Der Betrieb eines Freien Elektronen Lasers (FEL), bei dem die spontan emittierte Undulatorstrahlung ueber Wechselwirkung mit dem Elektronenstrahl selbst verstaerkt wird, setzt eine praezise Ausrichtung des Elektronenstrahls mit dem Photonenstrahl voraus. Um den Ueberlapp von Elektronen-und Photonenstrahl zu gewaehrleisten, wurde ein neuartiger Typ von Wellenleiter-Strahllagemonitor entwickelt, der in eine Vakuumkammer des Undulators des FELs der TESLA Test Facility (TTF) integriert ist. Vier um das Strahlrohr verteilte Wellenleiter koppeln ueber schmale Schlitze einen Bruchteil jenes elektromagnetischen Feldes aus, welches den Strahl begleitet. Die induzierten Signale haengen von der transversalen Strahlposition und der Strahlintensitaet ab. Mit vier Schlitz-Wellenleiter Paaren laesst sich ein lineares Signal ableiten, anhand dessen die Position des Elektronenstrahls bestimmt werden kann. Die induzierten Signale werden mittels eines stegbelasteten Wellenleiters in die erste Stufe eines bei 12 GHz arbeitenden Empfaengers zugefuehrt. Die vorliegende Arbeit beschreibt Design, Tests und Implementierung dieses neuartigen Typs von Strahllagemonitor. / The operation of a free electron laser working in the Self Amplified Spontaneous Emission mode (SASE FEL) requires the electron trajectory to be aligned with very high precision in overlap with the photon beam. In order to ensure this overlap, one module of the SASE FEL undulator at the TESLA Test Facility (TTF) is equipped with a new type of waveguide beam position monitor (BPM). Four waveguides are arranged symmetrically around the beam pipe, each channel couples through a small slot to the electromagnetic beam field. The induced signal depends on the beam intensity and on the transverse beam position in terms of beam--to--slot distance. With four slot--waveguide combinations a linear position sensitive signal can be achieved, which is independent of the beam intensity. The signals transduced by the slots are transferred by ridged waveguides through an impedance matching stage into a narrowband receiver tuned to 12 GHz. The present thesis describes design, tests, and implementation of this new type of BPM.

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.

Les lasers à électrons libres (LELs) à simple passage représentent actuellement la possibilité la plus prometteuse pour fournir des impulsions lumineuses de haute énergie (µJ à mJ) à des échelles de durée femtoseconde (1 fs = 10⁻¹⁵s) et des longueurs d’ondes ultra-courtes (résolution nanométrique i.e., jusqu’aux domaines de l’extrême-ultraviolet et des rayons X). Les LELs émettant dans l’extrême-ultraviolet sont une technologie encore jeune, si bien que de nombreuses questions restent ouvertes. Celles posées au sein de ce manuscrit concernent la configuration dite injectée, dans laquelle le processus est initié par une source externe cohérente (le “seed"). Nous nous concentrons particulièrement dans cette thèse sur les caractéristiques transverses et longitudinales de la lumière, sa cohérence, les propriétés de la phase temporelle et les liens directs entre le seed et l’émission LEL. La technique de génération dans un gaz noble d’harmoniques d’ordres élevés d’un laser femtoseconde (GHE) se montre à la fois complémentaire et en compétition avec les LELs. En compétition car les impulsions produites ont des qualités similaires à celles obtenues avec un LEL ; complémentaire car le rayonnement GHE peut être utilisé comme seed ou en combinaison avec la lumière LEL, par exemple pour effectuer des expériences mettant en jeu de multiples faisceaux. Bien que la GHE fournisse des impulsions moins puissantes, l’implémentation d’une telle source requiert un effort significativement moins important. Le taux de conversion harmonique, l’accordabilité et la qualité spatiale du faisceau généré, et la manière dont ces paramètres dépendent du laser générateur sont les problématiques traitées au sein de ce manuscrit. La volonté de la communauté scientifique d’effectuer des expériences novatrices demande des études profondes et l’optimisation des sources de GHE et des LELs. En particulier, sur la source LEL injectée FERMI@Elettra de Trieste, l’induction d’une dérive de fréquence dans le rayonnement a conduit à des résultats marquants. Entre autres, une méthode de génération d’impulsions scindées avec différentes longueurs d’ondes a été analysée et développée. Une telle possibilité ouvre la voie à l’utilisation des LELs injectés en tant que source autonome pour des installations de type pompe-sonde à deux couleurs. Plus généralement, l’étude des phénomènes mis en jeu dans les processus de GHE et du LEL ainsi que la caractérisation des propriétés de leur lumière sont des sujets intrinsèquement excitants, ayant des connexions directes avec de nombreux aspects fondamentaux de la physique. / Single-pass free-electron lasers (FELs) are currently the most promising facilities for providing light pulses with high energies (µJ to mJ) at femtosecond time scales (1 fs = 10⁻¹⁵s) and with ultrashort wavelengths (nanometer resolution i.e., down to extreme-ultraviolet and X-ray spectral regions). Extreme-ultraviolet FELs are still quite young so that many questions remain open. Those addressed within this manuscript concern the so-called seeded configuration, where an external coherent source (the “seed") initiates the process. In particular, we focus in this thesis on the transverse and longitudinal characteristics of the light, its coherence, the properties of the temporal phase and the direct correlations between the seed and the FEL emission. With regard to FELs, high-order harmonics of femtosecond laser pulses generated in noble gases (HHG technique) exhibit both competitive and complementary features. Competitive, because the produced pulses have similar assets as the ones provided by an FEL. Complementary, because the generated harmonics can be used as a seed or, in combination with FEL light, to perform multi-beam experiments. Even though less powerful pulses are produced by a HHG source, its implementation requires a significantly smaller effort. The efficiency of harmonic conversion, the tunability and spatial quality of the generated beam, and how these parameters depend on the driving laser are the issues discussed within this manuscript. The general will of the scientific community to perform novel experiments requires deep studies and optimization of FEL and HHG sources. In particular, on the seeded FEL facility FERMI@Elettra of Trieste, the induction of chirp in the radiation has led to remarkable results. Among others, a method of generation of split pulses with different wavelengths has been construed and developed. Such a possibility paves the way for the use of seeded FEL facilities as stand-alone sources for two-colour pump-probe setups. More generally, the study of phenomena involved in the FEL and HHG processes, together with the characterization of the light properties, are intrinsically exciting matters that have direct connections with fundamental aspects of physics. / Laser na proste elektrone (LPE, ang. free-electron laser - FEL) z enojnim prehodom je trenutno najbolj obetaven vir femtosekundnih (1 fs = 10⁻¹⁵ s) svetlobnih pulzov z visoko energijo (μJ do mJ) in ultra kratko valovno dolžino (nanometrska ločljivost, t.j., vse do spektralnega območja ekstremne ultravijolične in rentgenske svetlobe). LPE-ji, ki delujejo na področju ekstremne ultravijolične svetlobe, so razmeroma novi svetlobni viri, kar pomeni, da so glede njihovega delovanja odprta še mnoga vprašanja. V pričujočem doktorskem delu smo se ukvarjali predvsem z dvostopenjsko konfiguracijo, pri kateri LPE ojači zunanje (koherentno) elektromagnetno valovanje (seed). Osredotočili smo se na transverzalne in longitudinalne lastnosti proizvedene svetlobe, koherenco, lastnosti časovne faze ter na direktne korelacije med zunanjim virom (seed) in sevanjem LPE-ja. Poleg LPE-jev so v vzponu tudi svetlobni viri, ki temeljijo na generaciji visokih harmonikov (GVH, ang. high-order harmonic generation - HHG) v žlahtnih plinih. Ti svetlobni viri so zaradi podobnih lastnosti pulzov konkurenčni LPE-jem, po drugi strani pa predstavljajo komplementarne izvore svetlobe, ker jih je mogoče uporabiti v dvostopenjski LPE konfiguraciji kot vir zunanjega elektromagnetnega valovanja (seed) ali v kombinaciji z LPE-jem v eksperimentih z dvema ali več žarki. Kljub temu, da so ti svetlobni viri šibkejši v primerjavi z LPE-ji, je njihova izvedba bistveno lažja. V dizertaciji obravnavamo izkoristek harmonične pretvorbe virov, ki temeljijo na principu GVH, nastavljivost in prostorsko kakovost žarkov, ter odvisnost omenjenih parametrov od gonilnega laserja. Zaradi vse večje težnje po novih eksperimentih na vseh znanstvenih področjih sta ključna zelo natančno poznavanje delovanja in optimizacija LPE-jev in virov, ki temeljijo na GVH. Med bolj pomembne dosežke na LPE-ju FERMI@Elettra v Trstu spadajo možnost spreminjanja trenutne frekvence proizvedene svetlobe (ang. chirp) na podlagi katere je bila razvita metoda za generacijo razdeljenih pulzov z različnimi valovnimi dolžinami. S pomočjo te metode bo možno dvostopenjske LPE-je uporabljati kot samostojne vire svetlobe za poskuse v t.i. načinu « pump-probe ». V dizertaciji so predstavljene študije pojavov, ki so prisotni pri generaciji svetlobe v LPE-jih ter virih, ki temeljijo na GVH. Ti pojavi so, skupaj z metodami karakterizacije proizvedene svetlobe, tesno povezani s temeljnimi principi v fiziki.

<p>Metalloproteins, or proteins with a metal ion cofactor, are essential for biological function of both lower and higher level organisms. These proteins provide a multitude of functions from molecular transport, such as the hemoglobin transport of oxygen, to biologically important catalytic processes. As an example case, photosystem II (PSII) is studied as a representative metalloprotein. It was chosen based on the potential impact in the energy sector due to its ability to perform water oxidation using solar based energy. Understanding mechanisms by which the Mn₄Ca cluster inside PSII, also known as the oxygen evolving complex (OEC), can store energy as redox equivalents for splitting water will be essential for future development of analogous artificial systems. By using time resolved x-ray spectroscopy, the electron structure of the metal in the protein was probed through the catalytic cycle. While the applications mentioned herein are based on PSII from spinach, the developments in time-resolved x-ray spectroscopy techniques are also applicable to other metalloproteins.</p><p></p><p>By creating a new x-ray spectrometer we were able to capture the difference in x-ray emission spectra between two compounds differing in a single metal bound ligand, i.e. Mn^IV-OH and Mn^IV=O. This both establishes the functionality of the x-ray emission spectrometer and provides useful insight into the expected changes upon an oxygen double bond formation. This change in spectroscopic signal is discussed in context of the OEC which has been hypothesized to form a Mn^IV=O state.</p><p></p><p>A new sample delivery system and further developments to the x-ray spectrometer enabled both time-resolved x-ray absorption and time-resolved x-ray emission of PSII. These experiments show the potential of synchrotron sources for time-resolved x-ray spectroscopy. From our x-ray absorption measurements we were able to follow the electronic structure changes in time using a single incident photon energy. From the kinetic traces obtained, we show possible alternative interpretations of previous results showing a delay in reduction during the final step in water oxidation. From the x-ray emission spectroscopy (XES) measurements of PSII we were able to reproduce previous results within a limited collection time and give estimates for data size requirements for metalloproteins using this spectrometer. Between the results of both these measurements, we show the improved capability for time resolved measurements at synchrotrons.</p><p>The development of x-ray free electron lasers (XFELs) has also opened many opportunities for understanding faster electronic dynamics by providing femtosecond x-ray pulse durations with ~10¹² photons per pulse. While theoretical modeling of distortions to crystallographic data have been performed, little to no work has been done to understand under what conditions such an intense pulse will have on an impact on emission spectra. Here an atomistic model was developed, and data collected, to clarify the effects of sequential ionization, i.e. two single photons absorbed by the same atom at different times during a single pulse. Experimentally we found that XFELs easily achieve flux densities that invoke a different response than is classically observed for single photon absorption and emission for Mn^II which was used as a representative case for 3d transition metals in general. We also give parameters by which the onset of this damage can be predicted and an approximation to its effect on 3d transition metals. Additionally this work guides the work of future XFEL facilities as it shows that shorter pulses, currently believed to be able to escape x-ray induced distortions to crystallography data, is not a viable method for overcoming changes in x-ray emission spectra.</p><div><br></div>

No description available.

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.

L’obtention d’un Laser à Électrons Libres X (LEL-X) compact est un objectif majeur pour le développement des lasers. Plusieurs schémas prometteurs de LEL-X ont été proposés en utilisant à la fois l’accélération d’électrons dans les plasmas et des onduleurs optiques en régime Compton ou Compton inverse. Nous avons proposé un nouveau concept de LEL-X compact baptisé Raman XFEL, en combinant la physique des LEL en régime Compton, des lasers XUV conventionnels basés sur l’interaction laser plasma, et de l’optique non-linéaire. Nous étudions dans cette thèse les étapes préalables pour déclencher un effet laser à rayons X lors de l’interaction entre un paquet d’électrons libres relativistes et un réseau optique créé par l’interférence transverse de deux impulsions laser intenses. Dans cet objectif j’ai développé un code particulaire baptisé RELIC. Les études menées avec le code RELIC nous ont permis d’étudier la dynamique d’électrons relativistes et les processus d’injection du paquet d’électrons dans le réseau optique. Grâce à RELIC, nous avons distingué de nouveaux régimes d’interaction en fonction des paramètres du paquet d’électrons, ainsi que de la géométrie du réseau optique. Ces études ont été appliquées à l’amplification du rayonnement X et appuyées par des simulations PIC. RELIC a également permis de modéliser et d’analyser la première expérience réalisée en octobre 2015 sur l’installation laser ’Salle Jaune’ au Laboratoire d’Optique Appliquée (LOA). Cette première expérience a été une étape très importante pour la validation des modèles théoriques, et pour la réalisation future d’un laser à électrons libre X Raman. / The quest for a compact X-ray laser has long been a major objective of laser science. Several schemes using optical undulators are currently considered, in order to trigger the amplification of back scattered radiation, in Compton or inverse Compton regime. We have proposed a new concept of compact XFEL based on a combination between the physics of free electron lasers, of laser-plasma interactions, and of nonlinear optics. In this thesis, we study the necessary steps to trigger a X-ray laser during the interaction between a free relativistic electron bunch and an optical lattice created by the interference of two intense transverse laser pulses. For this purpose I developed a particular tracking code dubbed RELIC. RELIC allowed us to study the dynamics and injection process of a bunch of relativistic electrons into the optical lattice. Thanks to RELIC, we distinguished several interaction regimes depending on the relativistic electron bunch parameters, and on those of the optical lattice and its geometry. These studies are applied to the X ray amplification and supported by PIC simulations. RELIC also allowed us to model and analyze the first experiment conducted in october 2015 on the ”Salle Jaune” laser facility at LOA. This first experiment was very important to validate our theoretical models, and should prove to be an essential milestone for the development of a Raman X-ray free electron laser.

Near-field microscopy is a versatile technique for non-destructive detection of optical properties on the nanometer scale. Contrary to conventional microscopy techniques, the resolution in near-field microscopy is not restricted by the diffraction limit, but by the size of the probe only. Typically, wavelength-independent resolution in the range of few ten nanometers can be achieved. Many fundamental phenomena in solid states occur at such small length scales and can be probed by infrared and THz radiation. In the present work, nanoscale charge carrier distributions were investigated with near-field microscopy in classic semiconductors and state-of-the-art graphene field-effect transistors. A CO2 laser, the free-electron laser FELBE at the Helmholtz-Zentrum Dresden Rossendorf and a photoconductive antenna were applied as radiation sources for illumination of the samples. In the theoretical part of the work, the band model for charge carriers in semiconductors is briefly explained to derive typical charge carrier densities of such materials. The influence of the charge carriers to the light-matter interaction is introduced via the Drude model and evaluated for both infrared and THz radiation. In field-effect transistors, charge carrier density waves can occur when strong AC fields are coupled into the device. The phenomena in such transistors are introduced as a more complex material system. To describe the near-field coupling of the samples to the nanoscopic probe, the dipole model is introduced and extended for periodic charge carrier density, as elicited by low repetition-rate excitation lasers. Consequently, sidebands occur as new frequencies in the signal spectrum, allowing for a more sensitive probing of such transient processes. Experimental investigations of these sidebands were performed with a CO2 laser setup on a bulk germanium sample which was excited with femtosecond laser pulses. New frequencies up to the 8th sideband could be observed. The results show a characteristic near-field decay for all sidebands when the probe-sample distance is increased. A nanoscale material contrast in the sidebands signatures has been demonstrated via near-field scans on a gold / germanium heterostructure. Near-field signatures of graphene-field effect transistors have been examined utilizing FELBE. The results match the predicted behavior of charge carriers in such a device and in particular represent the first direct observations of the plasma waves. In collaboration with the group of Prof. Dr. Hartmut G. Roskos (Goethe-Universität Frankfurt), the plasma wave velocity in the graphene field-effect transistor has been derived via fitting to the model for two datasets on different devices from independent fabrications. The obtained velocity is in good agreement with literature values. The results promise the application of field-effect transistors as THz detectors and emitters and may lead to faster communication technology.:1 Introduction 2 Fundamentals 2.1 Semiconductors 2.2 Plasma Waves in Graphene Field-Effect Transistors 2.3 Near-Field Microscopy 2.3.1 Aperture-SNOM 2.3.2 Scattering-SNOM 2.4 THz Optics 3 SNOM-Theory 3.1 Dipole Model 3.2 Detection and Demodulation 3.3 Pump-induced Sidebands in SNOM 3.4 Field Enhancement by Resonant Probes 4 Near-Field Microscope Setups 4.1 FELBE THz SNOM 4.2 Pump-modulated s-SNOM 4.3 THz Time-Domain-Spectroscopy SNOM 5 Sideband Results 5.1 Pump-induced Sidebands in Germanium 5.2 Fluence Dependence 5.3 Higher-order sidebands 5.4 Oscillation Amplitude 5.5 Technical Aspects of the Sideband Demodulation 6 Field-Effect Transistors 6.1 Device Design 6.2 Data Analysis 6.3 Near-Field Overview Scans 6.4 Plasma Wave Examination 6.5 Conclusion 7 Discussion and Outlook A Appendix A.1 Scanning Probe Microscopy A.2 Atomic Force Microscope List of Figures Bibliography / Nahfeldmikroskopie ist eine vielseite Technik für das zerstörungsfreie Auslesen von optischen Eigenschaften auf der Nanoskala. Im Gegensatz zur konventionellen Mikroskopie ist die Auflösung nicht durch Beugungseffekte, sondern durch die Größe der genutzten Sonde begrenzt. Überlicherweise werden wellenlängenunabhängig Auflösungen von einigen zehn Nanometern erreicht. Viele fundamentale Prozesse in der Festkörperphysik treten auf Längenskalen dieser Größenordnung auf und können mit Infrarot- und THz-Strahlung untersucht werden. In dieser Arbeit wurden nanoskalige Ladungsträgerverteilungen mit Rasternahfeldmikroskopie untersucht, einerseits in klassischen Halbleitern, anderseits in state-of-the-art Graphen Feldeffekttransistoren. Zur Beleuchtung der Proben wurden ein CO2 Laser, der freie-Elektronen Laser FELBE am Helmholtz-Zentrum Dresden-Rossendorf und eine photoleitende Antenne verwendet. Im theoretischen Teil der Arbeit wird das Bändermodell für Ladungsträger in Halbleitern erklärt, um daraus typische Ladungsträgerdichten in diesen Materialien abzuleiten. Der Einfluss der Ladungsträger auf die Interaktion mit Strahlung wird durch das Drude-Modell eingeführt und für Infrarot- und THz-Strahlung abgeschätzt. In Graphen Feldeffekttransistoren können Ladungsträgerdichtewellen auftreten, wenn starke Wechselfelder in das Bauelement eingekoppelt werden. Die Prozesse in solchen Transistoren werden als komplexeres Materialsystem eingeführt. Um die Nahfeldkopplung der Proben an die Sonde zu beschreiben, wird das Dipol-Modell eingeführt und für periodische Ladungsträgerdichten erweitert, wie sie bspw. durch Pumplaser mit niedrigen Repetitionsraten erzeugt werden können. In der Folge entstehen Seitenbänder als neue Frequenzen im Signalspektrum, welche eine sensitivere Messung solcher transienten Prozesse ermöglichen. Experimentelle Untersuchungen des erweiterten Dipol-Modells wurden mit einem CO2 Laser Aufbau an einem Germaniumkristall durchgeführt, welcher mit Femtosekunden Laserpulsen angeregt wird. Neue Frequenzen im Spektrum konnten bis zu dem achten Seitenband beobachtet werden. Die Resultate zeigen den typischen Abfall des Nahfeldes, wenn der Abstand zwischen Sonde und Probe vergrößert wird. Ein Materialkontrast auf der Nanoskale im Seitenband-Signal konnte durch laterale Rasternahfeld-Scans auf einer Gold/Germanium Heterostruktur gezeigt werden. Die Nahfeldsignaturen der Graphen Feldeffekttransistoren wurden mit FELBE untersucht. Die Resultate stimmen mit dem vorausgesagtem Verhalten der Ladungsträger in einem solchen Bauteil überein und sind die erste direkte Beobachtung solcher Plasmawellen. In Kooperation mit der Gruppe um Prof. Dr. Hartmut G. Roskos (Goethe-Universität Frankfurt) wurde die Geschwindigkeit der Plasmawelle durch Regression der Daten berechnet. Dabei wurden zwei Datensätzen an Bauteilen von unabhängigen Fabrikationsprozessen genutzt. Die berechnete Geschwindigkeit ist in guter Übereinstimmung mit Literaturwerten. Die Resultate verheißen die Anwendung von Feldeffekttransistoren als THz Sender und Detektoren und könnten zu schnellerer Kommunikationstechnologie führen.:1 Introduction 2 Fundamentals 2.1 Semiconductors 2.2 Plasma Waves in Graphene Field-Effect Transistors 2.3 Near-Field Microscopy 2.3.1 Aperture-SNOM 2.3.2 Scattering-SNOM 2.4 THz Optics 3 SNOM-Theory 3.1 Dipole Model 3.2 Detection and Demodulation 3.3 Pump-induced Sidebands in SNOM 3.4 Field Enhancement by Resonant Probes 4 Near-Field Microscope Setups 4.1 FELBE THz SNOM 4.2 Pump-modulated s-SNOM 4.3 THz Time-Domain-Spectroscopy SNOM 5 Sideband Results 5.1 Pump-induced Sidebands in Germanium 5.2 Fluence Dependence 5.3 Higher-order sidebands 5.4 Oscillation Amplitude 5.5 Technical Aspects of the Sideband Demodulation 6 Field-Effect Transistors 6.1 Device Design 6.2 Data Analysis 6.3 Near-Field Overview Scans 6.4 Plasma Wave Examination 6.5 Conclusion 7 Discussion and Outlook A Appendix A.1 Scanning Probe Microscopy A.2 Atomic Force Microscope List of Figures Bibliography

An advent of powerful sources producing intense and ultrashort laser pulses containing high-energy photons opened up a wide range of possibilities to conduct experiments formerly achievable only through theoretical calculations and models. This thesis provides a complex overview of processes which occur right after arrival of the first photons, through lattice heating, up to resolidification and formation of irreversible changes. Irradiated spots and craters formed in various materials are examined employing a wide range of microscopic and spectroscopic methods which provide a deep insight into laser-induced modifications such as detachment of a graphene layer from SiC substrate or thermally-induced diffusion of tellurium inclusions through CdTe lattice. An increased emphasis is placed on beam characterization utilizing ablation and desorption imprints in suitable solids. A proper knowledge of the beam fluence profile may serve for evaluation of diverse damage thresholds as well as for modelling of the pulse propagation or consequent retrieval of otherwise unmeasurable opacity of warm dense aluminium plasma heated to temperatures exceeding tens of thousands of Kelvins. Moreover, the method of desorption imprints is extended to accurate characterization of pulses delivered at MHz repetition rate....

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.