In this thesis we investigate two potential applications of machine learning in the context of X-ray imaging and spectroscopy of biological samples, particularly such using X-ray free electron lasers (XFEL). We first investigate the possibility of using an emission spectrum, recorded from a sample after being probed by an incident X-ray, as a diagnostic tool. We produced a training dataset of simulated emission spectra, where the incident X-ray energy and fluence was varied as well as the sample density. The simulations were implemented using Cretin which is a radiation transfer code which model the behaviour of plasma. We then trained a dense neural network to predict the three above named features given an emission spectrum. The dependency between input and output is inherently non-linear, making neural networks a suitable method for these predictions. Our results show a mean prediction error of below 6% of the entire range of all three features. If a similar tool was to be implemented in real life XFEL experiments, it could provide useful information in the data analysis pipeline.   As a second focus of this thesis we aim to produce an application to be used by researchers in XFEL experiments. Given a set of input parameters, including the incident X-ray energy and fluence along with atomic content and density of the sample, our application generates an emission spectrum for the user. The application is based on a neural network trained on Cretin simulations. When evaluated by comparing the final model to simulations, our model was found to have a mean absolute percentage prediction error of 1.77%. In addition to this we include similar models that generate the time development of the electron temperature and mean ionization of the sample, since these properties are highly associated with the emission processes of plasma. We did this by training dense neural networks on a dataset consisting of simulations of the corresponding property. Finally we integrated our models in a graphical user interface web application, accessible via the QR code. With this approach, the desired data can be plotted in real-time in a user-friendly manner, without having to run complicated and time-consuming simulations. Our model is focused on biological samples and could be used as a reference tool in structural biology.

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.

X-ray free-electron lasers (XFELs) can achieve near-atomic resolution in imaging organic molecules. As a fourth-generation light source, modern XFELs can generate brilliant ultrashort X-ray pulses at MHz repetition rates. This allows XFELs to image single molecules with great detail, obtaining information about their dynamics and states through the interaction of the electrons within the molecule with the X-rays. A key challenge when imaging biomolecules (e.g. proteins, viruses, or bacteria) is to image the sample within its native environment, in solution. 3D-printed gas-accelerated liquid-sheet jet nozzles for liquid sample-delivery have yielded promising results in this respect, demonstrating that liquid sheets can be a reliable alternative to conventional sample-delivery methods, e.g. electrospray. Although the nozzles that this project uses have been successfully used for measurements at XFELs, the effect of nozzle design and liquid material-properties have not previously been explored. Therefore, the present report aims to explore different flow regimes of gas-accelerated liquid-sheet jets, and to study how the generated sheet jet depends upon different parameters, such as gas and liquid flow-rates, sample solution, and nozzle geometry. The findings suggest that low surface tension is crucial for producing large jets, and that higher viscosity may help to generate more stable sheet jets. However, further studies are required to draw definite conclusions.

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.

<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>

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.