PACE Solver Description: Fluid

This document describes the heuristic for computing treedepth decompositions of undirected graphs used by our solve fluid. The heuristic runs four different strategies to find a solution and finally outputs the best solution obtained by any of them. Two strategies are score-based and iteratively remove the vertex with the best score. The other two strategies iteratively search for vertex separators and remove them. We also present implementation strategies and data structures that significantly improve the run time complexity and might be interesting on their own

PACE Solver Description: PID^?

This document provides a short overview of our treedepth solver PID^{?} in the version that we submitted to the exact track of the PACE challenge 2020. The solver relies on the positive-instance driven dynamic programming (PID) paradigm that was discovered in the light of earlier iterations of the PACE in the context of treewidth. It was recently shown that PID can be used to solve a general class of vertex pursuit-evasion games - which include the game theoretic characterization of treedepth. Our solver PID^{?} is build on top of this characterization

Gitterbasierte Einzelschuss-Röntgenbildgebung am PHELIX-Laser

A highly topical field of research in the field of laboratory astrophysics and matter under extreme conditions is the investigation of plasmas and the resulting shocks, which laser facilities with the world’s highest energies and intensities are capable of generating. While radiation in the optical wavelength range can only be used to analyze the surfaces of optically non-transparent plasmas, the generation of short-pulsed X-ray backlighting makes it possible to study physical core quantities such as the density, compression and dynamics of the shock as well as structures within the shocked matter. X-ray backlighting can thus be used to image highly dynamic shock processes occurring on the time scale of a few nanoseconds. For imaging methods, the ability to record in single-shot mode is essential. This is possible with the grating-based approach pursued in this dissertation, which, in addition to the absorption contrast, provides additional image information, also referred to as differential phase contrast, due to its sensitivity to the phase shift imprinted on the X-ray radiation by the shocked medium under investigation. This dissertation provides an approach to as well as an understanding of the challenging framework conditions for establishing grating-based single-shot X-ray imaging at the Petawatt High-Energy Laser for Heavy Ion Experiments (PHELIX laser for short) at GSI Helmholtzzentrum für Schwerionenforschung GmbH. In addition to the relevant physical fundamentals for the imaging technique, results of two beamtimes at the PHELIX laser will be presented. Particular attention is paid to the alignment method of the portable grating interferometer used, which was developed during the preparation of the first beamtime. Furthermore, the conclusions drawn from the first beamtime and the associated optimization steps for the second beamtime are elaborated and documented by means of a comparative analysis with respect to the image quality achieved in both beamtimes. Finally, the investigations of the dynamics of shocks induced by the PHELIX laser in polymethyl methacrylate are presented.Ein hochaktuelles Forschungsfeld auf dem Gebiet der Laborastrophysik und der Materie unter extremen Bedingungen ist die Untersuchung von Plasmen und daraus hervorgehender Schocks, zu deren Erzeugung Laseranlagen mit den weltweit höchsten Energien und Intensitäten in der Lage sind. Während mit Strahlung im optischen Wellenlängenbereich nur die Oberflächen optisch nicht transparenter Plasmen analysiert werden können, wird durch die Erzeugung einer kurz gepulsten Röntgen-Hintergrundbeleuchtung die Möglichkeit geschaffen, physikalische Kerngrößen wie die Dichte, die Kompression und die Dynamik des Schocks sowie Strukturen innerhalb der geschockten Materie zu untersuchen. Mithilfe der Röntgen-Hintergrundbeleuchtung lassen sich somit auf der Zeitskala weniger Nanosekunden ablaufende, hoch-dynamische Schockprozesse abbilden. Für Bildgebungsmethoden ist hierfür die Fähigkeit zur Aufnahme im Einzelschuss-Modus essenziell. Diese ist mit dem im Rahmen der hier vorliegenden Dissertation verfolgten gitterbasierten Ansatz möglich, welcher neben dem Absorptionskontrast durch seine Sensitivität auf den Phasenschub, den das zu untersuchende geschockte Medium der Röntgenstrahlung aufprägt, zusätzliche Bildinformation, auch als differentieller Phasenkontrast bezeichnet, bietet. In dieser Dissertation wird ein Zugang zu den sowie ein Verständnis für die herausfordernden Rahmenbedingungen bei der Etablierung einer gitterbasierten Einzelschuss-Röntgenbildgebung am Petawatt Hoch-Energie Laser für SchwerIoneneXperimente (kurz: PHELIX-Laser) der GSI Helmholtzzentrum für Schwerionenforschung GmbH geschaffen. Neben den relevanten physikalischen Grundlagen für die Bildgebungstechnik werden Resultate zweier Strahlzeiten am PHELIX-Laser präsentiert. Dabei liegt besonderes Augenmerk auf der im Zuge der Vorbereitung der ersten Strahlzeit entwickelten Ausrichtungsmethode des verwendeten portablen Gitter-Interferometers. Des Weiteren werden die aus der ersten Strahlzeit gezogenen Schlüsse und damit verbundenen Optimierungsschritte für die zweite Strahlzeit herausgearbeitet und anhand einer gegenüberstellenden Analyse hinsichtlich der in beiden Strahlzeiten erzielten Bildqualität dokumentiert. Zuletzt erfolgt die Vorstellung der durchgeführten Untersuchungen der Dynamik von durch den PHELIX-Laser in Polymethylmethacrylat induzierten Schock

Noise Reduction for Single-Shot Grating-Based Phase-Contrast Imaging at an X-ray Backlighter

X-ray backlighters allow the capture of sharp images of fast dynamic processes due to extremely short exposure times. Moiré imaging enables simultaneously measuring the absorption and differential phase-contrast (DPC) of these processes. Acquiring images with one single shot limits the X-ray photon flux, which can result in noisy images. Increasing the photon statistics by repeating the experiment to gain the same image is not possible if the investigated processes are dynamic and chaotic. Furthermore, to reconstruct the DPC and transmission image, an additional measurement captured in absence of the object is required. For these reference measurements, shot-to-shot fluctuations in X-ray spectra and a source position complicate the averaging of several reference images for noise reduction. Here, two approaches of processing multiple reference images in combination with one single object image are evaluated regarding the image quality. We found that with only five reference images, the contrast-to-noise ratio can be improved by approximately 13% in the DPC image. This promises improvements for short-exposure single-shot acquisitions of rapid processes, such as laser-produced plasma shock-waves in high-energy density experiments at backlighter X-ray sources such as the PHELIX high-power laser facility

Single-exposure X-ray phase imaging microscopy with a grating interferometer

The advent of hard X-ray free-electron lasers enables nanoscopic X-ray imaging with sub-picosecond temporal resolution. X-ray grating interferometry offers a phase-sensitive full-field imaging technique where the phase retrieval can be carried out from a single exposure alone. Thus, the method is attractive for imaging applications at X-ray free-electron lasers where intrinsic pulse-to-pulse fluctuations pose a major challenge. In this work, the single-exposure phase imaging capabilities of grating interferometry are characterized by an implementation at the I13-1 beamline of Diamond Light Source (Oxfordshire, UK). For comparison purposes, propagation-based phase contrast imaging was also performed at the same instrument. The characterization is carried out in terms of the quantitativeness and the contrast-to-noise ratio of the phase reconstructions as well as via the achievable spatial resolution. By using a statistical image reconstruction scheme, previous limitations of grating interferometry regarding the spatial resolution can be mitigated as well as the experimental applicability of the technique

A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana

Motivation: Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating ‘omics’ data from various levels of the system in order to provide interpretations with respect to the energy state and to elicit conclusions about putative global energy-related response mechanisms in the cell