X-ray lasers are creating unprecedented research opportunities in physics,chemistry and biology. The peak brightness of these lasers exceeds presentsynchrotrons by 1010, the coherence degeneracy parameters exceedsynchrotrons by 109, and the time resolution is 105 times better. In theduration of a single flash, the beam focused to a micron-sized spot has the samepower density as all the sunlight hitting the Earth, focused to a millimetresquare. Ultrafast coherent X-ray diffractive imaging (CXDI) with X-ray lasers exploitsthese unique properties of X-ray lasers to obtain high-resolution structures fornon-crystalline biological (and other) objects. In such an experiment, thesample is quickly vaporised, but not before sufficient scattered light can berecorded. The continuous diffraction pattern can then be phased and thestructure of a more or less undamaged sample recovered% (speed of light vs. speed of a shock wave).This thesis presents results from the first ultrafast X-ray diffractive imagingexperiments with linear accelerator-driven free-electron lasers and fromoptically-driven table-top X-ray lasers. It also explores the possibility ofinvestigating phase transitions in crystals by X-ray lasers. An important problem with ultrafast CXDI of small samples such as single proteinmolecules is that the signal from a single measurement will be small, requiringsignal enhancement by averaging over multiple equivalent samples. We present anumerical investigation of the problems, including the case where samplemolecules are not exactly identical, and propose tentative solutions. A new software package (Hawk) has been developed for data processing and imagereconstruction. Hawk is the first publicly available software package in thisarea, and it is released as an open source software with the aspiration offostering the development of this field.

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. / <p>QC 20130514</p>

The thesis analyses the process of pair annihilation into one photon in a laser pulse. The theory of how to include pulse shapes in Strong Field QED and the resulting cross section is presented. The cross section is calculated and estimated for lasers of ELI and XFEL facilites. It is found that the effect may be experimentally verifiable at high frequency XFEL facilities for very finely tuned particle kinematics, but negligible at high intensity optical laser facilities such as ELI.

By means of N-body simulations we study the ion and electron dynamics in molecular first-row hydride clusters when exposed to intense and short X-ray pulses. We find that, for a particular range of X-ray intensities, fast protons are ejected from the system on a considerably shorter time scale than that of the screened core. As a consequence, the structure of heavy atoms is kept intact", which may be relevant in the context of X-ray based molecular imaging. Moreover the final charge states of the heavy ions are considerably lower than those of the ions in pristine atomic clusters exposed to the same laser pulses, which is in agreement with recent measurement of methane cluster at the LCLS in Stanford.

Modern physical experiments often demand advanced instrumentation based on advances in  technology. This work describes four instrumentation physics projects that are based on modern, high-capacity Field-Programmable Gate Arrays, making use of their versatility, programmability, high bandwidth communication interfaces and signal processing capabilities. In the first project, a jet-finding algorithm for the ATLAS detector at the LHC experiment at CERN was developed and implemented, and different verification methods were created to validate the functionality and reliability. The experiment uses a three level trigger system, where the first level uses custom FPGA-based hardware for analysis of collision events in real-time. The second project was an advanced timing and triggering distribution system for the new European X-Ray Free Electron Laser (XFEL) facility at DESY in Hamburg. XFEL will enable scientists to study nano structures on the atomic scale. Its laser pulses will have the strongest peak power in the world with extremely short duration and a high repetition rate, which will even allow filming of chemical reactions. The timing system uses modern FPGAs to distribute high-speed signals over optical fibers and to deliver clocks and triggers with high accuracy. The third project was a new data acquisition board based on high-speed ADCs combined with high-performance FPGAs, to process data from segmented Ge-detectors in real-time. The aim was to improve system performance by greatly oversampling and filtering the analog signals to achieve greater effective resolution. Finally, an innovative solution was developed to replace an aging system used at CERN and Stockholm University to test vital electronics in the Tile Calorimeters of the ATLAS detector system. The new system is entirely based on a commercial FPGA development board, where all necessary custom communication protocols were implemented in firmware to emulate obsolete hardware. / Inom området instrumenteringsfysik bedrivs forskning och utveckling av avancerade instrument, som används inom moderna fysikexperiment. Denna avhandling beskriver fyra projekt där programmerbara kretsar (FPGA) har nyckelfunktioner för att lösa krävande instrumenteringsuppgifter. Den första projektet beskriver utveckling och implementering av en algoritm för detektering av partikelskurar efter partikelkollisioner i LHC-experimentets ATLAS-detektor. Experimentet genererar 40 miljoner händelser per sekund, som måste analyseras i real-tid med hjälp av snabba parallella algoritmer. Resultatet avgör vilka händelser som är tillräckligt intressanta för fortsatt noggrannare analys. Den andra projektet beskriver utvecklingen av ett system som distribuerar klock- och trigger-signaler över ett 3 kilometers experimentområde med extrem precision, i den nya röntgenlaseracceleratorn XFEL vid DESY i Hamburg. Vid XFEL kommer man utforska nanostrukturer och till och med filma molekylers kemiska reaktioner. I den tredje projektet beskrivs utvecklingen av ett höghastighets datainsamlingssystem, för segmenterade Ge-detektorer. Genom att översampla signalen med hög hastighet kan man uppnå en bättre noggrannhet i mätningen än vad AD-omvandlarens egna upplösning medger. Detta leder i sin tur  till förbättrade systemprestanda. Slutligen beskrivs en innovativ lösning till ett test system för den elektronik, som Stockholms universitet har levererat till ATLAS detektorn. Det nya systemet ersätter det föregående testsystemet, som är baserad på föråldrade inte längre tillgängliga komponenter. Det nya systemet är dessutom också billigare eftersom det är baserat på ett standard FPGA utvecklingskort. / ATLAS experiment of the Large Hadron Collider experiment / European X-ray Free Electron Laser

Proteins are one of the most important molecules in biology. The wide range of functions of different proteins is also important for medical physics. Proteins are assembled by amino acids. These amino acids are connected by peptide bonds to form a protein. The function of a protein is decided by the composition and configuration of peptides, amino acids and their peptide bonds. Successful experiments with Xray Free-electron laser has lead to progress in structural biology, however there is still a need to crystallized samples in these experiments. In this project we have investigated three amino acids. These three amino acids are included in several protein that are hard to crystallize, glycine, valine and alanine. We have investigated their separate interatomic bonds by performing density functional calculations and evaluating the susceptibility of the bonds breaking in a typical time range of Xray Free-electron laser pulses. The results shows the fast dissipation of hydrogen atoms, bond shifting within the molecules during certain ionization degrees and the dissociation of the protein backbone after 20 fs.

abstract: Sample delivery is an essential component in biological imaging using serial diffraction from X-ray Free Electron Lasers (XFEL) and synchrotrons. Recent developments have made possible the near-atomic resolution structure determination of several important proteins, including one G protein-coupled receptor (GPCR) drug target, whose structure could not easily have been determined otherwise (Appendix A). In this thesis I describe new sample delivery developments that are paramount to advancing this field beyond what has been accomplished to date. Soft Lithography was used to implement sample conservation in the Gas Dynamic Virtual Nozzle (GDVN). A PDMS/glass composite microfluidic injector was created and given the capability of millisecond fluidic switching of a GDVN liquid jet within the divergent section of a 2D Laval-like GDVN nozzle, providing a means of collecting sample between the pulses of current XFELs. An oil/water droplet immersion jet was prototyped that suspends small sample droplets within an oil jet such that the sample droplet frequency may match the XFEL pulse repetition rate. A similar device was designed to use gas bubbles for synchronized “on/off” jet behavior and for active micromixing. 3D printing based on 2-Photon Polymerization (2PP) was used to directly fabricate reproducible GDVN injectors at high resolution, introducing the possibility of systematic nozzle research and highly complex GDVN injectors. Viscous sample delivery using the “LCP injector” was improved with a method for dealing with poorly extruding sample mediums when using full beam transmission from the Linac Coherent Light Source (LCLS), and a new viscous crystal-carrying medium was characterized for use in both vacuum and atmospheric environments: high molecular weight Polyethylene Glycol. / Dissertation/Thesis / Doctoral Dissertation Physics 2015

abstract: Serial crystallography (SX) is a relatively new structural biology technique that collects X-ray diffraction data from microcrystals via femtosecond pulses produced by an X-ray free electron laser (X-FEL) or by synchrotron radiation, allowing for challenging protein structures to be solved from microcrystals at room temperature. Because of the youth of this technique, method development is necessary for it to achieve its full potential. Most serial crystallography experiments have relied on delivering sample in the mother liquor focused into a stream by compressed gas. This liquid stream moves at a fast rate, meaning that most of the valuable sample is wasted. For this reason, the liquid jet can require 10-100 milligrams of sample for a complete data set. Agarose has been developed as a slow moving microcrystal carrier to decrease sample consumption and waste. The agarose jet provides low background, no Debye-Sherrer rings, is compatible for sample delivery in vacuum environments, and is compatible with a wide variety of crystal systems. Additionally, poly(ethylene oxide) which is amenable for data collection in atmosphere has been developed for synchrotron experiments. Thus this work allows sample limited proteins of difficult to crystallize systems to be investigated by serial crystallography. Time-resolved serial X-ray crystallography (TR-SX) studies have only been employed to study light-triggered reactions in photoactive systems. While these systems are very important, most proteins in Nature are not light-driven. However, fast mixing of two liquids, such as those containing enzyme protein crystals and substrates, immediately before being exposed to an X-ray beam would allow conformational changes and /or intermediates to be seen by diffraction. As a model, 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase (KDO8PS), has been developed for TR-SX. This enzyme initializes the first step of lipopolysaccharide synthesis by a net aldol condensation between arabinose-5-phosphate, phosphoenol pyruvate, and water. During this reaction, a short lived intermediate is formed and has been observed on a millisecond timescale using other methods. Thus KDO8PS is an ideal model protein for studying diffusion times into a crystal and short mixing times (<10 ms). For these experiments, microcrystals diffracting to high resolution have been developed and characterized. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

Serial Femtosecond X-ray crystallography (SFX) is a rapidly growing experimental technique by which the structure of a crystalline sample may be determined. The X- rays arrive at the sample in pulse trains of the order of femtoseconds. Each X-ray pulse train hits a unique crystal at a random orientation and produces a diffraction pattern on the detector and series of patterns is obtained, which is the reason for the denomination "serial". Here, the radiation damage done to a sample during an SFX experiment was studied by simulating diffraction patterns including damage. Throughout, a model reference structure in the form of a reflection list was used to simulate patterns. The aim was to minimise the effects of damage through a correction based on available damage data. Firstly, a simulation case with made-up damage data was performed. The made-up data was used to modify the structure factors such that they would appear damaged. After structural reconstruction, the same data was used to correct for the damage. This was done as a validation of the method pipeline. Secondly, a more realistic case, with actual simulated damage data and a distribution of incident intensities was carried out. The expectation value of the distribution was used to correct for damage. It is found for both cases that the damage correction improves the agreement between simulated data and the original model. This is a first step toward successfully correcting for radiation damage which would be a big step forward for SFX.

The European XFEL is an X-ray free electron laser research facility that generates ultrashort, high intensity flashes. Three SASE undulator systems are made of undulator segments and intersection components. Permanent magnets that form the segments, may potentially suffer demagnetization due to the stray radiation that comes from the interaction between electrons and the beam pipe. A gamma spectrometer (GR1-A, developed by Kromek) is planned to be placed at the entrance of one of the undulator segments of SASE1. Monte Carlo simulations, using Geant4, have been performed to study gamma radiation flux at possible measurement areas. The results show that in some cells the expected flux is larger than the maximum throughput, while for two segments there are areas which satisfy the limitations of the detector. An improvement of the geometry of the Geant4 code has also been done to make simulations more in line with the real systems. A comparison between dose results from the new and the former code shows that components placed at the intersections have a significant impact on dose distributions, especially quadrupole magnets.