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.

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.

The recent discovery of Cr4AlB4, a laminated ternary metal boride belonging to the family of layered MAB-phases, where the transition metal boride layers are interleaved by an A layer, has spurred theoretical investigation for novel M4AlB4 phases. In this study, first-principles calculations were applied in order to investigate the thermodynamical stability and mechanical properties of M4AB4 where M = Cr, Hf, Mo, Nb, Ta, Ti, V, W, Zr while the A layer was kept fixed as Al. The thermodynamical stability calculations validate the recently discovered Cr4AlB4 phase’s stability and suggest the neighboring phase Mo4AlB4 to be stable. Additionally, the phases Mo3AlB4, Mo2AlB2, Ti4AlB4 and Ti2AlB2 indicates phases close to stable with a formation enthalpy within the range of 0 < ∆H < 25 meV per atom compared to competing phases. Hence dynamical stability investigations were carried out, which indicates Mo4AlB4 to be dynamically stable. The stability of Mo4AlB4 does encourage synthesizing attempts to be kept in mind as a future project. Phase stability trends of the 111, 212, 314 and 414 compositions were discovered, where a 212, 314 and 414 composition is seen to be more stable for an M-element with lower electron configuration. Furthermore, the mechanical properties of the 414 compositions were investigated by systematically straining the unit cell in different directions. The bulk-, shear- and Young’s-modulus were derived and are presented, where Ti4AlB4 demonstrates values similar to the commended Ti2AlC MAX-phase. Finally, ductility plots are presented which purposes a linear trend between the elements of group IV, V and VI. Based on the results, further studies with a focus on the temperature and magnetization’s impact on the stability and mechanical properties are suggested.

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.