To understand the function of macromolecules like proteins it helps to know the structure of the molecule. Coherent diffraction imaging is an emerging method that might be used to figure out the structures of macromolecules. In this method diffraction patterns of the macromolecule are recorded by shining light on the molecule from many unknown orientations and detecting the pattern of the diffracted photons. By assembling the diffraction patterns in a specific way and finding the phase of the photons that gave rise to the diffraction patterns, it is theoretically possible to obtain the electronstructure of the molecule and thus the molecular structure. The assembling of several thousand diffraction patterns representing unknown orientations of the molecule is hard to do by hand, but there are several methods that can be used. The EMC (Expand-Maximize-Compress) algorithm is one of those methods. It is an iterative algorithm that tries to create a model describing the Fourier Transform of the electron density of the molecule by maximizing each diffraction patterns fit to the model. This work examines how sensitive the EMC algorithm is to datasets with few diffraction patterns or a low intensity of the light being diffracted by the molecule, for the proteins phytochrome and lysozyme. The result of the work could be used to make sure enough data in collected in real experiments. Diffraction patterns simulated with the program Condor is used in this work, instead of diffraction patterns from real experiments.EMC finds the correct model when the data set contains about 1/3 fewer photons for the smaller more symmetrical molecule lysozyme than it does for phytochrome. This might be because the shapes in lysozymes diffraction patterns are larger than in phyochrome’s patterns. For phytochrome the EMC algorithm assembled the diffraction patterns correctly, with fewest photons for the light intensity 0.764 J/μm2 and 1250 diffraction patterns. For lysozyme it was with an intensity 1.910 J/μm2 and 1425 diffraction patterns. More investigation of the data is needed to understand what factors that affect the EMC algorithms ability to assemble the diffraction patterns correctly. / För att förstå makromolekylers kemiska eller biologiska funktion so underlättar det om man känner till molekylens kemiska struktur. Med den nya tekniken “coherent diffraction imaging” ska det vara möjligt att lista ut makromolekylers struktur. I denna teknik detekterar man diffraktionsmönster av molekylen genom att belysa molekylen med ljus från många olika okända vinklar and registrera mönstret som skapas av det diffrakterade ljuset. Genom att sätta ihop alla dessa diffraktionsmönster på rätt sätt och sen återskapa fasen för ljuset i diffraktionsmönstret så kan man generera molekylens elektronstruktur och från elektronstrukturen kan man få tag i molekylens struktur. Att sätta ihop tio tusentals diffraktionsmönster med okända vinklar på rätt sätt är väldigt svårt att göra, men det finns flera olika metoder som kan användas. EMC (Expand-Maximize-Compress) är en sådan metod. EMC är en iterativ algoritm som skapar en modell av (Fourier transformen av) molekylens elektronstruktur genom att maximera hur bra diffraktionsmönstren passar med modellen. Detta arbete utreder hur bra EMC algoritmen är på att hitta rätt (Fourier transform av) elektronstruktur när väldigt få diffraktionsmönster används eller när intensiteten på ljuset som sprids av molekylen är lågt. Programmet Condor används för att generera teoretiska diffraktionsmönster för de 2 molekylerna lysozym och fytokrom. EMC används sedan med olika uppsättningar av intensitet och antal diffraktionsmönster för att skapa en modell av elektronstrukturen. EMC behövde ca 1/3 färre antal fotoner i sin modell för att hittar den rätta modellen av elektronstrukturen för den lilla symmetriskt formade molekylen lysozym än för fytokrom. Att det är lättare för EMC algoritmen att hitta den korrekta modellen för lysozym än fytokrom kan bero på att lysozyms diffraktionsmönster har större former/features eller på lysozyms storlek och form. EMC körningen som behövde minst antal fotoner för att hitta den korrekta elektronstrukturen för fytokrom hade intensiteten 0,764 J/μm2 på det inkommande ljuset och behövde 1250 diffraktionsmönster. För lysozym behövdes det 1,910 J/μm2 och 1425 diffraktionsmönster för att EMC algoritmen skulle hitta rätt modell av elektronstrukturen.

We are developing a tabletop extreme-ultraviolet source using high harmonic generation at Brigham Young University. The thesis goes over the theory of high harmonic generation using the three-step model. This tabletop source was designed for probing magnetic domains of iron nanoparticles. We present optimization of the 42 eV and 52 eV harmonics through phase matching. Phase matching consists of tuning the intensity of the IR beam and pressure of the gas medium. The target gas medium used for this thesis is argon. The 42 eV harmonic was optimized to 8.2 billion photons per second. This was used with a 1500 mm focal-length lens, 15 mm medium length, laser power of 1.53 Watts, and a pressure of 12 Torr of argon gas. The 52 eV harmonic was optimized to 1.5 billion photons per second with a 1500 mm focal-length lens, 20 mm medium length, laser power of 3.29 W, and 14.9 Torr of argon gas. There are two designs for selection of harmonics: 1) a tunable design consisting of a toroidal mirror and flat diffraction grating and 2) a set of normal-incidence extreme-ultraviolet mirrors designed for 42 or 52 eV photons. Magnetic imaging uses x-ray magnetic circular dichroism to obtain magnetic contrast and use it to visualize magnetic nanosystems. Therefore, the high harmonic source also needs to generate circularly polarized light. Generating circularly polarized high harmonics is possible with a bichromatic beam. This is achieved using an apparatus called the MAZEL-TOV designed by Oren Cohen’s group at Technion University in Israel. The MAZEL-TOV consists of a BBO crystal for second harmonic generation, a pair of pulse delay compensation plates, and a quarter-wave plate. These optics are placed inline with the laser beam. We have successfully optimized the circularly polarized extreme-ultraviolet harmonics with the MAZEL-TOV. A spectrometer was made to calibrate the harmonics in the MAZEL-TOV spectrum. The tabletop source was then used to demonstrated coherent diffraction imaging of two pinholes.

L'objectif de ce mémoire est dedévelopper de nouvelles méthodes d'imageriesans lentille en simple tir 2D et 3D avec dessources harmoniques XUV. Un intérêt particulierest porté aux techniques d'imageries permettantl'imagerie des objets biologiques et de phase.Dans un premier temps, on introduit la théorie del'imagerie dans lentille et on détaille lesméthodes utilisées au cours de cette thèse pourreconstruire le champ diffracté par l'objet quel'on souhaite imager. Les techniques d'imageriessont séparées en deux catégories : itératifs etholographiques. On discute des conditionsexpérimentales nécessaires à la reconstruction del'image de l'objet et on compare les avantagesrespectifs des deux types de méthodes. Puis, ondétaille les aspects expérimentaux du faisceauXUV obtenu par HHG et on couvre brièvementla théorie associée à ce processus. La sectionsuivante traite des paramètres et des techniquesde traitement des données influant sur la qualitéde l'image reconstruite en imagerie sans lentille.On montre comment améliorer lesreconstructions HERALDO dans un régime defaible flux de photons. On présente ensuite lesrésultats d'une technique de caractérisationcomplète de la cohérence spatiale d’un faisceauXUV en simple tir. Cette dernière est unparamètre critique de l'imagerie sans lentille. Al'aide d'un tableau non redondant de référencesponctuelles, on mesure la cohérence spatialepour chaque distance entre les références, sansaucune mesure du profil spatial du faisceau. Onmontre que la distribution de la cohérence estgaussienne et que son diamètre dépend desconditions de génération du faisceauharmonique. On étudie aussi quantitativementcomment l'accumulation de plusieurs tirs dediffraction diminue la cohérence apparente dufaisceau. Une expérience d'imagerie d'objets dephase avec une source harmonique pouvant êtreappliquée à des objets biologiques est ensuiteprésentée.A notre connaissance c'est la premièrereconstruction par méthode CDI d'objets dephase avec une source harmonique. La suite dumanuscrit présente les résultats de deuxexpériences visant à réaliser de l'imagerie 3D àl'échelle nanométrique avec une sourceharmonique. Tout d’abord, on présente unetechnique d'imagerie 3D simple tir. C'est lapremière expérience permettant unereconstruction 3D à partir d'une seuleacquisition, avec une résolution spatialenanométrique et une résolution temporellefemtoseconde, sans utiliser de connaissances apriori sur l'objet étudié. Cette technique possèdeun vaste spectre d'application, particulièrementpour l'étude structurelle d'échantillonsbiologiques sensibles aux dégâts d'irradiation.De plus, cette technique peut être facilementapplicable à des FELs et des synchrontrons pourobtenir de meilleures résolutions. La deuxièmeexpérience d'imagerie 3D est une preuve deconcept validant la faisabilité de lacryptomographie avec une source harmonique.Pour reconstruire le volume 3D de l'échantillon,la cryptotomographie utilise des figures dediffraction qui sont acquises pour desorientations de l'échantillon inconnues. Lerégime de faible flux dans lequel on se place nouspermet de simuler les paramètres d'une sourceharmonique fonctionnant dans la fenêtre de l'eau.On conclut que, le niveau du signal de diffractionest suffisant pour pouvoir identifier l'orientationde l'objet à partir des figures de diffractionenregistrées, dans des conditions expérimentalesoptimisées. Ainsi, avec suffisamment de figuresde diffraction enregistrées et assez d'orientationsde l'objet, on peut reconstruire le volume 3D del'objet. Ces résultats impliquent qu'uneexpérience de cryptotomographie d'objetsbiologiques avec une source harmoniquefonctionnant dans la fenêtre de l'eau seraitréalisable. / The aim of this dissertation is todevelop new lensless single shot imagingtechnique in 2D and 3D with XUV harmonicsources which can be applied to study biologicalobjects and phase objects. Firstly, we introducethe theory underlying lensless imagingtechniques and we describe the methods usedduring this thesis to reconstruct the light fielddiffracted by the studied object. The imagingtechniques are split in two categories: iterativeand holographic. The iterative methodsreconstruct the phase of the diffracted wavefront using constraints in the Fourier space andthe reel space. With the holographic techniques,the phase is encoded directly in the interferencefringes between the reference and the objectwithin the diffraction pattern. We discuss theexperimental parameters required to achieve animage reconstruction and we compare therespective advantages of the two types ofmethod. Then, we describe the experimentalparameters of the XUV beam produced by highharmonic generation (HHG) and we brieflyexplain the theory of the HHG. The next sectiondiscusses the parameters the quality of thereconstructed image. We show how to improvethe resolution and the signal to noise ratio usingthe HERALDO technique in the low fluxregime.We then show the result of a new technique forthe single shot characterization of the spatialcoherence of XUV beams. Indeed, the spatialcoherence is a critical parameter for coherentdiffractive imaging techniques. Using a NRA ofreference holes, we measure the spatialcoherence for each distance between each pairof holes, without the knowledge of the intensitydistribution on the sample. We show that thespatial coherence has a gaussian distribution andthat its diameter varies according to thegeneration parameters of the harmonic beam.We also study quantitatively the effect of multishotsaccumulation of the diffraction pattern onthe apparent coherence of the beam. We alsoshow the result of phase object imaging usingcoherent diffractive imaging with a harmonicsource. To our knowledge, this if the first timesuch result has been achieved. The rest of thedissertation present new lensless imaging 3Dtechniques using harmonic sources. The first ofthe last two experiments shown is a lenslesssingle shot stereo 3D technique. It is the first oneallowing a 3D reconstruction from a singleacquisition, with a nanometer spatial resolutionand a femtosecond temporal resolution, withoutusing \textit{a priori} knowledge of the samplestudied. This method has a vast spectrum ofapplication and is particularly interesting for thestructural study of biological sample sensitive toradiation damage and for the study of nonreversibledynamical phenomena in 3D.Furthermore, this can easily be implemented inFELs and synchrotrons to reach even betterspatial resolution. The second 3D experimentshown in this thesis is a proof of concept ofcryptotomography using a high harmonic sourcein a low flux regime. To reconstruct the 3Dvolume of the sample, cryptotomographie usesdiffraction pattern acquired for unknown sampleorientations and therefore non-classified. Thelow flux regime used here simulate the flux of aharmonic source generated in the water window.We conclude from this experiment that, with theproper experimental conditions, the diffractionsignal is sufficient to allow the classification byorientation of the diffraction patterns. Withenough diffraction pattern and angles of thesample recorded, we can achieve a 3Dreconstruction of the sample. This result impliesthat the cryptotomography of biological objectsusing a water window harmonic source ispossible.

Koherent Diffraktionsavbildning med en intensiv röntgenpuls från en Frielektronlaser har möjliggjort strukturbestämning av isolerade nanopartiklar som inte går att studera med hjälp av konventionella metoder, så som elektronmikroskopi. En mycket kort pulslängd tillsammans med spridningssignalens beroende av objektets elektroniska struktur medför också möjligheten att studera inducerad ultrasnabb dynamik med denna teknik. I detta projekt studerades joniseringspåverkan av Xe hos Xe-Ar core-shell-nanokluster. Enligt teorin har neutral Xe lägre spridningstvärsnitt under dess 3d-resonans än det motsvarande för fotonenergier över 3d-resonansen. Därför var en hög kontrast i klustren förväntad vid energier över dess 3d-resonans. I stället observerades mörkare regioner liknande hål i rekonstruktioner från de experimentella resultaten vid energier över 3d-resonansen hos Xe. En möjlig förklaring var jonisering av neutral Xe. För att undersöka detta skapades 3D modeller av Xe-Ar nanokluster för att simulera den interaktionen mellan intensiva röntgenpulser och nanokluster. Diffraktionsmönstren som genererades med hjälp av 3D-modellerna användes sedan för att utföra Iterativ fasrekonstruktion och rekonstruera partikeldensiteten. Brytningsindex av neutral Xe och de första tio jontillstånden hos Xe beräknades med hjälp av en modell konstruerad i detta projekt, kallad för step-model. Följaktligen introducerades samtliga jontillstånden hos Xe från 0 till 10 in i 3D modeller av Xe-Ar nanoklustren med brytningsindexen av jontillstånden uppskattade med hjälp av Kramers-Kronig-relationerna. Här antogs det att samtidigt som resonansen för varje Xe-jon förflyttas visar 𝛽 (det vill säga den imaginära komponenten i det komplexa brytningsindexet) som en funktion av fotonenergin, ett icke-monotoniskt beteende med en förändring i fotonenergin. Simuleringsresultaten erhållna med hjälp av Kramers-Kronig-relationerna visade en avtagande trend för 𝛽 i Xe-joner med en laddning> 4+ till skillnad från en ökning i 𝛽 för joner med en laddning <4+ relativt dess motsvarande för neutral Xe. Denna metod ansågs tillräcklig för att användas som en första approximation. Dessa resultat visade att ju mer Xe joniseras (och därför minskar 𝛽) desto mer transparenta blir Xe-jonerna under en laserpuls och därför ser de mörkare ut jämfört med Ar som har sin resonans långt ifrån fotonenergierna relevanta för detta projekt (660–760 eV). Vidare simulerades temporära förändringar i Xe-jonpopulationer för att bekräfta de erhållna simuleringsresultaten via step-model. En massiv energideposition då den intensiva röntgenpulsen träffar Xe-kärnorna initierar en serie av joniseringsmekanismer under de första få femtosekunderna av pulsen. Simuleringar för de jonpopulationer som uppstår och försvinner under förloppet av en 100 femtosekunder-lång röntgenpuls visade att jontillstånd mellan 1+ och 10+ är redan förbrukade efter några få femtosekunder vid 1016 W/cm2. Vid slutet av pulsen observerades endast högt laddade Xe-joner (upp till 35+). Den slutsats som drogs var därför att mörkare regioner som liknade hål och observerades i rekonstruktioner från experimentella data var en konsekvens av en förflyttning av resonansen hos de högt laddade Xe-joner (>4+) relativt dess motsvarande i en neutral Xe så att deras spridning minskar. / Coherent Diffraction Imaging with intense x-ray pulses from X-ray Free-Electron Lasers has enabled structure determination of isolated nanoparticles, that cannot be studied with conventional methods, such as electron microscopy. The very short pulse durations and the intrinsic dependence of the scattering signal on the electronic structure of the scattering object also allow studying ultrafast light-induced dynamics with this technique. In this project, the ionization impact of Xe on Xe-Ar core-shell nanoclusters was studied. Theory predicts that neutral Xe has a lower scattering cross-section below its 3d resonance than that at photon energies above its 3d resonance. Therefore, a high contrast in clusters above the neutral Xe’s 3d resonance is expected. However, in the experimental data, unusual dark features resembling holes were observed at energies above Xe’s 3d resonance. As possible explanation, ionization of neutral Xe was suggested. To investigate this, 3D models of Xe-Ar nanoclusters were created to simulate the interaction of intense x-ray pulses and nanoclusters. The diffraction patterns generated by these 3D models were used to perform Iterative Phase Retrieval to reconstruct the particle densities. The refractive indices of neutral Xe and Xe’s first ten ionic states were computed using a model designed in this project, called the step-model. Hence, each and every ionic state of Xe from 0 to 10 were introduced into the 3D models of the Xe-Ar nanoclusters with refractive indices of the ionic states estimated based on the Kramers-Kronig relations. Here, it was assumed that as the resonance is shifting for every ionic state of Xe, 𝛽 (i.e the imaginary component of the complex refractive index) as a function of photon energy shows a nonmonotonic behavior as the photon energy is varied. The simulation results by Kramers-Kronig relations showed a decrease in 𝛽 for ionic states > 4+ in contrast to an increase in 𝛽 for ions with charges < 4+ relative to that of neutral Xe. This approach was sufficient to be used as a first approximation. The results showed that Xe ions become more transparent to the laser pulse as their charge increases (and 𝛽 thereby decreases) and therefore they appear darker than Ar, which has its resonance far away from photon energies relevant for this project (660–760 eV). Furthermore, temporal changes in ionic populations of Xe were simulated to confirm the simulation results obtained by the step-model. The massive energy deposition upon interaction with the intense laser pulse launches a series of ionization events in the Xe cores during the first few fs of the x-ray pulse. The simulation of ionic populations emerging and depleting during the 100-fs-long 1016 W/cm2 x-ray pulse showed that ionic states 1+ to 10+ are depleted already after a few fs. By the end of the pulse, only highly charged (up to 35+) Xe ions are observed. Therefore, it was concluded that the dark features resembling holes in reconstructions from the experimental data were a consequence of a shift in the resonance of highly charged Xe ions (>4+) relative to that of neutral Xe so that their scattering decreases.

El conocimiento de las características interfaciales es de suma importancia para poder desarrollar materiales que sean capaces de dar lugar a reacciones electrocatalíticas eficientes. Por esta razón, en esta tesis se muestran diferentes estudios interfaciales sobre superficies monocristalinas de platino y cobre en diferentes electrolitos. Además se estudian las características de la interfase electrodoldisolución con superficies de platino modificadas con adátomos de hierro, cobalto y níquel. Para ello, se han empleado las técnicas de voltametría cíclica, espectroscopía infrarroja con transformada de Fourier, desplazamiento de carga con CO y salto de temperatura inducido por láser. Los resultados muestran cómo varía el campo eléctrico interfacial disminuye al aumentar el recubrimiento de hierro y níquel en la superficie de platino. Este efecto tiene un gran impacto en la reacción de evolución de hidrógeno, ya que la mejora electrocatalítica de esta reacción está relacionada con la energía de reorganización de las moléculas de agua, la cual, depende de la fortaleza del campo eléctrico interfacial. Los estudios realizados en medio alcalino para las diferentes superficies de cobre y platino sin modificar muestran una correlación entre el potencial de máxima entropía y las funciones de trabajo para cada una de las diferentes orientaciones atómicas superficiales. Por otro lado, debido a la aplicabilidad de las nanopartículas en los sistemas reales de conversión de energía, se realizaron experimentos de sincrotrón empleando la técnica de Bragg coherent difraction imaging con el objetivo de estudiar el deterioro de las nanopartículas en condiciones operando.