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Nucleic acids, such as DNA, play an essential role in all known forms of life; however, despite their fundamental importance, there is still a significant lack of understanding surrounding their functional behaviour. This thesis explores the structure and dynamics of DNA by employing methods based on fluorescence and through the use of computational calculations. Time-resolved fluorescence experiments have been performed on dinucleotides containing 2-aminopurine (2AP) in various alcohol-water mixtures. 2AP, a fluorescent analogue of the nucleobase adenine, has been used extensively to investigate nucleic acids because of its ability to be incorporated into their structures with minimal perturbation and its high sensitivity to its local environment. Direct solvent effects on 2AP were established through measurements on the free fluorophore. Analysis of the complex fluorescence decays associated with the dinucleotides was challenging but has provided insight into their conformational dynamics. Solvent polarity was found to play a significant role in determining both photophysical and conformational properties in these systems. The complicated fluorescence decay of 2AP in nucleic acids highlights the need for accurate and unbiased analysis methods. Various time-resolved fluorescence analysis methods, including iterative reconvolution and the exponential series method, have been investigated with real and simulated data to obtain an overview of their benefits and limitations. The main outcome of the evaluation is that no single method is preferred in all situations and there is likely to be value in using a combination when there is ambiguity in the interpretation of the results. Regardless of the analysis technique used, the parameterised description of the observed fluorescence decay is meaningless if the underlying physical model is unrealistic. The advance of computational methods has provided a new means to rigorously test the viability of proposed models. Calculations have been performed at the M06-2X/6-31+G(d) level of theory to investigate the stability of 2AP-containing dinucleotides in conformations similar to those observed in the double-helical structure of DNA. The results help to explain the similarity of the time-resolved fluorescence behaviour of 2AP in dinucleotide and DNA systems but also bring to light subtle differences that could perhaps account for experimental discrepancies. The recent emergence of advanced optical microscopy techniques has offered the prospect of being able to directly visualise nucleic acid structure at the nanoscale but, unfortunately, limitations of existing labelling methods have hindered delivery of this potential. To address this issue, a novel strategy has been used to introduce reversible fluorescence photoswitching into DNA at high label density. Photophysical studies have implicated aggregation and energy-transfer as possible quenching mechanisms in this system, which could be detrimental to its future application. The reliability of fluorescence photoswitching was investigated at ensemble and single-molecule level and by performing optical lock-in detection imaging. These developments lay the foundations for improved and sequence-specific super-resolution microscopy of DNA, which could offer new insights into the 3D nanoscale structure of this remarkable biopolymer. In summary, the work presented in this thesis outlines important observations and developments that have been made in the study of the structure and dynamics of nucleic acids.

<p>With 7 000 new cases in Sweden each year, breast cancer represents 30 percent of all female malignancies and is therefore the most commonly diagnosed cancer among women. There are limitations as to what can be done to prevent the disease but with the use of mammography screening the chances of finding and treating the disease at an early stage are increasing. Unfortunately, mammography screening is associated with radiation, which is an established risk factor for developing breast cancer. However, the newest screening technologies come with a reduced dose which decreases the risk of developing breast cancer due to the radiation.</p><p> </p><p>The effects of this lower dose compared to that of traditional technologies have not yet been studied and the purpose of this paper is therefore to assess the cost-effectiveness of the use of this new technology, with a focus on the number of radiation-induced cancers. A cost-utility analysis was performed where three different mammography technologies (one analogue and two digital) were compared. The total costs and QALYs of breast cancer generated by the use of these three technologies were calculated with the use of a Markov decision-analytic model, where a cohort of hypothetical 40 year-old women was followed throughout life.</p><p> </p><p>The results of the analysis showed that with the new digital technology (the PC-DR), one in 14 100 screened women develops breast cancer due to radiation while with the traditional mammography systems (SFM and the CR) this number is one in 3 500 and 4 300 screened women, respectively. Consequently, the number of induced cancers is decreased with up to 75 percent with the use of the PC-DR. Assuming that only the radiation dose differs between the three units, the analysis resulted in an incremental effect of 0.000269 QALYs over a life-time for the PC-DR when compared to SFM(0.000210 QALYs compared to the CR). The PC-DR was also associated with a 33 SEK (26 SEK) lower cost. Thus, if the only difference can be found in radiation dose, the PC-DR is the dominating technology to use since it is both more effective and costs less. However, it is possible that the PC-DR is more expensive per screening occasion than the other technologies and if so, the PC-DR would no longer be less costly. The study found that the scope for the possibility of excessive pricing is very small and under these circumstances, the willingness to pay for a QALY has to be considered when deciding what technology to invest in.</p>

Hybrid pixel detectors have been demonstrated to provide excellent quality detection of ionising photon radiation, particularly in X-ray imaging. Recently, there has been interest in developing a hybrid pixel detector specifically for photon dosimetry. This thesis is on the design, implementation, and preliminary characterisation of the Dosepix readout chip. Dosepix has 256 square pixels of 220 mm side-length, constituting 12.4 mm2 of photo-sensitive area per detector. The combination of multiple pixels provides many parallel processors with limited input flux, resulting in a radiation dose monitor which can continuously record data and provide a real-time report on personal dose equivalent. Energy measurements are obtained by measuring the time over threshold of each photon and a state machine in the pixel sorts the detected photon event into appropriate energy bins. Each pixel contains 16 digital thresholds with 16 registers to store the associated energy bins. Preliminary measurements of Dosepix chips bump bonded to silicon sensors show very promising results. The pixel has a frontend noise of 120 e-. In low power mode, each chip consumes 15 mW, permitting its use in a portable, battery-powered system. Direct time over threshold output from the hybrid pixel detector assembly reveal distinctive photo-peaks correctly identifying the nature of incident photons, and verification measurements indicate that the pixel binning state machines accurately categorise charge spectra. Personal dose equivalent reconstruction using this data has a flat response for a large range of photon energies and personal dose equivalent rates.

Spectral computed tomography with energy-resolving detectors has a potential to improve the detectability of images and correspondingly reduce the radiation dose to patients by extracting and properly using the energy information in the broad x-ray spectrum. A silicon photon-counting detector has been developed for spectral CT and it has successfully solved the problem of high photon flux in clinical CT applications by adopting the segmented detector structure and operating the detector in edge-on geometry. The detector was evaluated by both the simulation and measurements. The effects of energy loss and charge sharing on the energy response of this segmented silicon strip detector with different pixel sizes were investigated by Monte Carlo simulation and a comparison to pixelated CdTe detectors is presented. The validity of spherical approximations of initial charge cloud shape in silicon detectors was evaluated and a more accurate statistical model has been proposed. A photon-counting energy-resolving application specific integrated circuit (ASIC) developed for spectral CT was characterized extensively by electrical pulses, pulsed laser and real x-ray photons from both the synchrotron and an x-ray tube. It has been demonstrated that the ASIC performs as designed. A noise level of 1.09 keV RMS has been measured and a threshold dispersion of 0.89 keV RMS has been determined. The count rate performance of the ASIC in terms of count loss and energy resolution was evaluated by real x-rays and promising results have been obtained. The segmented silicon strip detector was evaluated using synchrotron radiation. An energy resolution of 16.1% has been determined with 22 keV photons in the lowest flux limit, which deteriorates to 21.5% at an input count rate of 100 Mcps mm−2. The fraction of charge shared events has been estimated and found to be 11.1% for 22 keV and 15.3% for 30 keV. A lower fraction of charge shared events and an improved energy resolution can be expected by applying a higher bias voltage to the detector. / <p>QC 20121123</p>

With 7 000 new cases in Sweden each year, breast cancer represents 30 percent of all female malignancies and is therefore the most commonly diagnosed cancer among women. There are limitations as to what can be done to prevent the disease but with the use of mammography screening the chances of finding and treating the disease at an early stage are increasing. Unfortunately, mammography screening is associated with radiation, which is an established risk factor for developing breast cancer. However, the newest screening technologies come with a reduced dose which decreases the risk of developing breast cancer due to the radiation.   The effects of this lower dose compared to that of traditional technologies have not yet been studied and the purpose of this paper is therefore to assess the cost-effectiveness of the use of this new technology, with a focus on the number of radiation-induced cancers. A cost-utility analysis was performed where three different mammography technologies (one analogue and two digital) were compared. The total costs and QALYs of breast cancer generated by the use of these three technologies were calculated with the use of a Markov decision-analytic model, where a cohort of hypothetical 40 year-old women was followed throughout life.   The results of the analysis showed that with the new digital technology (the PC-DR), one in 14 100 screened women develops breast cancer due to radiation while with the traditional mammography systems (SFM and the CR) this number is one in 3 500 and 4 300 screened women, respectively. Consequently, the number of induced cancers is decreased with up to 75 percent with the use of the PC-DR. Assuming that only the radiation dose differs between the three units, the analysis resulted in an incremental effect of 0.000269 QALYs over a life-time for the PC-DR when compared to SFM(0.000210 QALYs compared to the CR). The PC-DR was also associated with a 33 SEK (26 SEK) lower cost. Thus, if the only difference can be found in radiation dose, the PC-DR is the dominating technology to use since it is both more effective and costs less. However, it is possible that the PC-DR is more expensive per screening occasion than the other technologies and if so, the PC-DR would no longer be less costly. The study found that the scope for the possibility of excessive pricing is very small and under these circumstances, the willingness to pay for a QALY has to be considered when deciding what technology to invest in.

Gegenstand dieser Diplomarbeit ist die Untersuchung der Dynamik in dünnen Polymerfilmen anhand von einzelnen Molekülen. Zu diesem Zweck wurden dünne Filme (kleiner 100nm) hergestellt und mittels Einzelmoleküldetektion und zeitaufgelöster Einzelphotonenzählung analysiert, was eine orts- und zeitaufgelöste Untersuchung einzelner Farbstoffmoleküle ermöglicht. Ziel war es, festzustellen ob, und auf welchem Weg, die Dynamik der Umgebung in Fluktuationen der Fluoreszenzlebensdauer einzelner Moleküle sichtbar wird. Neben der Evaluierung der Untersuchungsmethoden wurden in dieser Arbeit zwei Arten von Sensormolekülen - DiD und Malachit Grün - näher untersucht. / The subject of this diploma thesis is the analysis of dynamics in thin polymer films using single molecules. Thin polymer films (less than 100nm) were produced and analysed by Single Molecule Detection (SMD) and Time Correlated Single Photon Counting (TCSPC). This allows a spatial and time resolved investigation of the single dye molecule. The aim was to ascertain if, and in which way, the dynamics of the environment are reflected by fluctuations of the fluorescence lifetime of the single molecule. In addition to evaluating the investigation methods two kinds of molecules - DiD and Malachite Green - were also analysed.

Contrast agents are often crucial in medical imaging for disease diagnosis. Novel contrast agents, such as gold nanoparticles (AuNPs) and lanthanides, are being ex- plored for a variety of clinical applications. Preclinical testing of these contrast agents is necessary before being approved for use in humans, which requires the use of small animal imaging techniques. Small animal imaging demands the detection of these contrast agents in trace amounts at acceptable imaging time and radiation dose. Two such imaging techniques include x-ray fluorescence computed tomography (XFCT) and photon-counting CT (PCCT). XFCT combines the principles of CT with x-ray fluorescence by detecting fluorescent x-rays from contrast agents at various projections to reconstruct contrast agent maps. XFCT can image trace amounts of AuNPs but is limited to small animal imaging due to fluorescent x-ray attenuation and scatter. PCCT uses photon-counting detectors that separate the CT data into energy bins. This enables contrast agent detection by recognizing the energy dependence of x-ray attenuation in different materials, independent of AuNP depth, and can provide anatomical information that XFCT cannot. To achieve the best of both worlds, we modeled and built a table-top x-ray imaging system capable of simultaneous XFCT and PCCT imaging. We used Monte Carlo simulation software for the following work in XFCT imaging of AuNPs. We simulated XFCT induced by x-ray, electron, and proton beams scanning a small animal-sized object (phantom) containing AuNPs with Monte Carlo techniques. XFCT induced by x-rays resulted in the best image quality of AuNPs, however high-energy electron and medium-energy proton XFCT may be feasible for on-board x-ray fluorescence techniques during radiation therapy. We then simulated a scan of a phantom containing AuNPs on a table-top system to optimize the detector arrangement, size, and data acquisition strategy based on the resulting XFCT image quality and available detector equipment. To enable faster XFCT data acquisition, we separately simulated another AuNP phantom and determined the best collimator geometry for Au fluorescent x-ray detection. We also performed experiments on our table-top x-ray imaging system in the lab. Phantoms containing multiples of three lanthanide contrast agents were scanned on our tabletop x-ray imaging system using a photon-counting detector capable of sustaining high x-ray fluxes that enabled PCCT. We used a novel subtraction algorithm for reconstructing separate contrast agent maps; all lanthanides were distinct at low concentrations including gadolinium and holmium that are close in atomic number. Finally, we performed the first simultaneous XFCT and PCCT scan of a phantom and mice containing both gadolinium and gold based on the optimized parameters from our simulations. This dissertation outlines the development of our tabletop x-ray imaging system and the optimization of the complex parameters necessary to obtain XFCT and PCCT images of multiple contrast agents at biologically-relevant concentrations. / Graduate

Computed tomography (CT) is a medical imaging technique used to create cross-section images of human bodies based on x-rays. The emerging photon-counting CT detector shows several advantages compared with the traditional energy integrating detector. This thesis is based on the new generation deep silicon photon-counting CT detector developed by KTH Medical Imaging group, with a 12×500μm^2 pixel size. A method is proposed to achieve high spatial resolution with low computation resource consumption.A Monte Carlo simulation has been done to simulate the photon interaction along with the charge transport process in the detector. The charge cloud distribution and induced current are used to make a precise estimation of the interaction position in the direction along the collecting electrodes. The feasibility of such a method under estimated electronic noise and other detector geometries has been checked. By having a high spatial resolution of around 1μm in one direction, it could be beneficial in phase contrast imaging.Besides the small pixel geometry, simulations on current photon-counting detector geometry, similar to what is used in clinics, have also been carried out, with a study of the charge carrier transport behavior and charge sharing possibility. The result shows that although the charge sharing event could be used to help estimate interaction position, its low proportion among total events leads to little resolution improvement. Another study on the induced current as a function of time has been presented. By reducing the electrode width while keeping the same pixel width, the induced current signal peak appears to be sharper. / Datortomografi (CT) är en medicinsk bildteknik som används för att skapa tvärsnittsbilder av människokroppen med hjälp av röntgenstrålar. Den nya CT-detektorn med fotonräkning har flera fördelar jämfört med den traditionella energiintegrerande detektorn. Den här avhandlingen bygger på den nya generationen av den djupa kiseldetektorn för CT-detektorn med fotonträkning i kisel som utvecklats av KTH:s grupp för medicinsk avbildning, med en pixelstorlek på 12×500μm^2. En metod föreslås för att uppnå hög spatial upplösning med begränsad kapacitet för beräkningar.En Monte Carlo-simulering har gjorts för att simulera fotoninteraktionen tillsammans med laddningstransportprocessen i detektorn. Laddningsmolnets fördelning och den inducerade strömmen används för att göra en exakt uppskattning av interaktionspositionen i riktningen längs de uppsamlande elektroderna. Genomförbarheten av en sådan metod med beräknat elektroniskt brus och andra detektorgeometrier har kontrollerats. Genom att ha en hög rumslig upplösning på cirka 1 μm i en riktning kan detta vara fördelaktigt vid faskontrastbildtagning.Förutom den lilla pixelgeometrin har simuleringar av den nuvarande geometrin för detektorer som räknar fotoner, liknande den som används på kliniker, också utförts, med en studie av transportbeteendet för laddningsbärare och möjligheten till laddningsdelning. Resultatet visar att även om laddningsdelningshändelsen kan användas för att hjälpa till att uppskatta interaktionspositionen, leder dess låga andel av de totala händelserna till en liten förbättring av upplösningen. En annan studie av den inducerade strömmen som en funktion av tiden har presenterats. Genom att minska elektrodbredden samtidigt som man behåller samma pixelbredd verkar den inducerade signaltoppen bli skarpare.

Point Cloud Registration with data measured from a photon-counting LIDAR sensor from a large distance (500 m - 1.5 km) is an expanding field. Data measuredfrom far is sparse and have low detail, which can make the registration processdifficult, and registering this type of data is fairly unexplored. In recent years,machine learning for point cloud registration has been explored with promisingresults. This work compares the performance of the point cloud registration algorithm Iterative Closest Point with state-of-the-art algorithms, with data froma photon-counting LIDAR sensor. The data was provided by the Swedish Defense Research Agency (FOI). The chosen state-of-the-art algorithms were thenon-learning-based Fast Global Registration and learning-based D3Feat and SpinNet. The results indicated that all state-of-the-art algorithms achieve a substantial increase in performance compared to the Iterative Closest Point method. Allthe state-of-the-art algorithms utilize their calculated features to obtain bettercorrespondence points and therefore, can achieve higher performance in pointcloud registration. D3Feat performed point cloud registration with the highestaccuracy of all the state-of-the-art algorithms and ICP.