Thesis advisor: Paul Davidovits / Aerosol particles are an important component of the Earth-Atmosphere system because of their influence on the radiation budget both directly (through absorption and scattering) and indirectly (through cloud condensation nuclei (CCN) activity). The magnitude of the raditaive forcing attributed to the direct and indirect aerosol effects is highly uncertain, leading to large uncertainties in projections of global climate change. Real-time measurements of aerosol properties are a critical step toward constraining the uncertainties in current global climate modeling and understanding the influence that anthropogenic activities have on the climate. The objective of the work presented in this thesis is to gain a more complete understanding of the atmospheric transformations of aerosol particles and how such transformations influence the direct and indirect radiative effects of the particles. The work focuses on real-time measurements of aerosol particles made with the Aerodyne Aerosol Mass Spectrometer (AMS) developed in collaboration with the Boston College research group. A key feature of the work described is the development of a lightscattering module for the AMS. Here we present the first results obtained with the integrated light scattering – AMS system. The unique and powerful capabilities of this new instrument combination are demonstrated through laboratory experiments and field deployments. Results from two field studies are presented: (1) The Northeast Air Quality Study (NEAQS), in the summer of 2004, conducted at Chebogue Point, Nova Scotia and (2) The Megacity Initiative: Local and Global Research Observations (MILAGRO) field campaign conducted in and around Mexico City, Mexico in March of 2006. Both field studies were designed to study the transformations that occur within pollution plumes as they are transported throughout the atmosphere. During the NEAQS campaign, the pollution plume from the Northeastern United States was intercepted as it was transported towards Europe. In this study, particles were highly processed prior to sampling, with residence times of a few days in the atmosphere. The MILAGRO campaign focused on the evolution of the Mexico City plume as it was transported north. During this study, regional and locally emitted particles were measured with residence times varying from minutes to days in the atmosphere. In both studies, the light scattering – AMS system provided detailed information about the density and composition of single particles, leading to important insights into how atmospheric processing transforms the particle properties. In Mexico City, the light scattering-AMS system was used for the first time as a true single particle mass spectrometer and revealed specific details about the atmospheric processing of primary particles from combustion sources.To quantify the radiative effects of the particles on climate, the processing and ultimate fate of primary emissions (often containing black carbon or soot) must be understood. To provide a solid basis for the interpretation of the data obtained during the field studies, experiments were conducted with a well characterized soot generation-sampling system developed by the Boston College research group. The laboratory soot source was combined with the light scattering – AMS system and a Cloud Condensation Nuclei Counter (CCNC) to measure the change in cloud-forming activity of soot particles as they are processed in the atmosphere. Because of the importance of black carbon in the atmosphere, several instruments have been developed to measure black carbon. In July of 2008, an intercomparison study of 18 instruments was conducted in the Boston College laboratory, with soot particles produced and processed to mimic a wide range of atmospherically-relevant conditions. Transformations in the physical, chemical, and optical properties of soot particles were monitored with the combined suite of aerosol instrumentation. Results from the intercomparison study not only calibrated the different instruments used in the study, but also provided critical details about how atmospheric processing influences the radiative effects of primary combustion particles. / Thesis (PhD) — Boston College, 2008. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Injection in the LHC is a delicate moment, since the LHC collimation system cannot offer adequate protection during beam transfer. For this reason, a complex chain of injection protection devices has been put in place. Among them, the SPS scrapers are the multi-turn cleaning system installed in the SPS aimed at halo removal immediately before injection in the LHC. The upgrade in luminosity of the LHC foresees beams brighter than those currently available in machine, posing serious problems to the performance of the existing injection protection systems. In particular, the integrity of beam-intercepting devices is challenged by unprecedented beam parameters, leading to interactions potentially destructive. In this context, a new design of scrapers has been proposed, aimed at improved robustness and performance. This thesis compares the two scraping systems, i.e. the existing one and the one proposed for upgrade. Unlike any other collimation system for regular halo cleaning, both are "fast" systems, characterised by the variation of the relative distance between the beam and the absorbing medium during cleaning, which enhances the challenge on energy deposition values. Assets/liabilities of the two systems are highlighted by means of numerical simulations and discussed, with particular emphasis on energy deposition in the absorbing medium, time evolution of the beam current during scraping and losses in the machine. Advantages of the system proposed for upgrade over the existing one are highlighted. The analysis of the existing system takes into account present operational conditions and addresses the sensitivity to settings previously not considered, updating and extending past studies. The work carried out on the upgraded system represents the first extensive characterisation of a multi-turn cleaning system based on a magnetic bump. Results have been obtained with the Fluka-SixTrack coupling, developed during this PhD activity from its initial version to being a state-of-art tracking tool for cleaning studies in circular machines. Relevant contributions to the development involve the handling of time-varying impact conditions. An extensive benchmark against a test of the scraper blades with beam has been carried out, to verify the reliability of results. Effcts induced in the tested blades confirm the high values of energy deposition predicted by the simulation. Moreover, the comparison with the time profile of the beam intensity measured during scraping allowed the reconstruction of the actual settings of the blades during the test. Finally, the good agreement of the quantitative benchmark against readouts of beam loss monitors finally proves the quality of the analyses and the maturity of the coupling.

Single particle electron cryomicroscopy (cryo-EM) is a method of structure determination that uses many randomly oriented images of the specimen to construct a three-dimensional density map. In this thesis, single particle cryo-EM has been used to determine the structure of intact adenosine triphosphate (ATP) synthase from bovine heart mitochondria, an approximately 550 kDa membrane protein complex. In respiring organisms, ATP synthase is responsible for synthesizing the majority of ATP, a molecule that serves as an energy source for many cellular reactions. In order to understand the mechanism of ATP synthase, knowledge of the arrangement of subunits in the intact complex is necessary. To obtain maps of intact ATP synthase showing internal density distributions by single particle cryo-EM, methodological improvements to image acquisition, map refinement, and data selection were developed. Further, a novel segmentation algorithm was developed to aid in interpretation of maps. The use of these tools allowed for construction and interpretation of two maps of ATP synthase, solubilized in different membrane mimetics, in which the arrangement of subunits could be identified. These maps revealed interactions within the complex important for its function. In addition, evidence was obtained for curvature of membrane mimetics around ATP synthase, suggesting a role for the complex in maintenance of mitochondrial membrane morphology.

Single particle electron cryomicroscopy (cryo-EM) is a method of structure determination that uses many randomly oriented images of the specimen to construct a three-dimensional density map. In this thesis, single particle cryo-EM has been used to determine the structure of intact adenosine triphosphate (ATP) synthase from bovine heart mitochondria, an approximately 550 kDa membrane protein complex. In respiring organisms, ATP synthase is responsible for synthesizing the majority of ATP, a molecule that serves as an energy source for many cellular reactions. In order to understand the mechanism of ATP synthase, knowledge of the arrangement of subunits in the intact complex is necessary. To obtain maps of intact ATP synthase showing internal density distributions by single particle cryo-EM, methodological improvements to image acquisition, map refinement, and data selection were developed. Further, a novel segmentation algorithm was developed to aid in interpretation of maps. The use of these tools allowed for construction and interpretation of two maps of ATP synthase, solubilized in different membrane mimetics, in which the arrangement of subunits could be identified. These maps revealed interactions within the complex important for its function. In addition, evidence was obtained for curvature of membrane mimetics around ATP synthase, suggesting a role for the complex in maintenance of mitochondrial membrane morphology.

This thesis addresses the observed fluorescence intermittency of single semiconductor nanocrystals, so called Quantum Dots (QDs), which is also referred to as blinking. Despite continuous excitation their fluorescence is randomly interrupted by dark periods that can last over several minutes. Especially the extraction of power law dwell time statistics in bright and dark states indicates very complex underlying processes that are not fully understood to date. Here two approaches are followed to reveal the nature of the blinking mechanism. One addresses the common threshold method for extraction of power law dwell times. Its performance is tested with simulations to a broad range of experimentally determined parameters. Strong deviations are found between input and extracted statistics dependent on input parameters themselves. A comparison with experimental data does not support the assignment of power law statistics for the bright state and indicates the existence of distinct blinking mechanisms. The second approach directly aims at the nature of the dark state, which is mostly attributed to charges in the QD or trap states in its vicinity. A method is developed to detect charging processes on single QDs with their fluorescence. Electrochemistry is combined with confocal microscopy also allowing evaluations of excited state lifetimes and emission spectra. Reduction and oxidation of the QD bands are successfully observed as a quenching of QD fluorescence. Single QD observations identify two independent blinking mechanisms, that are assigned to positive and negative charging. Positive charging is not only observed after hole injection but also the extraction of excited electrons. Three additional quenching mechanisms are identified, two of which are assigned to trap relaxation. Differences between two substrate electrodes demonstrate the importance of the substrate material.

During the last years we have seen the birth of free-electron lasers, a new type of light source ten billion times brighter than syncrotrons and able to produce pulses only a few femtoseconds long. One of the main motivations for building these multi-million dollar machines was the prospect of imaging biological samples such as proteins and viruses in 3D without the need for crystallization or staining. This thesis contains some of the first biological results from free-electron lasers. These results include 2D images, both of whole cells and of the giant mimivirus and also con- tains a 3D density map of the mimivirus assembled from diffraction patterns from many virus particles. These are important proof-of-concept experiments but they also mark the point where free-electron lasers start to produce biologically relevant results. The most noteworthy of these results is the unexpectedly non-uniform density distribution of the internals of the mimivirus. We also present Hawk, the only open-source software toolkit for analysing single particle diffraction data. The Uppsala-developed program suite supports a wide range fo algorithms and takes advantage of Graphics Processing Units which makes it very computationally efficient. Last, the problem introduced by structural variability in samples is discussed. This includes a description of the problem and how it can be overcome, and also how it could be turned into an advantage that allows us to image samples in all of their conformational states.

No description available.

In this thesis, we have explored the commonalities and connections between different classes of quantum systems that do not thermalize. Specifically, we have (1) shown that localized systems possess conservation laws like integrable systems, which can be constructed in a systematic way and used to detect localization-delocalization transitions , (2) studied the phenomenon of many-body localization in a model with a single particle mobility edge, (3) shown that interesting finite-size scaling emerges, with universal exponents, when athermal quantum systems are forced to thermalize through the application of perturbations and (4) shown that these scaling laws also arise when a perturbation causes a crossover between quantum systems described by different random matrix ensembles. We conclude with a brief summary of each chapter. In Chapter 2, we have investigated the effects of finite size on the crossover between quantum integrable systems and non-integrable systems. Using exact diagonalization of finite-sized systems, we have studied this crossover by obtaining the energy level statistics and Drude weight associated with transport. Our results reinforce the idea that for system size L → ∞, non-integrability sets in for an arbitrarily small integrabilitybreaking perturbation. The crossover value of the perturbation scales as a power law ∼ L−3 when the integrable system is gapless and the scaling appears to be robust to microscopic details and the precise form of the perturbation. In Chapter 3, we have studied the crossover among different random matrix ensembles CHAPTER 6. CONCLUSION 127 [Poissonian, Gaussian Orthogonal Ensemble (GOE), Gaussian Unitary Ensemble (GUE) and Gaussian Symplectic Ensemble (GSE)] realized in different microscopic models. We have found that the perturbation causing the crossover among the different ensembles scales to zero with system size as a power law with an exponent that depends on the ensembles between which the crossover takes place. This exponent is independent of microscopic details of the perturbation. We have also found that the crossover from the Poissonian ensemble to the other three is dominated by the Poissonian to GOE crossover which introduces level repulsion while the crossover from GOE to GUE or GOE to GSE associated with symmetry breaking introduces a subdominant contribution. Finally,we have conjectured that the exponent is dependent on whether the system contains interactions among the elementary degrees of freedom or not and is independent of the dimensionality of the system. In Chapter 4, we have outlined a procedure to construct conservation laws for Anderson localized systems. These conservation laws are found as power series in the hopping parameters. We have also obtained the conservation laws for the disorder free Aubry-Andre model, where the states are either localized or extended depending on the strength of a coupling constant. We have formulated a specific procedure for averaging over disorder, in order to examine the convergence of the power series. Using this procedure for the Aubry-Andre model, we show that integrals of motion given by our construction are well-defined in the localized phase but not so in the extended phase. Finally, we also obtain the integrals of motion for a model with interactions to lowest order in the interaction. In Chapter 5, we have studied many body localization and investigated its nature in the presence of a single particle mobility edge. Employing the technique of exact diagonalization for finite-sized systems, we have calculated the level spacing distribution, time evolution of entanglement entropy, optical conductivity and return probability to characterize the nature of localization. The localization that develops in the presence of interactions in these systems appears to be different from regular Many-Body Localization (MBL) in that the growth of entanglement entropy with time is linear (like in CHAPTER 6. CONCLUSION 128 a thermal phase) instead of logarithmic but saturates to a value much smaller than the thermal value (like for MBL). All other diagnostics seem consistent with regular MBL

Le travail de cette thèse a été consacré au développement d’un nouvelle technique SELFI (pour self-interferences, auto-interférences en anglais). Cette méthode permet d’obtenir une localisation tridimensionnelle d’émetteurs fluorescents individuels. Nous avons démontré que cela permet l'imagerie super-résolue en 3D et le suivie 3D de molécules uniques en profondeur dans des échantillons biologiques denses et complexes. La technique SELFI se base sur l'utilisation des interférences auto-référencées (également appelées « auto-interférences ») pour remonter à la localisation 3D d’un émetteur en une seule mesure. Ces interférences sont générées via l’utilisation d'un réseau de diffraction placé en sortie du microscope de fluorescence : le signal de fluorescence diffracte sur le réseau et les ordres interfèrent, après une courte propagation, sur le détecteur. Les interférences ainsi formées sont décodées numériquement pour remonter à la localisation 3D d'une molécule fluorescente au sein de l'échantillon. Une molécule unique peut ainsi être localisée avec une précision d'une dizaine de nanomètre, et cela jusqu'à une profondeur d'au moins 50µm au sein d'un échantillon biologique vivant épais (par exemple un tissu biologique).En combinant la méthode SELFI à différentes techniques de super-résolution (PALM, dSTORM et uPAINT), nous montrons que cette méthode de localisation tridimensionnelle permet de retrouver la hiérarchie et l'organisation de protéines dans des objets biologiques. En effectuant du SELFI-PALM, nous avons pu observer différentes protéines des points focaux d’adhésion (talin-C terminale et paxiline) et retrouver les différences de hauteur attendues, et ceux sur des échantillons de cellules vivantes. Ces résultats confirment la résolution accessible avec la technique SELFI (environ 25nm) même pour un faible nombre de photons collectés (environ 500 photons par molécule).Nous mettons en évidence la robustesse de la technique SELFI en reconstruisant des images de super-résolution 3D de structures denses en profondeur dans des échantillons tissulaires complexes. En effectuant du SELFI-dSTORM, nous avons observé le réseau d’actine sur des cellules cultivées en surface de la lamelle dans un premier temps, et à différentes profondeurs (25 et 50 microns) au sein de tissus artificiels dans un second temps.Du suivi 3D de particule unique a aussi été effectué sein de tissus biologiques vivants. Nous avons observé la diffusion libre de quantum dots à différentes profondeurs (jusqu’à 50 microns, limité par l’objectif utilisé) dans des tranches vivantes de cerveau.Nous avons appliqué la technique SELFI à la détection de récepteurs postsynaptiques NMDA. Cela nous a permis d'observer, sur des échantillons de neurones en culture primaire mais aussi au sein de tranches de cerveaux de rats, une différence d'organisation entre les deux sous-unités GluN2A et GluN2B de ce récepteur au glutamate.Enfin, nous avons démontré l'importance de suivre l'évolution de l'environnement des échantillons biologiques vivants lors des acquisitions permettant la détection de molécules individuelles. Grâce à l'utilisation additionnelle et simultanée de l'imagerie de phase quantitative, nous avons pu étudier la dynamique de la membrane cellulaire durant l’activation par un facteur de croissance. L'analyse corrélative entre les images de phase quantitative en lumière blanche et les détections de molécules fluorescentes uniques permet d'obtenir de nouvelles informations pertinentes sur l'échantillon étudié. / The work of this thesis was devoted to the development of a new technique SELFI (for self-interferences). This method unlocks the three-dimensional localization of individual fluorescent emitters. We have demonstrated that this allows 3D super-resolved imaging and 3D tracking of single molecules deep into dense and complex biological samples. The SELFI technique is based on the use of self-referenced interference to go back to the 3D location of a emitter in a single measurement. These interferences are generated using a diffraction grating placed at the exit of the fluorescence microscope: the fluorescence signal diffracts on the grating and, after a short propagation, the orders interfere on the detector. The formed interferences are digitally decoded to extract the 3D location of a fluorescent molecule within the sample. A single molecule can thus be localized with a precision of approximatively ten nanometers up to a depth of at least 50 µm in a thick living biological sample (for example a biological tissue).By combining the SELFI method with different super-resolution techniques (PALM, dSTORM and uPAINT), we show that this three-dimensional localization method grants the access to the hierarchy and organization of proteins in biological objects. By performing SELFI-PALM, we observed different proteins of the adhesion focal points (talin C-terminal and paxilin) and found the expected elevation differences, and those within living cell samples. These results confirm the resolution capability of the SELFI technique (about 25 nm) even for a small number of photons collected (about 500photons per molecule).We highlight the robustness of the SELFI technique by reconstructing 3D super-resolution images of dense structures at depth in complex tissue samples. By performing SELFI-dSTORM, we observed the actin network in cells grown on the surface of the coverslip at first, and at different depths (25 and 50 microns) within artificial tissues in a second time.3D single particle tracking has also been performed in living biological tissues. We observed the free diffusion of quantum dots at different depths (up to 50 microns) in living brain slices.We applied the SELFI technique to the detection of NMDA postsynaptic receptors. We observed, in primary culture of neurons but also within slices of rat brains, a difference in organization between the two subunits GluN2A and GluN2B of this glutamate receptor.Finally, we show the importance of following the evolution of the living biological sample environment during the acquisition of images leading to detections of single molecules. Thanks to the additional and simultaneous use of quantitative phase imaging, we were able to study cell membrane dynamics during the activation by a growth factor. The correlative analysis between white light quantitative phase images and single fluorescent molecule detections provides new relevant information on the sample under study.

Mitochondria are the power plant of most non-green eukaryotic cells. In order to understand mitochondrial functions and their regulation, knowledge of the spatiotemporal organization of their proteins is important. Mitochondrial membrane proteins can diffuse within membranes. They are involved in diverse functions e.g. protein import, cell respiration, metabolism, metabolite transport, fusion, fission or formation of the mitochondrial architecture. Furthermore, mitochondria compose of different subcompartments with different tasks. Especially, the inner mitochondrial membrane (IM), where the oxidative phosphorylation (OXPHOS) takes places, has a complex architecture with cristae extending into the matrix. The present work revealed the restricted localization of some mitochondrial proteins to specific membrane sections and linked it to their function or bioenergetic circumstances in the living cell. 
Single particle tracking (SPT) techniques like tracking and localization microscopy (TALM) allow to localize proteins with a precision below 20 nm. Additionally, tracking single proteins provides information about their mobility, dynamic and their spatiotemporal organization. TALM uses proteins, which were genetically tagged either with the HaloTag® (HaloTag) or the fSnapTag® (fSnapTag). These tags can be orthogonally and posttranslationally stained with specific and self-marking dyes. If the dyes are conjugated to the respective substrate of the tag. Single molecule labeling of mitochondrial proteins was performed substoichiometrically using membrane permeable rhodamine dyes, either tetramethylrhodamine (TMR) or silicon rhodamine (SiR). TALM allowed to localize proteins in different mitochondrial subcompartments. The gained trajectories and trajectory maps of mitochondrial proteins revealed their spatiotemporal organization. In the case of IM proteins like F1FO ATP synthase (Complex V - CV) a restricted diffusion in the CM, which is part of the continuous IM, was determined. The unimpeded diffusion of mitochondrial proteins in the outer mitochondrial membrane (OM) was compared with the mobility of IM proteins. The diffusion of mitochondrial IM proteins was restricted by the IM architecture and their diffusion coefficients were lower. Furthermore, significant differences of different mitochondrial IM proteins were compared, showing different localizations in the IM often coupled to their function, accompanied by different spatiotemporal organization and diffusion coefficients. Furthermore, a distinction was made between diffusion of proteins in the inner boundary membrane (IBM) and proteins that preferentially diffuse in the cristae membrane (CM). Evaluating trajectory maps, the different subcompartments in the IM were revealed by trajectories and the trajectory directionality, allowing the identification of mitochondrial proteins, which mark these subcompartments.
The morphology of mitochondria / mitochondrial networks and their bioenergetic parameters are linked to the metabolic states of the cell. In this work, the connection of the spatiotemporal protein organization of CV and the IM architecture was uncovered on the micro- and nanoscopic level and linked to the metabolic state of the cell. It was determined that the spatiotemporal organization of the CV was altered, when CV was inhibited. In addition, the bioenergetic influence of cells on the spatiotemporal behavior of CV and the reorganization of the IM architecture was investigated by TALM and compared with results of electron microscopy images. It was shown that starvation of cells led to a loss of cristae and thus to an increased mobility and spatiotemporal reorganization of CV. Taken together, the results presented in this work showed that a correctly functioning and active CV helps to maintain the IM architecture and both, the spatiotemporal organization of CV and the IM architecture were coupled to the metabolic state.. 
In order to investigate putative protein-protein interactions by colocalization and co-locomotion studies on single molecule level, dual color SPT is needed. Therefore, posttranslational and substoichimetric labeling as performed in TALM was tested for its potential of protein-protein interaction studies of mitochondrial membrane proteins. Here, a genetically double tagged translocase of the outer membrane subunit-20 (Tom20) (Tom20:HaloTag:fSnapTag) acted as a positive control. It turned out that substoichimetric, posttranslational labeling of mitochondrial proteins was not suitable for protein-protein interaction studies on mitochondrial proteins, because it was restricted by the low labeling degrees needed for TALM. However, dual-color TALM still allowed to study effects of proteins influencing the IM architecture and to study their influence on the spatiotemporal organization of CV. The co-transfection of Mic10, as the central protein of the mitochondrial inner membrane organizing system / mitochondrial contact site complex / mitochondrial organizing structure (MINOS / MICOS / MitOS (MINOS/MICOS)), altered the regular and aligned organization of the cristae. This was measured by a changed spatiotemporal organization of the CV, such as the loss of the perpendicular oriented of CV subunit-γ (CV-SUγ) cristae trajectories. In contrast to this, co-transfection of CV subunit-e (CV-SUe), important for dimerization of CV, increased the number of cristae trajectories. 
Mitochondria are three-dimensional (3D) cell organelles. Consequently, subcompartments like the IBM and CM are a 3D space in which CV is localized and diffuses. Thus, the diffusion of mitochondrial proteins is underestimated by two-dimensional SPT e.g. lateral confined diffusion can result from mitochondrial proteins diffusing along the z-axis of the microscope. In order to reveal the 3D spatiotemporal organization of CV, the potential of TALM to be extended to a 3D-SPT technique was investigated. Therto a cylindrical lens was installed in the emission path of a total internal reflection fluorescence (TIRF) microscope. This leads to an astigmatically distorted point spread function (PSF) of the fluorescent single molecule signals. This distortion allowed the reconstruction of single molecule localizations of CV to a superresolved image of the IM, in living cells. In addition, 3D-TALM enabled to display the 3D architecture of the IM by 3D trajectories of CV. 3D-TALM was able to detect whether CV diffuses in the IBM or in the CM, and extended the information about its mobility in the CM that it takes place in a disc-like manner. In this way it could be shown that CV is mobile within the cristae in all directions. Finally, 3D-TALM revealed an altered IM architecture caused by the metabolic state of the cell. As performed in two-dimensional TALM, the cells were kept under starving conditions. Here the now tubular IM architecture was revealed by 3D-TALM. The reversed metabolic state under improved respiratory conditions unexpectedly led to a more diverse IM architecture. These ultrastructural changes were also revealed by electron microscopy. Consequently, 3D-TALM enabled the study of IM architecture by tracking CV under different metabolic conditions, allowing an ultrastructural analysis of mitochondria in living cells. In addition, 3D TALM provided the spatiotemporal organization of CV under different metabolic conditions, so that the diffusion coefficients of CV could be related to changes in IM architecture caused by the metabolic condition.