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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
121

Modeling of Diffractive Signatures of Microlithographic Patterns

Mojtahedi, Simon January 2024 (has links)
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.
122

Theoretical Studies of Natural Gas Hydrates and H-bonded Clusters and Crystals

Liu, Yuan January 2016 (has links)
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.
123

Development and applications of theoretical algorithms for simulations of materials at extreme conditions

Mosyagin, Igor January 2017 (has links)
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.
124

Classifying the rotation of bacteria using neural networks / Rotationsklassificering av bakterier med neurala nätverk

Hedström, Lucas January 2019 (has links)
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.
125

Dual Energy CT as a Foundation for Proton Therapy Treatmen Planning - A pilot study

Näsmark, Torbjörn January 2019 (has links)
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.
126

Towards a tunable nanometer thick flat lens

Laurell, Hugo, Hillborg, Johan January 2018 (has links)
This report examines the cross sections of silver microresonators subjected to an incident light with different polarization. The microresonators had different geometries with and without broken symmetries. Cross section profiles for different microresonator configurations are interesting for the division of Material Physics, Uppsala University, when designing metamaterials to tune the optical response of the material. The goal is to form an insight of how the optical response can be tuned by choosing different geometries, varying the size and polarization of the incident light. In this project computer simulations in COMSOL were made to simulate the optical response of different microresonators. When the incident light interact with the silver microresonators plasmonic excitations is generated which in turn interacts with the light changing the phase and therefore the optical response. By increasing the radius of the disk silver microresonantors the resonance was found to shift to lower energies. For a geometry with a disk microresonator inside a ring microresonator the Fano resonances were dependent of the radius of the disk microresonator.
127

Relativistic light-matter interaction

Kjellsson Lindblom, Tor January 2017 (has links)
During the past decades, the development of laser technology has produced pulses with increasingly higher peak intensities. These can now be made such that their strength rivals, and even exceeds, the atomic potential at the typical distance of an electron from the nucleus. To understand the induced dynamics, one can not rely on perturbative methods and must instead try to get as close to the full machinery of quantum mechanics as practically possible. With increasing field strength, many exotic interactions such as magnetic, relativistic and higher order electric effects may start to play a significant role. To keep a problem tractable, only those effects that play a non-negligible role should be accounted for. In order to do this, a clear notion of their relative importance as a function of the pulse properties is needed.  In this thesis I study the interaction between atomic hydrogen and super-intense laser pulses, with the specific aim to contribute to the knowledge of the relative importance of different effects. I solve the time-dependent Schrödinger and Dirac equations, and compare the results to reveal relativistic effects. High order electromagnetic multipole effects are accounted for by including spatial variation in the laser pulse. The interaction is first described using minimal coupling. The spatial part of the pulse is accounted for by a series expansion of the vector potential and convergence with respect to the number of expansion terms is carefully checked. A significantly higher demand on the spatial description is found in the relativistic case, and its origin is explained. As a response to this demanding convergence behavior, an alternative interaction form for the relativistic case has been developed and presented. As a guide mark for relativistic effects, I use the classical concept of quiver velocity, vquiv, which is the peak velocity of a free electron in the polarization direction of a monochromatic electromagnetic plane wave that interacts with the electron. Relativistic effects are expected when vquiv reaches a substantial fraction of the speed of light c, and in this thesis I consider cases up to vquiv=0.19c. For the present cases, relativistic effects are found to emerge around vquiv=0.16c .
128

Photoluminescence Characteristics of III-Nitride Quantum Dots and Films

Eriksson, Martin January 2017 (has links)
III-Nitride semiconductors are very promising in both electronics and optical devices. The ability of the III-Nitride semiconductors as light emitters to span the electromagnetic spectrum from deep ultraviolet light, through the entire visible region, and into the infrared part of the spectrum, is a very important feature, making this material very important in the field of light emitting devices. In fact, the blue emission from Indium Gallium Nitride (InGaN), which was awarded the 2014 Nobel Prize in Physics, is the basis of the common and important white light emitting diode (LED). Quantum dots (QDs) have properties that make them very interesting for light emitting devices for a range of different applications, such as the possibility of increasing device efficiency. The spectrally well-defined emission from QDs also allows accurate color reproduction and high-performance communication devices. The small size of QDs, combined with selective area growth allows for an improved display resolution. By control of the polarization direction of QDs, they can be used in more efficient displays as well as in traditional communication devices. The possibility of sending out entangled photon pairs is another QD property of importance for quantum key distribution used for secure communication. QDs can hold different exciton complexes, such as the neutral single exciton, consisting of one electron and one hole, and the biexciton, consisting of two excitons. The integrated PL intensity of the biexciton exhibits a quadratic dependence with respect to the excitation power, as compared to the linear power dependence of the neutral single exciton. The lifetime of the neutral exciton is 880 ps, whereas the biexciton, consisting of twice the number of charge carriers and lacks a dark state, has a considerably shorter lifetime of only 500 ps. The ratio of the lifetimes is an indication that the size of the QD is in the order of the exciton Bohr radius of the InGaN crystal making up these QDs in the InGaN QW. A large part of the studies of this thesis has been focused on InGaN QDs on top of hexagonal Gallium Nitride (GaN) pyramids, selectively grown by Metal Organic Chemical Vapor Deposition (MOCVD). On top of the GaN pyramids, an InGaN layer and a GaN capping layer were grown. From structural and optical investigations, InGaN QDs have been characterized as growing on (0001) facets on truncated GaN pyramids. These QDs exhibit both narrow photoluminescence linewidths and are linearly polarized in directions following the symmetry of the pyramids. In this work, the neutral single exciton, and the more rare negatively charged exciton, have been investigated. At low excitation power, the integrated intensity of the PL peak of the neutral exciton increases linearly with the excitation power. The negatively charged exciton, on the other hand, exhibits a quadratic power dependence, just like that of the biexciton. Upon increasing the temperature, the power dependence of the negatively charged exciton changes to linear, just like the neutral exciton. This change in power dependence is explained in terms of electrons in potential traps close to the QD escaping by thermal excitation, leading to a surplus of electrons in the vicinity of the QD. Consequently, only a single exciton needs to be created by photoexcitation in order to form a negatively charged exciton, while the extra electron is supplied to the QD by thermal excitation. Upon a close inspection of the PL of the neutral exciton, a splitting of the peak of just below 0.4 meV is revealed. There is an observed competition in the integrated intensity between these two peaks, similar to that between an exciton and a biexciton. The high energy peak of this split exciton emission is explained in terms of a remotely charged exciton. This exciton state consists of a neutral single exciton in the QD with an extra electron or hole in close vicinity of the QD, which screens the built-in field in the QD. The InGaN QDs are very small; estimated to be on the order of the exciton Bohr radius of the InGaN crystal, or even smaller. The lifetimes of the neutral exciton and the negatively charged exciton are approximately 320 ps and 130 ps, respectively. The ratio of the lifetimes supports the claim of the QD size being on the order of the exciton Bohr radius or smaller, as is further supported by power dependence results. Under the assumption of a spherical QD, theoretical calculations predict an emission energy shift of 0.7 meV, for a peak at 3.09 eV, due to the built-in field for a QD with a diameter of 1.3 nm, in agreement with the experimental observations. Studying the InGaN QD PL from neutral and charged excitons at elevated temperatures (4 K to 166 K) has revealed that the QDs are surrounded by potential fluctuations that trap charge carriers with an energy of around 20 meV, to be compared with the exciton trapping energy in the QDs of approximately 50 meV. The confinement of electrons close to the QD is predicted to be smaller than for holes, which accounts for the negative charge of the charged exciton, and for the higher probability of capturing free electrons. We have estimated the lifetimes of free electrons and holes in the GaN barrier to be 45 ps and 60 ps, in consistence with excitons forming quickly in the barrier upon photoexcitation and that free electrons and holes get trapped quickly in local potential traps close to the QDs. This analysis also indicates that there is a probability of 35 % to have an electron in the QD between the photoexcitation pulses, in agreement with a lower than quadratic power dependence of the negatively charged exciton. InN is an attractive material due to its infrared emission, for applications such as light emitters for communication purposes, but it is more difficult to grow with high quality and low doping concentration as compared to GaN. QDs with a higher In-composition or even pure InN is an interesting prospect as being a route towards increased quantum confinement and room temperature device operation. For all optical devices, p-type doping is needed. Even nominally undoped InN samples tend to be heavily n-type doped, causing problems to make pn-junctions as needed for LEDs. In our work, we present Mg-doped p-type InN films, which when further increasing the Mg-concentration revert to n-type conductivity. We have focused on the effect of the Mg-doping on the light emission properties of these films. The low Mg doped InN film is inhomogeneous and is observed to contain areas with n-type conductivity, so called n-type pockets in the otherwise p-type InN film. A higher concentration of Mg results in a higher crystalline quality and the disappearance of the n-type pockets. The high crystalline quality has enabled us to determine the binding energy of the Mg dopants to 64 meV. Upon further increase of the Mg concentration, the film reverts to ntype conductivity. The highly Mg doped sample also exhibits a red-shifted emission with features that are interpreted as originating from Zinc-Blende inclusions in the Wurtzite InN crystal, acting as quantum wells. The Mg doping is an important factor in controlling the conductivity of InN, as well as its light emission properties, and ultimately construct InN-based devices. In summary, in this thesis, both pyramidal InGaN QDs and InGaN QDs in a QW have been investigated. Novel discoveries of exciton complexes in these QD systems have been reported. Knowledge has also been gained about the challenging material InN, including a study of the effect of the Mg-doping concentration on the semiconductor crystalline quality and its light emission properties. The outcome of this thesis enriches the knowledge of the III-Nitride semiconductor community, with the long-term objective to improve the device performance of III-Nitride based light emitting devices.
129

Polycapillary X-Ray Optics for Liquid-Metal-Jet X-Ray Tubes

Lindqvist, Malcolm January 2017 (has links)
Investigating and mapping fundamental processes in nature is a driving force for breakthroughs in research and technology. Doing so, requires knowledge of the smallest scales of the world. One way of performing measurements on these scales is through intense x-ray sources, which have improved greatly over the last decades. By combing these sources with state of the art optics, even higher flux densities can be reached, allowing for faster measurements and ground-breaking discoveries.  This study aims to explore the performance of polycapillary optics, when aligned to one of the most intense x-ray micro sources in the world, the liquid-metal-jet D2+. Knife edge scans were performed together with a photon-counting medipix x-ray camera to quantify focus properties such as, flux, flux density, transmission, gain and beam width. Measurements were conducted with a 20 μm source spot that was compared to a simulated 200 μm source spot, both at 260 W electron beam power. The data from vertical and horizontal scans were combined to reconstruct the 2D functionality of the polycapillary optic. The flux density were almost four times higher with the 20 μm spot compared to the simulated 200 μm spot. This result correlated with the condition for total external reflection and the local divergence. The conclusion is that the small source spot of the liquid-metal-jet source improves the efficiency of the polycapillary optic.  The efficiency could still be improved, if the deviation in the pointing accuracy could be minimized. Furthermore, the combination of liquid-metal-jet x-ray source and the polycapillary optic, achieved extremely high flux densities. This was specially compared to an x-ray source used for confocal micro XRF, where the flux was almost nine times higher with the liquid-metal-jet x-ray source. This allows for faster measurements within confocal micro XRF and other techniques demanding very high flux densities, but with low demands on beam divergence and spectral purity.
130

Luminescence properties of flexible conjugated dyes

Sjöqvist, Jonas January 2012 (has links)
In this licentiate thesis the luminescence properties of two flexible conjugated dyes have been studied. The first, Pt1, is a platinum(II) acetylide chromophore used in optical power limiting materials. The second is a set of optical probes known as luminescent conjugated oligothiophenes (LCOs), which are used to detect and characterize the protein structures associated with amyloid diseases such as Alzheimer’s disease. MM3 and CHARMM force field parameters have been derived for the Pt1 chromophore and LCOs, respectively, based on potential energy surface references calculated at the density functional theory (DFT)/B3LYP level of theory. The parameters have been used to perform room temperature molecular dynamics simulations of the chromophores in solvent, where tetrahydrofuran was used for Pt1 and water for the LCOs. Conformationally averaged absorption spectra were obtained, based on response theory calculations at the time-dependent DFT(TDDFT)/CAM-B3LYP level of theory for a selection of structures from the simulations. For one of the LCOs, p-HTAA, force field parameters were also created describing the dominant first excited state, based on TDDFT/B3LYP reference potential energy surfaces. These were used for molecular dynamics simulations of the chromophore in the excited state, allowing the creation of an emission spectrum. A theoretically obtained Stokes shift of 112 nm could be computed based on the absorption and emission spectra, which is in good agreement with the experimental value of 124 nm. In addition, a quantum mechanics/molecular mechanics study of the effects of solvation on the absorption properties of the p-HTAA chromophore in water has been conducted, resulting in two models for including these effects in the averaged spectra. The first includes explicit water molecules in the form of point charges and polarizable dipole moments, and results in an absorption wavelength that is blueshifted by 2 nm from a high quality reference calculation. The second model involves the complete removal of the solvent as well as the ionic groups of the chromophore. The resulting absorption wavelength is blueshifted by an additional 4 nm as compared to the first model, but requires only one fifth of the computational resources.

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