abstract: The fundamental building blocks for constructing complex synthetic gene networks are effective biological parts with wide dynamic range, low crosstalk, and modularity. RNA-based components are promising sources of such parts since they can provide regulation at the level of transcription and translation and their predictable base pairing properties enable large libraries to be generated through in silico design. This dissertation studies two different approaches for initiating interactions between RNA molecules to implement RNA-based components that achieve translational regulation. First, single-stranded domains known as toeholds were employed for detection of the highly prevalent foodborne pathogen norovirus. Toehold switch riboregulators activated by trigger RNAs from the norovirus RNA genome are designed, validated, and coupled with paper-based cell-free transcription-translation systems. Integration of paper-based reactions with synbody enrichment and isothermal RNA amplification enables as few as 160 copies/mL of norovirus from clinical samples to be detected in reactions that do not require sophisticated equipment and can be read directly by eye. Second, a new type of riboregulator that initiates RNA-RNA interactions through the loop portions of RNA stem-loop structures was developed. These loop-initiated RNA activators (LIRAs) provide multiple advantages compared to toehold-based riboregulators, exhibiting ultralow signal leakage in vivo, lacking any trigger RNA sequence constraints, and appending no additional residues to the output protein. Harnessing LIRAs as modular parts, logic gates that exploit loop-mediated control of mRNA folding state to implement AND and OR operations with up to three sequence-independent input RNAs were constructed. LIRA circuits can also be ported to paper-based cell-free reactions to implement portable systems with molecular computing and sensing capabilities. LIRAs can detect RNAs from a variety of different pathogens, such as HIV, Zika, dengue, yellow fever, and norovirus, and after coupling to isothermal amplification reactions, provide visible test results down to concentrations of 20 aM (12 RNA copies/µL). And the logic functionality of LIRA circuits can be used to specifically identify different HIV strains and influenza A subtypes. These findings demonstrate that toehold- and loop-mediated RNA-RNA interactions are both powerful strategies for implementing RNA-based computing systems for intracellular and diagnostic applications. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2019

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Every now and then, in the realms of science and art, we learn that some especially striking figure, who captures our attention, is from Utah. The achievements of the sons and daughters of the Utah pioneers reflect the substantial character of the work of the men and women who laid the foundation of Utah. This foundation was composed of material gathered from every worthy purpose engulfing character and cultural expression of the people. Among other accomplishments, Utah has had a notable development in musical art. Her achievements have not been a result of extraordinary circumstances, but from the long and continued devotion to the fundamentals of musical art and to a most unusual combination of qualities which may be described as her 'personality.' If we were to list the names of those who have contributed to the music history and musical growth of Utah, we would find Charles John Thomas, Ebeneezer Beesley, George Careless, David O. Calder, Evan Stephens, Anthony C. Lund, B. Cecil Gates, and many others. Since the writer has had an interest in the music of Utah, as a part of the history of the Church of Jesus Christ of Latter-day Saints, he was naturally attracted to the works of the men whose names have been listed. With the passing of time, the memory of these men begins to fade. An attempt will be made in this writing to preserve what information may be, at present, available in the way of books, brief newspaper notes, and magazine articles, as well as from prominent citizens who tho were intimately associated with the musician, Brigham Cecil Gates. It is not the purpose of this writing to give B. Cecil Gates' general biography, but to organize only those experiences which brought him into contact with music or musicians. The music we have today has been the contribution of many individuals, each building on the musical heritage of the other. By the same token the musicians of the future may be influenced by the work of the musicians of today. What did B. Cecil Gates contribute to the advancement of music in Utah? Did he help to maintain and improve the musical standards of the state? What did he accomplish as a musician? By a careful study of his life as a composer, director, and teacher of music, these questions can be answered.

The continued scaling of device dimensions in complementary metal oxide semiconductor (CMOS) technology within the sub-100 nm region requires an alternative high dielectric constant (high-k) oxide layer to counter high tunneling leakage currents, a metallic gate electrode to address polysilicon depletion, boron penetration and high polysilicon sheet resistance, and high mobility channel materials to boost the CMOS performance. Metal gates can also offer improved thermal and chemical stability, but their use requires that we improve our understanding of how the metal alloy phase, crystallographic orientation, and composition affect the electronic properties of the metal alloy-oxide interface. To replace n++ and p++ polysilicon gate electrodes and maintain scaled device performance requires metal gate electrodes with work functions within 0.2 eV of the silicon conduction and valence band edges, i.e., 5.0-5.2 and 4.1-4.3 eV, for PMOS and NMOS devices, respectively. In addition to work function and thermal/chemical stability, metal gates must be integrated into the CMOS process flow. It is the aim of this work to significantly expand our knowledge base in alloys for dual metal gates by carrying out detailed electrical and materials studies of the binary alloy systems of Ru with p-type metal Pt. Three n-type metals systems, Ru-Ta, Ru-Hf and Ru-Nb have also been partially investigated. This work also focuses on high mobility Ge p-MOSFETs for improved CMOS performance. DC magnetron sputtering has been used to deposit binary alloy films on thermally grown SiO2. The composition of the alloy films have been determined by Rutherford backscattering spectrometry and the identification of phases present have been made using x-ray and electron diffraction of samples. The microstructure of the phases of interest has been examined in the transmission electron microscope and film texture was characterized via x-ray diffraction. The electrical characterization includes basic resistivity measurements, and work function extraction. The work function has been determined from MOS capacitor and Schottky diodes. The need for electron and hole mobility enhancement and the progress in the development of high-k gate stacks, has lead to renewed interest in Ge MOSFETs. The p-MOS mobility data for Ge channel devices have been reported. The results indicate greater than 2 x improvements in device mobility as compared to standard Si device. A low frequency noise assessment of silicon passivated Ge p-MOSFETs with a TiN/TaN/HfO2 gate stack has been made. For the first time we also report results on low frequency noise characterisation for a Ge P+- n junctions with and without Ni germanidation.

Yes / Safety-critical systems are becoming larger and more complex to obtain a higher level of functionality. Hence, modeling and evaluation of these systems can be a difficult and error-prone task. Among existing safety models, Fault Tree Analysis (FTA) is one of the well-known methods in terms of easily understandable graphical structure. This study proposes a novel approach by using Machine Learning (ML) and real-time operational data to learn about the normal behavior of the system. Afterwards, if any abnormal situation arises with reference to the normal behavior model, the approach tries to find the explanation of the abnormality on the fault tree and then share the knowledge with the operator. If the fault tree fails to explain the situation, a number of different recommendations, including the potential repair of the fault tree, are provided based on the nature of the situation. A decision tree is utilized for this purpose. The effectiveness of the proposed approach is shown through a hypothetical example of an Aircraft Fuel Distribution System (AFDS). / DEIS H2020 Project under Grant 732242

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No / Synthetic Biology aspires to design, compose and engineer biological systems that implement specified behaviour. When designing such systems, hypothesis testing via computational modelling and simulation is vital in order to reduce the need of costly wet lab experiments. As a case study, we discuss the use of computational modelling and stochastic simulation for engineered genetic circuits that implement Boolean AND and OR gates that have been reported in the literature. We present performance analysis results for nine different state-of-the-art stochastic simulation algorithms and analyse the dynamic behaviour of the proposed gates. Stochastic simulations verify the desired functioning of the proposed gate designs.

This thesis introduces the emerging field of quantum computing, emphasizing its capability to surpass traditional computing by solving complex problems that are beyond the reach of classical computers. Unlike classical systems that operate with bits and logic gates, quantum computing utilizes qubits and quantum gates, exploiting the vast computational space offered by quantum mechanics. A focal point of this study is topological quantum computing, a novel approach designed to overcome the inherent vulnerability of quantum systems to errors, such as decoherence and operational inaccuracies. At the heart of this method lies the use of non-Abelian anyons, with a particular focus on Fibonacci anyons, whose unique topological characteristics and braiding operations present a viable path to fault-tolerant quantum computation. This thesis aims to elucidate how the braiding of Fibonacci anyons can be employed to construct the necessary quantum gates for topological quantum computing. By offering a foundational exploration of quantum computing principles, especially topological quantum computing, and detailing the process for creating quantum gates through braiding of Fibonacci anyons, the work sets the stage for further research and development in this transformative computing paradigm.

The aim of this dissertation was to research, through a comparative architectural analysis,whether the two urban districts Camden Town in north London and Greater Grand Crossing in south Chicago have or have not been gentrified and, if so, what kind of gentrification process they have gone through. The study was based on three questions: what buildings have been transformed in each area? How have the buildings been transformed? Have the functionsof the city districts been transformed with any particular focus in mind? The study found that Camden Town has been tourist gentrified, since the primary focus of the gentrification process was towards tourism and entertainment businesses where old Victorian, industrial buildings were transformed into venues for live music, shops and markets. In the case of Greater Grand Crossing however, it is not possible to establish that the area has been gentrified. Chicagoan artist Theaster Gates transformed several residential houses as part of a project, some of which remained residential, and some were made into spaces for cultural activities. However, the focus of the transformation was towards the already existing population and not towards potential gentrifiers.

Organic electrochemical transistors (OECTs) based on Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonic acid) (PEDOT:PSS) are a benchmark system in organic bioelectronics. In particular, the superior mechanical properties and the ionic-electronic transduction yield excellent potential for the field of implantable or wearable sensing technology. However, depletion-mode operation PEDOT:PSS-based OECTs cause high static power dissipation in electronic circuits, limiting their application in electronic systems. Hence, having control over the threshold voltage is of utmost technological importance. Here, PEDOT:PSS-based dual-gate OECTs with solid-state electrolyte where the threshold voltage is seamlessly adjustable during operation are demonstrated. It is shown that the degree of threshold voltage tuning linearly depends on the gate capacitance, which is a straightforward approach for circuit designers to adjust the threshold voltage only by the device dimensions. The PEDOT:PSS-based dual-gate OECTs show excellent device performance and can be pushed to accumulation-mode operation, resulting in a simplified and relaxed design of complementary inverters.