Nanophotonic and plasmonic research have seen many breakthroughs lately which has created a demand for automated design algorithms to optimize optical elements at the nanometer scale. This work focuses on plasmonic nanostructures that are small metal particles interacting with electromagnetic radiation on length scales typically less than the wavelength. Plasmonic effects from nanostructures are used for enhancing and manipulating electromagnetic fields at the nanometer scale which have seen many applications in sensing requiring an ultra-high sensitivity and a small resolution. This work is about how deep learning methods can be used for designing plasmonic gold nanostructures. In particular, we investigate how convolutional neural networks can be used to predict the optical properties of nanostructures and how conditional generative adversarial networks (cGAN) can be used for designing structures with desired optical properties. The data in this work consist of images with differently shaped nanostructures and the corresponding spectral data for the scattering cross section, the absorption cross section, the polarization rotation and the polarization ellipticity. Utilizing the convolutional EfficientNet architectures, we train a forward model to predict the spectral data of anisotropically shaped nanostructures with images of the structure shape as input. We achieve a mean squared error of 2.5 × 10−4, 2.5 ×10−4, 6.0 ×10−4, and 4.9 ×10−4 respectively for each variable which agrees with the literature for similar problems. For the inverse design models, we show that label projection can be used to improve the results of two common GAN architectures in combination with a novel label embedding network. We use the Wasserstein GAN method with gradient penalty for training the models to generate images of nanostructure shapes conditioned on spectral data. The best model achieves a pixelwise mean absolute error of 4.9×10−3 and an estimated spectral mean absolute error of 8.4×10−3 between original and generated images when trained on a dataset containing cylindrical dimer structures. Furthermore, we have shown that the pixelwise mean absolute error is reduced when more conditional input variables are added to the model and that the model can learn different nanostructure shapes when trained on a large dataset containing different anisotropic gold nanostructure shapes. The best pixelwise mean absolute error found is 1.1×10−2 and the estimated spectral mean absolute error is 1.7 × 10−2 on the full dataset using all available input data.

This thesis explores how the diffraction pattern in the near-field region of a chromium feature edge on a photomask gets altered for three scenarios: First, an analytical study using the Fresnel diffraction integral is performed that investigates what happens when the thin-mask approximation is omitted and the chromium layer is given a thickness. Another analytical study is performed where the edges of a test feature are altered to simulate deviations in the linewidth or a translation of the whole feature, image subtraction is then used to create a difference pattern by subtracting a reference diffraction pattern from the diffraction pattern created by the altered test feature. Lastly, a numerical study using Fourier optics is performed to investigate the effect that introducing four common defects: extrusions, intrusions, dark spots, and pinholes, around the edge will have on the diffraction pattern by subtracting the diffraction pattern from a reference half-plane and again analyzing the resulting difference pattern. Introducing a thickness to the chromium layer alters the diffraction pattern by creating a small crease around the area of the edge in reflective mode, resulting in something similar to a double edge. The high optical density of chromium nullified any effect the thickness had when viewing the system through transmission mode. A linear relation between a change in linewidth or translation of a feature and the peak intensity of the difference pattern is observed that might be used for edge detection. The defect diameter of an extrusion or intrusion seems to correlate in a quadratic way with the peak fringe intensity of the subtracted difference pattern along the x-axis as the defect is fully visible. For a dark spot or pinhole defect being translated away from a chromium edge, the central fringe along the y-axis of the difference pattern follows a sinusoidal curve as it translates further away from the edge. The amplitude of this curve is related to the defect size.

La première partie décrit trois expériences réalisées avec l'interféromètre atomique à jet de lithium supersonique développé à Toulouse. La seconde partie présente le nouvel interféromètre atomique à condensats de Bose-Einstein (CBE) développé dans le but de tester la neutralité de la matière. Les trois premières expériences exploitent l'interaction entre un atome de lithium et différents champs électromagnétiques. Une différence de potentiel électrique dépendant du temps a servi à moduler la phase des deux bras de notre interféromètre à des fréquences différentes, ce qui a permis une détection homodyne et hétérodyne d'ondes de matière. Une phase géométrique de la lumière (la phase de Pancharatnam) a été transférée à notre signal interférométrique par les réseaux de diffraction de Bragg ce qui a ajouté un nouvel outil à la panoplie permettant le contrôle d'ondes de matières. Enfin, un faisceau laser focalisé sur un seul des deux bras nous a permis de mesurer avec exactitude une des longueurs d'onde d'extinction du lithium (correspondant à une valeur de polarisabilité dynamique nulle). L'objectif du nouvel interféromètre à CBE est de réaliser une nouvelle mesure de la charge électrique résiduelle de la matière et en particulier des isotopes du rubidium 85Rb et 87Rb. Cette mesure nous permettra de connaître avec une plus grande sensibilité la différence de charge entre le proton et l'électron ainsi que la charge du neutron. Le principe de cette mesure repose sur une séparation spatiale importante entre les deux bras d'un interféromètre en fontaine ainsi que sur un temps de cycle de 5 s. Ces caractéristiques ont nécessité un travail de conception à la fois au niveau de la source (une puce à atome) et au niveau du phénomène de diffraction (séparation en impulsion importante) qui sera exposé dans un premier temps. Dans un second temps, les choix techniques en matière de chambre à vide, système laser et sources de champs magnétiques seront décrits et caractérisés. Enfin, les performances actuelles de cette source d'atomes froids seront présentées et comparées à nos attentes. / This thesis's first part describes the realization of three experiments using an atom interferometer operated with a lithium supersonic beam. The second part presents the development of a new BEC interferometer designed to test matter neutrality. The first three experiments rely on the interactions of lithium atom with different electromagnetic fields. A time dependent electric potential difference was used to produce phase modulation of both interferometer arms at different frequencies, leading to homodyne and heterodyne detection of atom waves. A geometric phase of light (the Pancharatnam phase) was successfully transferred to our interferometer signal during Bragg diffraction, enlarging the atom optics toolbox for phase control in an atom interferometer. Finally, a focused laser beam was used to measure accurately the value of one lithium tune-out wavelength (for which its dynamic polarizability is zero). The new BEC interferometer was designed to measure a possible non-zero electric charge of rubidium isotopes 85Rb and 87Rb with enhanced sensitivity to the electron-proton charge difference and neutron neutrality. This setup relies on a large spatial separation between the two interferometer arms in a fountain configuration aiming at a cycle time of 5s. These features required particular design work both on the atomic source (atom-chip) and the diffraction process (Large Momentum Transfer). The technical choices on the vacuum chambers, laser system and magnetic sources are described and characterized. Finally, the up-to-date cold-atom source performances is shown and compared to our expectations.

The objective of this master thesis was to provide the optimization of an ion-atom beam source for the improvement of its properties. The improvement of the parameters increases the efficiency of the source during the deposition of gallium nitride ultrathin films (GaN) being important in microeletronics and optoelectronics. After optimization, the depositions of GaN ultrathin films on Si(111) 7x7 at lower temperatures (

This Thesis contains details of the construction and characterisation of a compact apparatus for the cooling of ultracold atoms to quantum degeneracy, and their manipulation in flexible holographic optical traps. We have designed and built two iterations of this apparatus. The first version consists of a stainless steel single-cell vacuum chamber, in which we confine ⁸⁷Rb and ⁶Li or ⁷Li in a Magneto-Optical Trap. We characterise the alternative methods of pulsed atomic dispenser and Light Induced Atomic Desorption (LIAD) to rapidly vary the background pressure in the vacuum chamber with the view to enabling efficient evaporative cooling in the single chamber, loading MOTs of up to 10⁸ atoms using pulsed dispensers. The LIAD is found to be ineffective in loading large MOTs in this setup, while the pulsed dispensers method gradually increases the background pressure in the chamber over time. Based on the results of this first iteration, we designed and built a second single-chamber apparatus for cooling of ⁸⁷Rb to quantum degeneracy. The LIAD technique was used to successfully load MOTs containing 8x10⁷ atoms in this single pyrex cell with a rapidly-varying background pressure. The lifetime of an atomic cloud loaded from the MOT into a magnetic trap increased by a factor of 6 when LIAD was used. The holographic optical traps for cold atoms are generated using a Spatial Light Modulator, and we present our novel method for improving the quality of holographic light patterns to the point where they are suitable for trapping ultracold atoms using a feedback algorithm. As demonstrations of this new capability, we show power-law optical traps which provide an efficient, reversible route to Bose-Einstein Condensation and a dynamic ring trap for the investigation of superfluidity in cold atoms.

In this thesis H-bonded systems (natural gas hydrates, water clusters, and crystal ice) are studied by density functional theory (DFT) computations. Natural gas hydrates (NGHs) play an important role in energy and environmental fields: NGHs are considered as a promising backup energy resource in the near-future due to their tremendous carbon content; improper exploration of NGHs could induce geological disasters and aggravate the greenhouse effect. In addition, many technologies based on gas hydrates are being applied and developed. The thermodynamic stabilities of various water cavities in different clathrate crystalline phases occupied by hydrocarbon gas molecules are studied by dispersion-corrected hybrid functionals. The Raman spectra of C-C and C-H stretching vibrations of hydrocarbon molecules in various water cavities in the solid state are derived. The trends of C-H stretching vibrational frequencies are found to follow the prediction by the “loose cage ─| tight cage” model. In addition, the trends and origins of 13C NMR chemical shifts of hydrocarbon molecules in various NGHs are presented. These theoretical results will enlarge the database of C-C and C-H stretching vibrational frequencies and 13C NMR parameters of hydrocarbon molecules in NGHs, and provide valuable information to help identify the types of clathrate phases and varieties of guest molecules included in NGHs samples taken from natural sites. The behavior of water clusters may help to understand the properties of its liquid and solid states. The thermodynamic stabilities and IR spectra of a small-, medium-, and large-sized water cluster are studied in this work. After full optimization of (H2O)20,54,100 using the hybrid functional B3LYP, the electronic energies, zero-point energies, internal energies, enthalpies, entropies, and Gibbs free energies of the water clusters are computed. The OH stretching vibrational IR spectra of (H2O)20,54,100 are also presented and split into sub-spectra for different H-bond types based on the specific contributions from each group. It is found that the OH stretching vibrational frequencies of water are sensitive to the conformations of the H-bonds and the vibrations of the H-bonds belonging to different types are located in separated regions in the IR spectra. Thus, the spectroscopic fingerprints will reflect the H-bond topology of the water molecules in a water cluster. Ice XI has been suggested to be involved in the process of planetary formation as a considerable electric field might be formed from the ferroelectric ice XI in space. IR and Raman spectroscopic technology can be directly used to identify the occurrence of ferroelectric ice XI in laboratory or extraterrestrial settings. Due to the difficulty for DFT to describe non-covalent systems, the performance of 16 different DFT methods applied on the ice Ih, VIII, IX, and XI crystal phases are assessed. Based on the computational accuracy and cost, the IR and Raman spectra of ice Ih and XI are derived and compared. The librational vibrations are found to be the identifier which can be used to distinguish ice Ih and ice XI in the universe. In addition, the existence only one kind of H-bond in ice Ih is demonstrated from the overlapping sub-spectra for different types of H-bonded pair configurations in 16 isomers of ice Ih. The region of water under negative pressure is an exotic land in lack of exploitation. Guest free clathrate hydrate (clathrate ice) of sII type has been recently confirmed experimentally at negative pressure. Does any other clathrate ice phase exist at negative pressure region? Since clathrate hydrate are isostructural with silica clathrate minerals and semiconductor clathrates, and crystal structure prediction by analogy with known structures and first-principles computations is an effective way to find new crystalline phases of solid materials, we are motived to look for new clathrate ice phases from silica or semiconductor clathrate materials based on first-principles computations. Borrowing the idea new clathrate frameworks of ZnO and SiC can be constructed by connecting their bubble clusters in different ways, new clathrate ice phases (sL, sL_I, sL_II, and sL_III) are generated by connecting the water bubble clusters according to different rules. Using the non-local dispersion-corrected vdW-DF2 functional, clathrate ice sL with ultralow density (0.6 g/cm3) is predicted by first-principles phase diagram computations to be stable under larger negative pressures than the sII phase. The phase diagram of water is thus extended into the lower negative pressure region.

Electron beam induced current (EBIC) and atom probe tomography (APT) were used in this study to determine electrical activities and impurity compositions at extended defects in multicrystalline silicon (mc-Si) samples. The results provide, for the first time, information regarding the chemical species present at defects whose electrical activity has previously been measured. A new APT specimen fabrication process was developed with the ability to select a specific defect for APT analysis. Development of the APT specimen fabrication process proceeded by first selecting and optimising the preferential etching for nano-scale defect delineation. Three etchants were evaluated, namely Secco, Sirtl and Dash, from which the Secco etch was selected. Three parameters were optimised to produce etch pits with geometries that meet the requirements imposed by APT specimen fabrication methods. The optimum parameters were 0.05M potassium dichromate concentration, 20°C etch temperature, and 30sec etch time. In the second stage, marking techniques were developed in order for the defects to be located throughout the APT specimen fabrication process. However, it became apparent that the conventional APT specimen fabrication method could not be used to fabricate APT specimens containing selected defects in a mc-Si sample. This led to the development of a novel APT specimen fabrication approach which allowed APT specimens to be fabricated, reproducibly, containing grain boundaries and isolated dislocations. In order to evaluate accurately iron contamination in mc-Si, four atom probe parameters were optimised to maximise detection sensitivity: the evaporation rate, the laser beam energy, the pulse repetition rate and the specimen temperature. The optimisation process can be divided in to two parts. In the first part, a matrix of pre-sharpened single-crystal silicon specimens was subjected to a variety of experimental parameters. The optimised parameters were determined to be 0.3% evaporation rate, 0.5nJ beam energy, 160kHz repetition rate and 55K specimen temperature. The second part was to determine the iron detection efficiency –the percentage of detected Fe ions that can be correctly identified as Fe– and sensitivity using these parameters to analyse a specially prepared iron calibration specimen. The values were determined to be a detection efficiency of about 35% and sensitivity of 54ppm or 2.70x10¹⁸ atom/cm³. The APT specimen fabrication process and the optimised APT analysis parameters were used to analyse four extended defects in mc-Si samples subjected to three different processing conditions, namely gold-contaminated, as-grown and phosphorus diffusion gettering (PDG). The important aspects of the analysis are listed below: • Gold was not detected at the grain boundary and its associated dislocations in the gold-contaminated specimen. The binding enthalpy of gold to such defects is thus less than 0.63eV. • Iron was not detected in any specimen. • Copper was observed at the grain boundary in the as-grown specimen in the form of individual atoms as well as clusters with diameters ranging between 4nm and 9nm. The electrical activity of the grain boundary was about 58%. • Nickel and carbon were detected at the grain boundary in the post-PDG specimen with the former having platelet structures with diameters and thicknesses ranging between 4nm-7nm and 2nm-4nm, respectively. The recombination strength of the defect was about 22%. • Two nickel clusters were found at the isolated dislocation in the post-PDG specimen. The clusters were spherical with an average diameter of 10nm. The distance between the two clusters was 35nm. The recombination strength of the defect was about 4%.

Materials at extreme conditions exhibit properties that differ substantially from ambient conditions. High pressure and high temperature expose anharmonic, non-linear behavior, and can provoke phase transitions among other effects. Experimental setups to study that sort of effects are typically costly and experiments themselves are laborious. It is common to apply theoretical techniques in order to provide a road-map for experimental research. In this thesis I cover computational algorithms based on first-principles calculations for high-temperature and high-pressure conditions. The two thoroughly described algorithms are: 1) the free energy studies using temperature-dependent effective potential method (TDEP), and 2) a higher-order elastic constants calculation procedure. The algorithms are described in an easy to follow manner with motivation for every step covered. The Free energy calculation algorithm is demonstrated with applications to hexagonal close-packed Iron at the conditions close to the inner Earth Core’s. The algorithm of elastic constants calculation is demonstrated with application to Molybdenum, Tantalum, and Niobium. Other projects included in the thesis are the study of effects of van der Waals corrections on the graphite and diamond equations of state. / Material vid extrema förhållanden uppvisar egenskaper som skiljer sig avsevärt från omgivningsförhållanden. Högt tryck och hög temperatur exponera anharmonicity, icke-linjärt beteende, och kan framkalla fasövergångar bland andra effekter. Experimentella uppställningar för att studera denna typ av effekter är vanligtvis dyra och experiment själva är mödosam. Det är vanligt att tillämpa teoretiska metoder för att ge en färdplan för experimentell forskning. I denna avhandling täcker jag beräkningsalgoritmer baserat på första principer beräkningar för hög temperatur och högt tryck. De två grundligt beskrivna algoritmer är: 1) den fria energin studier med temperaturberoende effektiv potentiell metod (TDEP), och 2) en högre ordning elastiska konstantberäkningsproceduren. Algoritmerna beskrivs i en lätt att följa sätt med motivation för varje steg som omfattas. Den fria energiberäkningsalgoritm visas med program till hexagonal tätpackad järn på villkoren nära jordens inre kärna. Algoritmen av elastiska konstanter beräkning demonstreras med tillämpning till molybden, tantal, och niob. Andra projekt som ingår i avhandlingen är effekterna av van der Waals-korrigeringar på tillståndsekvation och elastiska konstanter i grafit och diamant.

Bacteria can quickly spread throughout the human body, making certain diseases hard or impossible to cure. In order to understand how the bacteria can initiate and develop into an infection, microfluidic chambers in a lab environment are used as a template of how bacteria reacts to different types of flows. However, accurately tracking the movement of bacteria is a difficult task, where small objects has to be captured with a high resolution and digitally analysed with computationally heavy methods. Popular imaging methods utilise digital holographic microscopy, where three-dimensional movement is captured in two-dimensional images by numerical reconstruction of the diffraction of light. Since numerical reconstructions become computationally heavy when a good accuracy is required, this master's thesis work focus on evaluating the possibility of using convolutional neural networks to quickly and accurately determine the spatial properties of bacteria. By thorough testing and analysis of state of the art and old networks a new network design is presented, designed to eliminate as many imaging issues as possible. We found that there are certain network design choices that help with reducing the overall error of the system, and with a well chosen training set with sensible augmentations, some networks were able to reach a 60% classification accuracy when determining the vertical rotation of the bacteria. Unfortunately, due to the lack of experimental data where the ground-truth is known, not much experimental testing could be performed. However, a few tests showed that images of high quality could be classified within the expected range of vertical rotation. / Bakterier kan snabbt sprida sig genom människokroppen, vilket försvårar starkt möjligheterna att kurera vissa sjukdomar. För att få en inblick i hur bakterier kan initiera och utvecklas till en infektion används som mall laborativa uppställningar med vätskekanaler i mikroskala när man söker förstå hur bakterier reagerar på olika typer av flöden. Att spåra dessa rörelser med god säkerhet är dock en utmaning, då man experimentellt söker fånga små skalor med hög upplösning, som sedan ska analyseras med datorintensiva metoder. Populära avbildningsmetoder använder sig utav digital holografisk mikroskopi, där tredimensionella rörelser kan fångas med hjälp av tvådimensionella bilder genom att numeriskt återskapa ljusets brytningsmönster mot objekten. Eftersom dessa metoder blir beräkningstunga när god säkerhet krävs så utforskar detta examensarbete möjligheterna att utnyttja faltningsnätverk för att snabbt och säkert bestämma vertikalrotationen hos bakterier avbildade med holografi. Genom nogranna tester av moderna samt äldre nätverk så presenteras en ny nätverksdesign, utvecklad i mål med att eliminera så många avbildningsproblem som möjligt. Vi fann att vissa designval vid nätverksutvecklingen kan hjälpa med att reducera klassificeringsfelen givet vårt system, och med en väl utvald träningsmängd med lämpliga justeringar så lyckades vi nå en klassificeringssäkerhet på över 60% med vissa nätverk. På grund av bristande experimentellt data där de riktiga värdena är kända så har ingen utförlig experimentell analys utförts, men några tester på experimentella bilder i god kvalité har visats ge resultat som tyder på en korrekt analys inom den förväntade vertikalrotationen.

The treatment plan for radiation therapy with protons is based on images from a computed tomography (CT) scanner. This is problematic since the photons in the x-ray beam from the CT scanner and the protons are affected differently by the tissue in the patient, which introduce an uncertainty in the track length of the protons. The hypothesis of this study is that a new generation of CT scanners (DECT), with the capacity to simultaneously scan the patient with two photon spectra of different mean energy, will improve the tissue characterisation and which in turn reduce the uncertainty in the track length of the protons. In this study, the accuracy and precision of a DECT-based method from the literature is compared to the conventional calibration method used today at the University clinics in Sweden to relate the attenuation of the photon beam to the slowing down of the protons. The methods are tested on CT images of a phantom, a plastic body containing tissue equivalent plastic inserts of known elemental composition. The results turned out to be inconclusive as there were large uncertainties in the measurements. The method has potential, as has been shown in the literature, but there are many questions that need to be answered before the method is ready to be implemented at the clinic. / En proton som färdas genom människokroppen deponerar endast en liten del av sin energi längs vägen innan den plötsligt deponerar allt i slutet på dess bana. Hur lång dess bana är beror på protonens ursprungliga energi och den atomära sammansättningen hos vävnaden den passerar igenom. Om sammansättningen är känd går det genom att justera den initiala energin bestämma banlängden. Denna egenskap gör protonen väldigt attraktiv för strålterpi, då det innbär möjligheten att behandla med hög precision samt bespara frisk vävnad onödig dos. Strålterapi med protoner planeras idag med bilder från en skiktröntgen (CT) som underlag. Ett problem med det är att röntgenstrålarna från CT-skannern påverkas annorlunda än protonerna av vävnaden, vilket introducerar en osäkerhet i protonernas banlängd. Hypotesen i denna studie är att en ny generation av CT-scanner (DECT), med möjlighet att simultant skanna patienten med två fotonspektran av olika medelenergi, på ett bättre sätt ska kunna bestämma den atomära sammansättningen för vävnaden och därmed reducera osäkerheten i protonernas banlängd. Noggrannhet och precision för en DECT-baserad metod från litteraturen jämförs med den SECT-baserade kalibreringsmetoden, som idag används på Universitetssjukhusen i Sverige för att relatera fotonstrålens dämpning i vävnaden till protonernas inbromsning. Metoderna testas på CT bilder av ett fantom, en plastkropp innehållandes olika cylindrar av vävnadsekvivalent plast med känd atomär sammansättning. Resultatet av den här studien är inte starkt nog för att bevisa hypotesen för studien. Det insamlade bildmaterialet innehåller höga brusnivåer jämfört med de som rapporteras i literaturen. Brusnivåer är så höga att det mesta av resultatet inte kan anses som statistiskt signifikant. Det är dessutom svårt att göra en direkt jämförelse av prestanda med befintlig teori för vävnadskaraktärisering, då bildmaterialet från de CT skanners som jämfördes är av olika typer. De resultat som publicerats i litteraturen visar att den DECT-baserade metoden har potential, men den här studien gör tydligt att det fortfarande finns frågor som måste besvaras innan metoden är redo att implementeras kliniskt.