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Coming dissertations at TekNat

  • Structured Data

    Author: Stephan Brandauer
    Publication date: 2018-12-20 08:33

    References are a programming language construct that lets a programmer access a datum invariant of its location.

    References permit aliasing -- several references to the same object, effectively making a single object accessible through different names (or paths). Aliasing, especially of mutable data, is both a blessing and a curse: when used correctly, it can make a programmer's life easier; when used incorrectly, for example through accidental aliases that the programmer is unaware of, aliasing can lead to hard to find bugs, and hard to verify programs.

    Aliases allow us to build efficient data structures by connecting objects together, making them immediately reachable. Aliases are at the heart of many useful programming idioms. But with great power comes great responsibility: unless a programmer carefully manages aliases in a program, aliases propagate changes and make parts of a program's memory change seemingly for no reason. Additionally, such bugs are very easy to make but very hard to track down.

    This thesis presents an overview of techniques for controlling how, when and if data can be aliased, as well as how and if data can be mutated. Additionally,...

  • Design of Rare Earth Free Permanent Magnet Generators

    Author: Petter Eklund
    Publication date: 2018-12-19 07:41

    Low speed permanent magnet (PM) synchronous generators (SGs) are commonly used in renewable energy. Rare earth (RE) PMs such as neodymium-iron-boron are a popular choice due to their high performance. In 2011 supply and cost issues were added to the previously existing environmental concerns regarding REPM raw materials as the world's major producer China imposed export restrictions. This thesis aims to investigate and propose design solutions for PMSGs that do not use REPMs. Two approaches are used: to design generators using the cheaper and more abundant ferrite PM materials, and to investigate how properties of new PM materials influence SG design.

    A ferrite PM rotor is designed to replace a REPM rotor in an experimental 12 kW wind power generator. The new design employs a flux concentrating spoke type rotor to achieve performance similar to the old REPM rotor while using ferrite PMs. The ferrite PM rotor design is built. The air gap length, magnetic flux density in the air gap, PM remanence, and voltage at both load and no load are measured. The generator has lower no load voltage than expected, which is mainly explained by lower than specified remanence of the...

  • Model Checking of Software Systems under Weak Memory Models

    Author: Tuan-Phong Ngo
    Publication date: 2018-12-17 09:08

    When a program is compiled and run on a modern architecture, different optimizations may be applied to gain in efficiency. In particular, the access operations (e.g., read and write) to the shared memory may be performed in an out-of-order manner, i.e., in a different order than the order in which the operations have been issued by the program. The reordering of memory access operations leads to efficient use of instruction pipelines and thus an improvement in program execution times. However, the gain in this efficiency comes at a price. More precisely, programs running under modern architectures may exhibit unexpected behaviors by programmers. The out-of-order execution has led to the invention of new program semantics, called weak memory model (WMM). One crucial problem is to ensure the correctness of concurrent programs running under weak memory models.

    The thesis proposes three techniques for reasoning and analyzing concurrent programs running under WMMs. The first one is a sound and complete analysis technique for finite-state programs running under the TSO semantics (Paper II). This technique is based on a novel and equivalent semantics for TSO, called Dual TSO...

  • Of spiders, bugs, and men : Structural and functional studies of proteins involved in assembly

    Author: Wangshu Jiang
    Publication date: 2018-12-14 13:44

    Protein assembly enables complex machineries while being economical with genetic information. However, protein assembly also constitutes a potential threat to the host, and needs to be carefully regulated.

    Sulfate is a common source of sulfur for cysteine synthesis in bacteria. A putative sulfate permease CysZ from Escherichia coli appears much larger than its apparent molecular mass when analyzed by chromatography and native gel. Clearly CysZ undergoes homo-oligomerization. Using isothermal titration calorimetry, we confirmed that CysZ binds to its putative substrate sulfate, and also sulfite with higher affinity. CysZ-mediated sulfate transport—in both E. coli whole cells and proteoliposomes—was inhibited in the presence of sulfite, indicating a feedback inhibition mechanism.

    Proteus mirabilis is a Gram-negative bacterium causing urinary tract infections. Its simultaneous expression of multiple fimbriae enables colonization and biofilm formation. Fimbriae are surface appendages assembled from protein subunits, with distal adhesins specifically recognizing host-cell receptors. We present the first three structures of P. mirabilis...

  • The Importance of Being Promiscuous : Understanding enzyme function, specificity, and evolution through structure

    Author: Annika Söderholm
    Publication date: 2018-12-14 13:41

    Enzymes are known to be amazingly specific and efficient catalysts. However, many enzymes also have so-called promiscuous functions, i.e., they are able to catalyze other reactions than their main one. The promiscuous activities are often low, serendipitous, and under neutral selection but if conditions arise that make them beneficial, they can play an important role in the evolution of new enzymes. In this thesis, I present three studies where we have characterized different enzyme families by structural and biochemical methods. The studies demonstrate the occurrence of enzyme promiscuity and its potential role in evolution and organismal adaptation.

    In the first study, I describe the characterization of wild type and mutant HisA enzymes from Salmonella enterica. In the first part of this study, we could clarify the mechanistic cycle of HisA by solving crystal structures that showed different conformations of wild type HisA in complex with its labile substrate ProFAR (N´-[(5´-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide). In the second part of this study, structures of mutant enzymes from a real-time evolution study provided us with an...