Rutherford backscattering spectrometry are performed at the Tandem Laboratory of Uppsala Univer-sity, providing information on thickness and composition of materials. To avoid the channelling effect,a wiggling routine has been created to randomly move the sample holding goniometer during the spec-trum acquisition. The aim of this project is to incorporate this routine into the batch measurement infrastructure.

The method of dipole orientation of protein complexes using electric fields plays a key role in the development of single particle imaging, since it enables orientation of the protein in vacuum. In the orientation process the protein is exposed to an external electric field along which the dipole axis of the protein will eventually align. Earlier studies using molecular dynamics simulations have implemented a constant electric field to examine the dipole orientation process. However, when injected into the electric field the protein experiences a gradually increasing field strength converging to some terminal field strength rather than a constant electric field. In order to examine the effects of the time-dependant nature of the electric field, in comparison to a constant one, fields with different time dependances were implemented in molecular dynamics simulations in vacuum performed with GROMACS. Ubiquitin was chosen as a model protein. The results of the study show time-increasing fields tend to result in slower orientation, but preserve the structure of the protein better than for a constant field. It was also shown that after 10 ns electric field exposure, with terminal field strengths greater  or equal to 0.6Vnm^-1, there was no apparent difference of the average degree of orientation of proteins within the time-increasing fields and the constant one. However, for fields of greater or equal to 1.5Vnm^-1 the constant field tended to result in a larger change of the protein structure.

The European X-Ray Free-Electron Laser facility (XFEL) provides ultra-short x-ray pulsesof high peak brilliance that are used in research to analyse atomic or molecular structures.The facility accelerates electrons and moves them through an undulator system consistingof several undulator cells containing permanent magnet poles supplying an alternatingmagnetic field, which causes the electrons to emit x-ray pulses. A concern is raised overthe deterioration of the permanent magnets due to radiation damage originating from strayradiation in the undulator system. The stray radiation is believed to be released by the highenergy electrons interacting with the beam pipe wall. In this study particle simulations aremade using the Monte Carlo particle transport code FLUKA to compare to previous sim-ulations and measurements performed at XFEL. A beam line model was made in FLUKA,simulating electron beams interacting with the vacuum pipe at several points. The sim-ulated energy deposition distribution along the undulator segment surface was fitted tomeasurement data of the dose over the magnets in different undulator cells at XFEL. Thisway the probability of the stray radiation originating from different electron beam interac-tion points could be studied. For the undulator cells that were studied the radiation wasfound to originate from interactions mainly in the gap between undulator segments. Forcell 4 and 12 it was found that radiation also originates from electron interactions with thebeam pipe inside the undulator segments. It was concluded that improvements can bemade in the simulation technique by simulating electron beam interactions at more posi-tions along the vacuum pipe’s longitudinal axis and around its lateral cross section. Furtherresearch is needed to find the impact of the alternating magnetic field over the undulatorsegments as well as to find which particles contribute to the radiation damage at XFEL. Asthe undulator cells had different relative contributions to the damaging dose from differentelectron beam interaction points it could be of interest to use the same method for fittingsimulated dose distributions to measurements of other undulator cells at XFEL.

In this master thesis project, a pulsed UV laser was designed and constructed. Also, the effects of absorption in a volume Bragg grating were investigated. The laser was diode pumped and constructed with Yb:KYW as gain medium. The lasing was at a wavelength of 1029.2 nm with a spectral bandwidth of 0.23 nm, locked by a volume Bragg grating that was used as input coupler for spectral control. Passive Q‑switching was used to generate pulses by placing a Cr:YAG saturable absorber inside the cavity. The laser generated radiation with a maximum peak power of 3.8 kW at an average power of 0.35 W, a repetition rate of 4 kHz and a pulse width of 16 ns. The maximum average power was 1.3 W with a peak power of 2 kW at a repetition rate of 20 kHz and with a pulse width of 20 ns. Through extra‑cavity second harmonic generation using an LBO crystal, green light at a wavelength of 514.7 nm was generated. The maximum average power was 130 mW with an optical conversion efficiency from the fundamental of around 10 %. Then, the second harmonic and the fundamental wave were mixed to generate UV light, at a wavelength of about 343 nm, by using a second LBO crystal. The maximum average power of UV was about 23 mW with an optical efficiency, with respect to the green, of approximately 20 %. One limitation of the laser was that the Cr:YAG was bleached not only by the circulating laser field, but also by remaining pump light. This resulted in decreasing peak power with increasing pump power, thus limiting the nonlinear conversion efficiencies. Thermal fracture of the Cr:YAG was a limiting factor for the intra-cavity average power, while burning of the coating on the Yb:KYW crystal limited the maximum peak power. The effects on a laser when using too high power for the level of absorption in a volume Bragg grating were also investigated. The effects of both resonant and non-resonant beams were investigated.  Since the intensity of a resonant beam decreases approximately exponentially in a volume Bragg grating, due to absorption, an uneven temperature distribution along the propagation axis is formed. This results in different thermal expansion and hence, results in a longitudinal chirp of the grating. The chirp caused a decrease in both reflectivity and spectral selectivity. The reflectivity of the particular grating used in these experiments decreased from 99.4 % to 93 %. In addition, it was experimentally shown that if a volume Bragg grating absorbs a non-negligible amount of a non-resonant beam, the thermal load will deform the volume Bragg grating. Therefore, it is not suitable to use such a grating the as input coupler of a laser cavity. / I detta examensarbete utformades och konstruerades en pulsad UV-laser. Dessutom undersöktes effekterna av absorption i ett volymbraggitter. Som laserkristall användes Yb:KYW vilken pumpades med en diodlaser. Lasring skedde vid 1029,2 nm med en bandbredd av 0,23 nm genom att ett volymbraggitter användes som inkopplingsspegel för att kontrollera spectrumet. Pulser generades genom passiv Q-switching med en Cr:YAG som mättnadsbar absorbator inne i kaviteten. Den maximala toppeffekten var 3,8 kW vid 0.35 W medeleffekt, 4 kHz repetitionsfrekvens och en pulsbredd på 16 ns. Den maximala medeleffekten var 1.3 W med en toppeffekt på 3,8 kW, 20 kHz repetitionsfrekvens och en pulsbredd på 20 ns. Genom frekvensdubbling i en LBO kristall genererades grönt ljus vid våglängden 514,7 nm. Den maximala medeleffekten var 130 mW med en optisk verkningsgrad från den fundamentala våglängden på 10 %. Sedan blandades det infraröda och det gröna ljuset i en andra LBO kristall för att generera UV-ljus, vid en våglängd om 343 nm. Den högsta medeleffekten av UV var cirka 23 mW med en optisk verkningsgrad, med avseende på det gröna ljuset, på ungefär 20%. En begränsning av laser var att Cr:YAG kristallen blektes inte enbart av lasern utan även av pumpen. Detta resulterade i fallande toppeffekt med ökande pumpeffekt, vilket begränsade effektiviteten i den ickelinjära konverteringen. Termisk fraktur på Cr:YAG kristallen var en begränsande faktor för cirkulerande medeleffekten i kaviteten, medan brännskador på Yb-kristallens antireflexbehandling begränsade toppeffekten. Effekterna i en laser vid användning av en alltför hög effekt i förhållande till nivån av absorption i ett volymbraggitter studerades också. Effekterna av både resonanta och ickeresonanta strålar undersöktes. Eftersom intensiteten av en resonant ståle minskar ungefär exponentiellt i ett volymbraggitter kommer temperaturen, på grund av absorption, fördelas ojämnt i propageringsriktningen. Detta resulterar i olika termiska expansion med en längsgående varierad gitterperiod som följd. Detta orsakar en minskning utav både reflektiviteten och den spektrala selektiviteten. Reflektiviteten i gittret som användes i dessa experiment minskade från 99,4 % till 93 %. Dessutom visades det experimentellt att om ett volymbraggitter absorberar en icke försumbar del av en ickeresonant stråle kommer värmebelastning att deformera volymenbraggittret. Därför är det inte lämpligt att använda ett sådant gitter som inkopplingsspegel i en laser.

The objective of this thesis has been to investigate novel host material configurations for high-power end-pumped Er-Yb co-doped, or Yb doped microchip lasers and try to increase their performance. In Er-Yb co-doped systems, the main limitation is the thermal shortcomings of the phosphate glass host material. The thesis presents some novel results that contribute to the search for a crystalline replacement. In Yb doped systems, most end-pumped schemes reported have been using relatively low-power single-emitter diodes. The thesis presents experiments with Yb:KGW microchips end-pumped by high-power diode bars. Another common limitation of end-pumped Yb microchip lasers is the thermal lens that destabilizes the cavity and decreases the beam quality. The approach to reduce the thermal lens by using an athermal propagation direction has been evaluated and the results are presented in the thesis. In the search for a crystalline host material for Er-Yb systems, borates have been found increasingly interesting. Consequently, we started out by investigating Gadolinium-calcium-oxoborate, GdCOB, which could be grown in platinum crucibles. It was found that the cw performance of such monolithic microchips is quite comparable to glass hosts in terms of slope efficiency, but the threshold is significantly larger. As for Q-switched performance, which is essential to most Er-Yb applications, the first efficient Q-switched results with a crystalline host is presented in the thesis. Similar to the cw regime, the slope efficiencies are comparable to glass, while the threshold is quite high. However, the perhaps most important parameter, maximum output power before thermal fracture, is neither significantly improved nor worsened compared with phosphate glass. This is believed to be due to higher threshold and a stronger thermal expansion that negates the benefit of a thermal conductivity that is only 2-3 times higher. To find a host material that could withstand higher pump powers, we turned our attention to the double-tungstates KGW and KYW, which have higher thermal conductivity and higher cross-sections. They have, however, energy level lifetimes which differ significantly from glass or borates and as a consequence, a thorough spectroscopic investigation has been undertaken to optimize dopant concentrations. Laser experiments on crystals with dopant concentrations based on this investigation are expected in the near future. When pumping Yb:KGW with a high-power diode bar, we achieved output powers of 9 – 12.4 W under different experimental conditions with incident powers of 18.3 – 26 W. The incident power of 26 W in one design was enough to fracture the crystal. Using a crystal cut for propagation along an athermal direction and comparing it with an identical b-cut crystal, we found that the thermal lens in the athermally oriented crystal was about a factor two weaker at the same absorbed power. / QC 20101116

Measurements of film mass flow rate for annular, diabatic steam-water flow in tubes are presented. The measurements were carried out with four axial power distributions and at several axial positions at conditions typical for boiling water reactors, i.e. 7 MPa pressure and total mass flux in a range from 750 to 1750 kg/m2s. The results show that the influence of the axial power distribution on the dryout power corresponds to a consistent tendency in the film flow rate and that the film tends to zero when dryout is approached. Furthermore it is demonstrated that two selected phenomenological models of annular flow well predict the present data. A model for additional entrainment due to boiling is shown to degrade the predictions. / QC 20101108

We studied the mutual neutralization of Li+ and H- at effective collision energies of a few hundred meV, which corresponds to temperatures of around 2000 K, in the double ion storage ring DESIREE.We present a new approach to match beam velocities and a new general analysis method for non-fragmenting mutual neutralization at DESIREE.Our results show two features, which we could clearly assign to the product channel into the electronically   excited  3s state of neutral lithium and an unresolved combination of 3p and 3d final state contributions.Branching fractions into 3s are extracted for ten different collision energies via spectral binning and compared to several theoretical investigations and two previous measurements, which focused on the heavier isotope deuterium.We find a significant isotope effect, as theoretically predicted, but in contrast to previous experimental results. The branching fractions agree well with different theoretical approaches using non-empirical couplings and  best with a combination of ab initio potentials and Landau-Zener transition probabilities.

Microphotonics has been offering a body of ideas to prospective applicationsin optics. Among those, the concept of photonic integrated circuits (PIC’s) has recently spurred a substantial excitement into the scientific community. Relisation of the PIC’s becomes feasible as the size shrinkage of the optical elements is accomplished. The elements based on photonic crystals (PCs) represent promising candidacy for manufacture of PIC’s. This thesis is devoted to tailoring of optical properties and advanced modelling of two types of photonic crystals: (Bi3Fe5O12/Sm3Ga5O12)m and (TiO2/Er2O3)m potentially applicable in the role optical isolators and optical amplifiers, respectively. Deposition conditions of titanium dioxide were first investigated to maximise refractive index and minimise absorption as well as surface roughness of titania films. It was done employing three routines: deposition at elevated substrate temperatures, regular annealing in thermodynamically equilibrium conditions and rapid thermal annealing (RTA). RTA at 500 oC was shown to provide the best optical performance giving a refractive index of 2.53, an absorption coefficient of 404 cm−1 and a root-mean-square surface roughness of 0.6 nm. Advanced modelling of transmittance and Faraday rotation for the PCs (Bi3Fe5O12/Sm3Ga5O12)5 and (TiO2/Er2O3)6 was done using the 4 × 4 matrix formalism of Višňovský. The simulations for the constituent materials in the forms of single films were performed using the Swanepoel and Višňovský formulae. This enabled generation of the dispersion relations for diagonal and off-diagonal elements of the permittivity tensors relating to the materials. These dispersion relations were utilised to produce dispersion relations for complex refractive indices of the materials. Integration of the complex refractive indices into the 4 × 4 matrix formalism allowed computation of transmittance and Faraday rotation of the PCs. The simulation results were found to be in a good agreement with the experimental ones proving such a simulation approach is an excellent means of engineering PCs.

To understand the function of macromolecules like proteins it helps to know the structure of the molecule. Coherent diffraction imaging is an emerging method that might be used to figure out the structures of macromolecules. In this method diffraction patterns of the macromolecule are recorded by shining light on the molecule from many unknown orientations and detecting the pattern of the diffracted photons. By assembling the diffraction patterns in a specific way and finding the phase of the photons that gave rise to the diffraction patterns, it is theoretically possible to obtain the electronstructure of the molecule and thus the molecular structure. The assembling of several thousand diffraction patterns representing unknown orientations of the molecule is hard to do by hand, but there are several methods that can be used. The EMC (Expand-Maximize-Compress) algorithm is one of those methods. It is an iterative algorithm that tries to create a model describing the Fourier Transform of the electron density of the molecule by maximizing each diffraction patterns fit to the model. This work examines how sensitive the EMC algorithm is to datasets with few diffraction patterns or a low intensity of the light being diffracted by the molecule, for the proteins phytochrome and lysozyme. The result of the work could be used to make sure enough data in collected in real experiments. Diffraction patterns simulated with the program Condor is used in this work, instead of diffraction patterns from real experiments.EMC finds the correct model when the data set contains about 1/3 fewer photons for the smaller more symmetrical molecule lysozyme than it does for phytochrome. This might be because the shapes in lysozymes diffraction patterns are larger than in phyochrome’s patterns. For phytochrome the EMC algorithm assembled the diffraction patterns correctly, with fewest photons for the light intensity 0.764 J/μm2 and 1250 diffraction patterns. For lysozyme it was with an intensity 1.910 J/μm2 and 1425 diffraction patterns. More investigation of the data is needed to understand what factors that affect the EMC algorithms ability to assemble the diffraction patterns correctly. / För att förstå makromolekylers kemiska eller biologiska funktion so underlättar det om man känner till molekylens kemiska struktur. Med den nya tekniken “coherent diffraction imaging” ska det vara möjligt att lista ut makromolekylers struktur. I denna teknik detekterar man diffraktionsmönster av molekylen genom att belysa molekylen med ljus från många olika okända vinklar and registrera mönstret som skapas av det diffrakterade ljuset. Genom att sätta ihop alla dessa diffraktionsmönster på rätt sätt och sen återskapa fasen för ljuset i diffraktionsmönstret så kan man generera molekylens elektronstruktur och från elektronstrukturen kan man få tag i molekylens struktur. Att sätta ihop tio tusentals diffraktionsmönster med okända vinklar på rätt sätt är väldigt svårt att göra, men det finns flera olika metoder som kan användas. EMC (Expand-Maximize-Compress) är en sådan metod. EMC är en iterativ algoritm som skapar en modell av (Fourier transformen av) molekylens elektronstruktur genom att maximera hur bra diffraktionsmönstren passar med modellen. Detta arbete utreder hur bra EMC algoritmen är på att hitta rätt (Fourier transform av) elektronstruktur när väldigt få diffraktionsmönster används eller när intensiteten på ljuset som sprids av molekylen är lågt. Programmet Condor används för att generera teoretiska diffraktionsmönster för de 2 molekylerna lysozym och fytokrom. EMC används sedan med olika uppsättningar av intensitet och antal diffraktionsmönster för att skapa en modell av elektronstrukturen. EMC behövde ca 1/3 färre antal fotoner i sin modell för att hittar den rätta modellen av elektronstrukturen för den lilla symmetriskt formade molekylen lysozym än för fytokrom. Att det är lättare för EMC algoritmen att hitta den korrekta modellen för lysozym än fytokrom kan bero på att lysozyms diffraktionsmönster har större former/features eller på lysozyms storlek och form. EMC körningen som behövde minst antal fotoner för att hitta den korrekta elektronstrukturen för fytokrom hade intensiteten 0,764 J/μm2 på det inkommande ljuset och behövde 1250 diffraktionsmönster. För lysozym behövdes det 1,910 J/μm2 och 1425 diffraktionsmönster för att EMC algoritmen skulle hitta rätt modell av elektronstrukturen.

Advances in experimental physics, specifically light sources emitting at an attosecond time scale, has enabled the time resolution of atomic processes like photoionization. Recent developments have allowed these sources to produce light with non-linear polarization. There exists various theoretical methods that can simulate experimental set-ups that make use of these attosecond sources. The aim of this thesis project was to extend two of these methods to be able to simulate circularly polarized light in order to both better model experimental results and come up with new potentially interesting experiments. This has resulted in an extended version of the Random Phase Approximation with Exchange method capable of simulating an ionization process by light of arbitrary polarization, as well as well as an extended version of the NewStock package that is capable of time-resolved simulation of matter interactions with arbitrary light pulses.