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).

In this thesis, an approximation is proposed to evaluate the steady-state performance of kanban controlled assembly systems. The approximation is developed for the systems with two components making up an assembly. Then, it is extended to systems with more than two components. A continuous-time Markov model is aggregated keeping the model exact, and this aggregate model is approximated replacing some state-dependent transition rates with constant rates. Decomposition of the approximate aggregate model into submodels guarantees product-form steady-state distribution for each subsystem. Finally, submodels are combined in such a way that the size of the problem becomes independent of the number of kanbans. This brings about the computational advantage in solving the combined model using numerical matrix-geometric solution algorithms. Based on the numerical comparisons with simulation, the exact model, an approximate aggregate model and another approximation in a previous study in the literature, the approximation is observed to be good in terms of accuracy with respect to computational burden and has the potential to be a building block for the analysis of systems that are more complex but closer to real-life applications.

A differential, membrane-based nanocalorimeter has been designed and constructed for thermal studies of mesoscopic samples at low temperatures. The calorimeter is intended for sample masses from mg to sub-μg and a broad temperature range from above room temperature down to the sub-K region. It allows concurrent use of ac steady state and relaxation methods. Effort was spent to achieve good absolute accuracy to enable investigations of the electronic contribution to the heat capacity of superconductors. The calorimeter consists of a pair of cells, each of which is a stack of heaters and thermometer in the center of a silicon nitride membrane, in total giving a background heat capacity less than 100 nJ/K at 300 K, decreasing to 10 pJ/K at 1 K. The device has several distinctive features: i) The resistive thermometer, made of a GeAu alloy, displays a high sensitivity, dlnR/dlnT ≈ −1 over the entire temperature range. ii) The sample is placed in direct contact with the thermometer, which is allowed to self-heat. The thermometer can thus be operated at high dc current to increase the resolution. iii) Data are acquired with a set of eight synchronized lock-in amplifiers measuring dc, 1st and 2nd harmonic signals of heaters and thermometer. iv) Absolute accuracy is achieved via a novel variable-frequency fixed-phase technique in which the measurement frequency is automatically adjusted during ac-calorimetry measurements to account for the temperature variation of the sample specific heat and the device thermal conductance. The properties of the empty cell and the effect of the thermal link between sample and cell were analytically studied. Practical expressions for describing the frequency dependence of heat capacity, thermal conductance, and temperature oscillation amplitude of the system were formulated. Comparisons with measurements and numerical simulations show excellent agreement. Calibration procedures are simple, but care should be taken to minimize thermal radiation effects. The experimental setup is operated with self-regulation of heater powers and thermometer bias, including compensation to zero the differential dc signal. As a result its high resolution and compact format, the calorimeter is well suited for studies of phase transitions and phase diagrams as well as electronic specific heat. The performance of the device is demonstrated by a study of the superconducting state of a small lead crystal. / En differentiell, membran-baserad nanocalorimeter har designats och tillverkats för termiska studier av mesoskopiska prover vid låg temperatur. Kalorimetern är avsedd för provmassor från mg till sub-μg och ett brett temperaturområde från över rumstemperatur till under 1 K. Den tillåter samtidig användning av både ac steady state och relaxations-metod. Fokus har lagts på att uppnå en god absolut noggrannhet för att möjliggöra studier av det elektroniska bidraget till värmekapaciteten hos supraledare. Kalorimetern består av två celler, var och en uppbyggd som en stack med värmeelement och termometer i mitten av ett kiselnitrid-membran, med en total bakgrundsvärmekapacitet på mindre än 100 nJ/K vid 300 K, minskande till 10 pJ/K vid 1 K. Kalorimetern har flera särdrag: i) Den resistiva termometern, gjord av en GeAu legering, visar en hög känslighet, dlnR/dlnT ≈ −1 över hela temperaturområdet. ii) Provet placeras i direkt kontakt med termometern, som tillåts att självvärma. Termometern kan alltså användas vid hög dc ström för att öka upplösningen. iii) Mätningarna genomförs med en uppsättning av åtta synkroniserade lock-in förstärkare, som mäter dc, grundfrekvens och 1:a övertonen hos värme-element och termometer. iv) Absolut noggrannhet uppnås genom en ny variabel-frekvens konstant-fas teknik där mätfrekvensen justeras automatiskt under ac-kalorimetrimätningar för att kompensera temperaturberoendet hos provets specifika värmekapacitet och kalorimetercellens värmeledningsförmåga. Egenskaperna hos den tomma cellen och inverkan av den termiska länken mellan prov och cell studerades analytiskt. Praktiska uttryck för att beskriva frekvens beroendet hos systemets värmekapacitet, värmeledningsförmåga, och temperaturoscillationer har formulerats. Jämförelser mellan mätningar och numeriska simuleringar visar mycket bra överensstämmelse. Kalibreringsförfarandet är enkelt, men försiktighet bör vidtas för att minimera värmestrålningseffekter. Experimentuppställningen drivs med självreglering av värmare och termometer, inklusive kompensation för att nollställa den differentiella dc signalen. Som en följd av dess höga upplösning och kompakta format är kalorimetern väl lämpad för studier av fasövergångar och fasdiagram såväl som det elektroniska specifika värmet. Kalorimeterns prestanda demonstreras genom en studie av det supraledande tillståndet hos en liten blykristall. / At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Accepted.

This is an experimental study into the permeability and compressibility properties of bagasse pulp pads. Three experimental rigs were custom-built for this project. The experimental work is complemented by modelling work. Both the steady-state and dynamic behaviour of pulp pads are evaluated in the experimental and modelling components of this project. Bagasse, the fibrous residue that remains after sugar is extracted from sugarcane, is normally burnt in Australia to generate steam and electricity for the sugar factory. A study into bagasse pulp was motivated by the possibility of making highly value-added pulp products from bagasse for the financial benefit of sugarcane millers and growers. The bagasse pulp and paper industry is a multibillion dollar industry (1). Bagasse pulp could replace eucalypt pulp which is more widely used in the local production of paper products. An opportunity exists for replacing the large quantity of mainly generic paper products imported to Australia. This includes 949,000 tonnes of generic photocopier papers (2). The use of bagasse pulp for paper manufacture is the main application area of interest for this study. Bagasse contains a large quantity of short parenchyma cells called ‘pith’. Around 30% of the shortest fibres are removed from bagasse prior to pulping. Despite the ‘depithing’ operations in conventional bagasse pulp mills, a large amount of pith remains in the pulp. Amongst Australian paper producers there is a perception that the high quantity of short fibres in bagasse pulp leads to poor filtration behaviour at the wet-end of a paper machine. Bagasse pulp’s poor filtration behaviour reduces paper production rates and consequently revenue when compared to paper production using locally made eucalypt pulp. Pulp filtration can be characterised by two interacting factors; permeability and compressibility. Surprisingly, there has previously been very little rigorous investigation into neither bagasse pulp permeability nor compressibility. Only freeness testing of bagasse pulp has been published in the open literature. As a result, this study has focussed on a detailed investigation of the filtration properties of bagasse pulp pads. As part of this investigation, this study investigated three options for improving the permeability and compressibility properties of Australian bagasse pulp pads. Two options for further pre-treating depithed bagasse prior to pulping were considered. Firstly, bagasse was fractionated based on size. Two bagasse fractions were produced, ‘coarse’ and ‘medium’ bagasse fractions. Secondly, bagasse was collected after being processed on two types of juice extraction technology, i.e. from a sugar mill and from a sugar diffuser. Finally one method of post-treating the bagasse pulp was investigated. The effects of chemical additives, which are known to improve freeness, were also assessed for their effect on pulp pad permeability and compressibility. Pre-treated Australian bagasse pulp samples were compared with several benchmark pulp samples. A sample of commonly used kraft Eucalyptus globulus pulp was obtained. A sample of depithed Argentinean bagasse, which is used for commercial paper production, was also obtained. A sample of Australian bagasse which was depithed as per typical factory operations was also produced for benchmarking purposes. The steady-state pulp pad permeability and compressibility parameters were determined experimentally using two purpose-built experimental rigs. In reality, steady-state conditions do not exist on a paper machine. The permeability changes as the sheet compresses over time. Hence, a dynamic model was developed which uses the experimentally determined steady-state permeability and compressibility parameters as inputs. The filtration model was developed with a view to designing pulp processing equipment that is suitable specifically for bagasse pulp. The predicted results of the dynamic model were compared to experimental data. The effectiveness of a polymeric and microparticle chemical additives for improving the retention of short fibres and increasing the drainage rate of a bagasse pulp slurry was determined in a third purpose-built rig; a modified Dynamic Drainage Jar (DDJ). These chemical additives were then used in the making of a pulp pad, and their effect on the steady-state and dynamic permeability and compressibility of bagasse pulp pads was determined. The most important finding from this investigation was that Australian bagasse pulp was produced with higher permeability than eucalypt pulp, despite a higher overall content of short fibres. It is thought this research outcome could enable Australian paper producers to switch from eucalypt pulp to bagasse pulp without sacrificing paper machine productivity. It is thought that two factors contributed to the high permeability of the bagasse pulp pad. Firstly, thicker cell walls of the bagasse pulp fibres resulted in high fibre stiffness. Secondly, the bagasse pulp had a large proportion of fibres longer than 1.3 mm. These attributes helped to reinforce the pulp pad matrix. The steady-state permeability and compressibility parameters for the eucalypt pulp were consistent with those found by previous workers. It was also found that Australian pulp derived from the ‘coarse’ bagasse fraction had higher steady-state permeability than the ‘medium’ fraction. However, there was no difference between bagasse pulp originating from a diffuser or a mill. The bagasse pre-treatment options investigated in this study were not found to affect the steady-state compressibility parameters of a pulp pad. The dynamic filtration model was found to give predictions that were in good agreement with experimental data for pads made from samples of pretreated bagasse pulp, provided at least some pith was removed prior to pulping. Applying vacuum to a pulp slurry in the modified DDJ dramatically reduced the drainage time. At any level of vacuum, bagasse pulp benefitted from chemical additives as quantified by reduced drainage time and increased retention of short fibres. Using the modified DDJ, it was observed that under specific conditions, a benchmark depithed bagasse pulp drained more rapidly than the ‘coarse’ bagasse pulp. In steady-state permeability and compressibility experiments, the addition of chemical additives improved the pad permeability and compressibility of a benchmark bagasse pulp with a high quantity of short fibres. Importantly, this effect was not observed for the ‘coarse’ bagasse pulp. However, dynamic filtration experiments showed that there was also a small observable improvement in filtration for the ‘medium’ bagasse pulp. The mechanism of bagasse pulp pad consolidation appears to be by fibre realignment. Chemical additives assist to lubricate the consolidation process. This study was complemented by pulp physical and chemical property testing and a microscopy study. In addition to its high pulp pad permeability, ‘coarse’ bagasse pulp often (but not always) had superior physical properties than a benchmark depithed bagasse pulp.