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Evaluation of several methods of fixing chicken skin for scanning electron microscopy (SEM) indicated standard chemical fixation using glutaraldehyde and osmium tetroxide followed by chemical dehydration with 2,2-dimethoxypropane to be the method of choice. SEM revealed that chicken skin has a convoluted surface. Two types of chicken skin, distinguishable on the basis of chemical composition and appearance were observed. Type I has a filamentous surface with 55% moisture and 25% fat, whereas Type II skin has a globular appearance, 52% fat and 33% moisture. The fatty acid profiles of Types I and II skin are the same. Bacteria have greater affinity for Type II than Type I skin. Attachment studies indicated that Salmonella typhimurium quickly attach to the skin surface and cannot be removed easily by washing with water or with water containing a surfactant. / Land and Food Systems, Faculty of / Graduate

The characterization of nanomaterials involved in dynamic processes are conventionally conducted using microscopy, spectroscopy and other physical/chemical methods through the pseudo-dynamic approach. In details, the dynamics processes are recorded by repeating or terminating the process multiple times. However, the above approach can lead to missing important transition information and inducing contamination for mechanistic studies. This motivates the efforts to develop real time characterization techniques which can probe the dynamic change of nanoparticles in their native operating environments. With the capability of probing structural change at the nanoscale, in situ transmission electron microscopy, has shown great potential in studies and applications of various processes. Targeting at conducting precise analysis, which has been limited by many uncertainties from electron beam effects and the miniaturized reaction cell used for TEM, the work presented herein pursues a quantitative characterization of a few electrochemical and biological processes through in situ liquid-phase transmission electron microscopy. In this work, the in situ transmission electron microscopy system is evaluated by comparing the in situ results with those from standard experiments to show its capabilities in studying dynamic processes. The in situ system is quantitatively calibrated to obtain the optimized observation conditions to avoid detectable electron beam interference, solution depletion and achieve sufficient resolution for analysis through micrometer thick liquid. These form the fundamentals for the in situ studies. Moreover, a comprehensive analysis protocol is established by incorporating multiple ex situ and post situ characterizations. Using this optimized in situ system, the mechanism of electrodeposition of gold on carbon electrode is studied. The in situ results allow quantitative analysis of the growth process. The prevailing diffusion limited three dimensional growth model is examined. A study of the effect of supporting electrolyte on the electrodeposition of palladium is also conducted. The self-limiting, surface diffusion and aggregation/recrystallization growth model is found to describe the early stage of growth, rather than the classical Volmer-Weber growth model. A further study is conducted on the structural evolution of palladium nanoparticles under electrochemical cycling. The mechanisms involved in this process, including electrodeposition, dissolution, hydrogen co-deposition and hydrogen desorption, are studied. The supporting electrolyte, HCl, is found to enhance the dissolution of deposited palladium clusters and induce movements and aggregation of the deposits during the hydrogen interaction process to form chain-like and irregular clusters, which provide direct experimental proof on the morphology formation of palladium with hydrogen involvement. Ultimately, the in situ technique is applied to the study of calcium phosphate biomineralization. Combined with multiple post situ characterization techniques, the study provides direct experimental evidence of the non-classical pre-nucleation and attachment growth of calcium phosphate structures. This demonstrates the potential of the in situ technique for studying the mechanisms involved in biological processes. / Dissertation / Doctor of Philosophy (PhD) / Nanostructured materials have been widely used in various fields. In situ transmission electron microscopy, a technique used to characterize nanomaterials involved in different dynamic processes in their operating environments, is an advanced tool over the traditional characterization methods such as ex situ microscopy and spectroscopy. However, there are several challenges in applying this in situ technique to processes occurring in liquid media. In this thesis, an in situ transmission electron microscopy system is applied to study the mechanisms of structural changes during different processes in liquids with both high spatial and temporal resolution. Protocols to evaluate and optimize the in situ system are developed to provide results comparable with those from their actual applications. Then in situ studies on the structural evolution of nanomaterials during electrochemical processes are performed and different theoretical models are applied to describe these processes. Finally, this technique is extended to investigate biomineralization to show its capabilities in future studies on biological processes.

Liquid cell electron microscopy has been proven to provide high spatial and temporal resolution for studying liquid layers and the solid-liquid interface at the micro and nano scale. The in situ environment allows for spatial and spectral characterization and quantification of the dynamics and kinetics involved with structural and chemical changes of nanostructures, which has seen application is fields of materials science, electrochemistry, corrosion, biomaterials, and nanophysics. The rapid growth of in situ liquid cell electron microscopy has motivated the fabrication of a custom liquid cell for improved control over the experimental conditions, including cell dimensions and materials. In this work, the process flow and micro-fabrication of a custom liquid cell system are proposed and executed, with proof of operation through the in situ imaging of suspended gold nanoparticles and electrochemical characterization. The in situ TEM system is improved upon by forming 1μm diameter holes through the viewing membranes, removing the background noise contribution from imaging electrons through the windows. This allows for high resolution liquid cell imaging. This improved system is used to study the oxidative etching conditions for palladium nanocrystals, which are commonly used as catalysis for hydrogen fuel cells. The dendritic etching is studied through native etching under exposure to hydrochloric acid without the presence of oxidizing species, followed by the radiolytic generation of oxidizing radicals via the microscope electron beam, and finally by the application of electrical biasing. / Thesis / Master of Applied Science (MASc) / Characterization of nanomaterials has been available for several decades and has aided in the improvement of material design, such as steel strength and corrosion resistance, electrical systems such as those involved in computers and smartphones, and biological sensing and detection. Observation of dynamic process which occur at the interface between solid and liquid phases, or purely within liquid layers, has always been a challenging topic due to the difficulty of finding a stable environment for both solids and liquids to exist at the nano scale within a measurement device. In situ liquid cell electron microscopy offers the ability to image this interface with real-time data acquisition for recording of dynamics and kinetics at the nano scale. Previous work has shown the liquid cell to provide high spatial and temporal resolution of systems in an environment which mimics their native operating conditions. This thesis addresses current developments for in situ systems and works to develop a custom liquid cell to further the applications of the liquid cell and provide improved control over experimental conditions. The work then aims to improve on current technology by increasing the spatial resolution obtainable. Finally, the technique is applied to study the structural changes of nanocrystals under various etching conditions as a demonstration of its’ capabilities.

Phase-transformation-induced microstructures, including twin domains, anti-phase domains and inversion domains have been analyzed using the scanning and transmission electron microscopy for BaTiO3, BaCeO3 and CaTiO3 of the perovskite structure. Differential etching rate was taken to identify the ferroelectric domains in tetragonal (t-) BaTiO3. Space group Pbnm (No. 62) usually adopted for the orthorhombic crystals by materials scientists is assumed throughout this research to avoid confusion of the plane and direction indices. Traditional contrast analysis was adopted for determining dislocation Burgers vectors (b) and fault vectors (R) in deformed and phase-transformed perovskites, synthetic ceramics (BaTiO3, BaCeO3 and CaTiO3) as well as natural minerals (CaTiO3), polycrystalline (BaTiO3, BaCeO3 and CaTiO3) as well as single crystal (CaTiO3). Atomic images for the structures of twin boundaries and anti-phase boundaries were taken by high resolution technique and image contrast enhancement was performed using fast Fourier transform. Failure of Friedel¡¦s law is adopted for determining if the crystal belongs to non-centrosymmetric point groups. Whether the twins are £_-, £\- or £k-type (i.e. anti-phase domain boundaries) is analysed from the contrast of extreme fringe patterns. Tilting experiments were performed on selected area diffraction patterns containing un-split row of reflections to ensure that the twin boundaries are the reflection or rotation type. Transformation twinning in all perovskites studied here follows the prediction by the relation of point group symmetries between the high- and low-symmetry phases, assuming continuous, diffusionless, second-order transitions that obey the restrictions imposed by the Landau theory of phase transition. Although such predictions of transformation-induced twinning are only permitted when crystallographic group-subgroup relationship exists and structural coherence retains between the high- and low-symmetry phases, experimental observations for r (rhombohedral) ¡÷ o-BaCeO3 and t ¡÷ o in CaTiO3 that are not related by group-subgroup, c (cubic) ¡÷ t (tetragonal) in CaTiO3 and and c (cubic) ¡÷ t (tetragonal) in BaTiO3 that are related by group-subgroup, are all consistent with the predictions from loss of point group symmetry elements and change of unit cell volume. In order that the Landau theory is conformed, however, an intermediate phase of either the lowest common supergroup (cubic Pm m) or highest common subgroup (monoclinic C2/c), with phase transition experiencing multistage pathways suggested by Christy and assumption of non-disruption conditions proposed by Guymont, was identified to bridge between two structures, such as rhombohedral and orthorhombic that are not group-subgroup related. Both the 90o and 180o ferroelectric twin domains in t-BaTiO3 are the reflection type and have been identified in pressureless-sintered ceramics. Further, fault vectors (R = £`<110]) for such domain boundaries were determined, boundary planes of {110) for the former, {100) and {220) for the latter deduced accordingly. The polar c-direction between adjacent domains was determined by differential etching rate across domain boundaries, convergent beam electron diffraction was also adopted for identification and confirmation of the c-axis for two types of domains in t-BaTiO3. Plastic deformation resulting from the thermodynamic driving force for sintering (?p) intensified by a multiplication factor £p) was evidenced microstructurally from analysing dislocations in pressureless-sintered BaTiO3 where a Frank-Read source was observed. Slip systems are activated for the effective stress acting on the slip plane along the slip direction has exceeded the critical value of resolved shear stress (£nCRSS) and yielding occurs. It has contributed to densification, i.e. the overall system shrinkage of a green powder compact, although if such contribution is at all significant requires studies of sintering kinetics to ascertain. Dislocation dissociation into the scallop-shaped half partials according to the following reactions is determined from analysing corresponding Burgers vectors. [010] + [001] ¡÷ [011] [001] + [10 ] ¡÷ [100] [001] + [110] ¡÷ [111] Both transformation twins lying in {110) and {112) and anti-phase domain boundaries with R = 1/2<111> are detected in o-BaCeO3. For orthorhombic (o-) BaCeO3, fault vectors of the latter R = 1/2<111> determined by contrast analysis was confirmed by high-resolution imaging, but on the contrary, fault vectors the former R = £`<110] and £`<021], respectively, could not be determined from such images. Utilizing the technique of large-angle convergent beam electron diffraction, such fault vectors and dislocation Burgers vectors determined by traditional contrast analysis have been confirmed. Both twinning and dislocations were observed in hot-pressed CaTiO3 prepared in a multi-anvil apparatus. Such twins are deformation twins since hot-pressing was conducted in the orthorhombic stable phase field at 1000oC under 8 GPa. Since fault vectors R = £`<110] determined for {112) and {110) twins are different from the transformation-induced twins in o-CaTiO3, R = £`<021] determined for the {112) twinning in natural perovskite may serve as a diagnostic feature for the deformation twins. Plastic deformation in hot-pressured sample was contributed by both slip and twinning. Slip occurred via slip systems with dislocations of b = [110] gliding in (110) is therefore {110}o <1 0>o (equivalent to {100}pc <001>pc, where pc for pseudo-cubic) often found in perovskites deformed at high temperatures. Another set of dislocations with b = [001] in screw orientation was also determined. APB with R = 1/2<111> detected in natural minerals suggests that the phase transition sequence in CaTiO3 is better described by: (c) ¡÷ t (I4/mcm) ¡÷ o (Pbnm) and such APB are generated from loss of the lattice point at I-centre (1/2,1/2,1/2) in the absence of a second orthorhombic Cmcm between t-I4/mcm and o-Pbnm reported before from neutron and X-ray powder diffraction studies.

Developments in scanning transmission electron microscopy (STEM) have opened up new possibilities for time-resolved imaging at the atomic scale. However, rapid imaging of single atom dynamics brings with it a new set of challenges, particularly regarding noise and the interaction between the electron beam and the specimen. This thesis develops a set of analytical tools for capturing atomic motion and analyzing the dynamic behaviour of materials at the atomic scale. Machine learning is increasingly playing an important role in the analysis of electron microscopy data. In this light, new unsupervised learning tools are developed here for noise removal under low-dose imaging conditions and for identifying the motion of surface atoms. The scope for real-time processing and analysis is also explored, which is of rising importance as electron microscopy datasets grow in size and complexity. These advances in image processing and analysis are combined with computational modelling to uncover new chemical and physical insights into the motion of atoms adsorbed onto surfaces. Of particular interest are systems for heterogeneous catalysis, where the catalytic activity can depend intimately on the atomic environment. The study of Cu atoms on a graphene oxide support reveals that the atoms undergo anomalous diffusion as a result of spatial and energetic disorder present in the substrate. The investigation is extended to examine the structure and stability of small Cu clusters on graphene oxide, with atomistic modelling used to understand the significant role played by the substrate. Finally, the analytical methods are used to study the surface reconstruction of silicon alongside the electron beam-induced motion of adatoms on the surface. Taken together, these studies demonstrate the materials insights that can be obtained with time-resolved STEM imaging, and highlight the importance of combining state-ofthe- art imaging with computational analysis and atomistic modelling to quantitatively characterize the behaviour of materials with atomic resolution.

M.Sc. / Despite several decades of extensive research and development in pharmaceutical chemistry, the poor solubility of lipophilic compounds in aqueous media remains a major barrier to their absorption, bioavailability and clinical efficacy. This poor solubility is also a problem in other areas such as the flavour and fragrance industry. In cosmetics, for example, poor aqueous solubility and instability of oily compounds causes problems in formulation and fragrance stability. One approach to overcome these difficulties is to encapsulate oily compounds in biocompatible materials. As a drug delivery system such an approach is attractive if the size of the capsule is reduced to the micrometer or nanometer scale. Naturally occurring polysaccharides like sodium alginate (NaALG) and chitosan (CS) are generally regarded as safe (GRAS) for use in human use and have therefore gained much attention recently. As a drug delivery system, this polymer matrix can be used to prevent drug degradation in the gastro intestinal tract (GIT) and often provides controlled release of the encapsulant. Cyclodextrins (CDs) on the other hand offer an alternative approach. These cyclic oligosaccharides have the ability to form non-covalent inclusion complexes with a range of organic compounds, and in so doing alter their physiochemical properties such as solubility. This study was aimed at exploring these concepts by using ALG and CS as an entrapment matrix for an essential oil, tagette oil (used as a model oily drug) that is insoluble in aqueous media. Alginate/chitosan (ALG/CS) nanoparticles were prepared in a 3-step procedure; emulsification of tagette oil in aqueous Na-ALG solution, followed by ionotropic pre-gelation of the ALG core with CaCl2 and further crosslinking with CS. Morphology and particle size measurements were performed by scanning and transmission electron microscopy (SEM and TEM), and Malvern Zetasizer.

We propose to interpret Cryogenic Electron Microscopy (CryoEM) data as a supervision for learning parameters of CryoEM microscopes. Following this formulation, we present a differentiable version of Transmission Electron Microscopy (TEM) Simulator that provides differentiability of all continuous inputs in a simulation. We demonstrate the learning capability of our simulator with two examples, detector parameter estimation and denoising. With our differentiable simulator, detector parameters can be learned from real data without time-consuming handcrafting. Besides, our simulator enables new way to denoising micrographs. We develop this simulator with the combination of Taichi and PyTorch, exploiting kernel-based and operator-based parallel differentiable programming, which results in good speed, low memory footprint and expressive code. We call our work as Differentiable TEM Detector as there are still challenges to implement a fully differentiable transmission electron microscope simulator that can further differentiate with respect to particle positions. This work presents first steps towards a fully differentiable TEM simulator. Finally, as a subsequence of our work, we abstract out the fuser that connects Taichi and PyTorch as an open-source library, Stannum, facilitating neural rendering and differentiable rendering in a broader context. We publish our code on GitHub.

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