Transmission electron tomography: quality assessment and enhancement for three-dimensional imaging of nanostructures

Nanotechnology has revolutionised humanity's capability in building microscopic systems by manipulating materials on a molecular and atomic scale. Nan-osystems are becoming increasingly smaller and more complex from the chemical perspective which increases the demand for microscopic characterisation techniques. Among others, transmission electron microscopy (TEM) is an indispensable tool that is increasingly used to study the structures of nanosystems down to the molecular and atomic scale. However, despite the effectivity of this tool, it can only provide 2-dimensional projection (shadow) images of the 3D structure, leaving the 3-dimensional information hidden which can lead to incomplete or erroneous characterization. One very promising inspection method is Electron Tomography (ET), which is rapidly becoming an important tool to explore the 3D nano-world. ET provides (sub-)nanometer resolution in all three dimensions of the sample under investigation. However, the fidelity of the ET tomogram that is achieved by current ET reconstruction procedures remains a major challenge. This thesis addresses the assessment and advancement of electron tomographic methods to enable high-fidelity three-dimensional investigations. A quality assessment investigation was conducted to provide a quality quantitative analysis of the main established ET reconstruction algorithms and to study the influence of the experimental conditions on the quality of the reconstructed ET tomogram. Regular shaped nanoparticles were used as a ground-truth for this study. It is concluded that the fidelity of the post-reconstruction quantitative analysis and segmentation is limited, mainly by the fidelity of the reconstructed ET tomogram. This motivates the development of an improved tomographic reconstruction process. In this thesis, a novel ET method was proposed, named dictionary learning electron tomography (DLET). DLET is based on the recent mathematical theorem of compressed sensing (CS) which employs the sparsity of ET tomograms to enable accurate reconstruction from undersampled (S)TEM tilt series. DLET learns the sparsifying transform (dictionary) in an adaptive way and reconstructs the tomogram simultaneously from highly undersampled tilt series. In this method, the sparsity is applied on overlapping image patches favouring local structures. Furthermore, the dictionary is adapted to the specific tomogram instance, thereby favouring better sparsity and consequently higher quality reconstructions. The reconstruction algorithm is based on an alternating procedure that learns the sparsifying dictionary and employs it to remove artifacts and noise in one step, and then restores the tomogram data in the other step. Simulation and real ET experiments of several morphologies are performed with a variety of setups. Reconstruction results validate its efficiency in both noiseless and noisy cases and show that it yields an improved reconstruction quality with fast convergence. The proposed method enables the recovery of high-fidelity information without the need to worry about what sparsifying transform to select or whether the images used strictly follow the pre-conditions of a certain transform (e.g. strictly piecewise constant for Total Variation minimisation). This can also avoid artifacts that can be introduced by specific sparsifying transforms (e.g. the staircase artifacts the may result when using Total Variation minimisation). Moreover, this thesis shows how reliable elementally sensitive tomography using EELS is possible with the aid of both appropriate use of Dual electron energy loss spectroscopy (DualEELS) and the DLET compressed sensing algorithm to make the best use of the limited data volume and signal to noise inherent in core-loss electron energy loss spectroscopy (EELS) from nanoparticles of an industrially important material. Taken together, the results presented in this thesis demonstrates how high-fidelity ET reconstructions can be achieved using a compressed sensing approach.

In vivo microvascular oximetry using multispectral imaging

This thesis describes the application of multispectral imaging to several novel oximetry applications. Chapter 1 motivates optical microvascular oximetry, outlines oxygen transport in the body, describes the theory of oximetry, and describes the challenges associated with in vivo oximetry, in particular imaging through tissue. Chapter 2 reviews various imaging techniques for quantitative in vivo oximetry of the microvasculature, including multispectral and hyperspectral imaging, photoacoustic imaging, optical coherence tomography, and laser speckle techniques. Chapter 3 describes a two-wavelength oximetry study of two microvascular beds in the anterior segment of the eye: the bulbar conjunctival and episcleral microvasculature. This study reveals previously unseen oxygen diffusion from ambient air into the bulbar conjunctival microvasculature, altering the oxygen saturation of the bulbar conjunctiva. The response of the bulbar conjunctival and episcleral microvascular beds to acute mild hypoxia is quantified and the rate at which oxygen diffuses into bulbar conjunctival vessels is measured. Chapter 4 describes the development and application of a highly novel non-invasive retinal angiography technique: Oximetric Ratio Contrast Angiography (ORCA). ORCA requires only multispectral imaging and a small perturbation of blood oxygen saturation to produce angiographic sequences. A pilot study of ORCA in human subjects was conducted. This study demonstrates that ORCA can produce angiographic sequences with features such as sequential vessel filling and laminar flow. The application and challenges of ORCA are discussed, with emphasis on comparison with other angiography techniques, such as fluorescein angiography. Chapter 5 describes the development of a multispectral microscope for oximetry in the spinal cord dorsal vein of rats. Measurements of blood oxygen saturation are made in the dorsal vein of both healthy rats, and in rats with the Experimental autoimmune encephalomyelitis (EAE) disease model of multiple sclerosis. The venous blood oxygen saturation of EAE disease model rats was found to be significantly lower than that of healthy controls, indicating increased oxygen uptake from blood in the EAE disease model of multiple sclerosis. Chapter 6 describes the development of video-rate red eye oximetry; a technique which could enable stand-off oximetry of the blood-supply of the eye with high temporal resolution. The various challenges associated with video-rate red eye oximetry are investigated and their influence quantified. The eventual aim of this research is to track circulating deoxygenation perturbations as they arrive in both eyes, which could provide a screening method for carotid artery stenosis, which is major risk-factor for stroke. However, due to time constraints, it was not possible to thoroughly investigate if video-rate red eye can detect such perturbations. Directions and recommendations for future research are outlined.

LHC main dipole magnet circuits: sustaining near-nominal beam energies

Crossing the Franco-Swiss border, the Large Hadron Collider (LHC), designed to collide 7 TeV proton beams, is the world's largest and most powerful particle accelerator the operation of which was originally intended to commence in 2008. Unfortunately, due to an interconnect discontinuity in one of the main dipole circuit's 13 kA superconducting busbars, a catastrophic quench event occurred during initial magnet training, causing significant physical system damage. Furthermore, investigation into the cause found that such discontinuities were not only present in the circuit in question, but throughout the entire LHC. This prevented further magnet training and ultimately resulted in the maximum sustainable beam energy being limited to approximately half that of the design nominal, 3.5-4 TeV, for the first three years of operation (Run 1, 2009-2012) and a major consolidation campaign being scheduled for the first long shutdown (LS 1, 2012-2014). Throughout Run 1, a series of studies attempted to predict the amount of post-installation training quenches still required to qualify each circuit to nominal-energy current levels. With predictions in excess of 80 quenches (each having a recovery time of 8-12+ hours) just to achieve 6.5 TeV and close to 1000 quenches for 7 TeV, it was decided that for Run 2, all systems be at least qualified for 6.5 TeV operation. However, even with all interconnect discontinuities scheduled to be repaired during LS 1, numerous other concerns regarding circuit stability arose. In particular, observations of an erratic behaviour of magnet bypass diodes and the degradation of other potentially weak busbar sections, as well as observations of seemingly random millisecond spikes in beam losses, known as unidentified falling object (UFO) events, which, if persist at 6.5 TeV, may eventually deposit sufficient energy to quench adjacent magnets. In light of the above, the thesis hypothesis states that, even with the observed issues, the LHC main dipole circuits can safely support and sustain near-nominal proton beam energies of at least 6.5 TeV. Research into minimising the risk of magnet training led to the development and implementation of a new qualification method, capable of providing conclusive evidence that all aspects of all circuits, other than the magnets and their internal joints, can safely withstand a quench event at near-nominal current levels, allowing for magnet training to be carried out both systematically and without risk. This method has become known as the Copper Stabiliser Continuity Measurement (CSCM). Results were a success, with all circuits eventually being subject to a full current decay from 6.5 TeV equivalent current levels, with no measurable damage occurring. Research into UFO events led to the development of a numerical model capable of simulating typical UFO events, reproducing entire Run 1 measured event data sets and extrapolating to 6.5 TeV, predicting the likelihood of UFO-induced magnet quenches. Results provided interesting insights into the involved phenomena as well as confirming the possibility of UFO-induced magnet quenches. The model was also capable of predicting that such events, if left unaccounted for, are likely to be commonplace or not, resulting in significant long-term issues for 6.5+ TeV operation. Addressing the thesis hypothesis, the following written works detail the development and results of all CSCM qualification tests and subsequent magnet training as well as the development and simulation results of both 4 TeV and 6.5 TeV UFO event modelling. The thesis concludes, post-LS 1, with the LHC successfully sustaining 6.5 TeV proton beams, but with UFO events, as predicted, resulting in otherwise uninitiated magnet quenches and being at the forefront of system availability issues.

Sequestering of Fe and Pb ions from Wastewater by Canarium schweinfurthii after carbonization and chemical treatment: Isothermal and Kinetic Modeling

In this paper agricultural waste; Canarium schweinfurthii was explored for the sequestering of Fe and Pb ions from wastewater solution after carbonization and chemical treatment at 400oC. Optimum time of 30 and 150 min with percentage removal of 95 and 98% at optimum pH of 2 and 6 was obtained for Fe and Pb ions. Kinetics model followed pseudofirst order as sum of absolute error (EABS) between Qe and Qc greater than that of pseudo second order. Parameters evaluated from isothermal equation (Freundlich and Langmuir) showed that KL and QO for Fe > Pb and R2 for Langmuir> Freundlich. The study reveals the suitability of the adsorbent for sequestering of Fe and Pb ions from industrial wastewater.

Gestão Técnica Centralizada em Edifícios da Força Aérea

A investigação centra-se na aplicação da Gestão Técnica Centralizada como instrumento para a melhoria da eficiência energética dos edifícios e infraestruturas da Força Aérea Portuguesa e diminuição de pessoal afeto à sua manutenção, tendo por base, dois casos de estudo, o edifício QC12 do Centro de Formação Militar e Técnica da Força Aérea e o ECOTERMOLAB, pertencente ao Instituto de Soldadura e Qualidade. Da análise desenvolvida conclui-se que o funcionamento dos edifícios ECOTERMOLAB e QC12, com controlo por GTC, representam anualmente uma diminuição de consumo energético em 30% e 44% respetivamente e, uma redução de 50% nos recursos humanos afetos à instalação do QC12. Da viabilidade económica obtiveram-se as métricas de Valor Atual Líquido e a Taxa Interna de Rentabilidade positivos e um Período de Recuperação do Investimento, de 11,5 anos para ECOTERMOLAB e 10,7 anos para QC12. Por fim, teceram-se algumas recomendações, dirigidas à Força Aérea Portuguesa, com o intento de melhorar a eficiência energética elétrica e a redução de recursos humanos afetos. Abstract: The research is focused in the application of the Centered Technique Management as an instrument to improve the Portuguese Air Force buildings and infrastructures’ energetic efficiency and to reduce the staff in charge of its maintenance, based on two study cases, QC 12 building in The Air Force Military and Technique Training Center and ECOTERMOLAB, which belongs to Instituto de Soldadura e Qualidade (Quality and Welding Institute). From the analysis, one can conclude that the functioning of the ECOTERMOLAB and QC12 buildings, with GTC control, represents an annual consumption of less 30% and 44% respectively and a 50% reduction in the human resources of the QC 12. From the economical viability, it was possible to get the figures of the Net Present Value and the Internal Rate of Return and a Period of Return on Investment of 11,5 years for ECOTERMOLAB and 10,7 years for QC 12. Finally, some recommendations to the Portuguese Air Force were made, aiming the improvement of the electrical energetic efficiency and a reduction in human resources.

Nonlinear development of matrix-converter instabilities

Matrix converters convert a three-phase alternating-current power supply to a power supply of a different peak voltage and frequency, and are an emerging technology in a wide variety of applications. However, they are susceptible to an instability, whose behaviour is examined herein. The desired “steady-state” mode of operation of the matrix converter becomes unstable in a Hopf bifurcation as the output/input voltage transfer ratio, q, is increased through some threshold value, qc. Through weakly nonlinear analysis and direct numerical simulation of an averaged model, we show that this bifurcation is subcritical for typical parameter values, leading to hysteresis in the transition to the oscillatory state: there may thus be undesirable large-amplitude oscillations in the output voltages even when q is below the linear stability threshold value qc.

Controlo de qualidade de matrizes de fotodíodos de avalanche no projecto "PET - Desenvolvimento de tecnologia PET para mamografia"

Dissertação mest. em Imagiologia Médica, Faculdade de Ciências e Tecnologia da Univ. do Algarve, 2006

Ligand effects on the structure and vibrational properties of the thiolated Au18 cluster

Most of the studies devoted to thiolated gold clusters suppose that their core and Au-S framework do not suffer from distortion independently of the protecting ligands (-SR) and it is assumed as correct to simplify the ligand as SCH3. In this work is delivered a systematic study of the structure and vibrational properties (IR and Raman) of the Au18(SR)14 cluster. The pursued goal is to understand the dependency of the displayed vibrational properties of the thiolated Au18 cluster with the ligands type. A set of six ligands was considered during calculations of the vibrational properties based on density functional theory (DFT) and in its dispersioncorrected approach (DFT-D)

Ligand effects on the optical and chiroptical properties of the thiolated Au18cluster

The effect of chiral and achiral ligands protecting the inner Au9 core of the Au18(SR)14 cluster is studied based on density functional theory (DFT) and its corrected long-range interaction (DFT-D) approach. It was found that the electronic properties (energy levels) depend on the specific ligands, which induce distinct distortions on the Au–S framework. However, the substitution of S-c-C6H11 as SCH3 ligands may be considered to be correct given the obtained resemblance to the displayed bonding, optical and chiroptical properties. A further comparison of the CD and UV spectra displayed by the Au18 cluster protected by chiral and achiral ligands attests that more intense profiles are featured by ligands including phenyl rings and/or oxygen atoms such that the Au18 cluster protected by either achiral metamercaptobenzoic acid (m-MBA) or achiral SPh ligands displays more intense UV and CD signals. These results provide new insight into the effect of ligands on thiolated gold clusters

Thiolated Au18cluster: preferred Ag sites for doping, structures, and optical and chiroptical properties

Recently, the X-ray determined structure of the thiolated Au18 cluster has been reported. In this communication, we addressed a study of structures and chiroptical properties of thiolated Au18 cluster doped with up to ten Ag atoms, which have been calculated by Time Dependent Density Functional Theory (TD-DFT). The number of Ag atoms was steadily varied and more stable isomers showed optical and Circular Dichroism (CD) spectra distinct from that found for the parent Au18 cluster. Doping with more than four Ag atoms results in enhancement of the oscillator strength of the HOMO–LUMO peak and it is expected that this feature can be exploited for photoluminescence applications.

On the structure of the Au18(SR)14 cluster

First principles calculations are used for a systematic search of the lowest-energy (most-stable) structure of the recently synthesized Au18(SR)14 cluster. A comparison of the calculated optical absorption and electronic circular dichroism spectra, which are highly sensitive to the cluster structure and chirality, with the experimental spectra of the glutathione-protected gold cluster, Au18(SG)14, is used to discriminate between low-energy isomers of the Au18(SR)14 (R = CH3) cluster. From the good agreement between calculated and measured spectra, it is predicted that the structure of the Au18(SR)14 cluster consists of a prolate Au8 core covered with two dimer (SR–Au–SR–Au–SR) and two trimer (SR–Au–SR–Au–SR–Au–SR) motifs. These results provide additional evidence on the existence of longer trimer motifs as protecting units of small thiolated gold clusters.

Long-term influence of chitin concentration on the resistance of cement pastes determined by atomic force microscopy

The presence of sulfates potentialize damage on cementbased materials, leading to structural failures. Therefore, structures must be designed to compensate for this effect. The mechanical properties of cement–chitin mixtures are investigated with different percentages of chitin (0.5, 1.3, and 2.1 wt.%) and aging of composite in a joint nanoscopic- and macroscopic-scale by experimental study. The objective is to increase the durability of concrete elements at coastal aquifers where concrete structures are in constant exposure to sulfate ions, chloride ions among others. Tapping mode AFM was used to characterize the surface structure and roughness of the cement pastes. To verify the chitin addition and the formation of sulfate-based aggregates Raman and IR spectra were recorded and are presented in this work. Then, force spectroscopy was used to obtain the nanomechanical properties at three different exposure times (1 day, 6 months, and 1 year) into water or a SO4 2 environment. Macroscopic parameters (e.g., compression strength of cylindrical probes) were assessed for comparison following standard guidelines. The results show a decrease of its mechanical properties as a function of the polymer concentration but more importantly, they correlate the elasticity and adhesion at the nanoscale with the behavior of the bulk material.