Taking the 'physical' out of physical education

Fluctuations in and out of equilibrium: Thermalization, quantum measurements and Coulomb disorder

This purely theoretical thesis covers aspects of two contemporary research fields: the non-equilibrium dynamics in quantum systems and the electronic properties of three-dimensional topological insulators. In the first part we investigate the non-equilibrium dynamics in closed quantum systems. Thanks to recent technologies, especially from the field of ultracold quantum gases, it is possible to realize such systems in the laboratory. The focus is on the influence of hydrodynamic slow modes on the thermalization process. Generic systems in equilibrium, either classical or quantum, in equilibrium are described by thermodynamics. This is characterized by an ensemble of maximal entropy, but constrained by macroscopically conserved quantities. We will show that these conservation laws slow down thermalization and the final equilibrium state can be approached only algebraically in time. When the conservation laws are violated thermalization takes place exponential in time. In a different study we calculate probability distributions of projective quantum measurements. Newly developed quantum microscopes provide the opportunity to realize new measurement protocols which go far beyond the conventional measurements of correlation functions. The second part of this thesis is dedicated to a new class of materials known as three-dimensional topological insulators. Also here new experimental techniques have made it possible to fabricate these materials to a high enough quality that their topological nature is revealed. However, their transport properties are not fully understood yet. Motivated by unusual experimental results in the optical conductivity we have investigated the formation and thermal destruction of spatially localized electron- and hole-doped regions. These are caused by charged impurities which are introduced into the material in order to make the bulk insulating. Our theoretical results are in agreement with the experiment and can explain the results semi-quantitatively. Furthermore, we study emergent lengthscales in the bulk as well as close to the conducting surface.

Growth and application of planar III-V semiconductor nanowires grown with MOCVD

The semiconductor nanowire has been widely studied over the past decade and identified as a promising nanotechnology building block with application in photonics and electronics. The flexible bottom-up approach to nanowire growth allows for straightforward fabrication of complex 1D nanostructures with interesting optical, electrical, and mechanical properties. III-V nanowires in particular are useful because of their direct bandgap, high carrier mobility, and ability to form heterojunctions and have been used to make devices such as light-emitting diodes, lasers, and field-effect transistors. However, crystal defects are widely reported for III-V nanowires when grown in the common out-of-plane <111>B direction. Furthermore, commercialization of nanowires has been limited by the difficulty of assembling nanowires with predetermined position and alignment on a wafer-scale. In this thesis, planar III-V nanowires are introduced as a low-defect and integratable nanotechnology building block grown with metalorganic chemical vapor deposition. Planar GaAs nanowires grown with gold seed particles self-align along the <110> direction on the (001) GaAs substrate. Transmission electron microscopy reveals that planar GaAs nanowires are nearly free of crystal defects and grow laterally and epitaxially on the substrate surface. The nanowire morphology is shown to be primarily controlled through growth temperature and an ideal growth window of 470 +\- 10 °C is identified for planar GaAs nanowires. Extension of the planar growth mode to other materials is demonstrated through growth of planar InAs nanowires. Using a sacrificial layer, the transfer of planar GaAs nanowires onto silicon substrates with control over the alignment and position is presented. A metal-semiconductor field-effect transistor fabricated with a planar GaAs nanowire shows bulk-like low-field electron transport characteristics with high mobility. The aligned planar geometry and excellent material quality of planar III-V nanowires may lead to highly integrated III-V nanophotonics and nanoelectronics.

Falling Out of the Sky

“Falling Out of the Sky” is a collection of poems, both formal and free verse, that explores an intimate familial landscape. In particular, these poems raise the question of what it means to be human through examinations of family mythology and its changes as bodies and memories become unreliable with time.

Improving protein yield from mammalian cells by manipulation of stress response pathways

Monoclonal antibodies are a class of therapeutic that is an expanding area of the lucrative biopharmaceutical industry. These complex proteins are predominantly produced from large cultures of mammalian cells; the industry standard cell line being Chinese Hamster Ovary (CHO) cells. A number of optimisation strategies have led to antibody titres from CHO cells increasing by a hundred-fold, and it has been proposed that a further bottleneck in biosynthesis is in protein folding and assembly within the secretory pathway. To alleviate this bottleneck, a CHO-derived host cell line was generated by researchers at the pharmaceutical company UCB that stably overexpressed two critical genes: XBP1, a transcription factor capable of expanding the endoplasmic reticulum and upregulating protein chaperones; and Ero1α, an oxidase that replenishes the machinery of disulphide bond formation. This host cell line, named CHO-S XE, was confirmed to have a high yield of secreted antibody. The work presented in this thesis further characterises CHO-S XE, with the aim of using the information gained to lead the generation of novel host cell lines with more optimal characteristics than CHO-S XE. In addition to antibodies, it was found that CHO-S XE had improved production of two other secreted proteins: one with a simple tertiary structure and one complex multi-domain protein; and higher levels of a number of endogenous protein chaperones. As a more controlled system of gene expression to unravel the specific roles of XBP1 and Ero1α in the secretory properties of CHO-S XE, CHO cells with inducible overexpression of XBP1, Ero1α, or a third gene involved in the Unfolded Protein Response, GADD34, were generated. From these cell lines, it was shown that more antibody was secreted by cells with induced overexpression of XBP1; however, Ero1α and GADD34 overexpression did not improve antibody yield. Further investigation revealed that endogenous XBP1 splicing was downregulated in the presence of an abundance of the active form of XBP1. This result indicated a novel aspect of the regulation of the activity of IRE1, the stress-induced endoribonuclease responsible for XBP1 splicing. Overall, the work described in this thesis confirms that the overexpression of XBP1 has an enhancing effect on the secretory properties of CHO cells; information which could contribute to the development of host cells with a greater capacity for antibody production.

Which way out of poverty? the human capital versus human capabilities approaches

La pobreza es un problema mundial que afecta a personas de diferentes maneras. El propósito de este artículo es explorar dos teorías principales que abordan la pobreza y la posibilidad de su superación, que son los enfoques de capital humano y de capacidades humanas. El enfoque del capital humano se centra exclusivamente en la faceta económica de la pobreza; en esta perspectiva, la pobreza se define como la falta de dinero y puede abordarse mediante el aumento de los ingresos financieros de las personas que viven en la pobreza. El enfoque de las capacidades humanas ve la pobreza como un problema multidimensional que va más allá de la economía para áreas como la salud, la educación y la libertad. Este enfoque se orienta hacia el cambio social y ayudar a las personas en situación de pobreza para descubrir y desarrollar su potencial. El autor considera que las capacidades humanas abarcan con mayor precisión el alcance de la pobreza y las personas afectadas por el mismo, aunque debido a su amplia gama ha sido difícil diseñar e implementar políticas eficaces que aborden todas las facetas de la pobreza.

Rare sex or out of reach equilibrium? The dynamics of F-IS in partially clonal organisms

Background: Partially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient (F-IS) over bar < 0. Yet in partially clonal species, both F-IS < 0 and F-IS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a state-and-time discrete Markov chain model to describe the dynamics of F-IS over time under increasing rates of clonality. Results: Results of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to F-IS = 0. Thus, although clonality alone does not lead to departures from Hardy-Weinberg expectations once reached the final equilibrium state, both negative and positive F-IS values can arise transiently even at intermediate rates of clonality. More importantly, such "transient" departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of F-IS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean (F-IS,F-infinity) over bar value expected at equilibrium. Conclusion: Our results argue for a dynamical interpretation of F-IS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean (F-IS) over bar values deviating from zero and/or a large variation of F-IS over loci are observed.

Keeping the Germans out of the straits: The five ottoman dreadnought thesis reconsidered

This article contests Sean McMeekin’s claims concerning Russian culpability for the First World War. McMeekin maintains that Ottoman rearmament, particularly the purchase of several battleships released onto the global arms market by South American states, threatened to create a situation where the Russian Black Sea Fleet would be outclassed by its Ottoman opposite number. Rather than waiting for this to happen, the tsarist regime chose to go to war. Yet, contrary to McMeekin’s claims, the Ottoman naval expansion never assumed threatening dimensions because the Porte was unable to purchase battleships from Chile or Argentina. As a result, it provided no incentive for Russia to go to war in 1914.

X-Ray powder diffraction laboratory @ University of Málaga (UMA)

X-Ray Powder Diffraction (XRPD) laboratory is a facility placed at Servicios Centrales de apoyo a la Investigación (SCAI) at University of Malaga (UMA) http://www.scai.uma.es/. This facility has three XRPD diffractometers and a diffractometer to measure high-resolution thin-films. X´Pert PRO MPD from PANalytical. This is a bragg-brentano (theta/2theta) with reflection geometry diffractometer which allows to obtain high resolution XRPD data with strictly monochromatic CuKα1 radiation (λ=1.54059Å) [Ge(111) primary monochromator] and an automatic sample charger. Moreover, it has parallel monochromatic CuKα1 radiation (λ=1.54059Å) with an hybrid Ge(220) monochromator for capillary and multiproposal (bulk samples up to 1 Kg) sample holders. The HTK1200N chamber from Anton Paar allows collecting high resolution high temperature patterns. EMPYREAN from PANalytical. This diffractometer works in reflection and transmission geometries with theta/theta goniometer, using CuKα1,2 radiation (λ=1.5418Å), a focusing X-ray mirror and a ultra-fast PIXCEL 3D detector with 1D and 2D collection data modes (microstructural and preferred orientation analysis). Moreover, the TTK450N chamber allows low temperature and up to 450ºC studies. A D8 ADVANCE (BRUKER) was installed in April 2014. It is the first diffractometer in Europe equipped with a Johansson Ge(111) primary monochromator, which gives a strictly monochromatic Mo radiation (λ=0.7093 Å) [1]. It works in transmission mode (with a sample charger) with this high resolution configuration. XRPD data suitable for PDF (Pair Distribution Function) analysis can be collected with a capillary sample holder, due to the high energy and high resolution capabilities of this diffractometer. Moreover, it has a humidity chamber MHC-trans from Anton Paar working on transmission mode with MoKα1 (measurements can be collected at 5 to 95% of relative humidity (from 20 to 80 ºC) and up to 150ºC [2]). Furthermore, this diffractometer also has a reaction chamber XRK900 from Anton Paar (which uses CuKα1,2 radiation in reflection mode), which allows data collection from room temperature to 900ºC with up to 10 bar of different gases. Finally, a D8 DISVOVER A25 from BRUKER was installed on December 2014. It has a five axis Euler cradler and optics devices suitable for high resolution thin film data collection collected in in-plane and out-of-plane modes. To sum up, high-resolution thin films, microstructural, rocking-curve, Small Angle X-ray Scattering (SAXS), Grazing incident SAXS (GISAXS), Ultra Grazing incident diffraction (Ultra-GID) and microdiffraction measurements can be performed with the appropriated optics and sample holders. [1] L. León-Reina, M. García-Maté, G. Álvarez-Pinazo, I. Santacruz, O. Vallcorba, A.G. De la Torre, M.A.G. Aranda “Accuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiations” J. Appl. Crystallogr. 2016, 49, 722-735. [2] J. Aríñez-Soriano, J. Albalad, C. Vila-Parrondo, J. Pérez-Carvajal, S. Rodríguez-Hermida, A. Cabeza, F. Busqué, J. Juanhuix, I. Imaz, Daniel Maspoch “Single-crystal and humidity-controlled powder diffraction study of the breathing effect in a metal-organic framework upon water adsorption/desorption” Chem. Commun., 2016, DOI: 10.1039/C6CC02908F.

Methane seep carbonates yield clumped isotope signatures out of equilibrium with formation temperatures

Methane cold seep systems typically exhibit extensive buildups of authigenic carbonate minerals, resulting from local increases in alkalinity driven by methane oxidation. Here, we demonstrate that modern seep authigenic carbonates exhibit anomalously low clumped isotope values (Delta(47)), as much as similar to 0.2 parts per thousand lower than expected values. In modern seeps, this range of disequilibrium translates into apparent temperatures that are always warmer than ambient temperatures, by up to 50 degrees C. We examine various mechanisms that may induce disequilibrium behaviour in modern seep carbonates, and suggest that the observed values result from several factors including kinetic isotopic effects during methane oxidation, mixing of inorganic carbon pools, pH effects and rapid precipitation. Ancient seep carbonates studied here also exhibit potential disequilibrium signals. Ultimately, these findings indicate the predominance of disequilibrium clumped isotope behaviour in modern cold seep carbonates that must be considered when characterizing environmental conditions in both modern and ancient cold seep settings.

Risk perception and correlates of alcohol use among out-of-school youth in motor parks in Lagos State, Nigeria

Background and Aim: The prevalence of alcohol use has increased globally. Out-of-school youth are a vulnerable group who might have missed opportunities for learning healthy behaviours in a formal school environment. The purpose of this study was to determine the risk perception, pattern of use, and correlates of alcohol use among out-of-school youth in Lagos, Nigeria. Methods: A cross-sectional study was conducted among 380 out-of-school youth in motor parks in Lagos State, Nigeria, using interviewer administered questionnaires. Results: The lifetime prevalence of alcohol use was 61.1%, while 55.5% were current drinkers. Beer (57.3%) was the most consumed type of alcohol, followed by distilled spirits (29.8%). Using the CAGE scoring system, more than half (57.8%) of the current drinkers had a drinking problem. Almost three quarters (70.1%) had experienced at least one episode of alcohol intoxication within the past month. A considerable number of current drinkers (63.5%) desired to reduce their alcohol intake or stop drinking, while 45.5% had made unsuccessful attempts to do so within the past year. Only 28.9% had received assistance to quit or reduce their drinking and of these less than half (39.3%) received assistance from a professional or healthcare worker. Males were more likely to be current drinkers and to have experienced episodes of alcohol intoxication. Parental and peer drinking were associated with alcohol use but not with intoxication. Conclusions: It is important to design specific programmes to reduce alcohol use among out-of-school youth in these settings.

Post-CMOS compatible high-throughput fabrication of AIN-based piezoelectric microcantilevers

A post-complementary metal oxide semiconductor (CMOS) compatible microfabrication process of piezoelectric cantilevers has been developed. The fabrication process is suitable for standard silicon technology and provides low-cost and high-throughput manufacturing. This work reports design, fabrication and characterization of piezoelectric cantilevers based on aluminum nitride (AlN) thin films synthesized at room temperature. The proposed microcantilever system is a sandwich structure composed of chromium (Cr) electrodes and a sputtered AlN film. The key issue for cantilever fabrication is the growth at room temperature of the AlN layer by reactive sputtering, making possible the innovative compatibility of piezoelectric MEMS devices with CMOS circuits already processed. AlN and Cr have been etched by inductively coupled plasma (ICP) dry etching using a BCl3–Cl2–Ar plasma chemistry. As part of the novelty of the post-CMOS micromachining process presented here, a silicon Si (1 0 0) wafer has been used as substrate as well as the sacrificial layer used to release the microcantilevers. In order to achieve this, the Si surface underneath the structure has been wet etched using an HNA (hydrofluoric acid + nitric acid + acetic acid) based solution. X-ray diffraction (XRD) characterization indicated the high crystalline quality of the AlN film. An atomic force microscope (AFM) has been used to determine the Cr electrode surface roughness. The morphology of the fabricated devices has been studied by scanning electron microscope (SEM). The cantilevers have been piezoelectrically actuated and their out-of-plane vibration modes were detected by vibrometry.