Reverse Osmosis (RO) filtration is capable of producing high quality drinking water with an ultra-low nutrient level. Therefore, a very low bacterial growth potential (BGP). BGP is a key bioassay to evaluate microbial quality and the biological stability of drinking water. Current methods to assess BGP in drinking water need to be adapted to the wide variety of water types due to results could highly vary from each, providing unreliable insights to the biological stability of the assessed water. This study evaluates the application of an FCM-based BGP assay for RO produced chlorinated drinking water. The approach combines (i) the standardization of a quenching agent concentration, (ii) the impact of sample pre-treatment such as filtration and pasteurization on the BGP of RO produced chlorinated water, (iii) the effect of different inoculums (an indigenous community and a mixture with bottled water) on the bacterial growth and their longevity after being stored, (iv) the use of BGP to assess the performance of carbon filters in removing chlorine and (v) the use of BGP to assess the effect of the addition of magnesium on bacterial growth. The results showed that high concentrations of sodium metabisulphite (> 7.5 mg/L) decrease the pH levels of the water,thus, inhibiting bacterial growth. Filtration had a significant effect on BGP values (2.62 x10^5 intact cells/mL) in comparison to pasteurization (9.02 x 10^4 intact cells/mL), when compared to the control. Using a mixture of water types as inoculum might provide a better insight to bacterial growth potential in water due to a higher consumption of nutrients. BGP demonstrated to be a sensitive tool to test the performance of carbonfilters applied to remove chlorine and its applicability to evaluate the biological stability of RO produced chlorinated drinking water. The concentrations of magnesium chloride tested in this study did not have a significant effect on cell numbers.

BACKGROUND - The development of Industry 4.0 increases the opportunities to both automate and digitize processes in the manufacturing industry. The steel industry has been around for many years, which means firmly anchored operations and both manual- and automated processes. To make better decisions, identify bottlenecks, and test new functions without having to stop the production, a digital model of the process can be helpful. Furthermore, with the rapid development of technology, digital models can be further developed into digital twins. A digital twin should be able to handle the communication between the physical- and digital world automatically and analyze data to make decisions in the process. RESEARCH QUESTIONS What are the challenges of developing a digital model representing a production line within a global steel manufacturing company? What opportunities could a digital model of a production line entail, and how could Industry 4.0 technologies create opportunities to further develop the digital model into a digital twin? METHODS - In this project, both a literature- and case study have been carried out. During the literature study, techniques that can be used to develop the digital model further have been investigated. During the case study, a digital model of a Quench Line was developed to gather practical experience of what it can mean to create a digital model of a manufacturing process within a steel manufacturing company. The model has been developed in MATLAB/Simulink. RESULTS - The most significant challenges when developing digital flow simulation models identified in this project were data management/access, handling variations, verifying the model, andlack of knowledge linked to digital models in general. The opportunities identified and confirmed in this project were that the model could be used to carry out new logistics planning, bottleneck analyses, and test new machine implementations. To further develop the digital model into a digital twin, Industry 4.0 technologies will be crucial. The technologies that will be useful are the Internet of Things, Artificial Intelligence, Machine Learning, Cloud Computing, and Big Data.

<p> In a postulated critical break LOCA in a CANDU reactor it is possible that heatup of a pressure tube (PT) causes ballooning contact with the calandria tube (CT). Stored heat in the PT is transferred out, yielding a high PT-CT heat flux, which can cause dry out of the CT and establishment of pool film boiling on the outer surface of the tube. The safety concern associated with this condition is that if the temperature of the CT experiencing film boiling gets sufficiently high then failure of the fuel channel may occur. However, quench heat transfer can limit the extent and duration of film boiling as has been experimentally observed. Current estimates of quench temperatures during pool film boiling are based primarily on experimental correlations. In this dissertation a novel mechanistic model of pool film boiling on the outside of a horizontal tube with diameter relevant to CT (approximately 130 mm) has been developed. The model is based in part upon characterizing the vapor film thickness for steady state film boiling under buoyancy driven natural convection flows around a tube located horizontally in a large liquid pool. Variations in steady state vapor film thickness as a function of the incident heat flux, the temperature of the CT outer wall, and the subcooling of the bulk liquid are analyzed. The calculated effective film boiling heat transfer coefficient is compared to available experimental data. Finally a transient equation is developed which quantifies the instability of the vapor film and a possible occurrence of rapid quench when a step change in governing parameters occurs, such as liquid subcooling. This mechanistic model can be employed in safety analysis to demarcate the conditions under which fuel channel failure will not occur in a postulated critical break LOCA.</p> / Thesis / Master of Applied Science (MASc)

This thesis investigates the impact of doping on the optical and structural characteristics of cerium oxide (ceria) nanoparticles synthesized using chemical precipitation. The dopants selected are samarium and neodymium, which have positive association energy with oxygen vacancies in the ceria host, and negative association lanthanides, holmium and erbium, as well as two metal dopants, aluminum and iron. Characteristics measured are absorption and fluorescence spectra and the diameter and lattice parameter of ceria. Analysis of the characteristics indicates qualitatively that the dopant controls the O-vacancy concentration and the ratio of the two cerium ionization states: Ce+3 and Ce+4. A novel conclusion is proposed that the negative association lanthanide dopants can act as O-vacancies scavengers in ceria while the O-vacancy concentration increases in ceria doped with positive association lanthanide elements. Doped ceria nanoparticles are evaluated in two applications: dissolved oxygen (DO) sensing and up-conversion. In the first application, ceria doped with either Sm or Nd and ceria doped with aluminum have a strong correlation between the fluorescence quenching with the DO concentration in the aqueous solution in which the ceria nanoparticles are suspended. Stern-Volmer constants (KSV) of doped ceria are found to strongly depend upon the O-vacancy concentration and are larger than some of the fluorescent molecular probes currently used to measure DO. The KSV measured between 25-50oC is found to be significantly less temperature dependent as compared to the constants of commercially-available DO molecular probes. In the second application, up-conversion, ceria nanoparticles doped with erbium and an additional lanthanide, either Sm or Nd, are exposed to IR radiation at 780 nm. Visible emission is only observed after the nanoparticles are calcinated at high temperature, greatly diminishing the concentration of O-vacancies. It is concluded that O-vacancies do not play a dominant role in up-conversion, unlike that drawn for down-conversion, where the fluorescence intensity is strongly correlated with the O-vacancy concentration. Correlations between annealing temperatures, dopant, and dopant concentrations with the power dependence of up-conversion on the pump and the origin of the intensities of the visible emission are presented. These studies show the promise of doped ceria nanoparticles. / Ph. D.

Yes / Bacteria sense their own population size, tune the expression of responding genes, and behave accordingly to environmental stimuli by secreting signaling molecules. This phenomenon is termed as quorum sensing (QS). By exogenously manipulating the signal transduction bacterial population behaviors could be controlled, which may be done through quorum quenching (QQ). QS related regulatory networks have been proven their involvement in regulating many virulence determinants in pathogenic bacteria in the course of infections. Interfering with QS signaling system could be a novel strategy against bacterial infections and therefore requires more understanding of their fundamental mechanisms. Here we review the development of studies specifically on the inhibition of production of N-acyl-homoserine lactone (AHL), a common proteobacterial QS signal. The opportunistic pathogen, Pseudomonas aeruginosa, equips the alkylquinolone (AQ)-mediated QS which also plays crucial roles in its pathogenicity. The studies in QQ targeting on AQ are also discussed. / University of Malaya High Impact Research Grants (UMC/625/1/HIR/MOHE/CHAN/01, A-000001-50001,and UMC/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027)

Yes / Lysinibacillus fusiformis strain RB21 is a quorum-quenching bacterium that is able to degrade quorum-sensing signaling molecules. Here, we present the first complete genome sequence of L. fusiformis strain RB21. The finished genome is 4.8 Mbp in size, and the quorum-quenching gene was identified. / University of Malaya for High Impact Research (UM-MOHE HIR) grant UM C/625/1/HIR/MOHE/CHAN/01, no. A000001-50001 and grant UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027

Le but de cette thèse est de sonder la flexibilité de NCp7 et de Δ(-)PBS, deux bio-molécules impliquées dans le second saut de brin de la transcription inverse du VIH. Deux stratégies expérimentales ont été mises en place. Un nouveau montage de spectroscopie ultra-rapide de fluorescence par down-conversion a été construit. Les dynamiques de quenching de la 2-aminopurine (2Ap), insérée en position 6, 8 et 10 de la boucle Δ(-)PBS ont pu être entièrement résolues à une résolution sub-ps. Pour chaque position, 4 temps de vie ont été révélés. Des mesures d'anisotropie confirment que les deux composantes < 5 ps sont liées à un empilement de la 2Ap avec les Guanines avoisinantes. Cet empilement est site-spécifique, prouvé par l'augmentation significative de leurs amplitudes lorsque la 2Ap est située près de la tige (position 10). La faible proportion de conformations reliées à un quenching collisionnel est significative de la faible exposition des 2Ap au solvant et de l'encombrement général de la boucle. La seconde approche avait pour but d'étudier l'effet du repliement du squelette protéique de [35-50] NCp7 autour de son atome de zinc par CID et par LID. Les spectres CID de la protéine nue sont expliqués par le modèle du proton mobile et une description détaillée d'un schéma de fragmentation spécifique autour du Tryptophane (Trp) a été soulignée, attribué une Lysine voisine. Un seul fragment issu de l'excitation à 266 nm a été identifié, son apparition entre en compétition avec les fragments CID du Trp. L'effet général du repliement autour du Zinc se traduit par une augmentation du taux de fragmentation autour du Trp et par une perte de spécificité pour le reste du spectre.Les flexibilités de Δ(-)PBS et NCp7 ont été respectivement évaluées par spectroscopie ultra-rapide de type down-conversion et par spectrométrie en phase gazeuse. La première méthode nécessite l'utilisation d'une sonde fluorescente non invasive, la 2-aminopurine (2Ap), placée en position 6, 8 et 10 de la boucle Δ(-)PBS. Notre résolution temporelle permet de résoudre entièrement les dynamiques locales de quenching et d'anisotropie de la 2Ap. Les composantes liées au quenching statique et quenching collisionnel ont été discriminées et révèlent les degrés d'empilement / encombrement locaux de la boucle. L'effet du repliement de [35-50] NCp7 autour de son atome de zinc a été étudié par CID et par LID à 266 nm. La protéine nue présente un interessant shéma de fragmentation autour du Tryptophane (Trp), exalté par la complexation avec le zinc, au prix une perte de spécificité pour le reste du spectre. Un seul fragment LID a été identifié, un mécanisme de sa formation est proposé. / This thesis aims to probe the flexibility of NCp7 and Δ(-)PBS, two biomolecules involved in the second strand transfer of the HIV's reverse transcription. We brought to the front two original experimental methods. A new ultrafast fluorescence down-conversion setup has been built, suitable for biological chromophore investigations. The quenching dynamics of 2-aminopurine (2Ap), site-mutated at the positions 6, 8 and 10 of Δ(-)PBS loop, were completely resolved under a ps scale. For each location, 4 decay times, were highlighted. Further anisotropy measurements confirmed that the two < 5 ps components correspond to stacking interactions of 2Ap with neighbouring Guanines. The site-specific aspect of the stacking were supported by a significant increase of their relative amplitudes when 2Ap were cloesly located to the stem (position 10). The minor portion of conformations involved with ps to ns collisional quenching suggests a low exposure of 2Ap towards the solvent as well as a general restriction of the loop. The second method planned to investigate the effet of the zinc-folding on [35-50] NCp7's peptidic backbone, thanks to CID and LID. The CID-generated spectra of the bare peptide were explained by the mobile proton model, and an exhaustive tryptophan (Trp) fragmentation pattern was described, mainly due to a neighbouring Lysin effects. Only one LID-fragment has been identified upon 266 nm excitation, probably created through a pathway competing with the generation of Trp fragments by CID. The main aspects related to zinc-folding are a general enhancement of the fragmentation ratios related to Trp and a loss of specificity for the remaining mass spectra parts.Δ(-)PBS et NCp7 has been respectively investigated by ultrafast down-conversion spectroscopy and gas-phase spectrometry. The first method implies the use of a non invasive fluorescent probe, named 2 aminopurine (2Ap), site mutated in position 6, 8 et 10 of the Δ(-)PBS loop. Our time resolution allows to fully depict the local quenching dynamics and anisotropy decays. The component related to static and collisional has been solved, thus describing different stacking degrees as well as local restrictions. The effect of [35-50] NCp7 folding around its zinc atom has been studied by CID and 266 nm LID. The bare protein displays an interesting fragmentation pathway around its Tryptophan (Trp), enhanced with zinc complexation, at the cost of a loss of specificity for the remaining mass spectra parts. Only one LID fragment has been identified, its occurence has been interpreted.

De fortes illuminations peuvent être dommageables voire même létales pour les organismes photosynthétiques. Une des stratégies utilisées pour se protéger de tels effets délétères consiste à augmenter la dissipation thermique de l’énergie absorbée en excès au niveau des antennes. Chez les cyanobactéries une protéine photo-active, l’Orange Carotenoid Protein (OCP), contrôle ce processus. Une fois photo-activée l’OCP interagit avec le coeur des phycobilisomes (PBs, les antennes collectrices majoritaires chez les cyanobactéries) et déclenche le mécanisme, entrainant à la fois une baisse de l’énergie parvenant aux photosystèmes et une diminution de la fluorescence des PBs. L’énergie absorbée en excès est dissipée sous forme de chaleur. Pour que les PBs regagnent leur pleine capacité de transfert, une autre protéine nommée Fluorescence Recovery Protein (FRP) est requise. La FRP accélère la désactivation de l’OCP. Dans ce manuscrit, je vais présenter ma contribution à la compréhension du mécanisme de photo-protection lié à l’OCP.J’ai continué la caractérisation de la FRP chez Synechocystis PCC 6803, organisme modèle utilisé dans nos études. J’ai montré que la FRP de Synechocystis est plus courte que ce qui est indiqué dans Cyanobase, commençant en fait à la méthionine 26. Mes résultats ont aussi révélé que la photo-protection n’a lieu que lorsque le ratio OCP/FRP est élevé.Le plus grand aboutissement de ma thèse a été la reconstitution in vitro du mécanisme de photo-protection lié à l’OCP en utilisant de l’OCP, de la FRP et des PBs isolés. J’ai montré que la lumière est requise uniquement pour la photo-activation de l’OCP et que l’attachement de l’OCP au PB ne demande aucune illumination. Ce n’est qu’une fois photo-activée que l’OCP peut interagir avec le PB et entrainer la diminution de fluorescence (quenching). En se basant sur les résultats obtenus in vitro nous avons proposé un modèle moléculaire pour le mécanisme de photo-protection lié à l’OCP. Le système de reconstitution in vitro a été utilisé pour évaluer l’importance d’un pont salin conservé (Arg155-Glu244) entre les deux domaines de l’OCP et a révélé que celui-ci stabilise la forme inactive de l’OCP. La photo-activation entraine rupture du pont salin, l’Arg155 étant ensuite impliquée dans l’interaction entre OCP et PB. Le site d’attachement de l’OCP au coeur du PB a aussi été étudié en utilisant le système in vitro. Nos résultats ont montré que les émetteurs terminaux du PB ne sont pas requis et que le site primaire de quenching est un trimère d’allophycocyanine émettant à 660nm. Enfin nous avons étudié les propriétés des états excités du caroténoïde dans l’OCP photo-activée, montrant qu’un de ces états a un caractère de transfert de charge très prononcé et peut avoir un rôle principal dans la dissipation de l’énergie. Nos résultats suggèrent fortement que non seulement l’OCP induit dissipation de l’énergie absorbée sous forme de chaleur mais aussi que l’OCP agit directement comme dissipateur d’énergie. / Strong light can cause damage and be lethal for photosynthetic organisms. An increase of thermal dissipation of excess absorbed energy at the level of photosynthetic antenna is one of the processes protecting against deleterious effects of light. In cyanobacteria, a soluble photoactive carotenoid binding protein, Orange Carotenoid Protein (OCP) mediates this process. The photoactivated OCP by interacting with the core of phycobilisome (PB; the major photosynthetic antenna of cyanobacteria) triggers the photoprotective mechanism, which decreases the energy arriving at the reaction centres and PSII fluorescence. The excess energy is dissipated as harmless heat. To regain full PB capacity in low light intensities, theFluorescence Recovery Protein (FRP) is required. FRP accelerates the deactivation of OCP.In this work, I present my input in the understanding of the mechanism underlying the OCPrelated photoprotection. I further characterized the FRP of Synechocystis PCC6803, the model organism in our studies. I established that the Synechocystis FRP is shorter than what it was proposed in Cyanobase and it begins at Met26. Our results also revealed the great importance of a high OCP to FRP ratio for existence of photoprotection. The most remarkable achievement of this thesis is the in vitro reconstitution of the OCPrelated mechanism using isolated OCP, PB and FRP. I demonstrated that light is only needed for OCP photoactivation but OCP binding to PB is light independent. Only the photoactivated OCP is able to bind the PB and quench all its fluorescence. Based on our in vitro experiments we proposed a molecular model of OCP-related photoprotection. The in vitro reconstituted system was applied to examine the importance of a conserved salt bridge (Arg155-Glu244) between the two domains of OCP and showed that this salt bridge stabilises the inactive form of OCP. During photoactivation this salt bridge is broken and Arg155 is involved in the interaction between the OCP and the PB. The site of OCP binding in the core of a PB wasalso investigated with the in vitro reconstituted system. Our results demonstrated that the terminal energy emitters of the PB are not needed and that the first site of fluorescence quenching is an APC trimer emitting at 660 nm. Finally, we characterised the properties of excited states of the carotenoid in the photoactivated OCP showing that one of these states presents a very pronounced charge transfer character that likely has a principal role in energy dissipation. Our results strongly suggested that the OCP not only induces thermal energy dissipation but also acts as the energy dissipator.

A new rising star in the carbon nanomaterial family is carbon dots. Carbon dots have received great attention due to their excellent luminescence and low toxicity. In this project, a new carbon dot derived from birch leaves is studied and characterized. The birch leaf carbon dot (BL-CD) exhibits narrow red photoluminescence (peak = 670 nm, full width at half maximum = 23 nm) with a photoluminescence quantum yield of 26% in dilute methanol solution.  The presence of the characteristic peaks of the pigment pheophytin-a in the absorption spectrum and the photoluminescence spectrum of the BL-CD and the absence of a crystal structure together with the narrow and excitation-independent photoluminescence indicate a carbon dot with a non-emissive amorphous structure with emissive molecular sites consisting of the pigment. The photoluminescence quenching of the BL-CDs in solid-state is reduced by the introduction of a hostmaterial. The use of a host enabled the employment of BL-CDs as the emitter in a light-emitting electrochemical cell (LEC). This project paves the way for further development of the environmentally friendly and sustainable BL-CD LEC.

In this diploma thesis was studied time-resolved fluorescence in polymer-surfactant system. At first aggregation numbers of cationic (cetyltrimethylammonium bromide), anionic (sodium dodecylsulfate) and nonionic (Triton X-100) surfactants were studied by steady-state and time-resolved fluorescence spectroscopy. These two methods were compared. Aggregation numbers by steady-state method were always lower than aggregation numbers measured by time-resolved method. Steady-state method of determination aggregation numbers is useless for surfactants with high aggregation number and for aerated samples. Addition of hyaluronan to surfactant system was studied. There was observed change in aggregation number after addition of hyaluronan and change in percentage of dynamic quenching after addition of hyaluronan. Hyaluronan affected aggregation number of cetyltrimethylammonium bromide and Triton X-100. Hyaluronan increased percentage of dynamic quenching in cetyltrimethylammonium bromide and in Triton X-100. Pyren in sodium dodecylsulfate was quenched by sphere of action with negligible percentage of dynamic quenching and addition of hyaluronan had no effect on quenching. As next goal of this thesis, the determination of the position of fluorescence probe pyrene in cetyltrimethylammonium bromide, sodium dodecylsulfate and Triton X-100 micelles was chosen. Position of pyrene changed with charge and structure of micelles. Next was studied how percentage of dynamic quenching by iodide compounds changes with different charge of micelle. In all cases majority of dynamic quenching was calculated.