A low temperature scanning tunneling microscope (LTSTM) was built that we could use in an ultra high vacuum (UHV) system. The scanning tunneling microscope (STM) was tested on an existing 3He cryostat and calibrated at room, liquid nitrogen and helium temperatures. We analyzed the operational electronic and vibration noises and made some effective improvements. To demonstrate the capabilities of the STM, we obtained atomically resolved images of the Au (111) and graphite surfaces. In addition, we showed that the stable tunneling junctions can be formed between the Pt/Ir tip and a superconducting thin film PbBi. We observed the atomic corrugation on Au (111) and measured the height of the atomic steps to be approximately2.53Å, which agrees with published values. In our images of the graphite surface, we found both the β atoms triangular structure, as well as the complete α-β hexagonal unit cell, using the same tip and the same bias voltage of 0.2V. The successful observation of the hidden α atoms of graphite is encouraging in regards to the possibility of imaging other materials with atomic resolution using our STM. We also demonstrated that stable tunneling junctions can be formed at various temperatures. To demonstrate this, the superconducting current-voltage and differential conductance-voltage characteristics of a PbBi film were measured from 1.1K to 9K From this data, the temperature dependent energy gap of the superconductor was shown to be consistent with the predictions of the Bardeen, Cooper, and Schrieffer (BCS) theory.

abstract: Vibrational spectroscopy is a ubiquitous characterization tool in elucidating atomic structure at the bulk and nanoscale. The ability to perform high spatial resolution vibrational spectroscopy in a scanning transmission electron microscope (STEM) with electron energy-loss spectroscopy (EELS) has the potential to affect a variety of materials science problems. Since 2014, instrumentation development has pushed for incremental improvements in energy resolution, with the current best being 4.2 meV. Although this is poor in comparison to what is common in photon or neutron vibrational spectroscopies, the spatial resolution offered by vibrational EELS is equal to or better than the best of these other techniques. The major objective of this research program is to investigate the spatial resolution of the monochromated energy-loss signal in the transmission-beam mode and correlate it to the excitation mechanism of the associated vibrational mode. The spatial variation of dipole vibrational signals in SiO2 is investigated as the electron probe is scanned across an atomically abrupt SiO2/Si interface. The Si-O bond stretch signal has a spatial resolution of 2 – 20 nm, depending on whether the interface, bulk, or surface contribution is chosen. For typical TEM specimen thicknesses, coupled surface modes contribute strongly to the spectrum. These coupled surface modes are phonon polaritons, whose intensity and spectral positions are strongly specimen geometry dependent. In a SiO2 thin-film patterned with a 2x2 array, dielectric theory simulations predict the simultaneous excitation of parallel and uncoupled surface polaritons and a very weak excitation of the orthogonal polariton. It is demonstrated that atomic resolution can be achieved with impact vibrational signals from optical and acoustic phonons in a covalently bonded material like Si. Sub-nanometer resolution mapping of the Si-O symmetric bond stretch impact signal can also be performed in an ionic material like SiO2. The visibility of impact energy-loss signals from excitation of Brillouin zone boundary vibrational modes in hexagonal BN is seen to be a strong function of probe convergence, but not as strong a function of spectrometer collection angles. Some preliminary measurements to detect adsorbates on catalyst nanoparticle surfaces with minimum radiation damage in the aloof-beam mode are also presented. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2020

abstract: Extended crystal defects often play a critical role in determining semiconductor device performance. This dissertation describes the application of transmission electron microscopy (TEM) and aberration-corrected scanning TEM (AC-STEM) to study defect clusters and the atomic-scale structure of defects in compound semiconductors. An extensive effort was made to identify specific locations of crystal defects in epitaxial CdTe that might contribute to degraded light-conversion efficiency. Electroluminescence (EL) mapping and the creation of surface etch pits through chemical treatment were combined in attempts to identify specific structural defects for subsequent TEM examination. Observations of these specimens revealed only surface etch pits, without any visible indication of extended defects near their base. While chemical etch pits could be helpful for precisely locating extended defects that intersect with the treated surface, this study concluded that surface roughness surrounding etch pits would likely mitigate against their usefulness. Defect locations in GaAs solar-cell devices were identified using combinations of EL, photoluminescence, and Raman scattering, and then studied more closely using TEM. Observations showed that device degradation was invariably associated with a cluster of extended defects, rather than a single defect, as previously assumed. AC-STEM observations revealed that individual defects within each cluster consisted primarily of intrinsic stacking faults terminated by 30° and 90° partial dislocations, although other defect structures were also identified. Lomer dislocations were identified near locations where two lines of strain contrast intersected in a large cluster, and a comparatively shallow cluster, largely constrained to the GaAs emitter layer, contained 60° perfect dislocations associated with localized strain contrast. In another study, misfit dislocations at II-VI/III-V heterovalent interfaces were investigated and characterized using AC-STEM. Misfit strain at ZnTe/GaAs interfaces, which have relatively high lattice mismatch (7.38%), was relieved primarily through Lomer dislocations, while ZnTe/InP interfaces, with only 3.85% lattice mismatch, were relaxed by a mixture of 60° perfect dislocations, 30° partial dislocations, and Lomer dislocations. These results were consistent with the previous findings that misfit strain was relaxed primarily through 60° perfect dislocations that had either dissociated into partial dislocations or interacted to form Lomer dislocations as the amount of misfit strain increased. / Dissertation/Thesis / Doctoral Dissertation Physics 2020

<p> Four stucturally distinct types of macromolecular antifreezes have been previously isolated from the sera of polar marine fish. When the water temperature surrounding these organisms drops below -0.7°C, the freezing point of their bodily fluids, any contact with surrounding ice will nucleate internal ice crystal growth. The antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) synthesized by the fish act to inhibit the growth of existing ice crystals in their sera through direct adsorption to the ice lattice. The α-helical structure of type I AFP from winter flounder has been solved to atomic resolution and its mechanism of ice binding has been proposed. The NMR solution structure of a type III AFP from ocean pout has identified proteins in this class to exist in a β-sandwich conformation, however their mechanism of action remains uncertain.</p> <p> To facilitate the pursuit of an x-ray crystal structure solution, we subcloned the gene for a type III AFP (HPLC6) into pET15b and expressed recombinant His-rHPLC6 AFP in E. coli. Purified rmHPLC6 product has been successfully crystallized, and heavy atom soaks were performed in order to attempt a structure solution by multiple isomorphous replacement. The lone tyrosine in this recombinant AFP has been successfully derivatized in solution with iodine, and the modified protein was crystallized. In order to optimize the measurement of anomalous scattering information, modifications to our data collection system were required. Cryocrystallography techniques were employed to improve the quality of collected data.</p> <p> The expression, purification, crystallization and optimized data collection on an iodine-derivatized type III AFP from ocean pout will be presented here. This work has been instrumental in providing the high quality x-ray data required to solve the crystal structure to atomic resolution. Future examination of the solved structure will promote an increased understanding of the ice-binding mechanism exhibited by this class of proteins.</p> / Thesis / Master of Science (MSc)

Diffusive Molecular Dynamics (DMD) is a class of recently developed computational methods for the simulation of long-term mass transport with a full atomic fidelity. Its basic idea is to couple a discrete kinetic model for the evolution of mass transport process with a non-equilibrium thermodynamics model that governs lattice deformation and supplies the requisite driving forces for kinetics. Compared to previous atomistic models, e.g., accelerated Molecular Dynamics and on-the-fly kinetic Monte Carlo, DMD allows the use of larger time-step sizes and hence has a larger simulation time window for mass transport problems. This dissertation focuses on the development, assessment and application of a DMD computational framework for the long-term, three-dimensional, deformation-diffusion coupled analysis of solute mass transport in nanomaterials. First, a computational framework is presented, which consists mainly of: (1) a computational model for interstitial solute diffusion, which couples a nonlinear optimization problem with a first-order nonlinear ordinary differential equation; (2) two numerical methods, i.e., mean field approximation and subcycling time integration, for accelerating DMD simulations; and (3) a high-performance computational solver, which is parallelized based on Message Passing Interface (MPI) and the PETSc/TAO library for large-scale simulations. Next, the computational framework is validated and assessed in two groups of numerical experiments that simulate hydrogen mass transport in palladium. Specifically, the framework is validated against a classical lattice random walk model. Its capability to capture the atomic details in nanomaterials over a long diffusive time scale is also demonstrated. In these experiments, the effects of the proposed numerical methods on solution accuracy and computation time are assessed quantitatively. Finally, the computational framework is employed to investigate the long-term hydrogen absorption into palladium nanoparticles with different sizes and shapes. Several significant findings are shown, including the propagation of an atomistically sharp phase boundary, the dynamics of solute-induced lattice deformation and stacking faults, and the effect of lattice crystallinity on absorption rate. Specifically, the two-way interaction between phase boundary propagation and stacking fault dynamics is noteworthy. The effects of particle size and shape on both hydrogen absorption and lattice deformation are also discussed in detail. / Ph. D. / Interstitial diffusion in crystalline solids describes a phenomenon in which the solute constituents (e.g., atoms) move from an interstitial space of the host lattice to a neighboring one that is empty. It is a dominating feature in many important engineering applications, such as metal hydrides, lithium-ion batteries and hydrogen-induced material failures. These applications involve some key problems that might take place over long time periods (e.g., longer than 1 s), while the nanoscale behaviors and mechanisms become significant. The time scale of these problems is beyond the capability of established atomistic models, e.g., accelerated Molecular Dynamics and on-the-fly kinetic Monte Carlo. To this end, this dissertation presents the development and application of a new computational framework, referred to as Diffusive Molecular Dynamics (DMD), for the simulation of long-term interstitial solute diffusion in advanced nanomaterials. The framework includes three key components. Firstly, a DMD computational model is proposed, which accounts for three-dimensional, deformation-diffusion coupled analysis of interstitial solute mass transport. Secondly, nu- merical methods are employed to accelerate the DMD simulations while maintaining a high solution accuracy. Thirdly, a high-performance computational solver is developed to implement the DMD model and the numerical methods. Moreover, regarding its application, the DMD framework is first validated and assessed in the numerical experiments pertaining to hydrogen mass transport in palladium crystals. Then, it is employed to investigate the atomic behaviors and mechanisms involved in the long-term hydrogen absorption by palladium nanoparticles with different sizes and shapes. The two-way interaction between hydrogen absorption and lattice deformation is studied in detail.

Die off-axis Elektronenholografie im Transmissionselektronenmikroskop (TEM) erlaubt die quantitative Rekonstruktion der komplexen Objektaustrittswelle mit atomarer Auflösung. Die Auswertung der Phase dieser Welle ermöglicht die Unterscheidung der Atomsorten bzw. das Zählen der Atome in Projektionsrichtung sowie die Bestimmung von Atompositionen. Damit ist ein TEM über die einfache Abbildung hinaus ein sehr leistungsstarkes Messgerät zur quantitativen Analyse kleinster Strukturen bis hin zur atomaren Skala. Die Prozedur von der Aufnahme eines hochaufgelösten Elektronenhologramms über die Rekonstruktion bis zur bildfehlerkorrigierten Objektwelle ist jedoch sehr umfangreich und teils sehr anfällig für Artefakte. Diese Arbeit zeigt unter kritischer Betrachtung der einzelnen Einflüsse, wie dieser Weg zu beschreiten ist, um schlussendlich zu einer artefaktfreien, interpretierbaren Objektwelle zu gelangen. Im letzten Jahrzehnt haben Bildfehler-Korrektoren die höchstauflösende Transmissions-elektronenmikroskopie auf instrumenteller Seite revolutioniert. Auch die off-axis Holografie kann eine ganze Reihe von Vorteilen aus diesem elektronenoptischen Zusatzsystem ziehen. Neben der Analyse dieser einzelnen Verbesserungen, insbesondere der Phasensignalauflösung, wird gezeigt, wie es das Cs-korrigierte TEM zu optimieren gilt, um schließlich bestmögliche Ergebnisse für quantitative Objektanalyse zu erzielen. Zwei Anwendungsbeispiele zeigen experimentelle Ergebnisse der Elektronenholografie mit Cs-korrigierten Mikroskopen. Bei der Analyse ferroelektrischer Nanoschichten erweisen sich die einzigartigen Möglichkeiten der holografischen Auswertung im Zusammenspiel mit der nunmehr hervorragenden Signalauflösung als äußerst nützlich, um die ferroelektrische Polarisation zu ermitteln. Die Objektwellenrekonstruktion der Korngrenze in einer Goldfolie demonstriert weitere Verbesserungen für die Holografie, wenn zusätzlich eine neuartige Elektronenquelle mit höherem Richtstrahlwert zum Einsatz kommt. Einzelne Goldatome werden mit einem Signal-Rausch-Verhältnis von ca. 10 in Amplitude und Phase messbar. / Off-axis electron holography in a transmission electron microscope (TEM) allows reconstructing the complex object exit-wave quantitatively with atomic resolution. Analyzing the phase shift of this wave gives access to the atomic species and enables counting the number of atoms in projection direction as well as determining atom positions. Therefore, a TEM is a very powerful measuring device for quantitative analysis of smallest structures down to the atomic scale beyond simple microscopic imaging. The procedure of the recording of a high-resolution electron hologram, its reconstruction, and after numerical aberration correction finally ending up with the object-exit wave, is quite comprehensive and partially susceptible to artifacts. This work shows how to manage this procedure in order to obtain an interpretable object exit-wave, which is free of artifacts. In instrumentation within the last decade aberration correctors have revolutionized high-resolution electron microscopy. Also off-axis holography can benefit from this electron optical add-on module. Besides the exploration of each improvement, in particular the phase detection limit, this work demonstrates, how to optimize the Cs-corrected TEM in order to get best possible results for quantitative object analysis. Two application examples show experimental results of electron holography with Cs-corrected microscopes. For the investigation of ferroelectric nanolayers, the unique possibilities of the holographic evaluation together with the strongly improved signal resolution turn out to be very useful when determining the ferroelectric polarization. The object wave reconstruction of the grain boundary in a gold film demonstrates further improvements for holography, when additionally using a new electron gun with improved brightness. Single gold atoms become measurable with a signal-noise-ratio of about 10 in amplitude and phase.

This thesis explores theoretical aspects of scanning transmission electron microscopy (STEM) and the comparison of simulation with experiment. / The long standing contrast mismatch problem between theory and experiment in conventional high resolution transmission electron microscopy (HRTEM) is examined using the principle of reciprocity and bright field scanning transmission electron microscopy (BFSTEM). It is found that quantitative agreement between theoretical and experimental images is possible provided that theory suitably accounts for the spatial incoherence of the source, and that experimental images are placed on an absolute scale with respect to the incident beam current. Agreement between theory and experimental image contrast is found to be independent of specimen thickness and probe defocus. / Core-loss electron energy-loss spectroscopy (EELS) is a powerful experimental tool with the potential to provide atomic-resolution information about the electronic structure at defects and interfaces in materials and nanostructures. Interpretation, however, is nonintuitive due to the nonlocal ionization potential. Novel improvements in microscope design and operating environment have enabled two dimensional chemical maps. This has permitted a more thorough theoretical analysis. This thesis compares experimental STEM EELS images of LaMnO3, BiSrMnO3 and Si samples to the relevant theoretical simulations. Image features which at first appear counter intuitive are discussed and explained with the accompanying theoretical simulations. It is demonstrated, using a sample of SrTiO3, that more direct interpretation of atomic resolution chemical maps is possible when using energy dispersive x-ray spectroscopy (EDS) in STEM. / This thesis considers extending chemical mapping in STEM EELS to three dimensions using depth sectioning. It explores, theoretically, the feasibility to depth section zone-axis aligned crystals that contain embedded impurities. In STEM EELS this is found to be possible for point defects but not for larger extended objects such as nanoparticles. / The theory describing the mechanism by which contrast is obtained in elastic scanning confocal electron microscopy (SCEM) is developed. It is shown that there is no first order phase contrast in SCEM and thus low image contrast. Finally, energy filtered scanning transmission electron microscopy (EFSCEM) is developed theoretically. The fundamental equation describing image formation is derived and an efficient computation method is developed to allow the rapid calculation of EFSCEM images.

Die off-axis Elektronenholografie im Transmissionselektronenmikroskop (TEM) erlaubt die quantitative Rekonstruktion der komplexen Objektaustrittswelle mit atomarer Auflösung. Die Auswertung der Phase dieser Welle ermöglicht die Unterscheidung der Atomsorten bzw. das Zählen der Atome in Projektionsrichtung sowie die Bestimmung von Atompositionen. Damit ist ein TEM über die einfache Abbildung hinaus ein sehr leistungsstarkes Messgerät zur quantitativen Analyse kleinster Strukturen bis hin zur atomaren Skala. Die Prozedur von der Aufnahme eines hochaufgelösten Elektronenhologramms über die Rekonstruktion bis zur bildfehlerkorrigierten Objektwelle ist jedoch sehr umfangreich und teils sehr anfällig für Artefakte. Diese Arbeit zeigt unter kritischer Betrachtung der einzelnen Einflüsse, wie dieser Weg zu beschreiten ist, um schlussendlich zu einer artefaktfreien, interpretierbaren Objektwelle zu gelangen. Im letzten Jahrzehnt haben Bildfehler-Korrektoren die höchstauflösende Transmissions-elektronenmikroskopie auf instrumenteller Seite revolutioniert. Auch die off-axis Holografie kann eine ganze Reihe von Vorteilen aus diesem elektronenoptischen Zusatzsystem ziehen. Neben der Analyse dieser einzelnen Verbesserungen, insbesondere der Phasensignalauflösung, wird gezeigt, wie es das Cs-korrigierte TEM zu optimieren gilt, um schließlich bestmögliche Ergebnisse für quantitative Objektanalyse zu erzielen. Zwei Anwendungsbeispiele zeigen experimentelle Ergebnisse der Elektronenholografie mit Cs-korrigierten Mikroskopen. Bei der Analyse ferroelektrischer Nanoschichten erweisen sich die einzigartigen Möglichkeiten der holografischen Auswertung im Zusammenspiel mit der nunmehr hervorragenden Signalauflösung als äußerst nützlich, um die ferroelektrische Polarisation zu ermitteln. Die Objektwellenrekonstruktion der Korngrenze in einer Goldfolie demonstriert weitere Verbesserungen für die Holografie, wenn zusätzlich eine neuartige Elektronenquelle mit höherem Richtstrahlwert zum Einsatz kommt. Einzelne Goldatome werden mit einem Signal-Rausch-Verhältnis von ca. 10 in Amplitude und Phase messbar. / Off-axis electron holography in a transmission electron microscope (TEM) allows reconstructing the complex object exit-wave quantitatively with atomic resolution. Analyzing the phase shift of this wave gives access to the atomic species and enables counting the number of atoms in projection direction as well as determining atom positions. Therefore, a TEM is a very powerful measuring device for quantitative analysis of smallest structures down to the atomic scale beyond simple microscopic imaging. The procedure of the recording of a high-resolution electron hologram, its reconstruction, and after numerical aberration correction finally ending up with the object-exit wave, is quite comprehensive and partially susceptible to artifacts. This work shows how to manage this procedure in order to obtain an interpretable object exit-wave, which is free of artifacts. In instrumentation within the last decade aberration correctors have revolutionized high-resolution electron microscopy. Also off-axis holography can benefit from this electron optical add-on module. Besides the exploration of each improvement, in particular the phase detection limit, this work demonstrates, how to optimize the Cs-corrected TEM in order to get best possible results for quantitative object analysis. Two application examples show experimental results of electron holography with Cs-corrected microscopes. For the investigation of ferroelectric nanolayers, the unique possibilities of the holographic evaluation together with the strongly improved signal resolution turn out to be very useful when determining the ferroelectric polarization. The object wave reconstruction of the grain boundary in a gold film demonstrates further improvements for holography, when additionally using a new electron gun with improved brightness. Single gold atoms become measurable with a signal-noise-ratio of about 10 in amplitude and phase.

This thesis concerns the application of aberration corrected scanning transmission electron microscopy (STEM) to the quantitative analysis of industrial Pd-Pt core-shell catalyst nanoparticles. High angle annular dark field imaging (HAADF), an incoherent imaging mode, is used to determine particle size distribution and particle morphology of various particle designs with differing amounts of Pt coverage. The limitations to imaging, discrete tomography and spectral analysis imposed by the sample’s sensitivity to the beam are also explored. Since scattered intensity in HAADF is strongly dependent on both thickness and composition, determining the three dimensional structure of a particle and its bimetallic composition in each atomic column requires further analysis. A quantitative method was developed to interpret single images, obtained from commercially available microscopes, by analysis of the cross sections of HAADF scattering from individual atomic columns. This technique uses thorough detector calibrations and full dynamical simulations in order to allow comparison between experimentally measured cross section to simulated ones and is shown to be robust to many experimental parameters. Potential difficulties in its applications are discussed. The cross section approach is tested on model materials before applying it to the identification of column compositions of core-shell nanoparticles. Energy dispersive X-ray analysis is then used to provide compositional sensitivity. The potential sources of error are discussed and steps towards optimisation of experimental parameters presented. Finally, a combination of HAADF cross section analysis and EDX spectrum imaging is used to investigate the core-shell nanoparticles and the results are correlated to findings regarding structure and catalyst activity from other techniques. The results show that analysis by cross section combined with EDX spectrum mapping shows great promise in elucidating the atom-by-atom composition of individual columns in a core-shell nanoparticle. However, there is a clear need for further investigation to solve the thickness / composition dualism.

Un microscope à force atomique (AFM) est utilisé pour caractériser des matériaux isolant ou semi-conducteur avec une résolution pouvant atteindre l'échelle atomique. Ce microscope est constitué d'un capteur de force couplé à une électronique de contrôle pour pouvoir correctement caractériser ces matériaux. Parmi les différents modes (statique et dynamique), nous nous focalisons essentiellement sur le mode dynamique et plus particulièrement sur le fonctionnement sans contact à modulation de fréquence (FM-AFM). Dans ce mode, le capteur de force est maintenu comme un oscillateur harmonique par le système d'asservissement. Le projet ANR Pnano2008 intitulé : ”Cantilevers en carbure de silicium à piézorésistivité métallique pour AFM dynamique à très haute fréquence" a pour objectif d'augmenter significativement les performances d'un FM-AFM en développant un nouveau capteur de force très haute fréquence. Le but est d'augmenter la sensibilité du capteur et de diminuer le temps nécessaire à l'obtention d'une image de la surface du matériau. Le système de contrôle associé doit être capable de détecter des variations de fréquence de 100mHz pour une fréquence de résonance de 50MHz. Etant donné que les systèmes présents dans l'état de l'art ne permettent pas d'atteindre ces performances, l'objectif de cette thèse fut de développer un nouveau système de contrôle. Celui-ci est entièrement numérique et il est implémenté sur une carte de prototypage basée sur un FPGA. Dans ce mémoire, nous présentons le fonctionnement global du système ainsi que ses caractéristiques principales. Elles portent sur la détection de l'écart de fréquence de résonance du capteur de force. / An atomic force microscope (AFM) is used to characterize insulating materials or semiconductors with a resolution up to the atomic length scale. The microscope includes a force sensor linked to a control electronic in order to properly characterize these materials. Among the various modes (static and dynamic), we focus mainly on the dynamic mode and especially on the frequency modulation mode (FM-AFM). In this mode, the force sensor is maintained as a harmonic oscillator by the servo system. The research project ANR Pnano2008 entitled: "metal piezoresistivity silicon carbide cantilever for very high frequency dynamic AFM" aims to significantly increase the performance of a FM-AFM by developing new very high frequency force sensors. The goal is to increase the sensitivity of the sensor and to decrease the time necessary to obtain topography images of the material. The control system of this new sensor must be able to detect frequency variations as small as 100mHz for cantilevers with resonance frequencies up to 50MHz. Since the state-of-the-art systems doe not present these performances, the objective of this thesis was to develop a new control system. It is fully digital and it is implemented on a FPGA based prototyping board. In this report, we present the system overall functioning and its main features which are related to the cantilever resonant frequency detection. This detection is managed by a phase locked loop (PLL) which is the key element of the system.