Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

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.

Un effort mondial existe actuellement dans le but de réaliser un ordinateur quantique. Un tel dispositif permettrait d'implémenter des algorithmes plus rapides que les algorithmes classiques pour certaines tâches (recherche dans des bases de données, factorisation d'entiers). Il permettrait également de simuler des systèmes quantiques de manière beaucoup plus efficace qu'un ordinateur classique. L'obtention de ce gain en puissance nécessite d'intriquer un grand nombre de bits quantiques (qubits). Celle ci suppose de pouvoir déplacer un qubit d'un point à un autre de l'espace. Dans cette thèse, nous démontrons une première étape vers le déplacement d'un qubit de spin électronique : un électron unique est déplacé, à la demande, entre deux boîtes quantiques distantes de quelques microns. Le transport est réalisé à l'aide d'une onde acoustique de surface qui entraîne l'électron. Le transfert a été réalisé avec une efficacité de 90 % et déclenché à la nanoseconde. Ces résultats ouvrent la voie à la réalisation d'expériences d'optique quantique électronique avec une détection évènement par évènement. L'envoi d'un électron sur deux initialement présents ouvre la voie à la génération de paires d'électrons distants et intriqués. / A global effort is pursued to realise a quantum computer. Such a dispositive will allow to implement faster algorithms for tasks like integer factoring and database search. It will also allow to simulate quantum system much more efficiently. than a classical system. This power gain necessitates to entangle a large number of qubits. This in turn requires the ability to transport a qubit in space. In this thesis, we demonstrate a first step: a single electron is transported on demand from one quantum dot to another quantum dot, micrometers away. The transport is realised thanks to a Surface Acoustic Wave (SAW) that drags the electron. The transfer is realised with an efficiency of 90 % and triggered within one nanosecond. These results open the way to the realisation of electron quantum optics experiments with an event per event detection. A work on the separation of two electron initially present in the quantum dot will lead to the generation of distant entangled particles.

Secondary multidrug transporters use the energy stored in transmembrane ion gradients to bind and extrude a variety of weakly related chemical structures. These polyspecific antiporters challenge the notions of high-affinity conformation and strict ion-substrate coupling, inherent to the alternating-access model of transport. In order to investigate the mechanism of secondary multidrug transport at a molecular level, we study LmrP, a Major Facilitator Superfamily (MFS) multidrug transporter from Lactococcus lactis, which relies on the proton-motive force to achieve the transport of its diverse substrates. We carried out Double Electron Electron (DEER) distance measurements to elucidate the conformational dynamics underlying the transport cycle. We monitored the conformational response of a library of labeled double cysteine mutants to the presence of ligand(s) and proton(s). We investigated the role of the lipid environment by performing the measurements on mutants reconstituted in nanoscale soluble lipid bilayers (nanodiscs). During this work, we have demonstrated that the transporter oscillates between two main conformations, the outward-open and the inward-open. We have shown that the protonation of conserved acidic residues is the driving force of the conformational transition. The lipid bilayer modulates the equilibrium and allows the transition to occur at higher and more physiological pH values. By using specific lipid compositions, we observe that the lipid headgroup is crucial in the regulation of the conformational equilibrium. Based on our data, we propose a model of secondary multidrug transport wherein substrate binding initiates the transport cycle by catalysing proton entrance from the extracellular side. Subsequent protonation of membrane-embedded acidic residues triggers a cascade of conformational changes that results in substrate extrusion to the extracellular side and proton release in the cytosol. We suggest the opening and closing of the extracellular site is tightly regulated while the cytoplasmic side is more flexible. To our knowledge, this work provides the first direct structural evidence of the role of the lipids in the regulation of the conformational dynamics of a membrane transporter. / La surexpression de transporteurs capables d’expulser des molécules cytotoxiques est un mécanisme connu de résistance aux antibiotiques de la cellule bactérienne. Certains transporteurs ont développé la capacité de reconnaitre et d’expulser des substrats de structures diverses, donnant lieu à une résistance multidrogue de la part de leur hôte. Ces transporteurs multidrogues sont présents dans une variété de classes de protéines, distribués dans tous les règnes du vivant. Parmi celles - ci, la famille MFS (Major Facilitator Superfamily) comprend la majorité des transporteurs multidrogues activé par une source d’énergie secondaire, et jouent un rôle crucial dans la propagation de maladies nosocomiales d’origine bactérienne. Une meilleure compréhension des mécanismes fondamentaux du transport multidrogue secondaire est le prérequis indispensable à l’élaboration de thérapies adaptées. En particulier, une description détaillée des changements conformationnels impliqués dans le transport, et une identification des mécanismes moléculaires qui permettent de lier la source d’énergie au transport fait actuellement défaut. Afin de pallier ce manque, ce travail vise à étudier LmrP (Lactococcus lactis multidrug resistance Protein) un transporteur MFS qui confère à son hôte Lactococcus lactis la résistance à divers antibiotiques et agents cytotoxiques de structure et de charge variable. Cette extrusion active est alimentée par un cotransport énergétiquement favorable de protons. Nous avons étudié le mécanisme de transport de LmrP à l’échelle moléculaire en utilisant la technique spectroscopique Double Electron Electron Resonance (DEER), qui permet de mesurer des variations de distances à l’échelle nanométrique, idéale pour observer les mouvements intramoléculaires d’un transporteur MFS. Différents aspects moléculaires susceptibles de réguler le cycle de transport sont étudiés de façon indépendante et couplée :le rôle des protons, des différents substrats, et de l’environnement lipidique. Sur base de cette cartographie conformationnelle, un mécanisme de transport couplant tous les acteurs moléculaires est proposé :la liaison du proton à un motif d’acides aminés conservé constitue la base de la transition conformationnelle, les divers substrats ayant pour rôle de permettre aux protons d’accéder à ce motif. La compétition substrat-proton est la base du transport couplé. Notre travail a mis en évidence le rôle fondamental de l’environnement lipidique, qui module l’équilibre conformationnel du transporteur en interagissant avec un ou plusieurs motif(s) conservé(s). Par ailleurs, notre étude questionne le paradigme actuel de transport au sein de la famille MFS car elle démontre que les changements conformationnels globaux passent par des réarrangements locaux et coordonnés. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

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.

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.

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.

In the present work three different proteins were investigated, namely IGPS, the SRII/HtrII complex and ChR2. EPR spectroscopy combined with SDSL were applied to investigate the relation of the respective protein dynamics and their functions. In case of IGPS spin label side chain dynamics were recorded and allow a classification of loop dynamics during catalysis. For SRII/HtrII an equilibrium of spin label side chain dynamics was found to reflect the equilibrium of the activated and deactivated states, which are responsible for signal transfer through the complex. Time-resolved analyses of side chain dynamics and trapping of intermediates of the light-triggered channel ChR2 identified conformational changes to occur during channel function. Thereby, the EPR spectroscopy proves to be a powerful tool to investigate proteins in context of structural changes during their protein function.

Theoretical formulations of secondary electron emission over the past 20 years have exceeded the confirming ability of available measurements. An instrument has been developed and tested for the purpose of obtaining simultaneous angle- and energy-resolved (AER) secondary and backscattered electron measurements for energetic electrons incident on conducting surfaces. The instrument is found to be in good working order and the data quality found to be excellent for nearly all angles and energies investigated. A representative set of AER measurements has been acquired for 1500 e V electrons normally incident on polycrystalline gold. The data have been used to construct angle-resolved (AR) spectra and energy-resolved (ER) angular distributions, which have been examined both as surface plots and cross sections. Analysis of the measurements strongly suggests that secondary electrons comprise the bulk of emitted electrons at energies much greater than the traditionally accepted maximum secondary electron energy of 50 eV. Additional evidence suggests the ability to investigate dominant secondary and backscattered electron production mechanisms in several energy domains.

Photoemission electron microscopy (PEEM) uses photoelectrons excited from material surfaces by incident photons to probe the interaction of light with surfaces with nanometer-scale resolution. The point resolution of PEEM images is strongly limited by spherical and chromatic aberration. Image aberrations primarily originate from the acceleration of photoelectrons and imaging with the objective lens and vary strongly in magnitude with specimen emission characteristics. Spherical and chromatic aberration can be corrected with an electrostatic mirror, and here I develop a triode mirror with hyperbolic geometry that has two adjacent, field-adjustable regions. I present analytic and numerical models of the mirror and show that the optical properties agree to within a few percent. When this mirror is coupled with an electron lens, it can provide a large dynamic range of correction and the coefficients of spherical and chromatic aberration can be varied independently. I report on efforts to realize a triode mirror corrector, including design, characterization, and alignment in our microscope at Portland State University (PSU). PEEM may be used to investigate optically active nanostructures, and we show that photoelectron emission yields can be identified with diffraction, surface plasmons, and dielectric waveguiding. Furthermore, we find that photoelectron micrographs of nanostructured metal and dielectric structures correlate with electromagnetic field calculations. We conclude that photoemission is highly spatially sensitive to the electromagnetic field intensity, allowing the direct visualization of the interaction of light with material surfaces at nanometer scales and over a wide range of incident light frequencies.