This thesis focus on memory-aware algorithms tailored for hierarchical memory architectures, found for instance within multicore processors. We first study the matrix product on multicore architectures. We model such a processor, and derive lower bounds on the communication volume. We introduce three ad hoc algorithms, and experimentally assess their performance.We then target a more complex operation: the QR factorization of tall matrices. We revisit existing algorithms to better exploit the parallelism of multicore processors. We thus study the critical paths of many algorithms, prove some of them to be asymptotically optimal, and assess their performance.In the next study, we focus on scheduling streaming applications onto a heterogeneous multicore platform, the QS 22. We introduce a model of the platform and use steady-state scheduling techniques so as to maximize the throughput. We present a mixed integer programming approach that computes an optimal solution, and propose simpler heuristics. We then focus on minimizing the amount of required memory for tree-shaped workflows, and target a classical two-level memory system. I/O represent transfers from a memory to the other. We propose a new exact algorithm, and show that there exist trees where postorder traversals are arbitrarily bad. We then study the problem of minimizing the I/O volume for a given memory, show that it is NP-hard, and provide a set of heuristics.Finally, we compare archival policies for BLUE WATERS. We introduce two archival policies and adapt the well known RAIT strategy. We provide a model of the tape storage platform, and use it to assess the performance of the three policies through simulation.

It has been conventional to simplify the thermo-mechanical modeling of solder joints by omitting the primary (transient) contributions to total creep deformation, assuming that secondary (steady-state) creep strain is dominant and primary creep is negligible. The error associated with this assumption has been difficult to assess because it depends on the properties of the solder joint and the temperature-time profile. This research examines the relative contributions of primary and secondary creep in Sn3.8Ag0.7Cu solder using the constant load creep and stress relaxation measurements for bulk tensile specimens and the finite element analysis of a chip resistor (trilayer) solder joint structure that was thermally cycled under multiple temperature ranges and ramp rates. It was found that neglect of primary creep can result in errors in the predicted stress and strain of the solder joint. In turn, these discrepancies can lead to errors in the estimation of the solder thermal fatigue life due to the changing proportion of primary creep strain to total inelastic strain under different thermal profiles. The constant-load creep and stress relaxation data for Sn3.8Ag0.7Cu span a range of strain rates 10(-8) 1/s < strain rate < 10(-4) 1/s, and temperatures 25°C, 75°C and 100°C. Creep and stress relaxation measurements show that transient creep caused faster strain rates during stress relaxation for a given stress compared to the corresponding minimum creep rate from constant-load creep tests. The extent of strain hardening during primary creep was a function of temperature and strain rate. A constitutive creep model was presented for Sn3.8Ag0.7Cu that incorporates both transient and steady-state creep to provide agreement for both creep and stress relaxation data with a single set of eight coefficients. The model utilizes both temperature compensated time and strain rate to normalize minimum strain rate and saturated transient creep strain, thereby establishing equivalence between decreased temperature and increased strain rate. The apparent activation energy of steady-state creep was indicative of both dislocation core and bulk lattice diffusion was the most sensitive model parameter. A saturation threshold was defined that distinguishes whether primary or secondary creep is dominant under either static or variable loading.

It has been conventional to simplify the thermo-mechanical modeling of solder joints by omitting the primary (transient) contributions to total creep deformation, assuming that secondary (steady-state) creep strain is dominant and primary creep is negligible. The error associated with this assumption has been difficult to assess because it depends on the properties of the solder joint and the temperature-time profile. This research examines the relative contributions of primary and secondary creep in Sn3.8Ag0.7Cu solder using the constant load creep and stress relaxation measurements for bulk tensile specimens and the finite element analysis of a chip resistor (trilayer) solder joint structure that was thermally cycled under multiple temperature ranges and ramp rates. It was found that neglect of primary creep can result in errors in the predicted stress and strain of the solder joint. In turn, these discrepancies can lead to errors in the estimation of the solder thermal fatigue life due to the changing proportion of primary creep strain to total inelastic strain under different thermal profiles. The constant-load creep and stress relaxation data for Sn3.8Ag0.7Cu span a range of strain rates 10(-8) 1/s < strain rate < 10(-4) 1/s, and temperatures 25°C, 75°C and 100°C. Creep and stress relaxation measurements show that transient creep caused faster strain rates during stress relaxation for a given stress compared to the corresponding minimum creep rate from constant-load creep tests. The extent of strain hardening during primary creep was a function of temperature and strain rate. A constitutive creep model was presented for Sn3.8Ag0.7Cu that incorporates both transient and steady-state creep to provide agreement for both creep and stress relaxation data with a single set of eight coefficients. The model utilizes both temperature compensated time and strain rate to normalize minimum strain rate and saturated transient creep strain, thereby establishing equivalence between decreased temperature and increased strain rate. The apparent activation energy of steady-state creep was indicative of both dislocation core and bulk lattice diffusion was the most sensitive model parameter. A saturation threshold was defined that distinguishes whether primary or secondary creep is dominant under either static or variable loading.

Nitroreductase from Enterobacter cloacae (NR) is a member of a large family of homologues represented in all branches of the tree of life. However the physiological roles of many of these enzymes remain unknown. NR has distinguished itself on the basis the diverse sizes and chemical types of substrates it is able to reduce (Koder et al 1998). This might be an evolved characteristic suiting NR for a role in metabolism of diverse occasional toxins. While there are numerous studies of determinants of substrate specificity, we know less about mechanisms by which enzymes can be inclusive. Therefore, we present a synthesis of NR's dynamics, stability, ligand binding repertoire and kinetic mechanism. We find that NR reduces para-nitrobenzoic acid (p-NBA) via a simple mechanism limited by the chemical step in which the nitro group is reduced (Pitsawong et al 2014). Thus, for this substrate, NR's mechanism dispenses with gating steps that in other enzymes can enforce substrate specificity. Our data demonstrate that substrate reduction is accomplished by rate-contributing hydride transfer from the flavin cofactor coupled to proton transfer from solvent, but do not identify specific amino acids with a role. This is consistent with our crystal structures, which reveal a spacious solvent-exposed active site bounded by a helix that moves to accommodate binding of substrate analogs (Haynes et al 2002). Because it is able to reduce TNT (trinitrotoluene), herbicides and pesticides, NR has important potential utility in bioremediation.

This thesis is a part of the French national project called MACAO (Modélisation Avancée de Composants Aéronautiques et Outils associés). In collaboration with Messier-Dowty company (a landing gears manufacturer), the thesis has contributed to better understand the actual literature studies in the field of aircraft tyre-road interaction modelling and therefore, to help making an optimal choice of model for a specifie application. The objectives have been to propose models for representing the tyre behaviour on the ground with respect to the aircraft run types. Physical oriented models are preferred. To complete this study, a literature survey of the previous researches in tyre modelling for steady­state responses is first carried out. Then, based on the main factors playing an important role in tyre modelling, it is proposed a classification for the physical and the semi-empirical models, which are also investigated. Based on this classification, the study requirements and the measurement data constraints, an a priori choice of suitable models are studied. A further investigation of the tyre deformation at pure lateral slip is carried out. It has allowed to physically describe the mechanism of generation of the longitudinal component of the tyre force at pure lateral slip. This force is refened as induced longitudinal force. By taking this force into consideration, it has been possible to explain why the self-aligning moment can drop to zero before the tyre gets to full sliding at pure lateral slip. Besides, the sensitivity analysis is proposed as a means for determining the parameters that have most influence on the model output and thus, are responsible for the output uncertainty.

The purpose of this study was to serve as a starting point in gaining understanding and experience of simulating a typical Pool Type Research Reactor with the thermal hydraulic software code Flownex®. During the study the following evaluations of Flownex® were done: * Assessment of the simplifying assumptions and possible shortcomings built into the software. * Definition of the applicable modelling methodology and further simplifying assumptions that have to be made by the user. * Evaluation of the accuracy and compatibility with the Pool Type Research Reactor. * Comparing the results of this study with similar studies found in the open literature. For the study the IAEA MTR 10 MW benchmark reactor (IAEA, 1992a) was used. A steady state simulation using Flownex® was done on a single fuel assembly, and this was compared with a model that was developed using the software package EES (Engineering Equation Solver). The results have shown good agreement between the different packages. After this verification, a steady state simulation of the entire core was done to obtain the characteristics of the reactor operating under normal condition. Finally, transient simulations were done on various LOFAs (Loss of Flow Accidents). The results of the various LOFAs were compared with studies that were previously done on the IAEA MTR 10 MW reactor. / Thesis (M.Ing. (Nuclear Engineering))--North-West University, Potchefstroom Campus, 2012.

The purpose of this study was to serve as a starting point in gaining understanding and experience of simulating a typical Pool Type Research Reactor with the thermal hydraulic software code Flownex®. During the study the following evaluations of Flownex® were done: * Assessment of the simplifying assumptions and possible shortcomings built into the software. * Definition of the applicable modelling methodology and further simplifying assumptions that have to be made by the user. * Evaluation of the accuracy and compatibility with the Pool Type Research Reactor. * Comparing the results of this study with similar studies found in the open literature. For the study the IAEA MTR 10 MW benchmark reactor (IAEA, 1992a) was used. A steady state simulation using Flownex® was done on a single fuel assembly, and this was compared with a model that was developed using the software package EES (Engineering Equation Solver). The results have shown good agreement between the different packages. After this verification, a steady state simulation of the entire core was done to obtain the characteristics of the reactor operating under normal condition. Finally, transient simulations were done on various LOFAs (Loss of Flow Accidents). The results of the various LOFAs were compared with studies that were previously done on the IAEA MTR 10 MW reactor. / Thesis (M.Ing. (Nuclear Engineering))--North-West University, Potchefstroom Campus, 2012.

Consider two Markovian N-policy queueing models in discrete time, one with batch arrival, the other with batch service. In this paper the transient behaviour of both models is studied and the analogous continuous time results are achieved by a limiting process. The steady state solution for the model with batch arrival is derived. (author's abstract) / Series: Forschungsberichte / Institut für Statistik

DNA polymerase epsilon (Pol ε) is a multi-subunit B-family DNA polymerase that is involved in leading strand DNA replication in eukaryotes. DNA Pol ε in yeast consists of four subunits, Pol2, Dpb2, Dpb3, and Dpb4. Pol2 is the catalytic subunit and Dpb2, Dpb3, and Dpb4 are the accessory subunits. Pol2 can be further divided into an N-terminal catalytic core (Pol2core) containing both the polymerase and exonuclease active sites and a C-terminus domain. We determined the X-ray crystal structure of Pol2core at 2.2 Å bound to DNA and with an incoming dATP. Pol ε has typical fingers, palm, thumb, exonuclease, and N-terminal domains in common with all other B-family DNA polymerases. However, we also identified a seemingly novel domain we named the P-domain that only appears to be present in Pol ε. This domain partially encircles the nascent duplex DNA as it leaves the active site and contributes to the high intrinsic processivity of Pol ε. To ask if the crystal structure of Pol2core can serve as a model for catalysis by Pol ε, we investigated how the C-terminus of Pol2 and the accessory subunits of Pol ε influence the enzymatic mechanism by which Pol ε builds new DNA efficiently and with high fidelity. Pre-steady state kinetics revealed that the exonuclease and polymerization rates were comparable between Pol2core and Pol ε. However, a global fit of the data over five nucleotide-incorporation events revealed that Pol ε is slightly more processive than Pol2 core. The largest differences were observed when measuring the time for loading the polymerase onto a 3' primer-terminus and the subsequent incorporation of one nucleotide. We found that Pol ε needed less than a second to incorporate the first nucleotide, but it took several seconds for Pol2core to incorporate similar amounts of the first nucleotide. B-family polymerases have evolved an extended β-hairpin loop that is important for switching the primer terminus between the polymerase and exonuclease active sites. The high-resolution structure of Pol2core revealed that Pol ε does not possess an extended β-hairpin loop. Here, we show that Pol ε can processively transfer a mismatched 3' primer-terminus between the polymerase and exonuclease active sites despite the absence of a β-hairpin loop. Additionally we have characterized a series of amino acid substitutions in Pol ε that lead to altered partitioning of the 3'primer-terminus between the two active sites. In a final set of experiments, we investigated the ability of Pol ε to displace the downstream double-stranded DNA while carrying out DNA synthesis. Pol ε displaced only one base pair when encountering double-stranded DNA after filling a gap or a nick. However, exonuclease deficient Pol ε carries out robust strand displacement synthesis and can reach the end of the templates tested here. Similarly, an abasic site or a ribonucleotide on the 5'-end of the downstream primer was efficiently displaced but still only by one nucleotide. However, a flap on the 5'-end of the blocking primer resembling a D-loop inhibited Pol ε before it could reach the double-stranded junction. Our results are in agreement with the possible involvement of Pol ε in short-patch base excision repair and ribonucleotide excision repair but not in D-loop extension or long-patch base excision repair.

The aim of this thesis is to develop a tractable method for approximating the steady-state behavior of continuous-review base-stock controlled assembly systems with Poisson demand arrivals and manufacturing and assembly facilities modeled as Jackson networks. One class of systems studied is to produce a single type of finished product assembling a number of components and another class is to produce two types of finished products allowing component commonality. The performance measures evaluated are the expected backorders, fill rate and the stockout probability for finished product(s). A partially aggregated but exact model is approximated assuming that the state-dependent transition rates arising as a result of the partial aggregation are constant. This approximation leads to the derivation of a closed-form steady-state probability distribution, which is of product-form. Adequacy of the proposed model in approximating the steady-state performance measures is tested against simulation experiments over a large range of parameters and the approximation turns out to be quite accurate with absolute errors of 10% at most for fill rate and stockout probability, and of less than 1.37 (&amp / #8776 / 2) requests for expected backorders. A greedy heuristic which is proposed to be employed using approximate steady-state probabilities is devised to optimize base-stock levels while aiming at an overall service level for finished product(s).