Synthesis & characterisation of group IV semiconducting nanowires

Semiconductor nanowires, particularly group 14 semiconductor nanowires, have been the subject of intensive research in the recent past. They have been demonstrated to provide an effective, versatile route towards the continued miniaturisation and improvement of microelectronics. This thesis aims to highlight some novel ways of fabricating and controlling various aspects of the growth of Si and Ge nanowires. Chapter 1 highlights the primary technique used for the growth of nanowires in this study, namely, supercritical fluid (SCF) growth reactions. The advantages (and disadvantages) of this technique for the growth of Si and Ge nanowires are highlighted, citing numerous examples from the past ten years. The many variables involved in this technique are discussed along with the resultant characteristics of nanowires produced (diameter, doping, orientation etc.). Chapter 2 outlines the experimental methodologies used in this thesis. The analytical techniques used for the structural characterisation of nanowires produced are also described as well as the techniques used for the chemical analysis of various surface terminations. Chapter 3 describes the controlled self-seeded growth of highly crystalline Ge nanowires, in the absence of conventional metal seed catalysts, using a variety of oligosilylgermane precursors and mixtures of germane and silane compounds. A model is presented which describes the main stages of self-seeded Ge nanowire growth (nucleation, coalescence and Ostwald ripening) from the oligosilylgermane precursors and in conjunction with TEM analysis, a mechanism of growth is proposed. Chapter 4 introduces the metal assisted etching (MAE) of Si substrates to produce Si nanowires. A single step metal-assisted etch (MAE) process, utilising metal ion-containing HF solutions in the absence of an external oxidant, was developed to generate heterostructured Si nanowires with controllable porous (isotropically etched) and non-porous (anisotropically etched) segments. In Chapter 5 the bottom-up growth of Ge nanowires, similar to that described in Chapter 3, and the top down etching of Si, described in Chapter 4, are combined. The introduction of a MAE processing step in order to “sink” the Ag seeds into the growth substrate, prior to nanowire growth, is shown to dramatically decrease the mean nanowire diameters and to narrow the diameter distributions. Finally, in Chapter 6, the biotin – streptavidin interaction was explored for the purposes of developing a novel Si junctionless nanowire transistor (JNT) sensor.

Effect of preantral follicle isolation technique on in-vitro follicular growth, oocyte maturation and embryo development in mice

Background: The use of mechanical and enzymatic techniques to isolate preantral follicles before in-vitro culture has been previously described. The aim of this study was to assess the effect of the isolation procedure of mouse preantral follicles on their subsequent development in vitro. Methods: Follicles were isolated either mechanically or enzymatically and cultured using an individual non-spherical culture system. Follicular development and steroidogenesis, oocyte in-vitro maturation and embryo development were assessed for both groups. Results: After 12 days of culture, follicles isolated mechanically had a higher survival rate but a lower antral-like cavity formation rate than follicles isolated enzymatically. Enzymatic follicle isolation was associated with a higher production of testosterone and estradiol compared with mechanical isolation. A stronger phosphatase alkaline reaction was observed after enzymatic isolation, suggesting that follicles isolated enzymatically had more theca cells than those isolated mechanically. However, both isolation techniques resulted in similar oocyte maturation and embryo development rates. Conclusions: Enzymatic follicular isolation did not affect theca cell development. Follicular steroidogenesis was enhanced after enzymatic isolation but the developmental capacity of oocytes was comparable to that obtained after mechanical isolation.

Pitfall of the LASH technique: An unsuspected leiomyosarcoma removed after morcellation

SCOPUS: ar.j

Afro-Cuban Bata Drum Aesthetics: Developing Individual and Group Technique, Sound and Identity

The Lucumi religion (also Santeria and Regla de Ocha) developed in 19th-century colonial Cuba, by syncretizing elements of Catholicism with the Yoruba worship of orisha. When fully initiated, santeros (priests) actively participate in religious ceremonies by periodically being possessed or "mounted" by a patron saint or orisha, usually within the context of a drumming ritual, known as a toque de santo, bembe, or tambor. Within these rituals, there is a clearly defined goal of trance possession, though its manifestation is not the sole measure of success or failure. Rather than focusing on the fleeting, exciting moments that immediately precede the arrival of an orisha in the form of a possession trance, this thesis investigates the entire four- to six-hour musical performance that is central to the ceremony. It examines the brief pauses, the moments of reduced intensity, the slow but deliberate build-ups of energy and excitement, and even the periods when novices are invited to perform the sacred bata drums, and places these moments on an equal footing with the more dynamic periods where possession is imminent or in progress. This document approaches Lucumi ritual from the viewpoint of bata drummers, ritual specialists who, during the course of a toque de santo, exercise wide latitude in determining the shape of the event. Known as omo Ana (children of the orisha Ana who is manifest in drums and rhythms), bata drummers comprise a fraternity that is accessible only through ritual initiation. Though they are sensitive to the desires of the many participants during a toque de santo, and indeed make their living by satisfying the expectations of their hosts, many of the drummers' activities are inwardly focused on the cultivation and preservation of this fraternity. Occasionally interfering with spirit possession, and other expectations of the participants, these aberrant activities include teaching and learning, developing group identity or signature sound, and achieving a state of intimacy among the musicians known as "communitas."

In situ synthesis of DNA microarray on functionalized cyclic olefin copolymer substrate.

Thermoplastic materials such as cyclic-olefin copolymers (COC) provide a versatile and cost-effective alternative to the traditional glass or silicon substrate for rapid prototyping and industrial scale fabrication of microdevices. To extend the utility of COC as an effective microarray substrate, we developed a new method that enabled for the first time in situ synthesis of DNA oligonucleotide microarrays on the COC substrate. To achieve high-quality DNA synthesis, a SiO(2) thin film array was prepatterned on the inert and hydrophobic COC surface using RF sputtering technique. The subsequent in situ DNA synthesis was confined to the surface of the prepatterned hydrophilic SiO(2) thin film features by precision delivery of the phosphoramidite chemistry using an inkjet DNA synthesizer. The in situ SiO(2)-COC DNA microarray demonstrated superior quality and stability in hybridization assays and thermal cycling reactions. Furthermore, we demonstrate that pools of high-quality mixed-oligos could be cleaved off the SiO(2)-COC microarrays and used directly for construction of DNA origami nanostructures. It is believed that this method will not only enable synthesis of high-quality and low-cost COC DNA microarrays but also provide a basis for further development of integrated microfluidics microarrays for a broad range of bioanalytical and biofabrication applications.

A versatile diffractive maskless lithography for single-shot and serial microfabrication.

We demonstrate a diffractive maskless lithographic system that is capable of rapidly performing both serial and single-shot micropatterning. Utilizing the diffractive properties of phase holograms displayed on a spatial light modulator, arbitrary intensity distributions were produced to form two and three dimensional micropatterns/structures in a variety of substrates. A straightforward graphical user interface was implemented to allow users to load templates and change patterning modes within the span of a few minutes. A minimum resolution of approximately 700 nm is demonstrated for both patterning modes, which compares favorably to the 232 nm resolution limit predicted by the Rayleigh criterion. The presented method is rapid and adaptable, allowing for the parallel fabrication of microstructures in photoresist as well as the fabrication of protein microstructures that retain functional activity.

Development of the morpholino gene knockdown technique in Fundulus heteroclitus: a tool for studying molecular mechanisms in an established environmental model.

A significant challenge in environmental toxicology is that many genetic and genomic tools available in laboratory models are not developed for commonly used environmental models. The Atlantic killifish (Fundulus heteroclitus) is one of the most studied teleost environmental models, yet few genetic or genomic tools have been developed for use in this species. The advancement of genetic and evolutionary toxicology will require that many of the tools developed in laboratory models be transferred into species more applicable to environmental toxicology. Antisense morpholino oligonucleotide (MO) gene knockdown technology has been widely utilized to study development in zebrafish and has been proven to be a powerful tool in toxicological investigations through direct manipulation of molecular pathways. To expand the utility of killifish as an environmental model, MO gene knockdown technology was adapted for use in Fundulus. Morpholino microinjection methods were altered to overcome the significant differences between these two species. Morpholino efficacy and functional duration were evaluated with molecular and phenotypic methods. A cytochrome P450-1A (CYP1A) MO was used to confirm effectiveness of the methodology. For CYP1A MO-injected embryos, a 70% reduction in CYP1A activity, a 86% reduction in total CYP1A protein, a significant increase in beta-naphthoflavone-induced teratogenicity, and estimates of functional duration (50% reduction in activity 10 dpf, and 86% reduction in total protein 12 dpf) conclusively demonstrated that MO technologies can be used effectively in killifish and will likely be just as informative as they have been in zebrafish.

Integrative Genomics Reveals a Role for GNA13 in Lymphomagenesis

Lymphomas comprise a diverse group of malignancies derived from immune cells. High throughput sequencing has recently emerged as a powerful and versatile method for analysis of the cancer genome and transcriptome. As these data continue to emerge, the crucial work lies in sorting through the wealth of information to hone in on the critical aspects that will give us a better understanding of biology and new insight for how to treat disease. Finding the important signals within these large data sets is one of the major challenges of next generation sequencing.

In this dissertation, I have developed several complementary strategies to describe the genetic underpinnings of lymphomas. I begin with developing a better method for RNA sequencing that enables strand-specific total RNA sequencing and alternative splicing profiling in the same analysis. I then combine this RNA sequencing technique with whole exome sequencing to better understand the global landscape of aberrations in these diseases. Finally, I use traditional cell and molecular biology techniques to define the consequences of major genetic alterations in lymphoma.

Through this analysis, I find recurrent silencing mutations in the G alpha binding protein GNA13 and associated focal adhesion proteins. I aim to describe how loss-of-function mutations in GNA13 can be oncogenic in the context of germinal center B cell biology. Using in vitro techniques including liquid chromatography-mass spectrometry and knockdown and overexpression of genes in B cell lymphoma cell lines, I determine protein binding partners and downstream effectors of GNA13. I also develop a transgenic mouse model to study the role of GNA13 in the germinal center in vivo to determine effects of GNA13 deletion on germinal center structure and cell migration.

Thus, I have developed complementary approaches that span the spectrum from discovery to context-dependent gene models that afford a better understanding of the biological function of aberrant events and ultimately result in a better understanding of disease.

FANTASIO: a versatile experimental set-up to investigate jet-cooled molecules

The design of a new apparatus, named FANTASIO, for studying jet-cooled molecules is described. It includes, around the same supersonic expansion cell, a high resolution Fourier transform spectrometer with single or multipass optics, a tunable diode laser spectrometer with optional cavity ring-down facilities, and a quadrupole mass spectrometer. Performance and operational procedures are illustrated.

Does an incremental filling technique reduce polymerization shrinkage stresses

It is widely accepted that volumetric contraction and solidification during the polymerization process of restorative composites in combination with bonding to the hard tissue result in stress transfer and inward deformation of the cavity walls of the restored tooth. Deformation of the walls decreases the size of the cavity during the filling process. This fact has a profound influence on the assumption-raised and discussed in this paper-that an incremental filling technique reduces the stress effect of composite shrinkage on the tooth. Developing stress fields for different incremental filling techniques are simulated in a numerical analysis. The analysis shows that, in a restoration with a well-established bond to the tooth-as is generally desired-incremental filling techniques increase the deformation of the restored tooth. The increase is caused by the incremental deformation of the preparation, which effectively decreases the total amount of composite needed to fill the cavity. This leads to a higher-stressed tooth-composite structure. The study also shows that the assessment of intercuspal distance measurements as well as simplifications based on generalization of the shrinkage stress state cannot be sufficient to characterize the effect of polymerization shrinkage in a tooth-restoration complex. Incremental filling methods may need to be retained for reasons such as densification, adaptation, thoroughness of cure, and bond formation. However, it is very difficult to prove that incrementalization needs to be retained because of the abatement of shrinkage effects.

Busbar sizing modeling tools: comparing an ANSYS® based 3D model with the versatile 1D model part of MHD-Valdis

The main goal of a cell stability MHD model like MHD-Valdis is to help locate the busbars around the cell in a way which leads to the generation of a magnetic field inside the cell that itself leads to a stable cell operation. Yet as far as the cell stability is concerned, the uniformity of the current density in the metal pad is also extremely important and can only be achieved with a correct busbar network sizing. This work compares the usage of a detailed ANSYS based 3D thermo-electric model with the one of the versatile 1D part of MHD-Valdis to help design a well balanced busbar network.

Identifying the damage mechanisms in paper using the acoustic emission monitoring technique

This paper investigates the use of the acoustic emission (AE) monitoring technique for use in identifying the damage mechanisms present in paper associated with its production process. The microscopic structure of paper consists of a random mesh of paper fibres connected by hydrogen bonds. This implies the existence of two damage mechanisms, the failure of a fibre-fibre bond and the failure of a fibre. This paper describes a hybrid mathematical model which couples the mechanics of the mass-spring model to the acoustic wave propagation model for use in generating the acoustic signal emitted by complex structures of paper fibres under strain. The derivation of the mass-spring model can be found in [1,2], with details of the acoustic wave equation found in [3,4]. The numerical implementation of the vibro-acoustic model is discussed in detail with particular emphasis on the damping present in the numerical model. The hybrid model uses an implicit solver which intrinsically introduces artificial damping to the solution. The artificial damping is shown to affect the frequency response of the mass-spring model, therefore certain restrictions on the simulation time step must be enforced so that the model produces physically accurate results. The hybrid mathematical model is used to simulate small fibre networks to provide information on the acoustic response of each damage mechanism. The simulated AEs are then analysed using a continuous wavelet transform (CWT), described in [5], which provides a two dimensional time-frequency representation of the signal. The AEs from the two damage mechanisms show different characteristics in the CWT so that it is possible to define a fibre-fibre bond failure by the criteria listed below. The dominant frequency components of the AE must be at approximately 250 kHz or 750 kHz. The strongest frequency component may be at either approximately 250 kHz or 750 kHz. The duration of the frequency component at approximately 250 kHz is longer than that of the frequency component at approximately 750 kHz. Similarly, the criteria for identifying a fibre failure are given below. The dominant frequency component of the AE must be greater than 800 kHz. The duration of the dominant frequency component must be less than 5.00E-06 seconds. The dominant frequency component must be present at the front of the AE. Essentially, the failure of a fibre-fibre bond produces a low frequency wave and the failure of a fibre produces a high frequency pulse. Using this theoretical criteria, it is now possible to train an intelligent classifier such as the Self-Organising Map (SOM) [6] using the experimental data. First certain features must be extracted from the CWTs of the AEs for use in training the SOM. For this work, each CWT is divided into 200 windows of 5E-06s in duration covering a 100 kHz frequency range. The power ratio for each windows is then calculated and used as a feature. Having extracted the features from the AEs, the SOM can now be trained, but care is required so that the both damage mechanisms are adequately represented in the training set. This is an issue with paper as the failure of the fibre-fibre bonds is the prevalent damage mechanism. Once a suitable training set is found, the SOM can be trained and its performance analysed. For the SOM described in this work, there is a good chance that it will correctly classify the experimental AEs.

A versatile characterization of causal relationships

This paper introduces a framework for representing versatile temporal relationships between events and their effects. The framework is based on a simple time model which characterizes each time element as a subset of the set of real numbers and allows expression of both absolute time values and relative temporal relations. The formalism presented here formally specifies the so-called most general temporal constraint (GTC), which guarantees the common-sense assertion that “the beginning of the effect cannot precede the beginning of the cause”. It is shown that there are in fact 8 possible causal relationships which satisfy GTC, including cases where, on the one hand, effects start simultaneously with, during, immediately after, or some time after their causes, and on the other hand, events end before, simultaneously with, or after their causes. The causal relationships characterized in this paper are versatile enough to subsume those representatives in the literature.

Numerical investigation of a source extraction technique based on an acoustic correction method

An aerodynamic sound source extraction from a general flow field is applied to a number of model problems and to a problem of engineering interest. The extraction technique is based on a variable decomposition, which results to an acoustic correction method, of each of the flow variables into a dominant flow component and a perturbation component. The dominant flow component is obtained with a general-purpose Computational Fluid Dynamics (CFD) code which uses a cell-centred finite volume method to solve the Reynolds-averaged Navier–Stokes equations. The perturbations are calculated from a set of acoustic perturbation equations with source terms extracted from unsteady CFD solutions at each time step via the use of a staggered dispersion-relation-preserving (DRP) finite-difference scheme. Numerical experiments include (1) propagation of a 1-D acoustic pulse without mean flow, (2) propagation of a 2-D acoustic pulse with/without mean flow, (3) reflection of an acoustic pulse from a flat plate with mean flow, and (4) flow-induced noise generated by the an unsteady laminar flow past a 2-D cavity. The computational results demonstrate the accuracy for model problems and illustrate the feasibility for more complex aeroacoustic problems of the source extraction technique.

A versatile policy toolkit supporting run-time policy reconfiguration

This paper describes an autonomics development tool which serves as both a powerful and flexible policy-expression language and a policy-based framework that supports the integration and dynamic composition of several autonomic computing techniques including signal processing, automated trend analysis and utility functions. Each of these technologies has specific advantages and applicability to different types of dynamic adaptation. The AGILE platform enables seamless interoperability of the different technologies to each perform various aspects of self-management within a single application. Self-management behaviour is specified using the policy language semantics to bind the various technologies together as required. Since the policy semantics support run-time re-configuration, the self-management architecture is dynamically composable. The policy language and implementation library have integrated support for self-stabilising behaviour, enabling oscillation and other forms of instability to be handled at the policy level with very little effort on the part of the application developer. Example applications are presented to illustrate the integration of different autonomics techniques, and the achievement of dynamic composition.