Characterization of the dynamic behavior of defect-bearing ablator materials subjected to extreme conditions is essential in advancing fusion energy as an reliable and abundant energy source. By understanding how materials evolve spatially and temporally we can minimize hydrodynamic instabilities, which are major contributing factors to energy yield degradation in inertial confinement fusion (ICF) experiments. In this thesis we demonstrate the capabilities of an ultrafast x-ray imaging (UXI) detector, the Icarus V2, where we capture multiple frames of single void-bearing sample compressed by a high-intensity laser shockwave. Using the Matter in Extreme Conditions (MEC) instrument at the Linac Coherent Light Source (LCLS), we conducted two experiments with the x-ray free electron laser (XFEL) multi-pulse mode, delivering four nanosecond-separated pulses to a sample impacted by a laser shockwave, obtaining multiframe images of a single sample in the holographic and direct imaging regime with the UXI detector. In contrast to the low temporal resolution provided by current cameras, the Icarus V2 can capture images with high temporal resolution, which can be used to determine the mechanisms that prevent thermonuclear ignition in ICF experiments. For images captured in the holographic regime at our XFEL energy of 8.23 keV, we realized that the shock front was obscured by strong phase-contrast effects. We recognized that by increasing the XFEL energy while in the holographic regime, more distinguishable features could be revealed behind and along the shock front. Alternatively, in the direct-imaging configuration we discovered that the evolution of microstructural features were directly recognizable in comparison to the holographic regime at lower XFEL energies. Overall, the images captured by the UXI in both regimes demonstrated our ability to obtain multiframe images of processes that occur over several nanoseconds for single samples, which has never been done before. Moreover, the capabilities of the UXI enable extraction of quantitative information over multiple frames, which can help with uncovering the underlying physics involved in high energy density (HED) physics experiments and other experiments involving non-repeatable ultrafast phenomena. Specifically, insight into the behavior of the void can be gained by performing phase retrieval on the images and obtaining the areal density of the materials during laser-shock ablation. Generally, the UXI improves data acquisition speed and operational efficiency, which extends this camera's functionality to experiments that occur at various time scales or experiments that require multiple images to be captured.

No description available.

abstract: Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These new methods include serial femtosecond crystallography, single particle imaging, solution scattering, and time resolved techniques. The XFEL is characterized by high intensity pulses, which are only about 50 femtoseconds in duration. The intensity allows for scattering from microscopic particles, while the short pulses offer a way to outrun radiation damage. XFELs are powerful enough to obliterate most samples in a single pulse. While this allows for a “diffract and destroy” methodology, it also requires instrumentation that can position microscopic particles into the X-ray beam (which may also be microscopic), continuously renew the sample after each pulse, and maintain sample viability during data collection. Typically these experiments have used liquid microjets to continuously renew sample. The high flow rate associated with liquid microjets requires large amounts of sample, most of which runs to waste between pulses. An injector designed to stream a viscous gel-like material called lipidic cubic phase (LCP) was developed to address this problem. LCP, commonly used as a growth medium for membrane protein crystals, lends itself to low flow rate jetting and so reduces the amount of sample wasted significantly. This work discusses sample delivery and injection for XFEL experiments. It reviews the liquid microjet method extensively, and presents the LCP injector as a novel device for serial crystallography, including detailed protocols for the LCP injector and anti-settler operation. / Dissertation/Thesis / Doctoral Dissertation Physics 2015

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.

Die Arbeit beschäftigt sich mit der neuartigen Wechselwirkung von intensiven und ultrakurzen Röntgenlaserpulsen mit atomaren endlichen Systemen, die derzeit durch eine neue Generation von Lichtquellen, sogenannter X-ray free-electron laser (XFEL) zugänglich gemacht wird. Eine der Vorzeigeanwendungen der XFELs ist die zukünftig potentiell mögliche Strukturbestimmung endlicher nicht-periodischer Systeme mit atomarer Auflösung durch Diffraktion. Hierbei stellt sich der durch die hohe notwendige Pulsintensität bedingte Strahlenschaden an dem System als limitierender Faktor heraus, der ein detailliertes Verständnis der durch Photoabsorption induzierten Dynamik voraussetzt, um diese Art der "Mikroskopie" zum Erfolg zu führen. Wir verwenden daher zur Beschreibung der laserinduzierten Dynamik ein mikroskopisches Modell in dem Photoionisation und inner-atomare Zerfallsprozesse durch quantenmechanische Raten behandelt werden und die Dynamik der Ionen und energetischen Elektronen in einer klassischen Molekulardynamik-Simulation erfasst wird. Eine Neuerung gegenüber bisherigen Modellen ist die Berücksichtigung der Ionisation von Atomen durch starke interne Felder in dem hoch-geladenen System. Durch eine Anwendung des Modells auf Neoncluster kann gezeigt werden, dass diese Feldionisation einen wichtigen Beitrag zur laserinduzierten Dynamik darstellt. Sie führt zur ultraschnellen Formation eines Nanoplasmas, welches sich im Kern des geladenen Clusters ansammelt und dort die Ladung der Clusterionen neutralisert. Hierdurch wird eine vorzeitige Coulomb-Explosion des Clusters vermieden. Es wird dargelegt, dass dieser Mechanismus der lokalen Schadensreduzierung durch die Einbettung des Clusters in ein Heliumtröpfchen auf den gesamten Cluster ausgeweitet werden kann, da durch Feldionisation und Migration von Elektronen die vollständige laserbedingte Aufladung des Clusters auf das Heliumtröpfchen transferiert wird. Eine Analyse der resultierenden Diffraktionsmuster bestätigt, dass der reduzierte Strahlenschaden am Cluster den Anwendungsbereich für Diffraktionsexperimente erheblich ausweitet. Kürzlich wurde am SLAC National Accelerator Laboratory der erste XFEL in Betrieb genommen. Eine Modifikation des Modells auf dort bereits erzielbare Wellenlängen wird genutzt um Vorhersagen über das Photoabsorptionsverhalten, aus dem alle weiteren Schäden folgen, an kleinen Neoncluster zu treffen. Hiermit lassen sich bereits jetzt durch den Vergleich zu Experimenten die wichtigen Schadensmechanismen und ihre theoretische Beschreibung testen. Es wird ferner das interessante Relaxationsverhalten des durch massive Photoionisation in XFEL-Strahlung erzeugten Elektronenplasmas untersucht. Diese neuartige Anregung erfolgt auf einer Femtosekunden-Zeitskala und produziert eine hohe Dichte an energetischen Elektronen. Wir beschreiben dieses Plasma durch ein generisches Modell seiner Vielteilchen-Dynamik. Hierbei kann der gesamte Parameterraum des Modells in vier Klassen unterteilt werden, die sich nach Anregungsgrad, der den Elektronenverlust des Plasmas regelt, und Anregungsdauer, die die transiente Dynamik beeinflusst, unterscheiden. Speziell der Bereich starker Anregung bei gleichzeitig kurzer Anregungsdauer zeigt ein interessantes neues Verhalten, bei dem sich eine Equilibrierung des Systems im Kontinuum andeutet.

Die Arbeit beschäftigt sich mit der neuartigen Wechselwirkung von intensiven und ultrakurzen Röntgenlaserpulsen mit atomaren endlichen Systemen, die derzeit durch eine neue Generation von Lichtquellen, sogenannter X-ray free-electron laser (XFEL) zugänglich gemacht wird. Eine der Vorzeigeanwendungen der XFELs ist die zukünftig potentiell mögliche Strukturbestimmung endlicher nicht-periodischer Systeme mit atomarer Auflösung durch Diffraktion. Hierbei stellt sich der durch die hohe notwendige Pulsintensität bedingte Strahlenschaden an dem System als limitierender Faktor heraus, der ein detailliertes Verständnis der durch Photoabsorption induzierten Dynamik voraussetzt, um diese Art der "Mikroskopie" zum Erfolg zu führen. Wir verwenden daher zur Beschreibung der laserinduzierten Dynamik ein mikroskopisches Modell in dem Photoionisation und inner-atomare Zerfallsprozesse durch quantenmechanische Raten behandelt werden und die Dynamik der Ionen und energetischen Elektronen in einer klassischen Molekulardynamik-Simulation erfasst wird. Eine Neuerung gegenüber bisherigen Modellen ist die Berücksichtigung der Ionisation von Atomen durch starke interne Felder in dem hoch-geladenen System. Durch eine Anwendung des Modells auf Neoncluster kann gezeigt werden, dass diese Feldionisation einen wichtigen Beitrag zur laserinduzierten Dynamik darstellt. Sie führt zur ultraschnellen Formation eines Nanoplasmas, welches sich im Kern des geladenen Clusters ansammelt und dort die Ladung der Clusterionen neutralisert. Hierdurch wird eine vorzeitige Coulomb-Explosion des Clusters vermieden. Es wird dargelegt, dass dieser Mechanismus der lokalen Schadensreduzierung durch die Einbettung des Clusters in ein Heliumtröpfchen auf den gesamten Cluster ausgeweitet werden kann, da durch Feldionisation und Migration von Elektronen die vollständige laserbedingte Aufladung des Clusters auf das Heliumtröpfchen transferiert wird. Eine Analyse der resultierenden Diffraktionsmuster bestätigt, dass der reduzierte Strahlenschaden am Cluster den Anwendungsbereich für Diffraktionsexperimente erheblich ausweitet. Kürzlich wurde am SLAC National Accelerator Laboratory der erste XFEL in Betrieb genommen. Eine Modifikation des Modells auf dort bereits erzielbare Wellenlängen wird genutzt um Vorhersagen über das Photoabsorptionsverhalten, aus dem alle weiteren Schäden folgen, an kleinen Neoncluster zu treffen. Hiermit lassen sich bereits jetzt durch den Vergleich zu Experimenten die wichtigen Schadensmechanismen und ihre theoretische Beschreibung testen. Es wird ferner das interessante Relaxationsverhalten des durch massive Photoionisation in XFEL-Strahlung erzeugten Elektronenplasmas untersucht. Diese neuartige Anregung erfolgt auf einer Femtosekunden-Zeitskala und produziert eine hohe Dichte an energetischen Elektronen. Wir beschreiben dieses Plasma durch ein generisches Modell seiner Vielteilchen-Dynamik. Hierbei kann der gesamte Parameterraum des Modells in vier Klassen unterteilt werden, die sich nach Anregungsgrad, der den Elektronenverlust des Plasmas regelt, und Anregungsdauer, die die transiente Dynamik beeinflusst, unterscheiden. Speziell der Bereich starker Anregung bei gleichzeitig kurzer Anregungsdauer zeigt ein interessantes neues Verhalten, bei dem sich eine Equilibrierung des Systems im Kontinuum andeutet.

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.

X-ray lasers bring us into a new world in photon science by delivering extraordinarily intense beams of x-rays in very short bursts that can be more than ten billion times brighter than pulses from other x-ray sources. These lasers find applications in sciences ranging from astrophysics to structural biology, and could allow us to obtain images of single macromolecules when these are injected into the x-ray beam. A macromolecule injected into vacuum in a microdroplet will be affected by evaporation and by the dynamics of the carrier liquid before being hit by the x-ray pulse. Simulations of neutral and charged water droplets were performed to predict structural changes and changes of temperature due to evaporation. The results are discussed in the aspect of single molecule imaging. Further studies show ionization caused by the intense x-ray radiation. These simulations reveal the development of secondary electron cascades in water. Other studies show the development of these cascades in KI and CsI where experimental data exist. The results are in agreement with observation, and show the temporal, spatial and energetic evolution of secondary electron cascades in the sample. X-ray diffraction is sensitive to structural changes on the length scale of chemical bonds. Using a short infrared pump pulse to trigger structural changes, and a short x-ray pulse for probing it, these changes can be studied with a temporal resolution similar to the pulse lengths. Time resolved diffraction experiments were performed on a phase transition during resolidification of a non-thermally molten InSb crystal. The experiment reveals the dynamics of crystal regrowth. Computer simulations were performed on the infrared laser-induced melting of bulk ice, giving a comprehension of the dynamics and the wavelength dependence of melting. These studies form a basis for planning experiments with x-ray lasers.

Coherent diffractive imaging (CDI) has become a very popular technique over the past two decades. CDI is a "lensless" imaging method which replaces the objective lens of a conventional microscope by a computational image reconstruction procedure. Its increase in popularity came together with the development of X-ray free-electron lasers (XFELs) which produce extremely bright and coherent X-rays. By facilitating these unique properties, CDI enables structure determination of non-crystalline samples at nanometre resolution and has many applications in structural biology, material science and X-ray optics among others. This work focuses on two specific CDI techniques, flash X-ray diffractive imaging (FXI) on biological samples and X-ray ptychography. While the first FXI demonstrations using soft X-rays have been quite promising, they also revealed remaining technical challenges. FXI becomes even more demanding when approaching shorter wavelengths to allow subnanometre resolution imaging. We described one of the first FXI experiments using hard X-rays and characterized the most critical components of such an experiment, namely the properties of X-ray focus, sample delivery and detectors. Based on our findings, we discussed experimental and computational strategies for FXI to overcome its current difficulties and reach its full potential. We deposited the data in the Coherent X-ray Database (CXIDB) and made our data analysis code available in a public repository. We developed algorithms targeted towards the needs of FXI experiments and implemented a software package which enables the analysis of diffraction data in real time. X-ray ptychography has developed into a very useful tool for quantitative imaging of complex materials and has found applications in many areas. However, it involves a computational reconstruction step which can be slow. Therefore, we developed a fast GPU-based ptychographic solver and combined it with a framework for real-time data processing which already starts the ptychographic reconstruction process while data is still being collected. This provides immediate feedback to the user and allows high-throughput ptychographic imaging. Finally, we have used ptychographic imaging as a method to study the wavefront of a focused XFEL beam under typical FXI conditions.  We are convinced that this work on developing strategies and algorithms for FXI and ptychography is a valuable contribution to the development of coherent diffractive imaging.

<p>This dissertation discusses the theoretical methods for quantum scattering in the context of x-ray scattering from electrons and classical scattering in the context of collisions between Rydberg atoms.</p> <p><br></p> <p>A method for describing non-relativistic x-ray scattering from bound electrons is presented. The approach described incorporates the full spatial dependence of the incident x-ray field and is non-perturbative in the incident x-ray field. The x-ray scattering probability obtained by numerical solution for the case of free-electrons is bench-marked with well known analytical free-electron results.</p> <p><br></p> <p>A recent investigation by Fuchs \emph{et al.} [Nat. Phys. 11, 964 (2015)] revealed an anomalous frequency shift of at least 800 eV in non-linear Compton scattering of high-intensity x-rays by electrons in solid beryllium. The x-ray scattering approach described is used to explore the role of binding energy, band structure, electron-electron correlation and a semi-Compton channel in the frequency shift of scattered x-rays for different scattered angles. The results of the calculation do not exhibit an additional redshift for the scattered x-rays beyond the non-linear Compton shift predicted by the free-electron model. </p> <p><br></p> <p>The interference between Compton scattering and nonlinear Compton scattering from a two-color field in the x-ray regime is theoretically analyzed for bound electrons. A discussion of the underlying phase shifts and the dependence of the interference effect on the polarizations of the incident and outgoing fields are presented. </p> <p><br></p> <p>The problem of using x-ray scattering to image the dynamics of an electron in a bound system is examined. Previous work on imaging electronic wave-packet dynamics with x-ray scattering revealed that the scattering patterns deviate substantially from the notion of instantaneous momentum density of the wave packet. Here we show that the scattering patterns can provide clear insights into the electronic wave packet dynamics if the final state of the scattered electron and the scattered photon momentum are determined simultaneously. The scattering probability is shown to be proportional to the modulus square of the Fourier transform of the instantaneous electronic spatial wave function weighted by the final state of the electron.</p> <p><br></p> <p>Collisional ionization between Rydberg atoms is examined. The dependence of the ionization cross section on the magnitude and the direction of orbital angular momentum of the electrons and the direction of the Laplace-Runge-Lenz vector of the electrons is studied. The case of exchange ionization is examined and its dependence on the magnitude of angular momentum of the electrons is discussed.</p> <p><br></p>