Abstract Diamond is nowadays regarded as a potential semiconductor material of the future, due to its extreme and unique properties. Some of these properties, in- clude its high hardness, highest breakdown ¯eld, high Debye temperature, high thermal conductivity, high hole and electron mobilities, large bandgap and op- tical transparency, among others. These properties make diamond suitable for high-temperature, high-speed and high-power electronic applicatons, as well as in other applications. However, defects associated with ion implantation have been shown to make it rather di±cult to obtain n-type doping in diamond. As such, an understanding of the nature of defects produced during ion implanta- tion of diamond remains a subject of great importance, if not essential, for the optimization of high-temperature, high-power electronic applications in partic- ular. In this respect, this study investigates the nature of the radiation damage generated within the collision cascades of multi-implantations of carbon ions in high-pressure, high-temperature single-crystal synthetic type Ib diamond, spread over a range of energies (50-150keV) and doses. This is achieved by means of the cold-implantation-rapid-annealing (CIRA) routine, and the anal- ysis of damage caused was done by using cross sectional transmission electron microscopy techniques. More precisely, the modes used to achieve this are the bright ¯eld transmission electron microscopy (BFTEM) coupled with selected area di®raction or SAD. At low dose implantation or at sub-critical implantation doses (2.5x1015 ions/cm2), it was found that the ion-damaged diamond layer consists of some threading dislocations, not homogeneously distributed which propagate from the surface into the ion-damaged diamond. In contrast to the sub-critical implantation doses , it was found that at very high implantation doses (7.0x1015 ions/cm2), i.e., above the critical dose (where diamond transforms to graphite upon annealing), the damaged diamond layer had some unconventional defect features close to the implanted surface.

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, June, 2013 / Diamond with its outstanding and unique physical properties offers the opportunity to be used as semiconductor material in future device technologies. Promising ap- plications are, among others, high speed and high-power electronic devices working under extreme conditions, such as high temperature and harsh chemical environments. With respect to electronic applications, a controlled doping of the material is neces- sary which is preferably done by ion implantation. The ion implantation technique allows incorporation of foreign atoms at de¯ned depths and with controlled spatial distribution which is not achievable with other methods. However, the ion implanta- tion process is always connected with the formation of defects which compensate and trap charge carriers thus degrading the electrical behaviour. It is therefore essential to understand the nature of defects produced under various implantation conditions. In this respect, this study involves the investigation of the nature of the radiation damage produced during the multi-implantation of carbon ions in synthetic high- pressure, high-temperature (HPHT) type Ib diamond spread over a range of energies from 50 to 150 keV and °uences, using the cold-implantation-rapid-annealing (CIRA) routine. Single energy implantation of carbon ions in synthetic HPHT (type Ib), at room temperature, was also performed. Both ion milling and FIB (Focused Ion Beam) milling were used to prepare thin specimen for transmission electron micro- scope (TEM) analysis. The unimplanted, implanted and annealed samples were characterized using trans- mission electron microscopy based techniques and Raman spectroscopy. ii iii In unimplanted type Ia natural diamond, a high density of platelets, exhibiting the typical contrast of both edge-on and inclined platelets on f100g planes was found. As-implanted HPHT type Ib diamond, implanted with single energy of 150 keV car- bon ions and °uence of 7£1015 ions cm¡2 revealed an amorphous diamond layer of about 80 nm in thickness while, for low °uence implantations, the damaged diamond retained its crystallinity after annealing at 1600 K. In addition, damaged diamond transformed into disordered carbon comprising regions with bent (002) graphitic fringes and regions of amorphous carbon when high °uence, i.e., one above the amor- phization/graphitisation threshold were used followed by rapid thermal annealing at 1600 K. Furthermore, the interface between the implanted and annealed layer and the diamond substrate at the end of the range, showed diamond crystallites, inter- spersed between regions of amorphous carbon and partially graphitized carbon. This indicates that solid phase epitaxial recrystallization regrowth in diamond does not occur.

A finalidade deste trabalho é aplicar a técnica de holografia em cristais fotorrefrativos para o estudo de propriedades mecânicas de microdispositivos, garantindo ainda a obtenção de uma geometria de arranjo holográfico simples e compacto. Foram feitas a análise de vibração e a análise de deformação de microdispositivos por meio da interferometria de média temporal e de dupla exposição, respectivamente. Como fontes de luz, foram utilizados diodos laser emitindo em 660nm, e um He-Ne laser emitindo em 632,8nm. Como meio fotorrefrativo de registro holográfico foi utilizado o cristal Bi12TiO20, (BTO) da família das selenitas. Foi proposto um arranjo óptico de holografia de reflexão do tipo Denisiuk, e a este arranjo foi adicionado um conjunto de lentes objetiva e ocular para formar uma configuração de microscópio composto, com o objetivo de obterem-se imagens holográficas de objetos de dimensões microscópicas. A gravação e a reconstrução do holograma se deram simultaneamente, devido à associação do cristal fotorrefrativo a uma câmera CMOS. Desta maneira, a observação dos hologramas foi feita em tempo real. Foram feitas, inicialmente, imagens de dupla exposição de piezorresistores MEMS (microelectromechanical systems), de geometria reduzida (2,96 x 0,6 mm2), e de dispositivos CMUT (Capacitive Micromachined Ultrasonic Transducers) com 640m de diâmetro. Através desta técnica foi possível medir deslocamentos de 0,33m a 4,3m. Foram obtidos também interferogramas de média temporal de cerâmicas e transdutores piezoelétricos, porém, iluminando apenas pequenas regiões destes objetos. Estas imagens mostraram qualidade razoável, indicando que é possível aplicar a técnica de interferometria em média temporal para objetos com amplitude de vibração entre 0,12m e 1,7m. Para investigar as potencialidades microscópicas foram feitas imagens de padrões de teste de resolução, onde foi possível visualizar estruturas com geometrias entre 2mm e 20m. / The aim of this work is to apply photorefractive crystals holography technique for the study of mechanical properties of micro-devices; it ensures obtaining a simple and compact geometry of holographic setup. Vibration and deformation analyses of micro-devices were performed using time average and double exposure interferometry, respectively. As light sources, it was used diode lasers emitting at 660nm, and He-Ne laser emitting at 632.8nm. As photorefractive holographic recording medium was used Bi12TiO20 (BTO) crystal, family of selenites. An optical setup of Denisiuk-type reflection holography was proposed, and this setup was added a set of objective and eyepiece lenses to form a compound microscope configuration, in order to obtain holographic images of objects with microscopic dimensions. Recording and reconstruction of the hologram occurred simultaneously, due to the combination of the photorefractive crystal to a CMOS camera. Thus, holograms observation occurs in real time. It was initially performed double exposure images of MEMS (microelectromechanical systems) piezoresistors, with reduced geometry (2.96 x 0.6 mm2), and CMUT (capacitive micromachined ultrasonic transducers) devices with 640m diameter. By this technique was possible measure displacements of 0.33m to 4.3m. Time average interferograms of Ceramics and piezoelectric transducers were also obtained, however, it illuminating only small regions of these objects. These images showed reasonable quality, indicating that it is possible apply the time average technique for objects with vibration amplitude between 0.12m e 1.7m. In order to investigate the microscopic potentialities images of resolution test chart were done, where it was possible to visualize structures with geometries between 20 m and 2mm.

Phase-contrast imaging is a method of imaging widely used in biomedical research and applications. It is a label-free method that exploits intrinsic differences in the refractive index of different tissues to differentiate between biological structures under analysis. The basic principle of phase-contrast imaging has inspired a lot of implementations that are suited for different applications. This thesis explores multiple novel implementations of phase-contrast imaging in the following order. 1, We combined scanning Oblique Back-illumination Microscope (sOBM) and confocal microscope to produce phase and fluorescence contrast images in an endomicroscopy configuration. This dual-modality design provides co-registered, complementary labeled and unlabeled contrast of the sample. We further miniaturized the probe by dispensing the two optical fibers in our old design. And we presented proof of principle demonstrations with ex-vivo mouse colon tissue. 2, Then we explored sOBM-based phase and amplitude contrast imaging under different wavelengths. Hyperspectral imaging is achieved by multiplexing a wide-range supercontinuum laser with a Michaelson interferometer (similar to Fourier transform spectroscopy). It features simultaneous acquisition of hyperspectral phase and amplitude images with arbitrarily thick scattering biological samples. Proof-of-principle demonstrations are presented with chorioallantoic membrane of a chick embryo, illustrating the possibility of high-resolution hemodynamics imaging in thick tissue. 3, We focused on increasing the throughput of flow cytometry with principle of phase-contrast imaging and compressive sensing. By utilizing the linearity of scattered patterns under partially coherent illumination, our cytometer can detect multiple objects in the same field of view. By utilizing an optimized matched filter on pupil plane, it also provides increased information capacity of each measurement without sacrificing speed. We demonstrated a throughput of over 10,000 particles/s with accuracy over 91% in our results. 4, A fourth part, which describes the principle and preliminary results of a computational fluorescence endomicroscope is also included. It uses a numerical method to achieve sectioning effect and renders a pseudo-3D image stack with a single shot. The results are compared with true-3D image stack acquired with a confocal microscope.

Estudos de placentação foram desenvolvidos em quatorze fêmeas de mocós em diferentes fases de gestação. As fêmeas foram pré-anestesiadas associando-se cloridrato de quetamina (15mg/kg) e midazolan (1mg/kg). Em seguida anestesiadas com isoflurano em associação com oxigênio com 100% de saturação. Após a anestesia realizou-se a cirurgia para a exposição das estruturas fetais e a coleta de dados. Macroscopicamente, identificou-se uma placenta discoidal, o saco vitelínico e o âmnio de aspecto transparente e avascular. Microscopicamente, o cordão umbilical apresentou duas artérias, uma veia e o ducto alantoideano, além de uma artéria e uma veia vitelínicas. A placenta mostrou uma relação mesometrial com o útero e apresentou-se constituída por lóbulos delimitados por regiões de interlóbulo e, perifericamente, uma região de sincício marginal contendo locais com espongiotrofoblasto e células trofoblásticas gigantes. A subplacenta esteve composta por lóbulos e por trofoblasto de natureza sincicial e celular. O saco vitelínico apresentou uma porção parietal sustentada pela membrana de Reichert´s e uma porção visceral muito vascularizada. Os estudos de placentação em mocós indicaram a presença de um útero bicórneo, uma placenta corioalantoídea discoidal e labiríntica, com barreira placentária hemocorial de subtipo hemomonocorial separando um fluxo sangüíneo materno-fetal do tipo contracorrente. / Placentation studies of fourteen rock cavy females in different gestation phases were conducted. Females were pre-anesthetized associating ketamine chloridrate (15mg/kg) and midazolan (1mg/kg). Soon afterwards, they were anesthetized by isoflurane inhalation in association with oxygen at 100% saturation. After anesthesia, the surgery allowed to exhibit fetal structures and then data collection was performed. Macroscopically, a discoidal placenta, vitelline sack and the amnion of a transparent aspect and avascular, were identified. Microscopically, the umbilical cord presented two arteries, a vein and the allantoid duct, besides an artery and a vitelline vein. The placenta showed a relationship between the mesometrium and the uterus and was constituted by lobes delimited by interlobular areas and, peripherically, by an area of marginal syncytium containing places with spongiotrophoblast and gigantic trophoblastic cells. The subplacenta was composed by lobules and by a trophoblast of syncytium and cellular nature. The vitelline sack showed a parietal portion sustained by the Reichert´s membrane and a well-vascularized visceral portion. The placentation studies in rock cavies indicated the presence of a bicornuate uterus, a chorioallantoid discoidal and labirynthic placenta, with a hemochorial placental barrier of hemomonochorial subtype separating the maternal-fetal countercurrent sanguine flow.

by Chan, Ray. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1994. / Includes bibliographical references (leaves [93-96]). / ACKNOWLEDGMENT / ABSTRACT / FIGURE CAPTIONS / TABLE CAPTIONS / INTRODUCTION / Chapter I. --- PRINCIPLES OF SEM / Chapter 1.1 --- STRUCTURE OF SEM --- p.1-1 / Chapter 1.2 --- IMAGE FORMATION --- p.1-6 / Chapter 1.2.1 --- Electron Beam-Specimen Interaction --- p.1-6 / Chapter 1.2.1.1 --- Electron scattering in solid specimen --- p.1-7 / Chapter 1.2.1.2 --- Electron range and spatial distribution --- p.1-7 / Chapter 1.2.1.3 --- Back scattered electrons(BE) --- p.1-8 / Chapter 1.2.1.4 --- Secondary electron(SE) --- p.1-9 / Chapter 1.2.1.5 --- Other signal types --- p.1-13 / Chapter 1.2.2 --- Types of Image Contrast --- p.1-14 / Chapter 1.3 --- DISTORTION AND NOISE --- p.1-17 / Chapter 1.3.1 --- Lens Aberration --- p.1-17 / Chapter 1.3.1.1 --- Spherical aberration --- p.1-17 / Chapter 1.3.1.2 --- Chromatic aberration --- p.1-18 / Chapter 1.3.1.3 --- Diffraction effect --- p.1-19 / Chapter 1.3.1.4 --- Axial astigmatism --- p.1-20 / Chapter 1.3.1.5 --- Spatial resolution calculation --- p.1-21 / Chapter 1.3.2 --- Image Defects --- p.1-22 / Chapter 1.3.2.1 --- Projection distortion --- p.1-22 / Chapter 1.3.2.2 --- Specimen tilting --- p.1-22 / Chapter 1.3.2.3 --- Moire effects --- p.1-22 / Chapter 1.3.3 --- Noise in SEM --- p.1-23 / Chapter II. --- SEM FOR IC TESTING / Chapter 2.1 --- QUANTITATIVE ANALYSIS OF VOLTAGE MEASUREMENT --- p.2-1 / Chapter 2.1.1 --- Energy Analysis of SEs --- p.2-1 / Chapter 2.1.2 --- Suppression of Local Fields --- p.2-2 / Chapter 2.1.3 --- "Elimination of Topography, Material Contrast and Work Function Variation" --- p.2-2 / Chapter 2.2 --- VOLTAGE RESOLUTION --- p.2-3 / Chapter 2.3 --- TIME RESOLUTION --- p.2-4 / Chapter 2.3.1 --- SE Generation Time --- p.2-4 / Chapter 2.3.2 --- SE Flight Time --- p.2-4 / Chapter 2.3.3 --- Required Voltage Resolution --- p.2-5 / Chapter 2.3.4 --- Electron Beam Pulse Width --- p.2-5 / Chapter 2.4 --- SPATIAL RESOLUTION --- p.2-5 / Chapter 2.5 --- CAPACITIVE COUPLING VOLTAGE CONTRAST --- p.2-6 / Chapter III. --- SEM TESTING TECHNIQUES / Chapter 3.1 --- CONVENTIONAL TESTING METHODS SYNOPSIS --- p.3-1 / Chapter 3.2 --- TESTING TECHNIQUES FOR SEM --- p.3-2 / Chapter 3.2.1 --- Static Mode --- p.3-2 / Chapter 3.2.2 --- Frequency Matching Mode --- p.3-3 / Chapter 3.2.2.1 --- Voltage coding --- p.3-4 / Chapter 3.2.2.2 --- Stroboscopy --- p.3-4 / Chapter 3.2.2.3 --- Waveform measurement --- p.3-6 / Chapter 3.2.2.4 --- Logic state mapping --- p.3-6 / Chapter 3.2.2.5 --- Frequency tracing --- p.3-7 / Chapter 3.2.2.6 --- Frequency mapping --- p.3-8 / Chapter 3.2.2.7 --- Logic state tracing --- p.3-9 / Chapter IV. --- CONVERT AMRAY 1830 INTO E-BEAM TESTER / Chapter 4.1 --- DESIGN CONSIDERATION --- p.4-1 / Chapter 4.1.1 --- Application Consideration --- p.4-1 / Chapter 4.1.2 --- Limitation of the AMRAY 1830 --- p.4-1 / Chapter 4.1.2.1 --- Detection system --- p.4-2 / Chapter 4.1.2.2 --- Scanning driver --- p.4-3 / Chapter 4.1.2.3 --- Beam blanker --- p.4-4 / Chapter 4.1.2.4 --- NibbleNet interface --- p.4-5 / Chapter 4.2 --- HARDWARE ARCHITECTURE --- p.4-6 / Chapter 4.2.1 --- SEM Circuit Varied --- p.4-7 / Chapter 4.2.1.1 --- Adding scanning relays --- p.4-7 / Chapter 4.2.1.2 --- Voltage clippers --- p.4-7 / Chapter 4.2.1.3 --- External scan interface in SEM --- p.4-9 / Chapter 4.2.2 --- PC Interface --- p.4-9 / Chapter 4.2.3 --- Driver Box --- p.4-10 / Chapter 4.2.3.1 --- Data preprocess unit --- p.4-10 / Chapter 4.2.3.2 --- Scanning preprocess unit --- p.4-12 / Chapter 4.2.3.3 --- Control unit --- p.4-12 / Chapter 4.2.4 --- Scanning Generation and Data Acquisition --- p.4-13 / Chapter 4.3 --- SOFTWARE DEVELOPED --- p.4-13 / Chapter 4.3.1 --- Function Library --- p.4-13 / Chapter 4.3.2 --- Integrated Environment --- p.4-14 / Chapter V. --- SYSTEM PERFORMANCE / Chapter 5.1 --- CHARACTERISTICS OF THE SCANNING DRIVERS --- p.5-1 / Chapter 5.1.1 --- Driver Output Changes with Acceleration Voltage --- p.5-2 / Chapter 5.1.2 --- Driver Output Changes with magnification --- p.5-3 / Chapter 5.1.3 --- Frequency Response --- p.5-4 / Chapter 5.1.4 --- Image Distortion --- p.5-7 / Chapter 5.2 --- INTEGRATED STUDY ENVIRONMENT --- p.5-9 / Chapter 5.2.1 --- Setting Status --- p.5-9 / Chapter 5.2.2 --- Image Scanning & Image Saving --- p.5-12 / Chapter 5.2.3 --- Static Probing --- p.5-15 / Chapter 5.2.4 --- Point Probing --- p.5-19 / Chapter 5.2.5 --- Frequency Matching --- p.5-20 / Chapter V. --- SUMMARY --- p.6-1 / REFERENCE / APPENDIX: / Chapter A. --- PROGRAM LISTING / Chapter B. --- CIRCUIT SCHEMATICS

This thesis presents an investigation into the development of plasmodesmata (PD), which are specialised pores in plant cell walls through which the cytosol and membranes of neighbouring cells are linked. Modification of PD from their initial single-tube (‘simple’) structures to branched (‘complex’) structures is an important part of tissue maturation as it allows cells to restrict the movement of syplasmically mobile molecules including hormones, RNAs and proteins. Conversion of PD from simple to complex is co-ordinated across large populations of cells to produce symplasmic domains, transport barriers, and preferential transport pathways. The development of PD is therefore intrinsic to the wider development and morphogenesis of cells, tissues, and organs. The aim of this project was to investigate the development of PD from simple to complex, particularly during the predictable, large-scale conversion of PD structure that accompanies the leaf transition from sink state to source. To study this I used transgenic plants expressing a GFP-tagged viral protein which accumulates specifically in complex PD, while leaving simple PD unlabelled. The project follows the development of complex PD from the early stages of leaf development to maturity using a range of microscopy techniques. Structured illumination microscopy was used to view labelled PD at super resolution, which gave new structural details about complex PD using a breakthrough technology. Conventional and high-throughput confocal and electron microscopy were used to localise PD within tissues in a broad survey of PD location in leaves to identify patterns of PD development. An imaging chamber was developed that allowed the development of complex PD to be viewed in real time and identified conditions that can trigger structural conversion of PD. Finally, a high-throughput microscopy study was performed to identify how hormones, sugar availability, environmental stresses, defence responses and inhibitors can affect PD development.

Wang, Jianpeng. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references. / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

Tissue cells exhibit varying responses according to the stiffness of their extracellular matrix (ECM). The mechanism of this stiffness sensing is not fully understood; however, it is known that cells probe stiffness by applying intracellular force to the ECM via integrin-mediated focal adhesions. The bonds between integrins and ECM have been described as “catch bonds�, and it is unclear how ECM viscoelasticity affects these bonds. We have observed the effects of ECM stiffness on the binding strength of integrins to ECM ligands by measuring the dissociation force of individual integrin-ligand bonds of 3T3 fibroblasts on collagen-coated polyacrylamide gels using atomic force microscopy. Results show that integrins exhibit higher rates of activation on stiff substrates. Furthermore, increased matrix stiffness results in the occurrence of larger, multi-bond dissociation events, which suggests that substrate stiffness may affect the cellular response by promoting integrin clustering as well as by modulating the maximum possible force between individual integrins and the ECM.

"In this thesis, a cell traction force microscopy method is developed for measuring traction forces of connective tissue cells. This method includes an improved methodology in traction force microscopy of live cells cultured on an elastic substrate. Tissue cells, such as skin and muscle cells respond to the mechanical stimuli of their microenvironment by adhering to their substrate and exerting forces on the proteins of the extracellular matrix (ECM). These forces are called cell traction forces. Fibroblasts are grown on polyacrylamide (PA) gels embedded with fluorescent beads and coated with different types of ECM ligands. Traction forces of NIH 3T3 fibroblasts are calculated from the measured deformations of PA gels by using a 3-D finite element method. The advantages of this method compared to the traditional methods of cell traction force microscopy (CTFM) are that this method takes into account the finite thickness of the substrate by applying a 3-D FEM analysis to reduce the errors of using an infinite half space approximation for a substrate with a finite thickness and that it uses a novel method for embedding the substrate with fluorescent markers that decreases the measurement uncertainties. In our approach fluorescent beads were embedded on the top of substrate instead of getting mixed with the gel. This decreases the effect of out-of-focus fluorescent beads on the measured deformation fields which enhances the accuracy of cell traction force measurements."