of the RBSOs. As expected, research organisations are a central actor in spin-offs’ networks, being the sole partner for some of them. But half of the RBSOs have moved beyond the academic sphere, being frequently a central element in tripartite technological relationships between research and other organisations and occupying an intermediation position in the network, thus potentially acting as facilitators in knowledge circulation and transformation. Also as expected, RBSOs are predominantly located in the main metropolitan areas and tend to relate with organisations similarly located. But while geographical proximity emerges as important in the choice of partners, in about half of the cases, RBSOs knowledge networks have extended beyond regional boundaries. Given their central position in the network this suggests a role as connectors across regions that will be explored in subsequent research.

Research-based spin-offs as agents of knowledge dissemination: evidence from the analysis of innovation networks

The paper addresses the role played by research-based spin-offs (RBSOs) as knowledge dissemination mechanisms, through their position in knowledge networks. For this purpose the paper analyses the formal networks established by Portuguese RBSOs, in the context of publicly funded research, technology and pre-commercial product development projects, and investigates their configuration across two levels. At organisational level, in order to understand whether RBSOs extend their reach beyond the academic sphere; and if they do, whether they connect to organisations located downstream in the knowledge value chain, and which is their position in networks involving both research organisations and other firms. At spatial level, in order to understand whether RBSOs extend their reach beyond the region where they are created, thus potentially acting as connectors between diverse regions. The analysis starts from the population of RBSOs created in Portugal until 2007 (327 firms) and identifies those that have established formal technological relationships, as part of projects funded by all the relevant programmes launched in the period 1993-2012. As a result, the analysis encompasses 192 collaborative projects and involves 82 spin-offs and 281 partners, of which only 20% are research organisations, the remaining being other firms and a variety of other downstream organisations. The results, although still preliminary, provide some insights into the knowledge networking behaviour of the RBSOs. As expected, research organisations are a central actor in spin-offs’ networks, being the sole partner for some of them. But half of the RBSOs have moved beyond the academic sphere, being frequently a central element in tripartite technological relationships between research and other organisations, and occupying an intermediation position in the network, thus potentially acting as facilitators in knowledge circulation and transformation. Also as expected, RBSOs are predominantly located in the main metropolitan areas and tend to relate with organisations similarly located. But while geographical proximity emerges as important in the choice of partners, in about half of the cases, RBSOs knowledge networks have extended beyond regional boundaries. Given their central position in the network, this suggests a role as connectors across regions that will be explored in subsequent research.

Position-dependent spin-orbit coupling for ultracold atoms

We theoretically explore atomic Bose-Einstein condensates (BECs) subject to position-dependent spin-orbit coupling (SOC). This SOC can be produced by cyclically laser coupling four internal atomic ground (or metastable) states in an environment where the detuning from resonance depends on position. The resulting spin-orbit coupled BEC (SOBEC) phase separates into domains, each of which contain density modulations-stripes-aligned either along the x or y direction. In each domain, the stripe orientation is determined by the sign of the local detuning. When these stripes have mismatched spatial periods along domain boundaries, non-trivial topological spin textures form at the interface, including skyrmions-like spin vortices and anti-vortices. In contrast to vortices present in conventional rotating BECs, these spin-vortices are stable topological defects that are not present in the corresponding homogenous stripe-phase SOBECs.

Thermal activation, long-range ordering, and topological frustration of artificial spin ice

Frustrated systems, typically characterized by competing interactions that cannot all be simultaneously satisfied, are ubiquitous in nature and display many rich phenomena and novel physics. Artificial spin ices (ASIs), arrays of lithographically patterned Ising-like single-domain magnetic nanostructures, are highly tunable systems that have proven to be a novel method for studying the effects of frustration and associated properties. The strength and nature of the frustrated interactions between individual magnets are readily tuned by design and the exact microstate of the system can be determined by a variety of characterization techniques. Recently, thermal activation of ASI systems has been demonstrated, introducing the spontaneous reversal of individual magnets and allowing for new explorations of novel phase transitions and phenomena using these systems. In this work, we introduce a new, robust material with favorable magnetic properties for studying thermally active ASI and use it to investigate a variety of ASI geometries. We reproduce previously reported perfect ground-state ordering in the square geometry and present studies of the kagome lattice showing the highest yet degree of ordering observed in this fully frustrated system. We consider theoretical predictions of long-range order in ASI and use both our experimental studies and kinetic Monte Carlo simulations to evaluate these predictions. Next, we introduce controlled topological defects into our square ASI samples and observe a new, extended frustration effect of the system. When we introduce a dislocation into the lattice, we still see large domains of ground-state order, but, in every sample, a domain wall containing higher energy spin arrangements originates from the dislocation, resolving a discontinuity in the ground-state order parameter. Locally, the magnets are unfrustrated, but frustration of the lattice persists due to its topology. We demonstrate the first direct imaging of spin configurations resulting from topological frustration in any system and make predictions on how dislocations could affect properties in numerous materials systems.

Cardiac T2-mapping using a fast gradient echo spin echo sequence - first in vitro and in vivo experience

Background: The aim of this study was the evaluation of a fast Gradient Spin Echo Technique (GraSE) for cardiac T2-mapping, combining a robust estimation of T2 relaxation times with short acquisition times. The sequence was compared against two previously introduced T2-mapping techniques in a phantom and in vivo. Methods: Phantom experiments were performed at 1.5 T using a commercially available cylindrical gel phantom. Three different T2-mapping techniques were compared: a Multi Echo Spin Echo (MESE; serving as a reference), a T2-prepared balanced Steady State Free Precession (T2prep) and a Gradient Spin Echo sequence. For the subsequent in vivo study, 12 healthy volunteers were examined on a clinical 1.5 T scanner. The three T2-mapping sequences were performed at three short-axis slices. Global myocardial T2 relaxation times were calculated and statistical analysis was performed. For assessment of pixel-by-pixel homogeneity, the number of segments showing an inhomogeneous T2 value distribution, as defined by a pixel SD exceeding 20 % of the corresponding observed T2 time, was counted. Results: Phantom experiments showed a greater difference of measured T2 values between T2prep and MESE than between GraSE and MESE, especially for species with low T1 values. Both, GraSE and T2prep resulted in an overestimation of T2 times compared to MESE. In vivo, significant differences between mean T2 times were observed. In general, T2prep resulted in lowest (52.4 +/- 2.8 ms) and GraSE in highest T2 estimates (59.3 +/- 4.0 ms). Analysis of pixel-by-pixel homogeneity revealed the least number of segments with inhomogeneous T2 distribution for GraSE-derived T2 maps. Conclusions: The GraSE sequence is a fast and robust sequence, combining advantages of both MESE and T2prep techniques, which promises to enable improved clinical applicability of T2-mapping in the future. Our study revealed significant differences of derived mean T2 values when applying different sequence designs. Therefore, a systematic comparison of different cardiac T2-mapping sequences and the establishment of dedicated reference values should be the goal of future studies.

Measurement of target single-spin asymmetry in charged kaon electroproduction on a transversely polarized 3He target

The subject of quark transverse spin and transverse momentum distribution are two current research frontier in understanding the spin structure of the nucleons. The goal of the research reported in this dissertation is to extract new information on the quark transversity distribution and the novel transverse-momentum-dependent Sivers function in the neutron. A semi-inclusive deep inelastic scattering experiment was performed at the Hall A of the Jefferson laboratory using 5.9 GeV electron beam and a transversely polarized ^{3}He target. The scattered electrons and the produced hadrons (pions, kaons, and protons) were detected in coincidence with two large magnetic spectrometers. By regularly flipping the spin direction of the transversely polarized target, the single-spin-asymmetry (SSA) of the semi-inclusive deep inelastic reaction ^{3}He^{uparrow}(e,e'h^{\pm})X was measured over the kinematic range 0.13 < x < 0.41 and 1.3 < Q^{2} < 3.1 (GeV)^{2}. The SSA contains several different azimuthal angular modulations which are convolutions of quarks distribution functions in the nucleons and the quark fragmentation functions into hadrons. It is from the extraction of the various ``moments'' of these azimuthal angular distributions (Collins moment and Sivers moment) that we obtain information on the quark transversity distribution and the novel T-odd Sivers function. In this dissertation, I first introduced the theoretical background and experimental status of nucleon spins and the physics of SSA. I will then present the experimental setup and data collection of the JLab E06-010 experiment. Details of data analysis will be discussed next with emphasis on the kaon particle identification and the Ring-Imaging Cherenkov detector which are my major responsibilities in this experiment. Finally, results on the kaon Collins and Sivers moments extracted from the Maximum Likelihood method will be presented and interpreted. I will conclude with a discussion on the future prospects for this research.

Oxidative stress and its haemodynamic consequences in chronic kidney disease

Chronic kidney disease (CKD) is associated with increased cardiovascular risk in comparison with the general population. This can be observed even in the early stages of CKD, and rises in proportion to the degree of renal impairment. Not only is cardiovascular disease (CVD) more prevalent in CKD, but its nature differs too, with an excess of morbidity and mortality associated with congestive cardiac failure, arrhythmia and sudden death, as well as the accelerated atherosclerosis which is also observed. Conventional cardiovascular risk factors such as hypertension, dyslipidaemia, obesity, glycaemia and smoking, are highly prevalent amongst patients with CKD, although in many of these examples the interaction between risk factor and disease differs from that which exists in normal renal function. Nevertheless, the extent of CVD cannot be fully explained by these conventional risk factors, and non-conventional factors specific to CKD are now recognised to contribute to the burden of CVD. Oxidative stress is a state characterised by excessive production of reactive oxygen species (ROS) and other radical species, a reduction in the capacity of antioxidant systems, and disturbance in normal redox homeostasis with depletion of protective vascular signalling molecules such as nitric oxide (NO). This results in oxidative damage to macromolecules such as lipids, proteins and DNA which can alter their functionality. Moreover, many enzymes are sensitive to redox regulation such that oxidative modification to cysteine thiol groups results in activation of signalling cascades which result in adverse cardiovascular effects such as vascular and endothelial dysfunction. Endothelial dysfunction and oxidative stress are present in association with many conventional cardiovascular risk factors, and can be observed even prior to the development of overt, clinical, vascular pathology, suggesting that these phenomena represent the earliest stages of CVD. In the presence of CKD, there is increased ROS production due to upregulated NADPH oxidase (NOX), increase in a circulating asymmetric dimethylarginine (ADMA), uncoupling of endothelial nitric oxide synthase (eNOS) as well as other mechanisms. There is also depletion in exogenous antioxidants such as ascorbic acid and tocopherol, and a reduction in activity of endogenous antioxidant systems regulated by the master gene regulator Nrf-2. In previous studies, circulating markers of oxidative stress have been shown to be increased in CKD, together with a reduction in endothelial function in a stepwise fashion relating to the severity of renal impairment. Not only is CVD linked to oxidative stress, but the progression of CKD itself is also in part dependent on redox sensitive mechanisms. For example, administration of the ROS scavenger tempol attenuates renal injury and reduces renal fibrosis seen on biopsy in a mouse model of CKD, whilst conversely, supplementation with the NOS inhibitor L-NAME causes proteinuria and renal impairment. Previous human studies examining the effect of antioxidant administration on vascular and renal function have been conflicting however. The work contained in this thesis therefore examines the effect of antioxidant administration on vascular and endothelial function in CKD. Firstly, 30 patients with CKD stages 3 – 5, and 20 matched hypertensive controls were recruited. Participants with CKD had lower ascorbic acid, higher TAP and ADMA, together with higher augmentation index and pulse wave velocity. There was no difference in baseline flow mediated dilatation (FMD) between groups. Intravenous ascorbic acid increased TAP and O2-, and reduced central BP and augmentation index in both groups, and lowered ADMA in the CKD group only. No effect on FMD was observed. The effects of ascorbic acid on kidney function was then investigated, however this was hindered by the inherent drawbacks of existing methods of non-invasively measuring kidney function. Arterial spin labelling MRI is an emerging imaging technique which allows measurement of renal perfusion without administration of an exogenous contrast agent. The technique relies upon application of an inversion pulse to blood within the vasculature proximal to the kidneys, which magnetically labels protons allowing measurement upon transit to the kidney. At the outset of this project local experience using ASL MRI was limited and there ensued a prolonged pre-clinical phase of testing with the aim of optimising imaging strategy. A study was then designed to investigate the repeatability of ASL MRI in a group of 12 healthy volunteers with normal renal function. The measured T1 longitudinal relaxation times and ASL MRI perfusion values were in keeping with those found in the literature; T1 time was 1376 ms in the cortex and 1491 ms in the whole kidney ROI, whilst perfusion was 321 mL/min/100g in the cortex, and 228 mL/min/100g in the whole kidney ROI. There was good reproducibility demonstrated on Bland Altman analysis, with a CVws was 9.2% for cortical perfusion and 7.1% for whole kidney perfusion. Subsequently, in a study of 17 patients with CKD and 24 healthy volunteers, the effects of ascorbic acid on renal perfusion was investigated. Although no change in renal perfusion was found following ascorbic acid, it was found that ASL MRI demonstrated significant differences between those with normal renal function and participants with CKD stages 3 – 5, with increased cortical and whole kidney T1, and reduced cortical and whole kidney perfusion. Interestingly, absolute perfusion showed a weak but significant correlation with progression of kidney disease over the preceding year. Ascorbic acid was therefore shown to have a significant effect on vascular biology both in CKD and in those with normal renal function, and to reduce ADMA only in patients with CKD. ASL MRI has shown promise as a non-invasive investigation of renal function and as a biomarker to identify individuals at high risk of progressive renal impairment.

Complete spin and orbital evolution of close-in bodies using a Maxwell viscoelastic rheology

In this paper, we present a formalism designed to model tidal interaction with a viscoelastic body made of Maxwell material. Our approach remains regular for any spin rate and orientation, and for any orbital configuration including high eccentricities and close encounters. The method is to integrate simultaneously the rotation and the position of the planet as well as its deformation. We provide the equations of motion both in the body frame and in the inertial frame. With this study, we generalize preexisting models to the spatial case and to arbitrary multipole orders using a formalism taken from quantum theory. We also provide the vectorial expression of the secular tidal torque expanded in Fourier series. Applying this model to close-in exoplanets, we observe that if the relaxation time is longer than the revolution period, the phase space of the system is characterized by the presence of several spin-orbit resonances, even in the circular case. As the system evolves, the planet spin can visit different spin-orbit configurations. The obliquity is decreasing along most of these resonances, but we observe a case where the planet tilt is instead growing. These conclusions derived from the secular torque are successfully tested with numerical integrations of the instantaneous equations of motion on HD 80606 b. Our formalism is also well adapted to close-in super-Earths in multiplanet systems which are known to have non-zero mutual inclinations.

ENZYME-FREE UBIQUITIN LIGATION. FROM NATIVE CHEMICAL LIGATION AND SPIN LABELING TO DIMERIZATION BY INTER-UBIQUITIN MIMICKING LINKAGE AND PH-DEPENDENT CONFORMATIONAL SWITCH

The delicate balance between the production and disposal of proteins is vital for the changes required in the cell to respond to given stimulus. Ubiquitination is a protein modification with a range of signaling outcomes when ubiquitin is attached to a protein through a highly ordered enzymatic cascade process. Understanding ubiquitination is a growing field and nowadays the application of chemical reactions allows the isolation of quantitative materials for structural studies. Therefore, in this dissertation it is described some of these suitable chemical methodologies to produce an isopeptide bond toward the polymerization of ubiquitin bypassing the enzymatic control with the purpose of showing if these chemical modifications have a direct impact on the structure of ubiquitin. First, the possibility of incorporating non-natural lysine analogs known as mercaptolysines into the polypeptide chain of Ubiquitin was explored when they were attached to ubiquitin by native chemical ligation at its C terminus. The sulfhydryl group was used for the attachment of a paramagnetic label to map the surface of ubiquitin. Second, the condensation catalyzed by silver nitrate was used for the dimer assembly. In particular, the main focus was on examining whether orthogonal protection and deprotection of each monomer have an impact on the reaction yield, since the synthetic strategy has been previously attempted successfully. Third, the formation of ubiquitin dimers was approached by building an inter-ubiquitin linkage mimicking the isopeptide bond with two approaches, the classic disulfide exchange as well as the thiol-ene click reaction by thermal initiation in aqueous conditions. After assembling the dimeric units, they were studied by Nuclear Magnetic Resonance, in order to establish a conformational state profile which depends on the pH conditions. The latter is a very important concept since some ligands have a preferred affinity when the protein-protein hydrophobic patches are in close proximity.