Utilizing density functional theory (DFT) the Vienna Ab initio Simulation Package (VASP) was used to calculate the Raman spectra for five single-walled carbon nanotubes (SWCNTs) with chiralities (4,4), (6,6), (8,0), (12,0) and (7,1). The radial breathing mode (RBM), when compared with experimental frequencies, shows good correlation. When compared to RBM:s calculated with tight binding the frequencies calculated with DFT displayed higher accuracy. The precision of G-band frequencies were inconclusive due to lack of experimental data. The frequencies did not agree well with the results from tight-binding theory. The correctness of the Raman activity estimations using results from DFT calculations was found to be questionable. An unknown mode, which was found to be highly Raman active in the calculated spectra of (4,4), (6,6), and possibly (8,0), and (12,0), is also discussed. It was concluded that further calculations on larger tubes, especially armchair tubes are relevant for future studies. Further verification of the determination of Raman activity is also needed. / F7042T - Project in Engineering Physics

The objectives of the present project were to set up, optimise and characterise a digitalholographic microscopy (DHM) laboratory set-up designed for the study of eyetissue and to implement and optimise digital data processing and noise reductionroutines. This work is part of a collaborative project aiming to provide quantitativemethods for the in vitro and in vivo characterisation of human corneal transparency.The laboratory set-up is based on a commercial laboratory microscope with zoomfunction (a “macroscope”). In continuation of previous work, we completed and optimised,and extended a software for holographic signal processing and numericalpropagation of the wavefront.To characterise the set-up and quantify its performances for standard operationand in its DHM configuration, we compare the magnification and resolution to theoreticalvalues for a given set of parameters. We determined the magnification factorand the rotation angle between the object and camera planes. With a laser wavelengthof 532 nm, a x1 objective and a zoom setting of x2.9 (which corresponds to aplane sample wavefront), we measured a magnification of 1.68. With the same parameters,we measure a holographic resolution of about 11 m. The wavefront phasecould be determined with a precision of a fraction of the wavelength.We subsequently performed analysis of the relative contribution of coherent noiseand implemented and evaluated several noise reduction routines. While the impactof coherent noise remained visible in the amplitude image, interferometric precisionwas obtained for the phase of the wavefront and the set-up was considered qualifiedfor its intended use for corneal characterisation.A first test measurement was performed on primate cornea.Subsequent work will address the further quantitative characterisation of the setupfor the full set of parameters (objectives, zoom positions, wavelengths), test measurementson samples with known transmission and light scattering properties (e.g.solutions of PMMA beads) and the comparison of the results with the predictions ofa theoretical model, and measurements on animal and human tissue.

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.

No description available.

Durch neue Ansätze zur Charakterisierung molekularer und nanokristalliner Materialien spiegelt die vorliegende Arbeit die Synergie von linearer Optik über Ultrakurzzeitphysik zur nichtlinearen Optik wider. Angefangen mit der linearen diffusen Reflektanz (Remission) zur Bestimmung des spektralen Reflexionsvermögens von Pulverpartikeln, erlaubt die hier gezeigte alternative Herangehensweise (s. Kapitel 2) nicht nur ein vereinfachtes Messen der Remission zur Analyse von Materialzusammensetzungen, Verunreinigungen und Co-Dotierungen, sondern eröffnet zudem über Monte-Carlo Simulationen, kombiniert mit der Kubelka-Munk Theorie und der Mie Streuung, auch den Zugang zu dem ansonsten experimentell unzugänglichen Absorptionskoeffizienten von nicht-transluzenten Proben. Die präsentierten Mess- und Simulationsergebnisse an Pulvertabletten aus Rutil-Titandioxid (TiO2) und Cer-dotierten Yttrium Aluminium Granat (YAG:Ce3+) sind mit den bisherigen in der Literatur vorliegenden Ergebnissen konsistent oder zumindest vergleichbar. Auch lassen sich nach Modifikation der Kubelka-Munk Funktion die Bandkanten-Energien Eg der mikro- und nanokristallinen Pulverproben mittels so genannter Tauc Plots verifizieren. Basierend auf einer starken Temperatur- und Konzentrationsabhängigkeit lassen sich die Emissionsspektren der oben genannten YAG:Ce3+-Leuchtstoffe aufgrund von Überlappung oder Verschiebung der energetischen Grundniveaus 2F5/2 und 2F7/2 variieren (s. Kapitel 3). Während sich bei Tieftemperaturen um 19K die doppelbandige Natur der Leuchtstoffe zeigt, verbreitern sich die Emissionsbanden bei Raumtemperatur zu einer Einzelbande, womit eine spektral sehr breite Fluoreszenz einhergeht. Mathematische Entfaltungen dieser Spektren zeigen jeweils den prozentualen Beitrag der Relaxation aus dem untersten angeregten Zustand 5d1 in einen der beiden Grundzustände 2F5/2 und 2F7/2 und ebenso den Einfluss der Temperatur und Cer-Konzentration. Tatsächlich führen die experimentellen Ergebnisse der vorliegenden Arbeit zu der Erkenntnis, dass eine der vier untersuchten YAG:Ce3+-Proben eine erhöhte Cer-Konzentration aufweisen muss. Anders als bei den schwach konzentrierten YAG:Ce3+-Proben ist die spektrale Doppelbande des stark konzentrierten Leuchtstoffs selbst bei 19K nur zu erahnen, während der Beitrag des 5d1 --> 2F7/2 Übergangs auf die Gesamtfluoreszenz retrograd zum 5d1 --> 2F5/2 Übergang mit steigender Temperatur sogar abnimmt. Im direkten Anschluss an die spektrale Vermessung der Proben folgen zeitaufgelöste Lebensdauermessungen zur Bestimmung der Nachleuchtdauern dieser Leuchtstoffe mittels Pikosekunden-Laserpulsen (ps-Pulse) (s. Kapitel 3.3). Auch hier stellen sich Unterschiede zwischen den genannten YAG:Ce3+-Proben heraus und untermauern erneut die Annahme unterschiedlicher Cer-Konzentrationen: Während die Nachleuchtdauer der niedrig konzentrierten Leuchtstoffe von der Temperatur nahezu unberührt bleibt, zeigt sich eine bemerkenswerte Temperaturabhängigkeit des 5d1 --> 2F5/2 Übergangs beim YAG:Ce3+ mit hohem Cer-Gehalt. Auf Basis sämtlicher experimenteller Erkenntnisse und einer ausgiebigen Literaturrecherche kann schließlich eine Fremddotierung der Leuchtstoff-Proben nahezu vollständig ausgeschlossen und ein Energieschema für die vorliegenden YAG:Ce3+-Leuchtstoffe mit den wichtigsten optischen Übergängen erstellt werden. In Hinblick auf potentielle holographische Applikationen wie der optischen Datenspeicherung oder Echtzeit-Holographie erweisen sich die in Polydimethylsiloxan eingebetteten photoschaltbaren Ruthenium-Sulfoxide aufgrund der äußerst geringen Beugungseffizienz von < 10−2 als nicht pragmatisch für die Praxis (s. Kapitel 4). Vergleichbare photoschaltbare Materialien, wie zum Beispiel Natriumnitrosylprussiat, erreichen hingegen Effizienzen von bis zu 100 %. Dennoch zeichnen sich die in Publikation 2 (s. Anhang A.2) vorgestellten Resultate an OSO-PDMS durch ihre äußerst hohe Qualität aus. Sowohl die dynamische Hologramm-Entstehung als auch die Rocking-Kurve folgen den physikalischen Theorien einwandfrei und lassen sich mit den bekannten mathematischen Anpassungen exakt wiedergeben, womit sich entsprechend intrinsische Größen ableiten lassen. Zudem beeindruckt der experimentelle Aufbau mit der präzisen Messung der oftmals nicht detektierbaren Nebenmaxima der gezeigten Rocking-Kurve sowie des Winkel-Multiplexings. Bemerkenswert ist außerdem aus physikalischer Sicht der immense Unterschied zwischen cw- und fs-Holographie. Hier deuten sich nichtlineare Effekte an, die zu der Erkenntnis führen, dass sich die bekannten Theorien mit cw-Lasern nicht ohne Weiteres deckungsgleich auf die Holographie mit ultrakurzen Laserpulsen anwenden lassen. Ein möglicher Erklärungsansatz ist in Kapitel 4.1 beschrieben. Einen praktischen Zweck zur Nutzung nichtlinearer Effekte erfüllt die vorgestellte Messmethode zur Unterscheidung polarer und nicht-polarer Materialien mittels intensiver fs- Puls-Anregung von sogenannten harmonischen (Upconversion-)Nanopartikeln (s. Kapitel 5). Denn anders als die zu Beginn behandelten Leuchtstoffe, weisen die harmonischen Nanopartikel eine starke Anti-Stokes Verschiebung durch Frequenzkonversion zweier oder dreier Photonen zu einem energiereicheren (kurzwelligen) Photon auf. Diese als SHG (second harmonic generation) und THG (third harmonic generation) bekannte Lichtemission wird spektral vermessen, wobei die zu Beginn der Arbeit beschriebenen linearen diffusen Reflektanzmessungen den zu erwartenden Spektralbereich ohne nennenswerte Absorption eingrenzen. Die eigens definierte Gütezahl fR, bestehend aus dem integrierten SHG- und THG-Emissionsspektrum einer Probe, kategorisiert dann die polare (fR > 1) oder nicht-polare (fR << 1) Natur des Materials.

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.

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.