VictorJuiz/thesis huggingface dataset:
Large-eddy Simulation of Premixed Turbulent Combustion Using Flame Surface Density Approach
Keywords: large-eddy simulation
turbulent combustion
flame surface density

In the last 10-15 years, large-eddy simulation (LES) has become well established for non-reacting flows, and several successful models have been developed for the transfer of momentum and kinetic energy to the subfilter-scales (SFS). However, for reacting flows, LES is still undergoing significant development. In particular, for many premixed combustion applications, the chemical reactions are confined to propagating surfaces that are significantly thinner than the computational grids used in practical LES. In these situations, the chemical kinetics and its interaction with the turbulence are not resolved and must be entirely modelled. There is, therefore, a need for accurate and robust physical modelling of combustion at the subfilter-scales. In this thesis, modelled transport equations for progress variable and flame surface density (FSD) were implemented and coupled to the Favre-filtered Navier-Stokes equations for a compressible reactive thermally perfect mixture. In order to reduce the computational costs and increase the resolution of simulating combusting flows, a parallel adaptive mesh (AMR) refinement finite-volume algorithm was extended and used for the prediction of turbulent premixed flames. The proposed LES methodology was applied to the numerical solution of freely propagating flames in decaying isotropic turbulent flow and Bunsen-type flames. Results for both stoichiometric and lean flames are presented. Comparisons are made between turbulent flame structure predictions for methane, propane, hydrogen fuels, and other available numerical results and experimental data. Details of subfilter-scale modelling, numerical solution scheme, computational results, and capabilities of the methodology for predicting premixed combustion processes are included in the discussions. The current study represents the first application of a full transport equation model for the FSD to LES of a laboratory-scale turbulent premixed flame. The comparisons of the LES results of this thesis to the experimental data provide strong support for the validity of the modelled transport equation for the FSD. While the LES predictions of turbulent burning rate are seemingly correct for flames lying within the wrinkled and corrugated flamelet regimes and for lower turbulence intensities, the findings cast doubt on the validity of the flamelet approximation for flames within the thin reaction zones regime.
Surface Templating Using a Photolabile Terpolymer to Construct Mixed Films of Oligomers and Oligonucleotides for DNA Biosensor Development
Keywords: mixed films
terpolymer
fluorescence
oligonucleotides
hybridization
selectivity
6-nitroveratyloxycarbonyl
photolabile

A photolabile terpolymer containing 6-nitroveratyloxycarbonyl (NVOC) protected amine, epoxy and trimethoxysilyl functionality in 1:3:2 monomer ratio was synthesized to template glass surfaces for specific site directed coupling of non-probe oligomers and probe oligonucleotides. Non-probe oligomers were introduced to the surface to control the environment of the probes by reducing probe-to-probe and probe-to-surface interactions. The trimethoxysilyl group served as the anchoring site for the terpolymer to be covalently bound to glass and silicon wafers. Amine terminated non-probe oligomers were coupled to the epoxy sites and thiolated 19-mer SMN1 probes were directed to the deprotected amine sites via the heterobifunctional linker, sulfosuccinimidyl-4-[maleimidomethyl]cyclohexane-1-carboxylate (sulfo-SMCC). Characterization of the terpolymer was done using 1H NMR, 13C NMR, MALDI-ToF and elemental analysis. NVOC deprotection was monitored by UV absorption, and surface characterization of the bound terpolymer on silicon wafers was investigated with XPS, ToF-SIMS, ellipsometry and static contact angle. Neutral polyethylene glycol (PEG), negatively charged methacrylic acid (MAA) oligomer and dC20 oligonucleotides were used as non-probe oligomers. The probe density on the surface was estimated to be 2.2 ± 0.3 x 10^12 molecules/cm2 and the presence of the oligomers on the surface did not significantly affect probe immobilization efficiency. The mixed films were functional for target hybridization and its selectivity towards partially-mismatched targets was investigated at different solution pH, ionic strength and temperature. It was demonstrated that pH can be tuned to ameliorate non-specific adsorption and ionic strength governed the selectivity of the surfaces. Improved selectivity was achieved at high salt concentration (1 M NaCl) on PEG and dC20 mixed films at room temperature. The MAA surface did not show significant improvements in selectivity. This indicated that charge of the oligomers does not dominate control of selectivity. The results suggested that the terpolymer construct played a role in depression of the melting temperature of the hybridized duplex to within 5 to 10 oC of room temperature. With the melting temperature shifted closer to room temperature, it is possible to improve selectivity for room temperature detections of single nucleotide polymorphism.
Studies in Physisorption and Chemisorption on Si(100)-2x1
Keywords: Surface Chemistry
STM

Scanning Tunneling Microscopy (STM) has been used to study the physisorption and chemisorption behaviour for three simple organic haloalkanes; 1,5 Dichloropentane (DCP), Bromomethane (CH3Br) and Chloromethane (CH3Cl)) on Si(100) 2x1, at temperatures ranging from 270 K to room temperature. The results were interpreted by Density Functional Theory (DFT) performed by collaborators at McGill University and the University of Liverpool. Physisorbed molecules of DCP were found to self assemble into stable lines aligned predominantly perpendicular to the Si dimer pair rows on the surface. A novel mechanism for line formation of Dichloropentane, termed, Dipole Directed Assembly (DDA), was elucidated by DFT calculations. For CH3Br three different patterns of dissociative attachment of reaction products (CH3 and Br/Cl) were observed, and assigned to three reaction pathways. These experimentally determined relative yields were used to obtain differences in reaction activation energy, Delta Ea, between the reaction pathways. These, in turn, were compared with computed differences in reaction barriers, Delta Eb, obtained ab initio for the same pathways by DFT. For CH3Cl, two single-molecule patterns of attachment were found, and a new reaction pathway for attaching CH3Cl in long chains of alternating CH3 and Cl was discovered. The mechanisms for chain growth were determined experimentally by examination of single molecular steps. This mechanism was explained ab initio by DFT to be the result of relative barrier heights for the possible chain-growth pathways.
Influence of Nickel and pH on Helicobacter pylori NikR
Keywords: Helicobacter pylori NikR
nickel
pH

Helicobacter pylori (H. pylori) is a gram-negative pathogenic bacterium that infects half of the world’s population. It resides in the human stomach, where it survives extremely acidic conditions. Efficient colonization by H. pylori requires urease and hydrogenase enzymes, both of which utilize nickel as a cofactor. The intracellular level of nickel in H. pylori is strictly maintained by a nickel-responsive transcription factor, HpNikR, which acts as a master regulator to control both activation of the urease genes and repression of a variety of other genes including its own. In addition to its role in nickel homeostasis, HpNikR has been implicated in the adaptive response of H. pylori to acidic environmental conditions. In this work, two representative genes, ureA and nikR, are confirmed to be regulated by HpNikR directly in response to changes in nickel concentration, with HpNikR binding to the promoter region of each gene. The binding sequences on the two promoters are distinct from each other and no consensus sequence could be identified from them. The binding affinity of HpNikR to the ureA promoter is much tighter than to the nikR promoter. Another signal that can activate the DNA-binding activity of HpNikR is a change in pH. Once HpNikR is activated by proton binding, it binds to the ureA promoter independently of nickel concentration, but still binds to the nikR promoter in a nickel-dependent manner. Several amino acids at the N-terminus of HpNikR, including Asp7, Asp8 and Lys6, are critical for the specific response of HpNikR to pH changes. In addition, the binding of HpNikR to distinct DNA sequences induces different degrees of DNA bending, which provides another possible means of gene regulation by HpNikR. The ability of HpNikR to differentially regulate distinct genes in response to several signals allows a graduated level of control of gene expression by HpNikR. In vivo studies to evaluate the physiological relevance of the above in vitro results have been initiated. Given the relatively low abundance of transcription factors in H. pylori, information about the effects of nickel and pH on HpNikR in vivo is important for understanding the multifaceted roles of HpNikR in fine-tuning the physiology of this organism. Ultimately this study may provide us with a better idea of how to control H. pylori-caused diseases.
Investigation of Nano-scale, Self-assembled, Polymeric Systems by Atomic Force Microscopy
Keywords: AFM
self-assembly
nanotechnology

The atomic force microscope (AFM) was used to study a series of self-assembled systems: alkanethiol self-assembled monolayer (SAM), diblock copolymer thin film, solid supported lipid bilayer membrane, and microgel with double interpenetrating polymer network. In the first system, packing and restructuring of self-assembled monolayers as exhibited by several alkanethiol systems (1-hexanethiol, 1-decanethiol, 11-ferrocenyl-1-undecanethiol) is demonstrated using conducting probe AFM (CP-AFM). Pressure is induced by an AFM tip, and simultaneously, electrical behavior is measured via detection of tunneling currents between metallic tip and substrate. The behavior is fit using a mechanical model that attempts to predict the observed junction resistance as a function of applied force with consideration for mechanical restructuring of the monolayer at higher loads. CP-AFM is also used to study self-assembled thin film of the diblock copolymer polystyrene- block-polyferrocenylsilane (PS-b-PFS) on gold substrate. Simultaneous height and electrical current imaging verify the phase separation of the two blocks of the polymer and additionally, distinguish each block due to differential conductivity. The phase separation of multi-component phospholipid bilayers (phosphatidylcholine/ sphingomyelin/ cholesterol) on supporting substrate into liquid-ordered and liquid-disordered phases is demonstrated using both topographical imaging, and the use of force map analysis through tip indentation and rupture measurements. The segregation and differential mechanical stiffness of the phases help to understand the important role of mechanical stability and rigidity membranes. An automated batch analysis process was implemented to facilitate the procedure. The mechanical properties of microfluidically produced microgels (cross-linked sodium alginate and poly(N-isopropylacrylamide)) are measured using indentation experiments, to evaluate the suitability of these gels as cell-mimics. Nanoscale heterogeneities were avoided by using a tipless cantilever. This body of work shows that the alginate content of these microgels can be varied to tune their mechanical properties and that a platform for mechanical measurement of cell and cell-mimics is possible.
Optimal and Robust Routing of Subscriptions for Unifying Access to the Past and the Future in Publish/Subscribe
Keywords: publish/subscribe
content-based routing
query
middleware
BPEL
workflow managment

A flexible, scalable, and asynchronous middleware abstract is needed for business process management, which involves thousands of tasks and a large number of running instances of large business processes. The content-based publish/subscribe system is an ideal candidate to serve as enterprise service bus for these applications. In the publish/subscribe paradigm, information providers called publishers disseminate publications to all subscribers who have expressed interests by registering subscriptions through a loosely coupled interface. However, the traditional publish/subscribe paradigm only supports stateless subscriptions, that is, event correlation is ignored. Moreover, subscribers can only receive publications issued after their subscriptions. There are many application contexts, however, where access to publications from the past is necessary,such as for replaying a business process execution to debug it. Even more interesting uses arise when data from the past can be correlated with those in the future. Therefore, new languages and new functionalities are needed in the standard publish/subscribe model in order to support business process management. A new subscription language PADRES SQL(PSQL) which can express event patterns and unify both historic and future views for subscribers. PADRES allows a subscriber to access data published both in the past and in the future. Furthermore, complex event detection happens in the broker network. The main difficulties of distributed event detection are routing a composite subscription, including where and how to decompose the composite subscription, and routing the individual parts of the subscription. Our composite subscription routing decisions are based on a cost model which minimizes the routing and detection delay. An adaptive subscription routing protocol is proposed to determine efficient location with dynamic changing workloads. PADRES also provides robust message delivery by exploring alternative paths in a cyclic overlay. Routing optimizations and efficient matching algorithms are studied to improve the performance of the extended publish/subscribe model. With the above features, we propose the Ninos system, the distributed business process execution architecture as a case study,which uses light-weight activity agents to carry out business process execution in a distributed environment. Ninos proves that decentralized business process execution is the trend for next generation products, and the publish/subscribe model is ideal to serve as an enterpriser service bus (ESB) for distributed applications.
The Experiences of Cancer Nurses’ Existential Care in Response to the Threat of Patients' Mortality within the Culture of Cure
Keywords: existential care
phenomenology

Patients are living longer with many types of cancer; however, often they face sudden possibilities of dying, not only due to their advancing illness but due to complications of their treatment. Consequently, they can express substantial existential distress. Nurses’ close proximity to patients puts them in an ideal place to assess and engage with patients’ existential distress; yet this kind of research has been scarce. The purpose of this doctoral thesis was to explore nurses’ experiences of being with patients facing the threat of mortality. Yalom describes this threat as the fear of death, isolation, anxiety and responsibility about freedom, and meaninglessness. The study took place in a cancer setting where care is highly technological and goals of cure dominate, specifically, two bone marrow transplant units of one institution in Canada. Benner’s methodology of interpretive phenomenology guided data collection and analysis of focused observations and interviews with 19 registered nurses. The experience of fighting cancer while preparing for the possibility of letting go was the main theme. Letting go did not reflect nurses’ intents to abandon life but to release patients (if only briefly) from perceived norms of the curative culture. More specifically, the main theme was characterized by: 1) working within the culture of cure and the possibilities of patients dying, 2) concern about “bursting the bubble of hope,” 3) whether to and how to respond to patients’ distress and dying, and 4) coping with patient involvement. In the context of responsive relationships (patients and their families, and healthcare colleagues), nurses reported engaging in communication about the threat of patients’ mortality, and responding with letting be and supporting families to let go, the management of technology and prevention of technological intrusions, and striving for patients to have “easier” deaths. Results indicate a potential to enhance nurses’ supportive care constituted by their perceived responsibility to engage and respond to patients’ existential distress. Moreover, this study suggests that more attention is warranted not only to policy, education, and research that focuses on patients’ existential well-being, but to the well-being of nurses working within tensions of curing and comforting.
Accretion Disks and the Formation of Stellar Systems
Keywords: stars: formation
planetary systems: protoplanetary disks
accretion, accretion disks
methods: numerical
stars: binary

In this thesis, we examine the role of accretion disks in the formation of stellar systems, focusing on young massive disks which regulate the flow of material from the parent molecular core down to the star. We study the evolution of disks with high infall rates that develop strong gravitational instabilities. We begin in chapter 1 with a review of the observations and theory which underpin models for the earliest phases of star formation and provide a brief review of basic accretion disk physics, and the numerical methods which we employ. In chapter 2 we outline the current models of binary and multiple star formation, and review their successes and shortcomings from a theoretical and observational perspective. In chapter 3 we begin with a relatively simple analytic model for disks around young, very massive stars, showing that instability in these disks may be responsible for the higher multiplicity fraction of massive stars, and perhaps the upper mass to which they grow. We extend these models in chapter 4 to explore the properties of disks and the formation of binary companions across a broad range of stellar masses. In particular, we model the role of global and local mechanisms for angular momentum transport in regulating the relative masses of disks and stars. We follow the evolution of these disks throughout the main accretion phase of the system, and predict the trajectory of disks through parameter space. We follow up on the predictions made in our analytic models with a series of high resolution, global numerical experiments in chapter 5. Here we propose and test a new parameterization for describing rapidly accreting, gravitationally unstable disks. We find that disk properties and system multiplicity can be mapped out well in this parameter space. Finally, in chapter 6, we address whether our studies of unstable disks are relevant to recently detected massive planets on wide orbits around their central stars.
c-Myb Dependent Smooth Muscle Cell Differentiation from Mouse Embryonic Stem Cells
Keywords: Biology
Genetics

Vascular smooth muscle cells (VSMC) serve as key constituents of the developing vasculature, ensuring stability of the nascent vessels, and are essential for the proper performance of the mature cardiovascular system. Pathological alterations in SMC biology, manifesting as perturbations in the differentiation state of SMC, play a pivotal role in the development and progression of various vascular diseases. Thus an understanding of the mechanisms and factors that control SMC differentiation underlies the potential for diagnostic and therapeutic advances. As such, this thesis aimed to implicate the c-Myb transcription factor in the process of SMC differentiation. For this purpose, in vitro assays were developed using the embryoid body (EB) model system, suitable for clarifying the molecular pathways and extrinsic factors that promote or obstruct SMC lineage specification and maturation to the contractile phenotype. Contractile activity was observed in the developing EBs, and further characterized as smooth muscle and cardiac contractions. Temporal induction of SM-specific markers preceded and paralleled contractile SMC appearance and their mRNA levels predicted the relative ability of distinct mouse ES cell (mESC) lines to generate EBs with contracting SMC. Using fluorescent SM-specific promoter-reporter gene strategy it was shown that spontaneous SM-contractions coincide with SM-myosin-heavy-chain (SM-MHC) promoter activity. Moreover, this technology was employed to generate SMC (SM-MHC+) in a scalable stirred-suspension culture system. This thesis addressed the effects of c-myb ablation on SMC differentiation both in vitro and in vivo. c-myb-/- mESC were unable to produce EBs with spontaneously contracting SMC, but gave rise to contracting cardiomyocytes unimpaired. Temporal patterns of myogenic and SM-specific gene expression levels during the course of differentiation revealed that, unlike wild-type EBs, c-myb-/- EBs lacked robust induction of these critical markers. Accordingly, c-myb-/- EBs exhibited significantly reduced SMC numbers. Additionally, in chimaeric EB model substantial contribution by c-myb-/- mESC was detrimental to the development of SM-contractions. To corroborate the in vitro data, chimaeric embryos and adult mice were used to demonstrate significantly reduced c-myb-/- cell contribution to vascular and visceral SMC lineages in vivo. Collectively, this thesis assigns a novel role for the c-Myb transcription factor and advances knowledge of in vitro SMC differentiation.