>Magister Scientiae - MSc / There are limited reports on virus population in haloalkaline environments; therefore the aim of this study was to investigate the genetic diversity and biology of bacteriophage communities in these environments. Bacteria were isolated to be used as phage hosts. One bacterium from Lake Magadi and four bacteria from Lake Shala were successfully isolated from sediment samples. A further two Lake Shala bacterial hosts from the IMBM culture collection were also used to isolate bacteriophages. Bacterial isolates were identified to be most closely related to Bacillius halodurans, Halomonas axialensis, Virgibacillus salarius, Bacillus licheniformis, Halomonas venusta, Bacillus pseudofirmus and Paracoccus aminovorans. Bacteriophages were screened using all bacteria against sediment samples from both Lake Shala and Lake Magadi. One phage was identified from Lake Magadi sediments (MGBH1) and two phages from Lake Shala sediments (SHBH1 and SHPA). TEM analysis showed that these phages belong to three different dsDNA phage families; Siphoviridae (MGBH1), Myoviridae (SHBH1) and Podoviridae (SHPA). All phages showed different genome sizes on agarose gel. Due to the small genome size, phage SHPA was chosen for further investigation. Partial, genome sequence analysis showed homology to both bacterial and phage proteins. A further investigation of phage diversity in this environment is essential using metagenomic approaches to understand these unique communities.

>Magister Scientiae - MSc / Magnetic luminescent nanoparticles of an iron oxide (Fe₃O₄) superparamagnetic core and an indium phosphide/zinc selenide (InP/ZnSe) quantum dot shell are reported. The magnetic nanoparticles (MNP’s) and quantum dots (QD’s) were each synthesized separately before conjugation. The MNP’s were functionalized with a thiol-group allowing the QD shell to bind to the surface of the MNP by the formation of a thiol-metal bond. The nanocomposite was capped with 3-mercaptopropionic acid, 1-propanethiol, 2-methyl-1-propanethiol and their properties investigated using the characterization techniques: high- resolution transmission electron microscopy (HR-TEM), energy-dispersive spectroscopy (EDS), UV-vis, scanning electron microscopy (SEM), superconducting quantum interference device (SQUID), and photoluminescence. These techniques yielded significant information on particle size, morphology, dispersion, and chemical composition including luminescence and florescence.

Transmission electron microscopy (TEM) is an important tool for the characterization of materials as it can provide clear understanding of the relationship between structure, property and composition of nanomaterials. For this, the in-situ TEM analysis is performed and requires specially manufactured sample holders. In particular, those designed to carry out electrical biasing can be used to understand not just the I-V characteristics but also the failure mechanism, structure-property relationship, Joule heating dynamics, electromigration, field emission properties, etc. at the nanoscale. The platforms holding the sample in most modern in-situ TEM holders rely on an insulating ceramic membrane which needs to be (almost) transparent to the imaging electron beam. Electrodes are defined through lithography and patterned on this membrane. Unfortunately, the presence of this membranes introduces several limitations such as electrostatic charging, reduction of image contrast and poor mechanical stability. To circumvent this issue it is necessary to fabricate a novel type of sample platform which does not rely on the presence of a membrane. In this work, novel membraneless sample-holding platforms were designed and manufactured using advanced microfabrication methods and tools. Besides fitting into an array of analytical tools, the novel platforms (or “chips”) can be subjected to thermal and/or chemical processing without compromising their function or structure. To test these, the electrical response of one-, two- and zero-dimensional nanoparticles were studied. Firstly, we investigated current-induced modifications in silver nanowires and expandable graphite flakes and studied various phenomenon involved. Along with these, corresponding ex-situ studies were also performed. Next, graphene oxide was explored as an alternative support platform for in-situ TEM. We successfully achieved temperature as high as 2000o C by Joule heating of graphene oxide. Furthermore, this graphene oxide platform was used as a heater and chemical processing substrate for investigating thermal stability and synthesis of inorganic nanoparticles, respectively.

Nanofluidics is an emerging field with many science and engineering applications. The physics of material transport through nanochannels are of interest in filtration, sensing, device miniaturization, and biomimetics. To address such ambitions with nanofluidic tools will require advancements in our understanding and control over nanofluidic systems. This work contributes to electrokinetic phenomena, characterization techniques, and applications in nanofluidics. Ion transport data through nanopipettes are used to validate a finite element model for nonlinear electrokinetic flows. With the model, we conclude that asymmetric surfaces induce fluid vortices and provide insight into supporting mathematical techniques. We then establish nanobubble-plugged nanopipettes as promising ionic devices due to the electrokinetic effects of three-phase interfaces. Using cryogenic transmission electron microscopy, ion current measurements, and extensive physical modeling, we conclude that nanobubble plugs are metastable, slow-growing, and induce strong current rectification and enhancement. All these insights let us study microbial surfaces using electrokinetic phenomena detected by a scanned nanopipette. Over immobilized Pseudomonas aerugonsa cells and Δphz-type biofilms, we detect topographic and surface charge properties due to voltage-dependent signals through a scanned nanopipette probe. Our efforts establish a fast hopping probe scanning ion conductance microscopy technique for long-range surface charge detection. Finally, we use an integrated carbon nanotube channel to demonstrate how solid-state charge can drive electrokinetic flows through Coulomb drag coupling.

Jednou z možností korekce sférické vady v elektronové mikroskopii je hexapólový korektor. Ačkoliv samotný princip korekce je poměrně dobře v literatuře popsán, jen relativně málo je věnováno samotnému seřízení hexapólového korektoru, jež je stěžejní pro správnou funkčnost. Práce je věnována analytickému rozboru vad seřízení a jejich vlivu na rozlišení obrazu za použití metody eikonálu a aberačních integrálů. Je ukázáno, že nejdůležitější roli v parazitických aberací hrají výchylky a náklon hexapólů. V závěru je pak popsáno, jakým způsobem je třeba hexapólový korektor seřídit pro odstranění parazitických vad.

This master thesis deals with conventional methods of bacterial cell analysis, polyhydroxyalkanoates, Raman spectroscopy and electron microscopy in the theoretical part. The production of polyhydroxybutyrate by selected thermophilic bacteria and their analysis by gas chromatography, cryogenic scanning electron microscopy and Raman spectroscopy is described in the experimental part. The chosen sample was analyzed by a transmission electron microscope. Comparing the results from previous mentioned methods it was found that the bacteria Schlegelella thermodepolymerans accumulated the highest amount of PHB. The lowest amount of PHB was obtained by bacteria Rubrobacter xylanophilus. The assumption that the PHB granules formed so-called needle-like plastic deformations during freeze-fracturing was affirmed by cryo-SEM photos analysis. Moreover, it was found that the bacterial cell characterization deduced from microscopic observation of samples corresponded to the description in the literature. TEM provided better resolution photos and in consequence the cells and PHB are more visible. The thesis is also focused on chemical fingerprint analysis of cells by Raman spectroscopy. Several biomolecules were identified by measured Raman spectra for the particular samples.

Les plasmons de surface (SP) sont des ondes électromagnétiques se propageant à l'interface entre deux milieux, typiquement un métal et un diélectrique. Les plasmons de surface ont la capacité de confiner le champ électromagnétique dans de très petite région de l’espace, typiquement quelques nanomètres, c’est à dire bien en dessous de la limite de diffraction de la lumière. Une conséquence de ce confinement sub-longueur d’onde de la lumière est que leur observation nécessite une résolution spatiale nanométrique - ce qui exclut l’utilisation de techniques optiques standard. Néanmoins, le microscope électronique en transmission à balayage (STEM) est un outil particulièrement adapté à l'étude des plasmons de surface car il emploie des électrons rapides ayant une longueur d’onde typique comprise entre 1 et 10 picomètres. Ainsi, durant la dernière décennie, les spectroscopies électroniques appliquées à la nano-optique se sont fortement développées, parmi elle comptent : la spectroscopie de perte d'énergie électronique (EELS), la spectroscopie cathodoluminescence (CL) ou l'interférométrie de Hanbury Brown et Twiss (HBT) appliquée à la CL. Dans cette thèse, j’ai exploré différents problèmes ouverts de la plasmonique et de la nano-optique dans le cadre particulier de la microscopie électronique. Dans le chapitre 3, je présente un formalisme prenant en compte à la fois la nature quantique et relativiste des expériences d’EELS en faisant appel notamment à des éléments de théorie quantique des champs. Dans le chapitre 4, nous démontrons que la réalisation d’une expérience d’EELS avec de tels faisceaux permet de mesurer des propriétés jusqu’alors inatteignable à l’échelle du nanomètre telle que la phase des plasmons, leurs chiralité optique voire même leur longueur de cohérence. Dans le chapitre 5, je présente plusieurs résultats théoriques et expérimentaux concernant des expériences de couplage. En particulier, j’étudie le phénomène contre-intuitif d’auto-hybridation qui est une conséquence de la nature non-hermitienne du problème aux valeurs propres associé aux résonances de plasmon et établit une analogie avec les systèmes quantiques ouverts. Enfin, au chapitre 6, je discute des récentes mesures de phonon réalisées dans un STEM grâce au développement de monochromateur électroniques. / Surface plasmons (SP) are electromagnetic waves propagating at the interface between two media typically a metal and a dielectric. SPs can confine electromagnetic fields in very short volumes (typically one to few nanometers), well below the light diffraction limit. This property has a tremendous number of applications ranging from fundamental physics (e.g. quantum optics) to applications (e.g. cancer therapy). However, the price to pay is that SPs suffer from huge ohmic losses in the metal which leads to very short lifetimes (typically few femtoseconds). Theoretically, this presence of dissipation dramatically hardens the theoretical description of SPs. Another consequence of the sub-wavelength confinement of light associated with SPs is that their observation requires a nanometric resolution - which excludes the use of standard optical techniques. Yet, the scanning transmission electron microscope (STEM) is a particularly suitable tool to study SPs as it employs fast electrons with typical wavelength from 1 to 10 picometers. Thus, the last decade has seen the tremendous development of electron-based spectroscopies applied to nano-optics such as electron energy loss spectroscopy (EELS), cathodoluminescence spectroscopy (CL) or STEM- Hanbury Brown and Twiss interferometry (HBT). In this thesis, I explored different open problems of plasmonics and nano-optics under the scope of electron microscopy and spectroscopies. In chapter 3, I develop a formalism taking into account both the quantum and relativistic nature of EELS experiments using elements of quantum field theory. In chapter 4, I apply the latter formalism to the case of EELS measurements of SPs using electrons with shaped phase. In chapter 5, I give several theoretical and experimental results on coupling experiments involving SPs. Particularly, I demonstrate a counterintuitive type of coupling, the so-called self- hybridization which is a consequence of the non-Hermitian nature of the LSP eigenproblem and draw analogy with open quantum system. Finally, in chapter 6, I discuss the recent result on vibrational EELS in monochromated STEM.

Hliníková slitina AA8079 připravena plynulým odléváním mezi válce je běžně používána pro výrobu tenké potravinářské fólie. Vzhledem k použité metodě odlévání a složení slitiny je struktura litého materiálu značně nehomogenní a obsahuje intermetalické fáze, které se shlukují v eutektických koloniích. Litý materiál tak vyžaduje tepelné zpracování před dalšími kroky výroby. Mikrostruktura materiálu po homogenizačních žíháních na různých teplotách je rozdílná, což ovlivňuje další zpracování. Po homogenizaci je materiál válcován což způsobuje snížení tažnosti. Rekrystalizační žíhání je vyžadováno po zválcování na střední tloušťku před finálním válcování, aby byla tažnost obnovena. Chování materiálu během rekrystalizačního žíhání je ovlivněno přítomnými fázemi, jejich velikostí a rozdělením. Byl studován vliv mikrostruktury po homogenizaci na rozdílných teplotách na rekrystalizaci, byla vyhodnocena kinetika rekrystalizace a byly identifikovány dva hlavní mechanismy ovlivňující rekrystalizaci - částicemi stimulovaná nukleace a Zenerův tlak.

Machine learning has been utilized in bio-imaging in recent years, however as it is relatively new and evolving, some researchers who wish to utilize machine learning tools have limited access because of a lack of programming knowledge. In electron microscopy (EM), immunogold labeling is commonly used to identify the target proteins, however the manual annotation of the gold particles in the images is a time-consuming and laborious process. Conventional image processing tools could provide semi-automated annotation, but those require that users make manual adjustments for every step of the analysis. To create a new high-throughput image analysis tool for immuno-EM, I developed a deep learning pipeline that was designed to deliver a completely automated annotation of immunogold particles in EM images. The program was made accessible for users without prior programming experience and was also expanded to be used on different types of immuno-EM images. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2020. / FAU Electronic Theses and Dissertations Collection

Dental amalgams have been used for centuries as major restorative materials for decaying teeth. Amalgams are prepared by mixing alloy particles which contain Ag, Sn, and Cu as the major constituent elements with liquid Hg. The study of microstructure is essential in understanding the setting reactions and improving the properties of amalgams. Until the work reported in this dissertation, optical microscopy (OM), scanning electron microscopy (SEM), and x-ray diffractometry (XRD) were used commonly to analyze amalgam microstructures. No previous systematic transmission electron microscopy (TEM) study has been performed due to sample preparation difficulties and composite structure of dental amalgams. The goal of this research was to carry out detailed microstructural and compositional studies of dental amalgams. This was accomplished using the enhanced spatial resolution of the TEM and its associated microanalytical techniques, namely, scanning transmission electron microscopy (STEM), x-ray energy dispersive spectroscopy (XEDS) and micro-microdiffraction (μμD). A new method was developed for thinning amalgam samples to electron transparency using the "wedge technique." Velvalloy, a low-Cu amalgam, and Tytin, a high-Cu amalgam, were the two amalgams characterized. Velvalloy is composed of a Ag₂Hg₃ (γ₁)/HgSn₇₋₉ (γ₂) matrix surrounding unreacted Ag₃Sn (γ) particles. In addition, hitherto uncharacterized reaction layers between Ag₃Sn(γ)/Ag₂Hg₃ (γ₂) and Ag₂Hg₃ (γ₁)/HgSn₇₋₉ (γ₂) were observed and analyzed. An Ag-Hg-Sn (β₁) phase was clearly identified for the first time. In Tytin, the matrix consists of Ag₂Hg₃ (γ₁) grains. Fine precipitates of Cu₆Sn₅ (η') are embedded inside the γ₁ and at the grain boundaries. These precipitates are responsible for the improved creep resistance of Tytin compared to Velvalloy. The additional Cu has completely eliminated the γ₂ phase which is the weakest component of amalgams. Ag-Hg-Sn (β₁) and large grains of Cu₆Sn₅ (η') are found adjacent to the unreacted alloy particles. Tytin alloy particles contain Cu₃Sn (ε) precipitates in a matrix of Ag₃Sn (γ) and Ag₄Sn (β). SEM was used to correlate the TEM findings in the context of the general microstructure. The results are in good agreement with those published in the literature. The microstructural details reported here, many of which were not previously available, will help provide insight into the deformation mechanisms of dental amalgams.