Optical Coherence Tomography (OCT) is a non-invasive high-resolutionmethod for measuring the reectance of scattering media in 1/2/3D, e.g.skin. The method has been used in a number of dierent medical elds andfor measurement of tissue optical properties.The software developed in this thesis is able to display features hidden ina shadowed volume by adding multiple OCT measurements taken at obliqueangles, a technique here called Multiple-Angle Oblique Optical CoherenceTomography (MAO-OCT).Three dierent objects with were measured at 5 to 9 angles. The measurementswere automatically and manually aligned in the software. They werealso tested with 6 dierent high pass intensity lters (HPIF) and reduced insize using 4 dierent methods to speed up calculations.The software's automatic alignment was tested with one tilted computergenerated test at 9 angles and with 5 dierent shadow strengths.With MAO-OCT it is possible to remove some eects of shadows in OCT,though it comes with a cost of reduced sharpness. The errors depend muchon the dierences in index of refraction in the sample.The software managed to automatically align 90% of the articial measurements,and 60% of the OCT measurements. The shadow strength andthe resize method had no noticeable eect on the automatic alignment of themeasurements.

Peripheral vision plays an important role for visually impaired people with central field loss. Furthermore, recent studies show that defocus in the image on the peripheral retina might influence the development of myopia. Apart from the refractive errors and astigmatism, off-axis aberrations such as coma and transverse chromatic aberration (TCA) also influence the image quality on the peripheral retina. Theory shows that the amount of TCA is quite large in peripheral vision especially in large off-axis angles. The aim of this study is to develop a method to measure the amount of TCA in the peripheral field of view of the human eye. The method which was used for this study was subjective and the amount of TCA was measured in the left eye of the three volunteer adult subjects. The method was based on measuring the TCA as a chromatic difference of position outside of the eye. The measurements were done in the nasal retina of the eye in seven angles from 0 deg eccentricity (fovea) to 60 deg eccentricity. To compare the experimental results with theoretical values two schematic eye models were implemented in ZEMAX optical design software; a reduced eye model and a wide angle eye model. The results showed the expected increase of TCA with off-axis angle. The measurements for two subjects were in good agreement with the eye models. The magnitudes for TCA varied between subjects, one reason for this can be related to the different shapes of the eye in different subjects. The third subject had different values for TCA. This difference led us to investigate the reliability and the repeatability of the method in more detail.

Trapped Rydberg ions with their extraordinary properties serve as very good candidatesfor quantum computing and quantum simulation. The strong dipole-dipoleinteraction in Rydberg ions enables fast entangling gates between qubits. The entanglementdoes not involve motional quantum state to exchange information, whichmakes it suitable to perform gate operations in a long ion string. In this report,preliminary studies for cooling the trapped ions using polarization gradient coolingand addressing of single ion in a long ion string have been done. The results showthat for cooling of multiple ions in a linear chain, a combination of Doppler coolingand polarization gradient cooling provides better cooling as compared to Dopplercooling alone. Simulations for single ion addressing shows that the focusing of thebeams on the ions can be further improved by using additional optics described bythe simulation. Better focusing is essential to deliver higher laser intensities to theion such that the Rabi frequency is higher. This is important for improving the delity of gate operation in long ion strings.

Irradiation induced void swelling is problematic for the application of austenitic steels under high dose irradiation. In this thesis, the swelling is characterized by dislocation bias. The dislocation bias is obtained using the finite element method, accounting for fcc copper and nickel under electron irradiation. The methodology is implemented with the interaction energies between an edge dislocation and point defects. Analytically derived interaction energies, which are based on elasticity theory, are compared with interaction energies obtained from atomistic model using semi-empirical atomic potentials as physics basis. The comparison shows that the description of analytical interaction energies is inaccurate in the dislocation core regions. The bias factor dependence on dislocation density and temperature is presented and discussed. At high temperatures or low dislocation densities, the two approaches tend to converge. However, the dislocation bias based on the interaction energies from the two approaches, reveals larger discrepancy for nickel than for copper. The impact on dislocation bias from the different stacking fault energies of copper and nickel is elaborated. Nickel, which has a larger stacking fault energy, is predicted to have larger swelling rate than copper under the same irradiation conditions. / <p>QC 20130530</p>

Single-particle imaging, or SPI, is a method used to obtain the three-dimensional structure of particles. Repeatedly aiming X-rays at samples of a particle produces diffraction patterns, which are combined to a best-fit three-dimensional model of the particle. SPI of proteins can be improved by orienting the protein before imaging. Protein dipole orientation makes use of a protein's dipole moment and an external electric field to generate torque, which can orient the protein. A protein subject to an electric field may however result in damage of the protein's geometrical structure, or insufficient protein orientation, depending on the magnitude of the electric field. Sufficient protein orientation without substantial protein damage is possible in an interval of electric field strengths. The results in this report reveal that the method of SPI can be further improved. With a protein being fully oriented in an electric field, it is possible to reduce the electric field strength and yet sustain sufficient orientation, with some constraints. Longer times for imaging and less structural damage to the protein are hence possible. This study implements Molecular Dynamics (MD) and the most extensively used open-source MD software, GROMACS, with ubiquitin as a sample protein. / Single-particle imaging, eller SPI, är en metod som används för att erhålla den tredimensionella strukturen hos partiklar. Genom att upprepade gånger rikta röntgenstrålar mot prover av en partikel produceras diffraktionsmönster, som kombineras till en anpassad tredimensionell modell av partikeln. SPI av proteiner kan förbättras genom att i förväg rikta proteinet. I dipolorientering av ett protein utnyttjas proteinets dipolmoment och ett yttre elektriskt fält för att generera vridmoment, vilket kan rikta proteinet. Ett protein som utsätts för ett yttre elektriskt fält kan dock resultera i att proteinets geometriska struktur skadas, eller att proteinets riktning avviker avsevärt, beroende på magnituden av det elektriska fältet. Det är möjligt att rikta ett protein inom ett intervall av elektrisk fältstyrka utan att proteinet skadas avsevärt. Resultaten i denna rapport avslöjar att metoden för SPI kan förbättras ytterligare. Med ett protein som i förväg riktats i ett elektriskt fält är det möjligt att sänka fältstryrkan och ändå upprätthålla riktningen, med vissa begränsningar. Längre tid för avbildning och mindre omfattande strukturella skador möjliggörs med detta. Denna studie implementerar Molecular Dynamics (MD) och den mest använda programvaran med öppen källkod för MD-simuleringar, GROMACS, med proteinet ubiquitin som prov.

The X-ray tube is one of the most common types of X-ray sources, which is widely used in research laboratories and industry. Electrons are accelerated towards a metallic target to generate X-ray photons, thus creating a significant thermal load on the metal. In order to reduce the risk of damage, some techniques, such as the focus line principle or the installation of a very thin target, are implemented in most cases. In addition, the geometry of the target is chosen to maximise the amount of X-rays for the intended application. The aim of this thesis is to investigate how the incident angle of the electron beam, consequence of the line focus principle, and the thickness of the target influence the total photon yield of the source. Monte Carlo simulations of electron/photon transport have been made with a modified version of the PENELOPE program using a novel variance reduction technique. The results from the calculations are validated with experiments conducted with a prototype source, in the laboratory of Excillum AB. Since thermal capabilities and X-ray yield have opposite dependence on target angle and thickness, by combining the thermal results from Sara Högnad$\acute{\mathrm{o}}$ttir's thesis and the ones produced in this thesis, it is possible to isolate an optimal configuration of the source. In this geometry, the best compromise between high brightness and high maximum allowed power is found.

With the passage of time and the advancement of our industrial civilization, environmental concerns have become more and more recognized since the 1990s. Carbon dioxide reduction reactions are capable of converting carbon dioxide into valuable hydrocarbons and reducing the carbon emission from the combustion of fossil fuels. This is a promising direction for sustainable energy resources given that the scarcity of fossil fuels is becoming more threatening to the survival of mankind. In recent years, oxide-derived metal nanostructures have been synthesized and show unique catalytic features. Recently, Sloan et al. synthesized a novel oxide-derived copper nanocube structure, which showed a high selectivity toward ethylene over methane and low overpotentials. In this work, the presence of subsurface oxygen in the catalyst surface is tested with density functional theory (DFT) calculations, as a complement to experimental x-ray photoelectron spectroscopy. Due to limitations on the scale of modeling with DFT, the results indicate a very low stability of subsurface oxygen, which give rise to a question if subsurface oxygen would be stable with a reasonably large cluster model. Self-consistent charge density functional tight binding (SCC-DFTB) is adopted to investigate a nanocube model. In this model, a manually reduced cuprious oxide nanocube is constructed and investigated. Subsurface oxygen atoms close to facets are found to be more stable inside. A higher degree of disorder is proposed to be the cause of this difference in stabilizing subsurface oxygen atoms between the slab and nanocube models. The presence of subsurface oxygen enhances the adsorption of CO on the Cu(100) surface, increasing the likelihood for adsorbed CO molecules to dimerize, which is the rate determining step for ethylene production on Cu(100) under low-overpotential conditions. With subsurface electronegative atoms such as oxygen or fluorine, it is also found that the d-band scaling relation could be broken.

Three particles interacting via Coulomb forces represents a fundamental problem in quantum mechanics whose approximate solution provides some insight into the more complex analysis associated with few-body problems. We have investigated resonance states composed of three particles interacting via Coulombic and more general potentials in non-relativistic quantum mechanics, using the complex scaling method. My calculations have been applied to two different physical systems: (i) an investigation of the possibility of resonances in the $p e \mu$ system, which has been suggested as a possible reason for unexpected results from a recent measurement of the proton radius in muonic hydrogen (ii) a calculation of resonances in positron-hydrogen scattering, which shows that we can represent this system with the accuracy needed for future scattering calculations. The basis set used is built from Gaussians in Jacobi coordinates, thus automatically including mass-polarisation effects which cannot be neglected in muonic systems.

This thesis presents three different series of high energy (keV) collision experiments as well as a brief scientific introduction to the field. In the first series, protonated glycine and leucine were collided with carbon dioxide and a beam attenuation method was applied to determine their total fragmentation cross sections. A technique was also presented for how to restore the resolution in mass spectra obtained with a hemispherical electrostatic analyzer followed by a position sensitive detector (micro-channel plate equipped with a resistive anode). In the second series of experiments, Collision Induced Dissociation (CID) and Electron Capture Induced Dissociation (ECID) studies were performed on the nucleotide adenosine 5'-monophosphate anion (AMP-) in water complexes.  The two dissociation techniques revealed different fragmentation patterns and a numerical solvent evaporation model was used to interpret the spectra. It was then found that the CID and ECID processes were associated with different internal energy distributions. The third experiment concerned ECID of the protonated dipeptide glycine-alanine ([GA+H]+) in complexes with water, methanol, acetonitrile or crown ether. Depending on the attached molecular species, different ratios between the two competing channels ammonia loss and N-Cα bond cleavage were observed. Quantum chemical calculations revealed that a notable shift in the location of the captured electron occurred for the case of two acetonitriles and one crown ether compared to the bare ion and the ion in complexes with either water or methanol. Finally, this thesis will discuss developments of the electrospray ionization platform as well as the new Double ElectroStatic IonRing ExpEriment (DESIREE) facility.

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