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Performance is an important aspect of computer systems since it directly affects user experience. One way to analyze and predict performance is via performance modeling. In recent years, multi-core systems have made processors more powerful while keeping power consumption relatively low. However the complicated design of these systems makes it difficult to analyze performance. This thesis presents performance modeling techniques for cache performance and synchronization cost on multi-core systems. A cache can be designed in many ways with different configuration parameters including cache size, associativity and replacement policy. Understanding cache performance under different configurations is useful to explore the design choices. We propose a general modeling framework for estimating the cache miss ratio under different cache configurations, based on the reuse distance distribution. On multi-core systems, each core usually has a private cache. Keeping shared data in private caches coherent has an extra cost. We propose three models to estimate this cost, based on information that can be gathered when running the program on a single core. Locks are widely used as a synchronization primitive in multi-threaded programs on multi-core systems. While they are often necessary for protecting shared data, they also introduce lock contention, which causes performance issues. We present a model to predict how much contention a lock has on multi-core systems, based on information obtainable from profiling a run on a single core. If lock contention is shown to be a performance bottleneck, one of the ways to mitigate it is to use another lock implementation. However, it is costly to investigate if adopting another lock implementation would reduce lock contention since it requires reimplementation and measurement. We present a model for forecasting lock contention with another lock implementation without replacing the current lock implementation.

Lipopolysaccharides (LPS), major virulence determinants in Gram–negative bacteria, are responsible for many pathophysiological responses and can elicit strong immune responses. In order to better understand the role of LPS in host–pathogen interactions and elucidate the immunogenic properties of LPS outer core oligosaccharide, an all α–linked Escherichia coli R3 outer core pentasaccharide was first synthesized with a propyl amino linker at the reducing end. This oligosaccharide was also covalently conjugated to a carrier protein (CRM197) via the reducing end propyl amino linker. An immunological analysis demonstrated that this glycoconjugate can elicit specific anti-pentasaccharide antibodies with in vitro bactericidal activity. These findings will contribute to further exploring this pentasaccharide antigen as a vaccine candidate. Human milk oligosaccharides (HMOs) are a family of diverse unconjugated glycans that exist in human milk as one of the major components. Characterization, quantification and biofunctional studies of HMOs remain a big challenge due to their diversity and complexity. The accessibility of homogenous HMOs library is essential to solve these issues which have beset academia for several decades. In this study, an efficient chemoenzymatic strategy, namely Core Synthesis/Enzymatic Extension (CSEE), for rapid production of diverse HMOs was reported. Based on 3 versatile building blocks and 4 robust glycosyltransferases, a library of 31 HMOs were chemoenzymatically synthesized and characterized by MS and NMR. CSEE indeed provides a practical approach to harvest structurally defined HMOs for various applications. Glycoproteins are extremely important for all life on the planet. Glycoproteins play important roles in various biological processes. Increasing evidences demonstrate that glycosylation of proteins could improve stability of proteins by stabilizing their tertiary structure and protecting them from proteolysis. Besides, glycosylation of proteins could provide targeting effects through glycan-lectin interaction. Furthermore, carbohydrates play crucial roles in humoral immunity in that many sugar epitopes are identified as antigens for antibodies. Glycoprotein could boost strong T cells mediated intercellular immune responses because homogeneous antigens present on the surface of proteins by multivalent bonds. In this study, the three advantages of glycoproteins, namely stabilizing proteins, targeting effects and eliciting immunological response, were extensively explored by broad collaboration with other groups.

The past trend of increasing processor throughput by increasing the clock frequency and the instruction level parallelism is no longer feasible due to extensive power consumption and heat dissipation. Therefore, the current trend in computer hardware design is to expose explicit parallelism to the software level. This is most often done using multiple, relatively slow and simple, processing cores situated on a single processor chip. The cores usually share some resources on the chip, such as some level of cache memory (which means that they also share the interconnect, e.g., a bus, to that memory and also all higher levels of memory). To fully exploit this type of parallel processor chip, programs running on it will have to be concurrent. Since multi-core processors are the new standard, even embedded real-time systems will (and some already do) incorporate this kind of processor and concurrent code. A real-time system is any system whose correctness is dependent both on its functional and temporal behavior. For some real-time systems, a failure to meet the temporal requirements can have catastrophic consequences. Therefore, it is crucial that methods to derive safe estimations on the timing properties of parallel computer systems are developed, if at all possible. This thesis presents a method to derive safe (lower and upper) bounds on the execution time of a given parallel system, thus showing that such methods must exist. The interface to the method is a small concurrent programming language, based on communicating and synchronizing threads, that is formally (syntactically and semantically) defined in the thesis. The method is based on abstract execution, which is itself based on abstract interpretation techniques that have been commonly used within the field of timing analysis of single-core computer systems, to derive safe timing bounds in an efficient (although, over-approximative) way. The thesis also proves the soundness of the presented method (i.e., that the estimated timing bounds are indeed safe) and evaluates a prototype implementation of it. / Den strategi som historiskt sett använts för att öka processorers prestanda (genom ökad klockfrekvens och ökad instruktionsnivåparallellism) är inte längre hållbar på grund av den ökade energikonsumtion som krävs. Därför är den nuvarande trenden inom processordesign att låta mjukvaran påverka det parallella exekveringsbeteendet. Detta görs vanligtvis genom att placera multipla processorkärnor på ett och samma processorchip. Kärnorna delar vanligtvis på några av processorchipets resurser, såsom cache-minne (och därmed också det nätverk, till exempel en buss, som ansluter kärnorna till detta minne, samt alla minnen på högre nivåer). För att utnyttja all den prestanda som denna typ av processorer erbjuder så måste mjukvaran som körs på dem kunna delas upp över de tillgängliga kärnorna. Eftersom flerkärniga processorer är standard idag så måste även realtidssystem baseras på dessa och den nämnda typen av kod.  Ett realtidssystem är ett datorsystem som måste vara både funktionellt och tidsmässigt korrekt. För vissa typer av realtidssystem kan ett inkorrekt tidsmässigt beteende ha katastrofala följder. Därför är det ytterst viktigt att metoder för att analysera och beräkna säkra gränser för det tidsmässiga beteendet hos parallella datorsystem tas fram. Denna avhandling presenterar en metod för att beräkna säkra gränser för exekveringstiden hos ett givet parallellt system, och visar därmed att sådana metoder existerar. Gränssnittet till metoden är ett litet formellt definierat trådat programmeringsspråk där trådarna tillåts kommunicera och synkronisera med varandra. Metoden baseras på abstrakt exekvering för att effektivt beräkna de säkra (men ofta överskattade) gränserna för exekveringstiden. Abstrakt exekvering baseras i sin tur på abstrakta interpreteringstekniker som vida används inom tidsanalys av sekventiella datorsystem. Avhandlingen bevisar även korrektheten hos den presenterade metoden (det vill säga att de beräknade gränserna för det analyserade systemets exekveringstid är säkra) och utvärderar en prototypimplementation av den. / Worst-Case Execution Time Analysis of Parallel Systems / RALF3 - Software for Embedded High Performance Architectures

Different scenarios for assembling rod-like and spherical colloidal particles using binary mixtures of partially miscible liquids were investigated experimentally. Suitable rod-like colloids were developed first. The subsequent studies of colloids in binary liquids consisted, on one hand, of systems where particles were partially wetted by both phases and, on the other hand, of systems where particles were completely wetted by the minority phase. A simple method to prepare large quantities of micrometer-sized akagan eite-silica core-shell rods was developed. These were proven to be very versatile, with the possibility of modifying their properties on different levels. The aspect ratio is simply controlled by a gradual growth of the silica shells. From them, hollow silica rods and rods with an increased responsiveness to a magnetic field could be obtained in straightforward ways. Bijels were prepared by trapping rod-like particles on a percolating liquid-liquid interface. The familiar bicontinuous organization of liquid domains was observed after structural arrest. At a fixed volume per particle it is demonstrated that for rod-like particles the domain size decreases faster with increasing quantity of particles than in the case of spherical particles. Additionally, the packing of the rods at the interface was elucidated, revealing several characteristic features. In particle-stabilized droplet emulsions rapid evaporation of the continuous phase and eventual full mixing of the liquid phases can leave a cellular network of particles. The formation and eventual stability of these networks were investigated in detail with confocal microscopy. When colloids are completely wetted by the minority component of an asymmetric binary mixture there can be substantial temperature and composition regimes outside the binodal where shear-induced aggregation can take place. This happens as adsorbed layers present at the particle surfaces coalesce and bind particles through a liquid bridge. Depending on particle concentration, percolating networks can form of rods wetted by the minority phase after temperature quenching such a system just across the binodal.

published_or_final_version / Endodontics / Master / Master of Dental Surgery

Precooling, or a reduction in core temperature (Tc) has been demonstrated to be a potent enhancer of endurance running performance, however there is no known mechanism for this improvement. By holding the exercise workload constant, changes in variables such as running economy (RE), heart rate, and ventilation (VE) can be determined as a result of precooling. Improved running economy, or a reduced oxygen cost of a specific workload, is linked to improved exercise performance. Purpose: To determine the changes in flexibility, RE, heart rate, VE, and Tc during running at a constant workload following cool water immersion and to determine any sex-specific responses. Methods: Fourteen well-trained runners (8 males and 6 females) completed four treadmill runs at a sex-specific velocity (8.0 mph for females and 8.6 mph for males). The first two runs served as accommodation trials. The third and fourth runs were preceded by either cool water immersion (24.8oC) for 40 minutes or quiet sitting. Oxygen consumption, heart rate, Tc, VE, and flexibility were measured during both experimental trials. Results: Running economy did not change as a result of the precooling treatment, whereas Tc and heart rate were reduced by 0.4oC and 5 beats per minute, respectively. Minute ventilation was reduced in the female subjects only (1.4 liters/min). Sex differences were apparent in Tc, heart rate, VE, and flexibility response. Conclusion: While the precooling procedure was effective in reducing Tc and heart rate, RE did not change. Thus, improvements in RE cannot explain the dramatic enhancements of endurance running performance that often occur post-cooling. Differences between male and female subjects in response to precooling were identified, most notably in VE.

The research programme at the University of Canterbury includes the development and applications of partial core inductors and transformers for high voltage testing of generator insulation. Unlike a conventional full core transformer, a partial core transformer has no limbs and yokes. A partial core transformer is a compromise between a full core and coreless transformer. It is superior to its full core counterpart as far as cost, weight and ease of transportation are concerned. Partial core transformers have a low magnetising reactance and hence draw a high magnetising current. This characteristic makes them a perfect fit in applications where the load is capacitive in nature, such as a.c. power frequency high voltage testing of generator insulation and cable testing etc. The work carried out for this thesis focuses on automatically controlling the amount of reactive power on the supply side of a partial core transformer. The considered design includes a third winding around the existing two windings. A power electronic controller is connected to the third winding, which modifies the VAr absorption characteristics of the magnetically coupled supply winding. Two options are considered to achieve continuous reactive power control in the partial core transformer as explained below. First, a thyristor controlled reactor (TCR) is proposed as the VAr controller. It is modelled using PSCAD/EMTDC software. Simulations reveal the design criteria, overall performance and the limitations of the suggested proposal. The TCR connected tertiary winding takes the capacitive burden of the supply. The model demonstrates the ability of the automatically controlled TCR to provide a continuous variation of reactive power without significant under or over compensation. This feature limits the supply current to its real component only, so the supply provides only the losses of the system. Second, a voltage source converter is considered as the VAr controller. This is modelled in PSCAD/EMTDC and a hardware prototype is designed and built. Based on the analysis, the control algorithm (including a digital PI controller) is implemented using an 8 bit micro-controller, PIC18LF4680. The prototype is tested in the laboratory for both active and inductive load conditions as seen from the supply side. Performance of the hardware prototype is discussed in detail. The PSCAD/EMTDC model and the hardware prototype successfully demonstrate the feasibility of a STATCOM controlled partial core transformer. The proposed system is capable of compensating a wide range of capacitive loads as compared with its TCR counterpart. It is proved that the system is very robust and remains dynamically stable for a large system disturbance such as change in load from full capacitive to inductive and vice versa. This confirms that the system is capable of providing continuous VAr control.