Stuttgart, Univ., Diss., 2006.

Freiburg i. Br., Univ., Diss., 2007.

Frankfurt (Main), University, Diss., 2007. / Erscheinungsjahr an der Haupttitelstelle: 2007.

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.

A quantum mechanical state may be transferred between locations using quantum teleportation.Specically information encoded in the polarized state of a light pulse maybe teleported onto the collective spin state of an ensemble of atoms. This thesis providesa theoretical framework for achieving such a teleportation protocol experimentally.

Le cinéma d’Atom Egoyan présente la particularité d’être difficilement classable, par son obstination à maintenir son caractère "fermé", sans craindre d’explorer ses possibilités dans des champs cinématographiques divers. Le sentiment de perte de sens, qui traverse l’organisation de son œuvre, semble jouer le rôle le plus important quant à la réception de ses films. La recherche essaye de commenter son univers filmique captivant, préférant l’examiner par l’autre côté, là où il se tait et se cache, tout en empêchant la lecture lucide d’une analyse filmique. Se fondant d’abord sur le rôle capital du découpage, nous essayons de comprendre comment le cinéaste canadien bâtit son univers aporétique, à l’aide de toute sorte de figure de juxtaposition. Essayer d’assimiler la construction d’un tel univers d’observer comment les personnages, finalement, y vivent. Lutter contre l’inquiétude, qui touche parfois même la terreur, équivaut, chez Egoyan à la lutte de ses personnages contre le découpage. La perte de sens, ne pourrait qu’être le résultat d’une vérité filmique désarmée. / Atom Egoyan’s cinema is special in that it is not easily classifiable, since it manages to retain its ‘closed’ character while, at the same time, not afraid to explore its potential in various cinematic fields. The organization of his work is permeated by the sense of losing ‘sense’, which is a characteristic of modernism, and seems to be playing an important role in the way his films are shot. This research attempts to comment on his fascinating cinematic universe, daring to examine its other side, the one which, as it remains hidden and silent, resists straightforward filmic analysis. Based on the predominant role of decoupage in his films, we attempt to understand how the Canadian director constructs his paradoxical universe, employing all kinds of juxtapositional forms. Attempting to assimilate the construction of such a universe can have but one objective, and that is to observe how its characters inhabit it. Toiling against anxiety which sometimes borders on terror is equivalent in Egoyan’s work with the struggle of his characters against decoupage. The loss of ‘sense’ is nothing if not the result of a disarmed cinematic truth.

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.

Clinical heavy ion beams provide the most accurate means of external radiation treatment of tumors available. The study of energetic heavy ions on individual cells have been hampered by shortcomings in available detector technology. The fluorescence nuclear track detector developed by the Landauer Inc. is a small chiplike detector with all the properties needed for these kinds of studies. It is biocompatible, autoclavable, does not require post-irradiation chemical processingand allows the readout of a sufficient number of physical parameters for the determination of a particle’s radiobiological and physical properties. Previous studies in clinical spread-out Bragg peaks have shown a discrepancy in what is detected to what is seen in Monte Carlo radiation transport simulations. While the fluence of heavy primary ions agrees to within one percent, the detection of fragments is underestimated by at least an order of magnitude. In this thesis the performance of the track-recording has been assessed for light ion fragmentsfrom hydrogen, helium and carbon primary particles in physically optimised spread-out Braggpeaks. The underestimation of light ion fragments for carbon beams, mentioned in previousstudies, was reproduced. The underestimation of light ion fragments is prevalent also for helium primary particles. No significant amount of lost tracks are seen in hydrogen beams. The analysis verifies the hypothesis that the detection of large angle trajectories for light ion fragments is not a principal limitation of the detector. The underestimation most probably stems from some limiting features of the readout and image analysis procedure.

In this project laser absorption spectroscopy was performed on a flame in a Fabry-Pérot cavity, using an optical frequency comb. Optical frequency comb spectroscopy is a technique that allows broadband ultra-sensitive detection of molecular species in gas phase. Optical frequency combs are generated by femtosecond mode-locked lasers, which generate short pulses and whose spectrum consists of a comb of sharp laser lines covering a broad spectral range. Doing spectroscopy with optical frequency combs can hence be compared to measurements with thousand of synchronised continuous wave lasers simultaneously, which enables broadband sensitive measurements in short acquisition times. A Vernier spectrometer uses the filtering ability of the cavity to allow sequential transmission of parts of the frequency comb spectrum. Its technical simplicity and robustness make it a good candidate for measuring in turbulent environments. The aim of the project was to implement continuous-filtering Vernier spectroscopy in a setup for measuring absorption spectra in air and in a flame. This was done by using an Er:fiber femtosecond laser emitting in the near-infrared wavelength range and a Fabry-Pérot cavity containing the flame. The cavity, which consists of two highly reflective mirrors, lets the light of the comb interact with the molecules in the flame for each of the many round-trips it perform; thus increasing the sensitivity to absorption. An active locking mechanism was implemented to stabilize the coupling of the optical frequency comb to the cavity. The locking allowed multiple measurements to be averaged which reduced noise. A galvanometer scanner was added to the system which was used to measure a broad part of the comb spectrum. Hot water absorption lines were detected in the swept comb spectrum and a candidate absorption peak for OH absorption was recorded. The spectrometer today has opportunities for improvements. A frequency calibration should be implemented which is essential for making estimates of reactant/product concentrations in combustion processes.

Ce mémoire présente la conception et réalisation d'un montage expérimental pour le développement d'un interféromètre à atomes froids de 87Rb guidés sur un microcircuit à atomes, l'objectif final étant la réalisation d'un capteur inertiel de rotations. Nous avons ainsi étudié théoriquement le confinement magnétique des atomes dans un guide circulaire. Une telle étude nous a permis d'identifier les principales problématiques liées à la propagation sur une orbite stable d'un paquet d'onde atomique dans un guide magnétique, à savoir: la rugosité du potentiel de guidage, les défauts du potentiel associés au motif de micro fils employés pour créer ce potentiel, et les pertes par effet Majorana. Dans cette thèse nous proposons des solutions originales à ces problèmes basés sur des études précédentes et sur les résultats de nos calculs. Du point de vue expérimental, nous avons monté une nouvelle expérience d'atomes froids dont la principale caractéristique est d'être compacte et donc transportable pour des mesures locales de vitesses de rotations. Nous avons donc, au cours de ce travail, assemblé un système à ultra vide efficace, développé un banc optique très compacte comprenant des sources laser pour le refroidissement et piégeage des atomes, un laser de Bragg pour la réalisation de l'interféromètre atomique, ainsi que toute l'électronique de contrôle de cette expérience. / This manuscript present the design and realization of an experimental setup for the development of a cold atom interferometer using 87Rb atoms guided on an atom chip, the final goal being the realization of an inertial sensor for rotation measurements. We have therefore study theoretically the magnetic confinement of these atoms in a circular guide. Such a study allowed us to identify the main challenges linked to the atomic wave packet propagation along a stable circular orbit in a magnetic guide, namely: the roughness of the guiding potential, the magnetic potential defects associated to the pattern of the micro wires used to produce this potential, and the Majorana losses. In this thesis we propose original solutions to these questions based on preliminary studies and on the results of our calculations. From the experimental point of view, we have assembled a new cold atom experiment with the main feature of being compact and therefore transportable for in situ measurement of rotations. We have along this work put together an efficient ultra high vacuum system, developed a compact optical bench containing the laser sources for cooling and trapping, a Bragg laser for the atom interferometer, as well as all the needed electronics to control the experiment.