Дисертації з теми "European X-Ray Free Electron Laser"

Recenti sviluppi nella progettazione di impianti di luce di sincrotrone di quarta generazione riguardano la produzione di fasci di luce nella banda dei raggi X con elevate caratteristiche in termini di brillanza, coerenza e impulsi estremamente brevi ( femtosecondo ) . I principali schemi per la produzione della radiazione XFEL riguardano l’impiego di ondulatori con differenti modalità di seeding. L’utilizzo dei fasci di radiazione XFEL nelle linee di luce per applicazioni di imaging, spettroscopia e diffrazione, ha determinato un costante sforzo sia nello sviluppo di dispositivi ottici in grado di selezionare e focalizzare il fascio su dimensioni nanometriche, che nella sperimentazione di tecniche “lensless” in grado di superare i limiti imposti dall’utilizzo di tali dispositivi . I risultati ottenuti nella produzione dei fasci hanno consentito nuove possibilità di indagine nella struttura dei materiali su distanze atomiche nella definizione, senza precedenti di dettagli su scale temporali del femtosecondo, permettendo lo studio, non solo di strutture atomiche in condizioni di equilibrio stabile quanto di stati della materia velocemente dinamici e di non equilibrio. CXDI e Spettroscopia Strutturale Ultraveloce risolte in tempo sono alcune delle tecniche in cui l’utilizzo della radiazione XFEL apre nuove possibilità di indagine agli stati transienti della materia permettendo la ricostruzione della dinamica di processi chimico –fisici su intervalli temporali finora inaccessibili .

The ability to diagnose the structure of a material at extreme conditions of high-pressure and high-temperature is fundamental to understanding its behaviour, especially since it was found that materials will adopt complex crystal structures at pressures in the Terapascal regime (1TPa). Static compression, using the diamond anvil cell coupled with synchrotron radiation has to date been the primary method for structural studies of materials at high pressure. However, dynamic compression is the only method capable of reaching pressures comparable to the conditions found in the interior of newly discovered exo-planets and gas giants where such exotic high-pressure behaviour is predicted to be commonplace among materials. While generating extreme conditions using shock compression has become a mature science, it has proved a considerable experimental challenge to directly observe and study such phase transformations that have been observed using static studies due to the lack of sufficiently bright X-ray sources. However, the commissioning of new 4th generation light sources known as free electron lasers now provide stable, ultrafast pulses of X-rays of unprecedented brightness allowing in situ structural studies of shock compressed materials and their phase transformation kinetics in unprecedented detail. Bismuth, with its highly complex phase diagram at modest pressures and temperatures, has been one of the most studied systems using both static and dynamic compression. Despite this, there has been no structural characterisation of the phases observed on shock compression and it is therefore the ideal candidate for the first structural studies using X-ray radiation from a free electron laser. Here, bismuth was shock compressed with an optical laser and probed in situ with X-ray radiation from a free electron laser. The evolution of the crystal structure (or lack there of) during compression and shock release are documented by taking snapshots of successive experiments, delayed in time. The melting of Bi on release from Bi-V was studied, with precise time scans showing the pressure releasing from high-pressure Bi-V phase until the melt curve is reached off-Hugoniot. Remarkable agreement with the equilibrium melt curve is found and the promise of this technique has for future off-Hugoniot melt curve studies at extreme conditions is discussed. In addition, shock melting studies of Bi were performed. The high-pressure Bi - V phase is observed to melt along the Hugoniot where melting is unambiguously identified with the emergence of a broad liquid-scattering signature. These measurements definitively pin down where the Hugoniot intersects the melt curve - a source of some disagreement in recent years. Evidence is also presented for a change in the local structure of the liquid on shock release. The impact of these results are discussed. Finally, a sequence of solid-solid phase transformations is observed on shock compression as well as shock release and is detected by distinct changes in the obtained diffraction patterns. The well established sequence of solid-solid phase transformations observed in previous static studies is not observed in our experiments. Rather, Bi is found to exist in some metastable structures instead of forming equilibrium phases. The implications these results have for observing reconstructive phase transformations in other materials on shock timescales are discussed.

Hard x-ray free-electron lasers are novel sources of coherent x-rays with unprecedented brightness and very short pulses. The radiation from these sources enables a wide range of new experiments that were not possible with previous x-ray sources. Many of these experiments require the possibility to focus the intense x-ray beam onto small samples. This Thesis investigates the possibility to use diffractive zone plate optics to focus the radiation from hard x-ray free-electron lasers. The challenge for any optical element at free-electron laser sources is that the intensity in a single short pulses is high enough to potentially damage the optics. This is especially troublesome for zone plates, which are typically made of high Z elements that absorb a large part of the incident radiation. The first part of the Thesis is dedicated to simulations, where the temperature behavior of zone plates exposed to hard x-ray free-electron laser radiation is investigated. It is found that the temperature increase in a single pulse is several hundred Kelvin but still below the melting point of classical zone plate materials, such as gold, tungsten, and iridium. Even though the temperature increases are not high enough to melt a zone plate it is possible that stresses and strains caused by thermal expansion can damage the zone plate. This is first investigated in an experiment where tungsten gratings on diamond substrates are heated to high temperatures by a pulsed visible laser. It is found that the gratings are not damaged by the expected temperature fluctuations at free-electron lasers. Finally, a set of tungsten zone plates are tested at the Linac Coherent Light Source where they are exposed to a large number of pulses at varying fluence levels in a prefocused beam. Damage is only observed at fluence levels above those typically found in an unfocused x-ray free-electron laser beam. At higher fluences an alternative is to use a diamond zone plate, which has significantly less absorption and should be able to survive much higher fluence. Damage in diamond structures is investigated during the same experiment, but due to a remaining tungsten etch mask on top of the diamond the results are difficult to interpret. Additionally, we also demonstrate how the classical Ronchi test can be used to measure aberrations in focusing optics at an x-ray free-electron laser in a single pulse. The main result of this Thesis is that tungsten zone plates on diamond substrates can be used at hard x-ray free-electron laser sources.

QC 20130514

L’étude des processus de fusion partielle dans les intérieurs planétaires revêt une importance capitale dans la compréhension de l’évolution d’une planète. Ceci est d’autant plus important dans le contexte du nombre croissant de découvertes d’exoplanètes aux histoires potentiellement très variées. Un des outils expérimentaux majeurs pour l’étude des intérieurs planétaires est la cellule à enclume de diamant (DAC), permettant d’amener des échantillons de tailles micrométriques à des conditions de pression de l’ordre de dizaines à centaines de GPa et des températures de l’ordre de plusieurs milliers de Kelvins. L’étude des propriétés physiques de ces échantillons, tel que leur diagramme de phase, peuvent être analysés grâce à la diffraction des rayons X (XRD), des rayonnements générés en synchrotron. Ces expériences peuvent cependant souffrir de la technique de chauffage laser continu qui génère de forts gradients de température au sein des échantillons et peuvent mener à de la migration chimique au sein de la zone chauffée. L’analyse in situ des échantillons se fait alors sur une composition différente de la composition initiale, qui ne correspond pas forcément à celle envisagée. Cette thèse propose une nouvelle approche expérimentale, consistant à effectuer un chauffage laser court de 250 ns afin de limiter la migration chimique. Ce montage expérimental a été testé sur des alliages de Fer du système ternaire Fe-Si-O, les résultats pouvant par exemple s’appliquer dans le contexte de cristallisation du noyau externe liquide de la Terre. Nos expériences ont été menées au European X-ray Free Electron Laser (EuXFEL), une installation scientifique produisant une source pulsée de rayon X (série de pulses d’une durée individuelle de 30 fs constituant un train à une fréquence de 4.5 MHz (un pulse toutes les 221.5 ns) à forte brillance. Combiné au chauffage laser d’une fraction de µs, les expériences au EuXFEL permettent d’obtenir une résolution temporelle de l’évolution de l’échantillon lors de son refroidissement, permettant notamment d’observer la séquence de cristallisation. Une mesure de la température de surface par pyrométrie optique avec caméra streak (SOP) est effectuée simultanément aux autres mesures, avec une résolution temporelle inférieure à la µs. Les mesures effectuées au EuXFEL ne permettent pas de résoudre entièrement l’étendue des gradients de pression et de température ni d’appréhender tous phénomènes se produisant lors des expériences. Pour compenser ces lacunes, un modèle numérique basé sur l’analyse d’éléments finis (FEM) reproduisant les expériences a été développé. Ce modèle utilise les propriétés des matériaux aux conditions de pression et température sondées, notamment les équations d’état les dépendances en pression et température des propriétés de matériaux (ρ, K, G, κ, Cp, chaleur latente…). Pour reproduire les expériences, les valeurs du modèle sont ajustées en minimisant l’erreur moyenne par rapport aux mesures SOP. La FEM fournit des cartographies de température et de pression des échantillons. En combinant les données de XRD et les températures extraites du modèle, il est possible de remonter aux conditions précises de température et de pression des échantillons lors de leurs changements de phase. Cela permet aussi d’évaluer le degré d’homogénéité en température et en pression (évaluation de la pression thermique) au sein de la zone sondée par les rayons X. Les modèles permettent également l’étude des déformations en DAC et de calculer la répartition des contraintes qui peut être un facteur important dans certaines conditions. Enfin, des expériences utilisant les rayons X pour chauffer l’échantillon sont également reproduites avec les modèles et des pistes sont explorées pour remonter aux propriétés des matériaux tels que la conductivité thermique
The study of partial melting processes in planetary interiors is of prime importance to understand planetary evolution mechanisms. This is even more true when considering the increasing number of exoplanetary discoveries which likely acknowledged a high variety of histories. A main experimental tool for to study deep planetary interior conditions is the diamond anvil cell (DAC), allowing to raise pressures on micron-sized samples up to hundreds of GPa and at temperatures up to thousands of Kelvins. The study of sample’s physical properties such as their phase change pressures and temperatures (P,T) can be analyzed in X-ray generating synchrotron facilities, using the X-ray diffraction (XRD) properties of minerals. Those experiments may yet suffer from the continuous laser heating technique which generates strong temperature gradients within the samples and may lead to chemical migration in the heated zone. The sample in-situ analysis is then achieved on a composition diverging from the initial one which does not necessarily correspond to what was intended to be measured. This thesis suggests a new experimental approach consisting in using a short and intense (250 ns) laser heating pulse in order to limit that chemical migration. This experimental setup was tested on iron alloys of the Fe-Si-O ternary system, results on such compositions being for instance applicable on in the context of Earth’s liquid outer core crystallization. Our experiments are run at the European X-ray Free Electron Laser (EuXFEL) facility which generates a high brilliance pulsed X-ray source (series of 30 fs pulses at frequencies up to 4.5 MHz (one pulse each 221.5 ns). Combined to the µs fraction laser heating, the EuXFEL experiments allow to obtain a temporal resolution of the sample evolution during its cooling, allowing to observe crystallization sequences. A streak optical pyrometry (SOP) surface temperature measurement is achieved simultaneously to the XRD with time resolution below the µs-scale. However, measurements achieved at the EuXFEL do not allow to fully resolve the extent of the phenomena occurring during experiments. To compensate this lack of information, we developed a numerical model based on the finite element method (FEM) to reproduce the achieved experiments. This model uses the material properties (such as ρ, K, G, κ, Cp and latent heat) at the experimental pressure and temperature conditions including their P,T dependencies when available. Equations of state (EoS) related variations where included in the model for the related parameters. To reproduce the experiments, the model values are adjusted by minimizing the mean error compared to the SOP data. Combining experimental XRD with best-fitting model temperatures, it is possible to get back to the P, T conditions during the samples phase change. In addition, the FEM furnishes temperature and pressure maps highlighting e.g. sample internal gradients and allowing to evaluate the degree of homogeneity of P and T, both assumed to be critical parameter in chemical migration. Models allow as well to calculate the constraint distribution in the DAC assemblage which can be an important factor in certain conditions. Finally, experiments directly using X-rays to heat the sample were achieved, analyzed and reproduced by modelling. Using the models, the possibility of deducing material properties such as thermal conductivity from best fits to experimental data are explored

This thesis describes various design options for beam spreaders to allow the inclusion of multiple beam lines as an integral part of X-ray Free Electron Laser (FEL) facilities. The accelerator configuration driving an X-ray FEL follows a linear geometry so as to maintain the ultra-bright properties of the electron beam generated at the injector. Bending the beam is typically restricted only to the bunch compressor chicane in order to avoid an increase in transverse emittance due to the emission of coherent synchrotron radiation. Unlike storage ring based light sources, X-ray FELs serve either one experiment at a time or a number of experiments (quasi-simultaneously) by splitting the radiation from a single FEL line; the radiation pulse repetition rate is set by the injector and the technology used for acceleration. Multiple beam lines provide flexibility in experiments and provide access for a greater number of users. However, in providing multiple beam lines, bending the electron beam is unavoidable and its high quality (i.e. low emittance, low energy spread and high peak current) must be ensured by very careful design of the beam spreader. Two main aspects of the beam spreader design (namely, the options for switching and the lattice design) have been studied and are presented here in detail. Two lattice design concepts, one based on a Triple Bend Achromat magnetic lattice and the other based on a Double Bend Achromat magnetic lattice, are discussed. The relative merits, advantages and disadvantages of these design options are detailed, including mitigation of the effects from coherent synchrotron radiation which include increases in both the beam emittance and energy spread. Experimental studies related to the Triple Bend Achromat arc on the ALICE facility are used to recommend beam diagnostics and instrumentation in different spreader design concepts. The results presented in this thesis will be central to the design of an optimised beam spreader for any future UK X-FEL facility.

X-ray crystallography has been around for 100 years and remains the preferred technique for solving molecular structures today. However, its reliance on the production of sufficiently large crystals is limiting, considering that crystallization cannot be achieved for a vast range of biomolecules. A promising way of circumventing this problem is the method of serial femtosecond imaging of single-molecules or nanocrystals utilizing an X-ray free-electron laser. In such an approach, X-ray pulses brief enough to outrun radiation damage and intense enough to provide usable diffraction signals are employed. This way accurate snapshots can be collected one at a time, despite the sample molecule exploding immediately following the pulse due to extreme ionization. But as opposed to in conventional crystallography, the spatial orientation of the molecule at the time of X-ray exposure is generally unknown. Consequentially, assembling the snapshots to form a three-dimensional representation of the structure of interest is cumbersome, and normally tackled using algorithms to analyze the diffraction patterns. Here we explore the idea that the explosion data can provide useful insights regarding the orientation of ubiquitin, a eukaryotic regulatory protein. Through two series of molecular dynamics simulations totaling 588 unique explosions, we found that a majority of the carbon atoms prevalent in ubiquitin are directionally limited in their respective escape paths. As such we conclude it to be theoretically possible to orient a sample with known structure based on its explosion pattern. Working with an unknown sample, we suggest these discoveries could be applicable in tandem with X-ray diffraction data to optimize image assembly.

The arrival of 4th generation light-sources has opened up new regimes in X-ray-matter interactions. A billion times spectrally brighter than the preceding X-ray sources, free-electron-lasers (FELs) can deposit large amounts of energy into a system in less than 100 fs. Since the absorption of x-rays is reasonably well understood and the pulse length is so short, the plasma conditions created are well characterized. The work presented in this thesis relates to a series of experiments where solid aluminium foils were heated with the focussed FEL radiation. The way that the opacity of the FEL heated foil would affect the observed emission spectrum is investigated. The extent to which the opacity influences the emission spectra is found to have intensity and photon energy dependencies. The transmission of the x-ray pulse used to generate a solid-density aluminium plasma is studied in both simulation work using the collisional-radiative code SCFLY and experiment. The phenomenon of saturable absorption is seen to occur, caused by the system being ionized to such an extent that none of the ions present can absorb the x-ray photons through K-shell photoionization. The use of the FEL beam in a split and delay scheme was also explored. Simulations of the time dependent changes in transmission and what may be observed were performed.

The advances achieved using X-ray Free Electron Lasers such as the Linac Coherent Light Source (LCLS), have revolutionised the routine production of uniform solid-density plasmas. Pulses of X-rays above 1 keV and with durations shorter than 100 fs attaining intensities on target of around 10¹⁷ Wcm^-2 are now routinely created. Through simple single-photon photoionization events with atoms in ambient solid conditions, it is possible to create uniform samples that are simultaneously hot, dense, and highly ionized which may be easily modelled. This thesis describes measurements of the spectrally-resolved X-rays emitted from solid-density magnesium targets of varying sub-μm thicknesses isochorically heated by an X-ray laser. The data exhibit a thickness-independent source function, allowing the extraction of a measure of the opacity to K-shell X-rays within well-defined regimes of electron density and temperature, extremely close to Local Thermodynamic Equilibrium conditions by fitting to the simple 1D slab solution of the equation of radiative transfer. The deduced opacities at the peak of the K-α transitions of the ions are consistent with those predicted by detailed atomic-kinetics calculations. The extracted opacities transpire to be robust to a plethora of variations in X-ray drive conditions, including the shape, pulse-length, and energy content. Furthermore the approximations in using the 1D slab solution are examined in detail and found to be good. A full three-dimensional model of the plasma is advanced which includes attenuation, line-of-sight effects, full longitudinal and transverse gradients, and photon time-of-flight effects. The results from this model are found to also agree with the simpler 1D slab solution. This novel method of elucidating opacities may complement other methods based on absorption and could be important for further benchmarking of opacities in solar-interior relevant conditions.

This thesis presents experimental studies of water and ice at near-atmospheric pressures using intense x-rays only accessible at synchrotrons and free-electron lasers. In particular, it focuses on the deeply supercooled, metastable state and its implications on ice nucleation. The local structure of the liquid phase was studied by x-ray scattering over a wide temperature range extending from 339 K down to 227 K. In order to be able to study the deeply supercooled liquid, micron-sized water droplets were evaporatively cooled in vacuum and probed by ultrashort x-ray pulses. This is to date the lowest temperature at which measurements of the structure have been performed on bulk liquid water cooled from room temperature. Upon deep supercooling, the structure evolved toward that of a low-density liquid with local tetrahedral coordination. At ~230 K, where the low-density liquid structure started to dominate, the number of droplets containing ice nuclei increased rapidly. The estimated nucleation rate suggests that there is a “fragile-to-strong” transition in the dynamics of the liquid below 230 K, and its implications on water structure are discussed. Similarly, the electronic structure of deeply supercooled water was studied by x-ray emission spectroscopy down to 222 K, but the spectral changes expected from the structural transformation remained absent and explanations are discussed. At high fluence, the non-linear dependence of the x-ray emission yield indicated that there were high valence hole densities created during the x-ray pulse length due to Auger cascades, resulting in reabsorption of the x-ray emission. Finally, the hydrogen-bonded network in water was studied by x-ray absorption spectroscopy and compared to various ices. It was found that the pre-edge absorption cross-section, which is associated with distorted hydrogen bonds, could be minimized for crystalline ice grown on a hydrophobic BaF2(111) surface with low concentration of nucleation centers.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 3: Manuscript. Paper 4: Manuscript. Paper 5: Manuscript. Paper 6: Manuscript.

The advent of the 4th generation X-ray sources paves the way for a new phase of experimental investigation of Hot-Dense plasmas. At the Linac Coherent Light Source (LCLS), pulses of keV X-rays, shorter than 100 fs, and with intensities up to 10¹⁸ W·cm^-2, are routinely produced, allowing for the production of uniform samples of solid-density plasmas. The simple single-photon X-ray absorption mechanism can be easily modelled, so that the plasma conditions can be accurately retrieved, without relying on diagnostic techniques that are not benchmarked in this high density regime. The work presented here describes the results of the first experiment where the LCLS interacts with a solid Al target, isochorically heating it at temperatures up to 190 eV. The system is described by the SCFLY non-LTE model, where the density and temperature are computed self consistently, as a consequence of the detailed atomic processes, rather than imposed by the user. The approximations affecting the simulations are discussed in detail. The code is first validated, by modelling the charge state distribution measured in a previous experiment (L. Young et. al), where the LCLS interacts with a Ne gas, a simplified (collisionless) problem. Then it is used to model the K-alpha spectroscopic data obtained for Al. The plasma evolution, explained by SCFLY simulations, is found to be primarily determined by collisions, whose visible effects on the experimental spectra are discussed. By varying the wavelength of the laser and observing the change in the K-alpha fluorescence, the K-edges for different ions in the plasma were determined, leading to a charge resolved measurement of continuum lowering in the HDM system. The results disagree with the widely used Stewart-Pyatt model, with the disagreement increasing for higher charge states, but are consistent with the older Ecker-Kroell model. These results have profound implications for dense plasma modelling.

A novel, no-contact approach to X-ray mirror bending control is presented here, proposed for use on the beamlines of the European X-ray Free Electron Laser (XFEL) project. A set of mirrors with tunable bending radii are desired, that will maintain their optical properties even as the beam incidence causes local heating. Various mechanical bending mechanisms have been proposed and used on other beamlines, which can take up a lot of physical space, demanding more vacuum power, while using expensive high precision servomotors. Rather than bend the mirror by mechanical means, it is proposed to heat the mirror to produce the desired bending. This could work two ways. One scenario calls for a finely tunable heat lamp to irradiate the back surface of the mirror while the X-ray laser heats the front side. With appropriate tuning, simulations show that this approach can keep the mirror flat, and perhaps produce a circular profile. The second scenario is similar to the first, but a thin film of tungsten is added to the back of the silicon mirror. This scenario calls for the temperature of the mirror to change homogenously to affect the desired bending, and in this case the profile should be cylindrical. In both scenarios the uneven nature of the incident radiation causes distortions that may be undesirable. Both scenarios are simulated and it is shown that the stress produced by a metal film may minimize this distortion. The response time of the mirror and configuration of both the heating and cooling mechanism are also considered.

In the European XFEL, electrons bunches are accelerated up to 20 GeV and thenenter undulators where coherent X-rays are produced which can be used for imaging atva molecular level. Electrons may stray from the path and hit the permanent magnets inthe undulators. It is well known that ionizing radiation can affect the magnetic characteristics of permanent magnets. The undulators are therefore equipped with a type of semiconductor dosimeters, RADFETs, so that the potential damage from ionizing radiation to the magnets can be measured and corrected for. It is also known that heat will be generated from air-coils in the accelerator which can change the ambient temperature around the dosimeters up to 25 K. All semiconductor technology is highly susceptible totemperature. This report investigates the fading characteristics of the RADFET under different temperatures and times after irradiation. It also investigates the dose responseunder dierent temperatures and estimates the magnitude of errors in measured dose which can be expected if temperatures are not accounted for. It is seen that a delta T of a few K can have a large impact on RADFETs' ability to both record and retain dose. A strong time dependence is also seen. The fading is the largest during irradiation andthen slows down exponentially, stabilizing after 1 to 2 months. An increase from 20 deg C to 26 deg C will increase the fading by 2 Gy/h during irradiation, and 0.015 Gy/h weeks afterirradiation. It is estimated that dose measurements at XFEL can have errors of up to 14% if long-term fading is not accounted for. A model for estimating long-term fading as a function of temperature is proposed.

All across physics research, incoherent and coherent light sources are extensively utilized. Especially highly brilliant X-ray sources such as third generation synchrotrons or free-electron lasers have become an invaluable tool enabling experimental techniques that are unique to these kinds of light sources. But these sources have developed to large scale facilities and a demand in compact laboratory scale sources providing radiation of similar quality arises nowadays. This thesis focuses on Traveling-Wave Thomson-Scattering (TWTS) which allows for the realization of ultra-compact, inherently synchronized and highly brilliant light sources. The TWTS geometry provides optical undulators, through which electrons pass and thereby emit radiation, with hundreds to thousands of undulator periods by utilizing pulse-front tilted lasers pulses from high peak-power laser systems. TWTS can realize incoherent radiation sources with orders of magnitude higher photon yield than established head-on Thomson sources. Moreover, optical free-electron lasers (OFELs) can be realized with TWTS if state-of-the-art technology in electron accelerators and laser systems is utilized. Tilting the laser pulse front with respect to the wavefront by half of this interaction angle optimizes electron and laser pulse overlap by compensating the spatial offset between electrons and the laser pulse-front at the beginning of the interaction when the electrons are far from the laser pulse axis. The laser pulse-front tilt ensures continuous overlap between electrons and laser pulse while the electrons cross the laser pulse cross-sectional area. Thus the interaction distance can be controlled in TWTS by the laser pulse width rather than laser pulse duration. Utilizing wide, petawatt class laser pulses allows realizing thousands of optical undulator periods. This thesis will show that TWTS OFELs emitting ultraviolet radiation are realizable today with existing technology for electron accelerators and laser systems. The requirements on electron bunch and laser pulse quality of these ultraviolet TWTS OFELs are discussed in detail as well as the corresponding requirements of TWTS OFELs emitting in the soft and hard X-ray range. These requirements are derived from scaling laws which stem from a self-consistent analytic description of the electron bunch and radiation field dynamics in TWTS OFELs presented within this thesis. It is shown that these dynamics in TWTS OFELs are qualitatively equivalent to the electron bunch and radiation field dynamics of standard free-electron lasers which analytically proves the applicability of TWTS for the realization of an optical free-electron laser. Furthermore, experimental setup strategies to generate the pulse-front tilted TWTS laser pulses are presented and designs of experimental setups for the above examples are discussed. The presented setup strategies provide dispersion compensation, required due to angular dispersion of the laser pulse, which is especially relevant when building compact, high-yield hard X-ray TWTS sources in large interaction angle setups. An example of such an enhanced Thomson source by TWTS, which provides orders of magnitude higher spectral photon density than a comparable head-on interaction geometry, is presented, too
Inkohärente und kohärente Lichtquellen werden in allen Feldern der physikalischen Forschung intensiv eingesetzt. Im Besonderen ermöglichen hoch-brilliante Röntgenquellen, wie Synchrotrone der dritten Generation und Freie-Elektronen Laser, einzigartige Experimentiertechniken wodurch diese zu unverzichtbaren Werkzeugen wurden. Sie sind allerdings auch im Umfang zu Großforschungseinrichtungen herangewachsen. Um den hohen Bedarf an hoch-brillianten Lichtquellen zu decken, besteht daher die Notwendigkeit neuartige und kompakte Quellen zu entwickeln welche auf dem Maßstab eines Labors realisierbar sind. Diese Dissertation widmet sich der Traveling-Wave Thomsonstreuung (TWTS) welche die Realisierung ultra-kompakter, intrinsisch synchronisierbarer und hoch-brillianter Röntgenquellen ermöglicht. TWTS ist eine Methode der Streuung von Laserpulsen an relativistischen Elektronen. Dabei durchquert ein Elektronenpuls mit nahezu Lichtgeschwindigkeit einen Laserpuls. Während der Durchquerung beginnen die Elektronen im Feld des Laserpulses zu oszillieren wobei sie Strahlung emittieren. Die ausgesandte Strahlung besitzt eine deutlich kürzere Wellenlänge als das Laserfeld aufgrund der hohen Elektronengeschwindigkeit und der damit verbundenen großen Dopplerverschiebung. Das besondere an TWTS ist, dass Elektronen- und Laserpropagationsrichtung einen Winkel einschließen sowie pulsfrontverkippte Hochleistungslaserpulse eingesetzt werden. Dadurch können um Größenordnungen längere Interaktionsdistanzen als in herkömmlichen frontalen Thomsonstreuungsanordnungen erreicht werden. TWTS ermöglicht dadurch die Realisierung optischer Freie-Elektronen Laser (OFEL) und inkohärenter Strahlungsquellen mit einer um Größenordnungen erhöhten Photonenausbeute gegenüber Thomsonstreuungsquellen in frontalen Interaktionsanordungen. Werden modernste Elektronenbeschleuniger und Lasersysteme genutzt, dann ist der Betrieb optischer Freie-Elektronen Laser bereits heute mit TWTS möglich. Das wird in der Dissertation am Beispiel eines Vakuumultraviolettstrahlung emittierenden TWTS OFEL gezeigt. Dessen Anforderungen an die Qualität der Elektronen- und Laserpulse werden im Detail in der Arbeit besprochen sowie weitere Beispiele weicher und harter Röntgenstrahlung emittierender TWTS OFEL präsentiert. Diese Anforderungen werden anhand von Skalierungsvorschriften ermittelt welche aus einer selbstkonsistenten, 1.5 dimensionalen Theorie zur Wechselwirkung zwischen Elektronen und Laserfeld in TWTS abgeleitet sind. Sowohl die Theorie zur Wechselwirkung als auch die Ableitung der Skalierungsvorschriften sind Teile dieser Dissertation. Eine wichtige Erkenntnis der Theorie ist die qualitative Äquivalenz von Elektronen- und Strahlungsfeldbewegungsgleichungen in TWTS zu denen herkömmlicher Freie-Elektronen Laser. Das beweist analytisch die Möglichkeit zur Realisierung eines OFEL mit TWTS. Einen weiteren wichtigen Teil dieser Dissertation bildet die Arbeit zur Generierung der Laserpulse mit verkippter Pulsfront. Optische Aufbauten zur Verkippung der Laserpulsfront werden vorgestellt und für einige der präsentierten TWTS OFEL ausführlich dargelegt. Die Aufbauten verkippen nicht nur die Laserpulsfront sondern gewähren gleichzeitig Kontrolle über die Laserpulsdispersionen. Dadurch kann während der gesamten Interaktionen eine ausreichend hohe Qualität des Laserfeldes sichergestellt werden, was für TWTS OFEL und inkohärente TWTS Lichtquellen mit großem Interaktionswinkel unbedingt notwendig ist. Ein Beispiel einer inkohärenten TWTS Lichtquelle wird ebenfalls präsentiert. Diese emittiert Strahlung mit einer um Größenordnungen höheren spektrale Photonendichte als eine herkömmliche Thomsonquelle in einer frontalen Streuanordnung mit vergleichbaren Laser- und Elektronenpulsen

Récemment, la mise au point de techniques de radiographie à résolution temporelle a ajouté la dimension temporelle à la recherche dans le domaine de la biologie structurale et celles-ci se sont avérées être d'excellents outils pour suivre l'évolution structurale des protéines lors d'une réaction. En particulier, les sources de rayons X de 4ème génération (appelées lasers à électrons libres et à rayons X), avec des impulsions de l'ordre de la femtoseconde et des fluences extrêmement élevées, sont capables de sonder des ensembles de molécules essentiellement gelées dans le temps dans des conditions physiologiques. Après un aperçu des études publiées dans la littérature scientifiques, une introduction de base des techniques utilisées est présentée, accompagnée d'une description du dispositif expérimental et du flux de réduction des données. Les deux derniers chapitres sont consacrés à la présentation des résultats obtenus au cours de deux séries d'expériences réalisées au LCLS (SLAC, Menlo Park, CA, USA), pour étudier les changements structuraux des protéines dans la réaction de photodissociation prototypique du monoxyde de carbone chez des hemoprotéines. Au cours de la première expérience, la modification structurelle globale de trois hemoprotéines a été sondée par une technique de diffusion à résolution temporelle, afin d'observer d'éventuelles différences dans ce que l'on appelle le ''protein quake'' lié à la structure de la protéine. Dans la deuxième expérience, le site actif de la myoglobine a été sondé au cours de la même réaction par absorption de rayons X. Les spectres XANES à résolution temporelle ont été comparés à des calculs théoriques, dans le cadre de la théorie de la diffusion multiple, afin d'obtenir une image détaillée de la dynamique ultrarapide. Un bref projet secondaire portait à mesurer précisément des modèles de diffusion statique de la carboxyhémoglobine, afin de définir ses structures d'équilibre multiple par comparaison avec des combinaisons linéaires de structures cristallographiques connues. En conclusion, dans cette thèse de doctorat, nous avons essayé d'apporter quelques petits éléments dans la compréhension de la dynamique ultrarapide des protéines, en appliquant à la fois des méthodes d'analyse standard (Guinier), mais aussi des méthodes presque inexplorées (calculs de diffusion multiple sur des données à résolution temporelle). Selon le système et le niveau de détail requis, ces méthodes, appliquées ici aux à des systèmes modèles, peuvent être considérées d'excellents outils dans la recherche ultérieure sur des protéines plus complexes
Recently, the development of time resolved X-ray techniques has added the time dimension to structural biology studies, and have proven to be great tools to track proteins during the course of a reaction, or a specific conformational change. In particular the 4th generation X-ray sources (so called X-ray Free-Electron Lasers), with femtosecond pulses and extremely high fluences, are capable of probing ensembles of molecules essentially frozen in time under physiological conditions. After an overview of the past studies in the field, a basic introduction of the used techniques, the description of the experimental set-up and the flow of data reduction are presented. The last two chapters are devoted to present the results obtained during two separate sets of experiments, conducted at the XPP beamline of the Linac Coherent Light Source (SLAC, Menlo Park, CA, USA), to study the protein's structural changes, upon prototypical photo-dissociation reaction of carbon monoxide from heme proteins. During the first experiment, the global structural modification of three heme proteins has been probed by means of time resolved scattering technique, in order to observe eventual differences in the so called “protein-quake” depending on the protein's structure. In the second experiment, the active site of myoglobin was probed, during the same reaction, by X-ray absorption. The time resolved XANES spectra have been compared with theoretical calculations, in the framework of the multiple scattering theory, in order to retrieve a detailed picture of the ultra-fast dynamics. A further small side-project dealt with the precise measurement of static scattering patterns of carboxy hemoglobin with the goal of defining its multiple equilibrium structures by comparison with linear combinations of known crystallographic structures. In conclusion, in this Ph.D. thesis we tried to add some small pieces in the understanding of ultra-fast proteins dynamics by applying both standard (Guinier) and almost unexplored (multiple scattering calculations on time resolved data) analysis methods: depending on the system and the level of details required, these methodologies, here applied on model systems, can be considered excellent tools for further research on more complicated proteins

X-ray crystallography is a form of microscopy that allows the three-dimensional arrangement of atoms belonging to molecules within crystals to be determined. In this method, a crystal is illuminated with a beam of X-rays and the diffracted amplitudes resulting from the illumination are measured and computationally processed to enable the electron density of the unit molecule, or the unit cell, constituting the crystal to be calculated. The recent development of the X-ray free-electron laser (XFEL) provides new routes for determining molecular structures via its ability to generate intense but brief X-ray pulses. These new instruments enable diffraction measurements to be obtained from crystals that have a small number of unit cells, referred to as nanocrystals, and molecular structure determination via this technique is known as serial femtosecond nanocrystallography (SFX). This thesis is concerned with the characterisation of diffraction data obtained from SFX experiments and the techniques for reconstructing the electron density of the molecule from such data. The noise characteristics of diffraction measurements from nanocrystals is developed. Methods for directly inverting nanocrystal diffraction to obtain the electron density of the molecule are analysed and an approach to ameliorate the effect of noise is proposed and evaluated by simulation. A model for diffraction by nanocrystals that include the effects of different unit cell arrangements and incomplete unit cells on the crystal surface is also developed and explored by simulation. The diffraction by finite crystals is shown to be equal to the incoherent average over a set of unit cells that contain different molecular arrangements related to the symmetry of the crystal at hand. The problem of image reconstruction under this circumstance is investigated. The more general problem of reconstructing multiple, unrelated, objects from their averaged diffraction is also explored and uniqueness properties along with reconstruction algorithms developed. The problem of reconstructing multiple, related, unit cells is studied and preliminary results are obtained. These results show that iterative phase retrieval algorithms can in principle be adapted to reconstruct the electron density of a crystalline specimen from the data obtained in SFX and the retrieval of phases from the diffracted intensity averaged over multiple objects is feasible.

The recent availability of X-ray Free Electron Lasers (XFELs) has opened a completely new and unexplored regime for the study of light-matter interactions. The extremely bright intensities delivered by XFELs can couple many photons into the target, turning well known interactions such as photoionization and scattering into new, non-linear, complex many-body phenomena. This thesis reports theoretical investigations aiming to improve the understanding of the fundamental processes and dynamics triggered by intense X-ray pulses, with a special focus in finite systems such as molecules and clusters. Sequential multiple photoionization in atomic clusters was investigated, where previous observations were extended for higher charge states where direct photoionization is frustrated. Through a rate equation study and subsequent molecular dynamics simulations, it was found that frustrated ionization is partially responsible for the low-energy peak observed in the electron energy spectrum. The influence of plasma evaporation over the formation of the sequential low-energy peak was also investigated, identifying the effects of the system size and photon energy. Multiple channel ionization was also investigated for the case of fullerenes. This is done through a series of studies, starting from a simplified rate equation scheme, and culminating with full molecular dynamics simulations. From these results, a good insight was obtained over the origin, physical meaning, and relevant parameters that give rise to the complicated features observed in the electronic spectra. The mechanisms responsible of all these features are expected to be present in other systems, making these results quite general. Diffractive imaging of biomolecules was studied in a final step, with a particular focus on the influence of intramolecular charge transfer mechanisms. To this end a conformer of T4 Lysozyme was used, a representative enzyme with well known structure. Charge migration is found to allow for additional processes such as proton ejection, a mechanism which enables an efficient release of energy from the system. This mechanism considerably suppresses structural damage for heavy ions, improving the quality of the measured diffraction patterns.

Since the discovery of lasers, the quest for new powerful sources of radiation has become an exciting fields of both fundamental and applied research. Indeed, light sources are nowadays one of the most powerful tools for matter investigation. Free electron lasers (FELs) represent the next step in the evolution of the light sources, with the potential to overcome the lack of coherent sources in the x-ray spectral range. After a general introduction to the characteristics and mechanisms of seeded FEL I will introduce the FERMI FEL facility, which is the first user facility in the XUV spectral range based seeded high-gain harmonic generation. Then I will report different approaches that I followed to improve the performance of the FERMI FEL. In particular, I will focus on experiments aimed at measuring and controlling the polarization of the FEL pulse, and at generating multi-color FEL pulses for pump-probe experiments. Furthermore I will present the experiments I carried out in order to assess the effect on the FEL performance of a laser heater, which is a device that is used to control the energy spread of the electron beam.

The recent development of free-electron lasers operating at XUV and X-ray wavelengths are proving vital for the exploration of matter in extreme conditions. The ultra-short pulse length and high peak brightness these light sources provide, combined with a tunable X-ray wavelength range, makes them ideally suited both for creating high energy density samples and for their subsequent study. In this thesis I describe the work done on the XUV free-electron laser FLASH in Hamburg, aimed at creating homogeneous samples of warm dense matter through the process of volumetric XUV photo-absorption, and the theoretical work undertaken to understand the process of high-intensity laser-matter interactions. As a first step, we have successfully demonstrated intensities above 10¹⁷ Wcm-2 at a wavelength of 13.5 nm, by focusing the FEL beam to micron and sub-micron spot sizes by means of a multilayer-coated off-axis parabolic mirror. Using these record high intensities, we have demonstrated for the first time saturable absorption in the XUV. The effect was observed in aluminium and magnesium samples and is due to the bleaching of a core-state absorption channel by the intense radiation field. This result has major implications for the creation of homogeneous high energy density systems, as a saturable absorption channel allows for a more homogeneous heating mechanism than previously thought possible. Further, we have conducted soft X-ray emission spectroscopy measurements which have delivered a wealth of information on the highly photo-excited system under irradiation, immediately after the excitation pulse, yet before the system evolves into the warm dense matter state. Such strongly photo-excited samples have also been studied theoretically, by means of density functional theory coupled to molecular dynamics calculations, yielding detailed electronic structure information. The use of emission spectroscopy as a probe for solid-density and finite-temperature systems is discussed in light of these results. Theoretical efforts have further been made in the study of the free-free absorption of aluminium as the system evolves from the solid state to warm dense matter. We predict an absorption peak in temperature as the system heats and forms a dense plasma. The physical significance of this effect is discussed in terms of intense light-matter interactions on both femtosecond and picosecond time-scales.

The newly emerging technology of X-ray free-electron lasers (XFELs) has the potential to revolutionise molecular imaging. XFELs generate very intense X-ray pulses and predictions suggest that they may be used for structure determination to atomic resolution even for single molecules. XFELs produce femtosecond pulses that outrun processes of radiation damage and permit the study of structures at room temperature and of structural dynamics. While the first demonstrations of flash X-ray diffractive imaging (FXI) on biological particles were encouraging, they also revealed technical challenges. In this work we demonstrated how some of these challenges can be overcome. We exemplified, with heterogeneous cell organelles, how tens of thousands of FXI diffraction patterns can be collected, sorted, and analysed in an automatic data processing pipeline. We improved  image resolution and reduced problems with missing data. We validated, described, and deposited the experimental data in the Coherent X-ray Imaging Data Bank. We demonstrated that aerosol injection can be used to collect FXI data at high hit ratios and with low background. We reduced problems with non-volatile sample contaminants by decreasing aerosol droplet sizes from ~1000 nm to ~150 nm. We achieved this by adapting an electrospray aerosoliser to the Uppsala sample injector. Mie scattering imaging was used as a diagnostic tool to measure positions, sizes, and velocities of individual injected particles. XFEL experiments generate large amounts of data at high rates. Preparation, execution, and data analysis of these experiments benefits from specialised software. In this work we present new open-source software tools that facilitates prediction, online-monitoring, display, and pre-processing of XFEL diffraction data. We hope that this work is a valuable contribution in the quest of transitioning FXI from its first experimental demonstration into a technique that fulfills its potentials.

Investigations of soft matter using ultrashort high intensity pulses have been made possible through the advent of X-ray free-electrons lasers. The last decade has seen the development of a new type of protein crystallography where femtosecond dynamics can be studied, and single particle imaging with atomic resolution is on the horizon. The pulses are so intense that any sample quickly turns into a plasma. This thesis studies the ultrafast transition from soft matter to warm dense matter, and the implications for structural determination of proteins.                    We use non-thermal plasma simulations to predict ultrafast structural and electron dynamics. Changes in atomic form factors due to the electronic state, and displacement as a function of temperature, are used to predict Bragg signal intensity in protein nanocrystals. The damage processes started by the pulse will gate the diffracted signal within the pulse duration, suggesting that long pulses are useful to study protein structure. This illustrates diffraction-before-destruction in crystallography. The effect from a varying temporal photon distribution within a pulse is also investigated. A well-defined initial front determines the quality of the diffracted signal. At lower intensities, the temporal shape of the X-ray pulse will affect the overall signal strength; at high intensities the signal level will be strongly dependent on the resolution. Water is routinely used to deliver biological samples into the X-ray beam. Structural dynamics in water exposed to intense X-rays were investigated with simulations and experiments. Using pulses of different duration, we found that non-thermal heating will affect the water structure on a time scale longer than 25 fs but shorter than 75 fs. Modeling suggests that a loss of long-range coordination of the solvation shells accounts for the observed decrease in scattering signal. The feasibility of using X-ray emission from plasma as an indicator for hits in serial diffraction experiments is studied. Specific line emission from sulfur at high X-ray energies is suitable for distinguishing spectral features from proteins, compared to emission from delivery liquids. We find that plasma emission continues long after the femtosecond pulse has ended, suggesting that spectrum-during-destruction could reveal information complementary to diffraction.

Recent improvements in deep learning architectures, combined with the strength of modern computing hardware such as graphics processing units, has lead to significant results in the field of image analysis. In this thesis work, locally connected architectures are employed to reduce noise in flash X-ray diffraction images. The layers in these architectures use convolutional kernels, but without shared weights. This combines the benefits of lower model memory footprint in convolutional networks with the higher model capacity of fully connected networks. Since the camera used to capture the diffraction images has pixelwise unique characteristics, and thus lacks equivariance, this compromise can be beneficial. The background images of this thesis work were generated with an active laser but without injected samples. Artificial diffraction patterns were then added to these background images allowing for training U-Net architectures to separate them. Architecture A achieved a performance of 0.187 on the test set, roughly translating to 35 fewer photon errors than a model similar to state of the art. After smoothing the photon errors this performance increased to 0.285, since the U-Net architectures managed to remove flares where state of the art could not. This could be taken as a proof of concept that locally connected networks are able to separate diffraction from background in flash X-Ray imaging.

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.

Les protéines fluorescentes photocommutables (RSFPs) ont la propriété de passer d’un état fluorescent à un état non-fluorescent en réponse à la lumière. Cette propriété en fait des outils de marquage pour la microscopie de super-résolution (ou nanoscopie). Le mécanisme de photocommutation implique l’isomérisation du chromophore ainsi qu’un changement d’état de protonation de ce dernier. Le mécanisme a été très étudié par différentes approches de spectroscopie et de simulation mais reste encore mal compris, l’ordre séquentiel des évènements est notamment encore débattu. Certains de ces évènements de la photocommutation se déroulent à des échelles de temps très courtes, ce qui rend difficile l’étude structurale par cristallographie des rayons X à l’aide des sources synchrotron actuelles dont la résolution temporelle est encore limitée. Les lasers à électrons libres (XFELs) sont une nouvelle source de rayons X produisant des impulsions suffisamment courtes pour permettre l’étude structurale des intermédiaires précoces ou à courte durée de vie qui se forment ou cours de la photocommutation, et suffisamment brillantes pour permettre la collecte de données cristallographiques sur des cristaux de tailles nano- et micrométrique. L’utilisation de ce nouveau genre d’instrument a permis l’émergence de la cristallographie sérielle, une nouvelle approche de la cristallographie des rayons X. Cette approche a depuis été adaptée aux lignes synchrotrons.Le travail présenté ici se focalise sur l’étude de rsEGFP2, une protéine fluorescente photocommutable de la famille de la GFP. Il y est décrit la mise au point d’un protocole de microcristallisation permettant l’obtention d’échantillons en vue d’une expérience de cristallographie résolue en temps au XFEL. Un mécanisme de photocommutation y est proposé à travers le résultat de deux expériences sur les deux XFELs actuellement opérationnels, à des échelles de temps différentes, dévoilant un chromophore « twisté » à l’état excité ainsi qu’un état cis protoné de ce dernier. La caractérisation structurale des variants de rsEGFP2 par cristallographie d’oscillation « classique » combinée à la découverte fortuite d’une conformation alternée du chromophore dans l’état non-fluorescent, issue d’expérience de cristallographie sérielle, apporte un complément d’explication des propriétés photophysiques de la protéine
Reversibly switchable fluorescent proteins (RSFPs) are able to reversibly toggle between a fluorescent on-state and a non-fluorescent off-state under visible light irradiation. This property makes them a suitable marker used in super-resolution microscopy (or nanoscopy). The photo-switching mechanism involves isomerisation of the chromophore and a change of its protonation state. This mechanism has been well studied but remains poorly understood. The structural nature and the sequential order of atomistic events are still under debate. Some of them take place on the ultra-fast time scale and make structural investigation by X-ray crystallography impossible using current synchrotron radiation sources whose temporal resolution they offer is limited. X-ray free electron lasers (XFELs) are a new kind of X-ray source producing femtosecond pulses that allow structural investigation of ultra-fast intermediates during photoswitching. They are also so bright that crystallographic data collection from micro- and nanometer-sized crystals became possible. The bright and short XFEL pulses required a new methodology to be developed, the so-called serial crystallography methodology. This method is now being adapted to synchrotron radiation facilities.Here is presented a time-resolved crystallography study of the reversibly switchable green fluorescent protein 2 (rsEGFP2). A microcrystallization protocol is described allowing the preparation of suitable samples in large amounts for time-resolved serial crystallography experiments. A photoswitching mechanism of rsEGFP2 is proposed based on crystallographic results obtained from data collected at the two XFEL facilities currently fully operational, i.e. the LCLS in the USA and SACLA in Japan. In particular, the structure of two photoswitching intermediates have been determined, one featuring a twisted chromophore in the excited state and the other displaying a protonated cis isomer of the chromophore in the ground state. The structural characterization of rsEGFP2 variants by traditional oscillation crystallography combined with the serendipitous discovery of an alternate chromophore conformation in the off-state during an XFEL experiment provided unique insight into the photophysical behavior of the protein

Les impulsions ultra-brèves de rayonnement ultraviolet extrême (UVX) ont un grand champ d’application dans les domaines tels que le diagnostic de plasmas, la spectroscopie ou l’étude de la dynamique ultrarapide dans les atomes et les molécules.Aujourd’hui, il existe trois sources délivrant ce genre d’impulsions. Les harmoniques d’ordre élevé (HHG, en anglais) générés dans les gaz rares ou sur les solides peuvent fournir des impulsions attosecondes. Cependant, leur énergie, le plus souvent de l’ordre du nanojoule, limite les applications. L’amplification des impulsions harmoniques dans les plasmas créés par laser (SXRL, en anglais) a démontré pouvoir fournir des énergies de plusieurs dizaines de microjoules. Des énergies plus élevées peuvent être obtenues avec les lasers à électrons libres (LEL) UVX injectés, mais ce sont des Très Grandes Infrastructures ayant un accès limité.Ces dernières années, des progrès significatifs ont été réalisé avec chacune des ces sources, avec pour objectif la génération d’impulsions plus brèves. Il est devenu nécessaire de développer des nouvelles techniques de métrologie temporelle des impulsions UVX ultra-brèves. De plus, beaucoup d’expériences, comme ceux impliquant des phénomènes non-linéaires, nécessitent de hautes intensités UVX. La focalisation efficace des impulsions de faibles énergies peut significativement augmenter le domaine d’application. De bons fronts d’onde sont nécessaires pour focaliser les impulsions UVX à haute intensité, et les optiques doivent aussi être de bonne qualité et alignées avec précision.Dans cette thèse, les propriétés spatiales des harmoniques d’ordre élevé ont été extensivement étudiées grâce à un senseur de front d’onde UVX. Cet appareil couplé à une source HHG a démontré être utile pour la caractérisation de table et à la longueur d’onde ainsi que pour l’optimisation de systèmes optiques UVX.Le problème de la mise en place de la complète caractérisation temporelle d’impulsions UVX est aussi discuté en détail, et deux nouveaux schémas pour la reconstruction d’impulsions de LEL injectés et de lasers X à plasma sont présentés. Finalement, la première implantation d’un système d’amplification à dérive de fréquence (CPA, en anglais) sur un LEL UVX est présentée et son implantation pour les lasers X à plasmas est aussi discutée
Ultrashort pulses of extreme-ultraviolet (XUV) radiation have a wide range of applications in fields such as plasma probing, spectroscopy, or the study of ultrafast dynamics in atoms and molecules.Nowadays, there are three main sources of such pulses. High-order harmonic generation (HHG) in rare gases or solid surfaces is able to provide attosecond pulses. However, their limited energy, of the order of nanojoules, limits its number of applications. The amplification of high-harmonic pulses in laser-driven plasmas (SXRL) has been demonstrated to provide energies of tens of microjules. Higher pulse energies can be obtained from seeded XUV free-electron lasers (FELs), large-scale facilities with more limited accessibility.In recent years, significant progress has been made with each of these sources towards the generation of shorter pulses. It is thus necessary to develop new techniques for full temporal metrology of ultrashort XUV pulses. Additionally, many experiments, such as those involving nonlinear phenomena, require high XUV intensities. Efficient focusing of low-energy pulses can significantly increase their range of application. Good wavefronts are required in order to focus XUV pulses to high intensities, and the optics must be of high quality and precisely aligned.In this thesis, the spatial properties of high-harmonic pulses are extensively explored thanks to the use of an XUV Hartmann wavefront sensor. This device is also proven here to be useful for tabletop, at-wavelength characterization and optimization of XUV optical systems with HHG sources.The problem of performing full temporal characterization of XUV pulses is also discussed in detail, and two new schemes for complete pulse reconstruction for seeded XUV FELs and seeded SXRLs are presented. Finally, the first implementation of chirped pulse amplification (CPA) in a seeded XUV FEL is reported, and its implementation in seeded SXRLs is discussed as well

In order to understand the behaviour and function of proteins, their three dimensional structure needs to be known. Determination of macro-molecules’ structures is done using X-ray diffraction or electron microscopy, where the resulting diffraction pattern is used for molecular reconstruction. These methods are however limited by radiation damage.The aim of this work is to study radiation damage of peptides in proteins using computer simulations. Increased understanding of the atomic and molecular dynamics can contribute to an improvement of the method ofimaging biological molecules. To be able to describe the processes that take place as accurately as possible, the problem must treated quantum mechanically.Thus, the simulations are performed with molecular dynamics based on first principles. In order to capture the dynamics of the excited states of the molecule when exposed to X-rays, time-dependent density functional theory with delta self-consistent field is used. These simulations are compared to ground state simulations. The results of the thesis conclude that the excited and ground state simulations result in differences in the dynamics, which are most pronounced for lager molecules.

This thesis investigates the use of high-power lasers for synchrotron radiation sources with high brilliance, from the EUV to the hard X-ray spectral range. Hereby lasers accelerate electrons by laser-wakefield acceleration (LWFA), act as optical undulators, or both. Experimental evidence shows for the first time that LWFA electron bunches are shorter than the driving laser and have a length scale comparable to the plasma wavelength. Furthermore, a first proof of principle experiment demonstrates that LWFA electrons can be exploited to generate undulator radiation. Building upon these experimental findings, as well as extensive numerical simulations of Thomson scattering, the theoretical foundations of a novel interaction geometry for laser-matter interaction are developed. This new method is very general and when tailored towards relativistically moving targets not being limited by the focusability (Rayleigh length) of the laser, while it does not require a waveguide. In a theoretical investigation of Thomson scattering, the optical analogue of undulator radiation, the limits of Thomson sources in scaling towards higher peak brilliances are highlighted. This leads to a novel method for generating brilliant, highly tunable X-ray sources, which is highly energy efficient by circumventing the laser Rayleigh limit through a novel traveling-wave Thomson scattering (TWTS) geometry. This new method suggests increases in X-ray photon yields of 2-3 orders of magnitudes using existing lasers and a way towards efficient, optical undulators to drive a free-electron laser. The results presented here extend far beyond the scope of this work. The possibility to use lasers as particle accelerators, as well as optical undulators, leads to very compact and energy efficient synchrotron sources. The resulting monoenergetic radiation of high brilliance in a range from extreme ultraviolet (EUV) to hard X-ray radiation is of fundamental importance for basic research, medical applications, material and life sciences and is going to significantly contribute to a new generation of radiation sources and free-electron lasers (FELs).

2013/2014
The present work of thesis is situated within the framework of the study of disordered systems as liquids and glasses. A liquid is a system characterized by long range translational invariance and by a short range ordered structure. In the liquid state, contrarily to the crystalline one, there is not structural periodicity and all we learnt from solid state physics (Block’s theorem, phonons, Brillouin’s zones, eigen-states of plane waves, etc.) must be fully revised. The macroscopic collective properties of condensed matter are the result of inter and intra-molecular interactions that are typified by characteristic time and space scales. A longstanding and powerful tool to investigate the collective nature of the microscopic processes inside the system is the acoustic spectroscopy. While in the case of crystalline phase we could take advantage of the periodical structure of the system, limiting our investigation to the so called first Brillouin zone, in order to characterize a disordered system we need to explore a widest as possible spectral range to access the all time and space scales in which the dynamical phenomena occur. This approach can be called Broad Band Acoustic Spectroscopy . My PhD activity was devoted to the development of new experimental methods and techniques allowing the exploration with continuity of dynamics evolving with timescales from tenth’s of ns’s to ps’s. I could test such Broad Band Acoustic Spectroscopy on a prototypical sample: acetonitrile, the liquid with highest dipole moment, known for its many different inter- and intra-molecular dynamics. Using several experimental and computational approaches I could characterize the main dynamical processes for such compound in its whole liquid phase. Thanks to the crossing of the all acquired information, it was possible to identify a mutual influence between different relaxations whose behaviour otherwise was not possible to correctly understand. After a brief introduction to contextualize the Broad Band Acoustic Spectroscopy in disordered systems, in Chapter 1 is presented an overview of the experimental techniques used to perform the measurements within this work. In this chapter, the first my original contribution to the extension of acoustic spectral range finds the place. Thanks to the design and realization of particular spatial filters it is now possible to perform Brillouin Light Scattering experiments with angle tunabil- ity without incurring in annoying spurious contributions issues. In the chapter are also recalled the main physical principles at the ground of every presented tech- nique, in particular stressing the complementarity of the energy and time resolved spectroscopies. Because all the information from the inner dynamics of the sample are mediated by the acoustic modes interaction, Chapter 2 is dedicated to the formalism of the density fluctuations, highlighting the differences between the hydrodynamic model, valid at macroscopic length-scales, and the memory functions approach, necessary to describe the mesoscopic region where the characteristic length-scales of the acoustic modes are comparable to the inter-particles distances. In Chapter 3 are shown the experimental results obtained thanks to the Broad Band Spectroscopy in the whole temperature range of the liquid phase of acetoni- trile. We could first measure some thermodynamical quantities by a non linear spectroscopy named Transient Grating, shedding light on the literature debate on them. Among the obtained results, we appreciated a temperature dependency of the heat capacity ratio which is usually considered a constant. Starting from these results and using the filtering approach introduced in Chapter 1, we could profitably study the vibrational relaxation of acetonitrile discovering some relevant discrepan- cies with previous studies. In this way we demonstrated the importance to avoid eventual spurious contributions and to have complementary information from dif- ferent spectral domains. Then there will be shown the results for the so called structural relaxation, obtained in the high energy domain by Inelastic X-ray Scat- tering. A really interesting correlation has been found with the result obtained by the ultrafast response of the Transient Grating method. Once again, to obtain such comparison was necessary to combine the information arising from many different spectral ranges, fact that highlights the utility and endorses the multi-techniques broad band acoustic spectroscopy method. The temperature dependence of the aforementioned relaxation processes sug- gested to evaluate if any coupling there exist between the two. This is exactly what we were able to appreciate in the deep-UV domain and we proposed a phenomeno- logical model to give a picture of the occurring interaction. To further investigate such dynamics coupling effect, could be extremely useful to explore the soft-UV spectral range but so far any technique was able to access such energy domain. In Chapter 4 we thus present our innovative solution to the problem: a novel table top Fabry-Perot interferometer conceived to operate with UV laser source and with only reflecting optics. The last chapters of the thesis describe my contribution to the forthcoming Free Electron Laser (FEL) based experiment to further increase the accessible spectral range to the acoustic spectroscopy: the TIMER project. In particular I will show the result obtained with the pilot experiment named “mini-TIMER” in which we could demonstrate the feasibility of a Transient Grating experiment in the Extreme Ultra Violet (EUV) domain. When TIMER will be operative it will be the first experimental setup able to probe the EUV mesoscopic region of crucial importance for the study of glasses and nano-structures. This result paves the way to a new class of intriguing experiments only matter of theoretical considerations so far: the so called four wave mixing experiments with elemental selectivity.
Il presente lavoro di tesi si colloca nell’ambito dello studio dei sistemi disordi- nati quali liquidi e vetri. Un liquido ´e un sistema caratterizzato da invarianza traslazionale a lungo raggio e da una struttura ordinata a corto raggio. Lo stato liquido, a differenza di quello cristallino, non gode di una periodicit`a strutturale e tutto ci`o che avevamo imparato dalla fisica dello stato solido (teorema di Block, fononi, zone di Brillouin, autostati di onde piane, etc.) deve essere completamente rivisto. Le propriet`a collettive della materia sono il risultato di interazioni a livello inter- e intra-molecolare identificate da caratteristiche scale temporali e spaziali. Uno strumento ormai affermato e utile per lo studio della natura collettiva dei processi microscopici attivi all’interno del sistema ´e la spettroscopia acustica. Mentre nel caso della fase cristallina si poteva sfruttare la natura periodica della struttura del sistema, limitando lo studio alla cosiddetta prima zona di Brillouin, per caratteriz- zare un sistema disordinato ´e necessario esplorare un intervallo spettrale il pi`u ampio possibile cosí da poter aver accesso alle scale spazio-temporali in cui le dinamiche avvengo. Questo tipo di approccio pu`o essere chiamato Spettroscopia Acustica ad Ampia Banda Spettrale . Il mio dottorato ´e stato dedicato allo sviluppo di nuovi metodi e tecniche speri- mentali per esplorare con continuit`a i processi dinamici la cui evoluzione avviene su scale di tempi tra le decine di ns e i ps. Tale Spettroscopia Acustica ad Ampia Banda Spettrale ´e stata testata su un campione prototipo di acetonitrile, il liquido con il pi´u alto momento di dipolo esistente, noto per le sue molteplici dinamiche di orgine inter- e intra-molecolare. Usando diversi approcci sperimentali e computazionali ´e stato possibile caratterizzare i principali processi di rilassamento per tale composto in tutta la sua fase liquida. Combinando poi tutte le informazioni acquisite, ´e stato possibile indentificare una mutua influenza tra i diversi processi di rilassamento il cui comportamento altrimenti sarebbe rimasto incompreso. Dopo una breve introduzione per contestualizzare la Spettroscopia Acustica ad Ampia Banda Spettrale nell’ambito dei sistemi disordinati, nel Capitolo 1 viene offerta una panoramica delle tecniche sperimentali usate per effettuare le misure nel corso di questo lavoro. Trova posto in questo capitolo la descrizione del mio primo originale contributo all’estensione dell’intervallo spettrale acustico. Grazie alla progettazione e realizzazione di particolari filtri spaziali ´e ora possibile effet- tuare esperimenti di diffusione di luce Brillouin con angolo di scattering variabile senza dover incorrere in fastidiosi problemi di contributi spuri. Nel capitolo vengono anche richiamati i principali elementi di fisica alla base di ogni tecnica, marcando in particolare la caratteristica di complementariet`a tra esperimenti risolti in tempo e in energia. Siccome tutte le informazioni a proposito delle dinamiche interne del campione sono mediate dall’interazione coi modi acustici, il Capitolo 2´e dedicato al formalismo delle fluttuazioni di densit`a, evidenziando le differenze tra il modello idrodinamico, valido per scale spaziali macroscopiche, e l’approccio delle funzioni memoria, nec- essario per descrivere la regione mesoscopica dove le dimensioni caratteristiche dei modi acustici diventano confrontabili con le distanze tra le particelle. Nel Capitolo 3 sono riportati i risultati sperimentali ottenuti mediante la Spet- troscopia Acustica ad Ampio Intervallo Spettrale nell’intero range di temperature in cui l’acetonitrile permane allo stato liquido. Per prima cosa, attraverso un tecnica fotonica di spettroscopia non lineare (Transient Grating) ´e stato possibile misurare alcune variabili termodinamiche, potendo fare chiarezza tra i vari contributi presenti in letteratura. Tra i risultati ottenuti, la dipendenza in temperatura del rapporto tra i calori specifici laddove usualmente viene considerata costante. Partendo da questi risultati e usando l’approccio di filtraggio introdotto nel Capitolo 1, ´e stato possibile studiare il rilassamento vibrazionale dell’acetonitrile scoprendo alcune ril- evanti discrepanze con i precedenti lavori riportati in letteratura. Abbiamo cosí dimostrato l’importanza di eliminare eventuali contributi spuri e di poter attingere a informazioni complementari da diversi domini spettrali. Verr`a inoltre mostrato il risultato dello studio del cosiddetto rilassamento strutturale effettuato nel range di alte energie grazie allo Scattering di raggi X. Una interessante correlazione si ´e po- tuta riscontrare tra i risultati di questo esperimento e quelli ottenuti con la tecnica Transient Grating nella sua risposta ultraveloce. Ancora una volta, per ottenere tale risultato ´e stato necessario combinare informazioni provenienti da molti inter- valli spettrali diversi, confermando la validit`a di un approccio multi-tecnica come quello della spettroscopia acustica a larga banda spettrale. L’andamento in tem- peratura dei suddetti processi di rilassamento suggerivano di valutare la presenza di un eventuale accoppiamento tra i due fenomeni. ´E esattamente ci`o che abbiamo osservato esplorando il dominio del profondo ultravioletto e per il quale abbiamo proposto un modello fenomenologico in grado di fornire una rappresentazione delle interazioni in gioco. Per poter approfondire tale fenomeno di accoppiamento sarebbe estremamente utile poter esplorare l’intervallo spettrale degli UV soffici, ma fino ad oggi nessuna tecnica era in grado accedere a tale range. Nel Capitolo 4 mostriamo la nostra innovativa soluzione al problema: un nuovo interferometro Farby-Perot “table-top”, concepito per lavorare con una sorgente UV laser e con sole ottiche riflettive. Gli ultimi capitoli della tesi descrivono il mio contributo al prossimo esperi- mento avente come sorgente di luce un laser ad elettroni liberi: il progetto TIMER, destinato ad aumentare ulteriormente il range spettrale sperimentalmente acces- sibile con la spettroscopia acustica. In particolare, mostrer`o i risultati ottenuti nell’esperimentopilotachiamato“mini-TIMER”graziealqualedimostratolapossibilit`a di effettuare un esperimento Transient Grating anche nel range spettrale dell’estremo UV (EUV). Quando TIMER sar`a operativo sar`a il primo setup sperimentale in grado di sondare la regione mesoscopica nell’EUV, zona di cruciale importanza per lo studio dei vetri e delle nanostrutture. Questo risultato apre inoltre la strada ad una nuova classe di interessanti esperimenti ad oggi oggetto solo di considerazioni teoriche: i cosiddetti esperimenti di “four wave mixing” combinati con la selettivit`a elementale che la radiazione EUV pu`o fornire.
XXVI Ciclo
1985

Atoms, molecules and clusters all constitute building blocks of macroscopic matter. Therefore, understanding the electronic and geometrical properties of such systems is the key to understanding the properties of solid state objects.

In this thesis, some atomic, molecular and cluster systems (clusters of O₂, CH₃Br, Ar/O₂, Ar/Xe and Ar/Kr; dimers of Na; Na and K atoms) have been investigated using synchrotron radiation, and in the two last instances, laser light. We have performed x-ray photoelectron spectroscopy (XPS) on all of these systems. We have also applied ultraviolet photoelectron spectroscopy (UPS), resonant Auger spectroscopy (RAS) and near-edge x-ray absorption spectroscopy (NEXAFS) to study many of the systems. Calculations using ab initio methods, namely density functional theory (DFT) and Møller-Plesset perturbation theory (MP), were employed for electronic structure calculations. The geometrical structure was studied using a combination of ab initio and molecular dynamics (MD) methods.

Results on the dissociation behavior of CH₃Br and O₂ molecules in clusters are presented. The dissociation of the Na₂ molecule has been characterized and the molecular field splitting of the Na 2p level in the dimer has been measured. The molecular field splitting of the CH₃Br 3d level has been measured and the structure of CH₃Br clusters has been determined to be similar to the structure of the bulk solid. The diffusion behavior of O₂, Kr and Xe on large Ar clusters, as a function of doping rate, has been investigated. The shake-down process has been observed from excited states of Na and K. Laser excited Na atoms have been shown to be magnetically aligned. The shake-down process was used to characterize the origin of various final states that can be observed in the spectrum of ground-state K.

abstract: One of the most important issues in femtosecond free electron laser X-ray diraction is to reconstruct the 3D charge density of molecule from a mass of diraction snapshots. In order to determine the orientation of single molecule from diraction patterns, we rst determine the moments and products of inertia of this from 2D experiment data (diraction patterns or EM images to obtain the elements of the inertia tensor. If diraction patterns from uniformly random orientations or some preferred orientations are collected, the principal axes of the molecule can be extracted, together with the Euler angles which relate the principal axes of the molecule to the laboratory frame axes. This is achieved by nding the maximum and minimum values for the measured moments from many single-molecule patterns. Simulations for GroEL protein indicates that the calculation of the autocorrelation help eliminate the Poisson noise in Cryo- EM images and can make correct orientation determination. The eect of water jacket surrounding the protein molecule is studied based on molecular dynamics simulation result. The intensities from water and interference is found to suppress those from protein itself. A method is proposed and applied to the simulation data to show the possibility for it to overcome the water background problem. The scattering between Bragg re ections from nanocrystals is used to aid solution of the phase problem. We describe a method for reconstructing the charge density of a typical molecule within a single unit cell, if suciently nely-sampled diraction data are available from many nanocrystals of dierent sizes lying in the same orientations without knowledge of the distribution of particle size or requiring atomic-resolution data. Triple correlation of the diraction patterns are made use of to reconiii
Dissertation/Thesis
Ph.D. Physics 2011

abstract: Photosystem II (PSII) is a large protein-cofactor complex. The first step in photosynthesis involves the harvesting of light energy from the sun by the antenna (made of pigments) of the PSII trans-membrane complex. The harvested excitation energy is transferred from the antenna complex to the reaction center of the PSII, which leads to a light-driven charge separation event, from water to plastoquinone. This phenomenal process has been producing the oxygen that maintains the oxygenic environment of our planet for the past 2.5 billion years. The oxygen molecule formation involves the light-driven extraction of 4 electrons and protons from two water molecules through a multistep reaction, in which the Oxygen Evolving Center (OEC) of PSII cycles through 5 different oxidation states, S0 to S4. Unraveling the water-splitting mechanism remains as a grant challenge in the field of photosynthesis research. This requires the development of an entirely new capability, the ability to produce molecular movies. This dissertation advances a novel technique, Serial Femtosecond X-ray crystallography (SFX), into a new realm whereby such time-resolved molecular movies may be attained. The ultimate goal is to make a “molecular movie” that reveals the dynamics of the water splitting mechanism using time-resolved SFX (TRSFX) experiments and the uniquely enabling features of X-ray Free-Electron Laser (XFEL) for the study of biological processes. This thesis presents the development of SFX techniques, including development of new methods to analyze millions of diffraction patterns (~100 terabytes of data per XFEL experiment) with the goal of solving the X-ray structures in different transition states. ii The research comprises significant advancements to XFEL software packages (e.g., Cheetah and CrystFEL). Initially these programs could evaluate only 8-10% of all the data acquired successfully. This research demonstrates that with manual optimizations, the evaluation success rate was enhanced to 40-50%. These improvements have enabled TR-SFX, for the first time, to examine the double excited state (S3) of PSII at 5.5-Å. This breakthrough demonstrated the first indication of conformational changes between the ground (S1) and the double-excited (S3) states, a result fully consistent with theoretical predictions. The power of the TR-SFX technique was further demonstrated with proof-of principle experiments on Photoactive Yellow Protein (PYP) micro-crystals that high temporal (10-ns) and spatial (1.5-Å) resolution structures could be achieved. In summary, this dissertation research heralds the development of the TR-SFX technique, protocols, and associated data analysis methods that will usher into practice a new era in structural biology for the recording of ‘molecular movies’ of any biomolecular process.
Dissertation/Thesis
Doctoral Dissertation Chemistry 2015

abstract: Structural details about viruses and their components are important for understanding the many steps in a virus life-cycle, including entry into host cells, replication, assembly, and release of progeny virions. X-ray crystallography and electron microscopy, including cryo-EM, have been used extensively for virus structural studies. Recent advances with cryo-EM have significantly advanced the field with near-atomic resolution structures of viruses being achievable. X-ray free-electron lasers (XFELs) are a novel, developing method to solve structures for non-crystalline single particle targets like viruses. Diffraction patterns can be collected directly from particles at room temperature. High quality, homogeneous virus preparations are critical for both cryo-EM and XFEL studies. Thus, optimization of virus growth and sample preparation are important steps in virus structural studies. The work described in this thesis focused on optimization of protocols for growth and purification of bacteriophage PR772 for XFEL and complementary cryo-EM studies. PR772 is one of several model viruses used in the single particle initiative (SPI) experiments at the SLAC National Laboratory Accelerator Laboratory Linac Coherent Light Source (LCLS). SPI is a collaborative international effort that works towards identifying and solving challenges of high-resolution single particle imaging using XFELs. Single particle diffraction snapshots were collected from PR772 particles prepared with optimized protocols. PR772 preparations were also used for cryo-EM imaging, with the goal to obtain a high-resolution structure of the virus. The optimization and characterization employed to assure samples suitable for XFEL and cryo-EM are detailed, along with data collected with both approaches.
Dissertation/Thesis
Masters Thesis Microbiology 2019