Throughout this thesis work, surface nanocarbon synthesis on metal catalyst surfaces was investigated as the first step of carbon nanotube production mechanism. Study was aimed to make a comparison between the performances of selected catalyst surfaces and to find most probable mechanism for the nanocarbon synthesis on the metal catalyst surface. Formation of nanocarbon from the acetylene as carbon source on the selected Fe(111), Ni(111) and Ni(100) surfaces were studied by means of quantum mechanics. Density functional theory (DFT) was implemented periodically by using Vienna Ab-initio Simulation Package (VASP) code for the computations required. Relative energy profiles of the interested mechanisms were generated by the usage of equilibrium geometry calculations, climbing image nudged elastic band (CI-NEB) calculations and transition state calculations. Formation step of surface nanocarbon, with the decomposition of the carbon source, is the rate determining step of carbon nanotube production. Therefore, results of the nanocarbon synthesis study were related to carbon nanotube synthesis. For the mechanistic study, surface-acetylene complex was obtained by the adsorption of the acetylene on the chosen catalyst surface. Then three different mechanisms were studied for the dehydrogenation process. These processes were named as direct hydrogen-hydrogen interaction, hydrogen atom desorption and surface-hydrogen interaction methods. Among these methods surface-hydrogen interaction methods resulted in minimum activation barriers for all three surfaces used and said to be the most probable mechanism. Finally, relative energy profiles of the mechanisms were compared for the Fe(111), Ni(100) and Ni(111) surfaces and performance of Fe(111) for CNT synthesis was found better than the others.

The generation of a functional nervous system requires that neuronal cells and axons navigate precisely to their appropriate targets. The Eph Receptor Tyrosine Kinases (RTKs) and their ephrin ligands have emerged as one of the important guidance cues for neuronal and axon navigation. However, the molecular mechanisms of how Eph RTKs regulate these processes are still incomplete. The purpose of this work was to contribute to the understanding of how Eph receptors regulate axon guidance by identifying and characterizing components of the Caenorhabditis elegans Eph RTK (VAB-1) signaling pathway. To achieve this objective I utilized a hyper active form of the VAB-1 Eph RTK (MYR-VAB-1) that caused penetrant axon guidance defects in the PLM mechanosensory neurons, and screened for suppressors of the MYR-VAB-1 phenotype. Through a candidate gene approach, I identified the adaptor NCK-1 as a downstream effector of VAB-1. Molecular and genetic analysis revealed that the nck-1 gene encodes for two isoforms (NCK-1A and NCK-1B) that share similar expression patterns in parts of the nervous system, but also have independent expression patterns in other tissues. Genetic rescue experiments showed that both NCK-1 isoforms can function in axon guidance, but each isoform also has specific functions. In vitro binding assays showed that NCK-1 binds to VAB-1 in a kinase dependent manner. In addition to NCK-1, WSP-1/N-WASP was also identified as an effector of VAB-1 signaling. Phenotypic analysis showed that nck-1 and wsp-1 mutants had PLM axon over extension defects similar to vab-1 animals. Furthermore, VAB-1, NCK-1 and WSP-1 formed a complex in vitro. Intriguingly, protein binding assays showed that NCK-1 can also bind to the actin regulator UNC-34/Ena, but genetic experiments suggest that unc-34 is an inhibitor of nck-1 function. Through various genetic and biochemical experiments, I provide evidence that VAB-1 can disrupt the NCK-1/UNC-34 complex, and negatively regulate UNC-34. Taken together, my work provides a model of how VAB-1 RTK signaling can inhibit axon extension. I propose that activated VAB-1 can prevent axon extension by inhibiting growth cone filopodia formation. This is accomplished by inhibiting UNC-34/Ena activity, and simultaneously activating Arp2/3 through a VAB-1/NCK-1/WSP-1 complex. / Thesis (Ph.D, Biology) -- Queen's University, 2011-07-28 16:20:31.957

Nous avons montré que la molécule recombinante humaine CD146 soluble (rh-sCD146) a un effet chimiotactique et angiogénique sur les cellules dérivées de progéniteurs endothéliaux (PEC) en augmentant leur capacité à migrer, à proliférer et à former des pseudo-capillaires. Des expériences réalisées in vivo sur un modèle d'ischémie de la patte chez le rat ont montré que des injections locales répétées de rh-sCD146 permettent une diminution significative du taux d'auto-amputation des animaux et une augmentation du taux de perfusion sanguin de la patte et de la densité capillaire. Dans une 2ème partie du travail, nous avons montré que l'angioplastie coronaire induit une hausse significative du nombre de cellules endothéliales circulantes (CEC) 6h après l'intervention (H6). Les lésions endothéliales, évaluées par la mesure de la variation du nombre de CEC (H6-H0), sont plus élevées chez les non-répondeurs par rapport aux bons répondeurs au Clopidogrel et sont corrélées à l'index VASP / We showed that the recombinant human soluble CD146 (rh-sCD146) has a chemotactic and angiogenic effect on endothelial progenitor derived cells (EPC) by increasing their ability to migrate, to proliferate and to form pseudo- capillaries. In an in vivo experiments model of ischemia in the rat by femoral artery ligation we showed that repeated local injections of rh-sCD146 for 12 days allows a significant reduction in the rate of animals self-amputation and an increase in the rate of blood perfusion of the leg and in the capillary density. In a second part of the work, we have shown that percutaneous coronary intervention induced a significant rise in circulating endothelial cells (CEC) levels 6h after the procedure (H6). The endothelial injury, assessed by CEC delta-change between H6 and H0, was significantly higher in the high on-treatment platelet reactivity group compared with the good responders to Clopidogrel and correlated with the Vasodilatator-Stimulated Phosphoprotein index

This thesis involves a case study in the use of parallelism to improve the performance of an application for computational research on molecules. The application, VASP, was migrated from a machine with 4 nodes and 16 single-threaded processors to a machine with 60 nodes and 120 dual-threaded processors. When initially migrated, VASP's performance deteriorated after about 17 processing elements (PEs), due to network contention. Subsequent modifications that restrict communication amongst VASP processes, together with additional support for threading, allowed VASP to scale up to 112 PEs, the maximum number that was tested. Other performance-enhancing optimizations that were attempted included replacing old libraries, which produced improvements of about 10%, and prefetching, which degraded, rather than enhanced, VASP performance.

Development is punctuated by morphogenetic rearrangements of epithelial tissues, including complete detachment of individual motile cells during epithelial-mesenchymal transition (EMT). Dramatic actin rearrangements occur as cell-cell junctions are dismantled and cells become independently motile during EMT. Characterizing dynamic actin rearrangements and identifying actin machinery driving these rearrangements is essential for understanding basic mechanisms of cell-cell junction remodeling; yet, neither the precise series of actin rearrangements at cell-cell junctions that accompany EMT, nor the machinery that controls actin rearrangement during EMT, have been identified. This work represents a detailed study of junctional actin reorganization in cells undergoing EMT, identifies actin regulatory proteins that control this actin reorganization, and defines the specific function of one regulatory protein, zyxin, in EMT. Using immunofluorescence and live cell imaging of HGF induced scattering of MDCK cells, dynamic actin rearrangement events occurring during EMT are characterized. Junctional actin characteristic of cell-cell adherent cells is rearranged into contractile medial actin networks linked to the junctional membrane in the initial steps of cell scattering. This actin rearrangement is accompanied by dynamic redistribution of specific actin regulatory proteins, namely α-actinin and zyxin-VASP complexes. α-Actinin mediates higher order structure of junctional actin. Zyxin-VASP complexes mediate linkage of dynamic medial actin networks to adherens junction membranes. Zyxin regulation of actin-membrane linkage controls whether cell migration during EMT occurs independently in solitary cells or is coordinated through tissues. The functional analysis employed here uses novel, quantitative methods that define specific cellular EMT ‘phenotypes’ to reveal the precise role of zyxin in EMT. Constitutive active zyxin mutants exhibit persistent actin-membrane linkages and a scattering phenotype in which cells migrate without loss of cell-cell adhesion. Zyxin is proposed to regulate EMT progression by regulating disruption or maintenance of actin membrane linkages at cell-cell junctions. Zyxin alters the ability of cells to fully detach and migrate independently during EMT and may be an important regulator of morphogenetic plasticity.

No description available.

This thesis investigates the lithium-ion dynamics and structural changes in the novel cathode material LiFeV2O7 by solid-state NMR spectroscopy and density functional theory (DFT). With the escalating demand for high-performance lithium-ion batteries (LIBs), exploring cathode materials that can offer superior energy density, cycle stability, and safety is crucial. LiFeV2O7 presents a fascinating structure because it incorporates two transition metals capable of undergoing redox processes, a feature highly beneficial for lithium-ion batteries. The research employs advanced DFT calculations to predict the electronic structure and 7Li NMR shifts. These theoretical insights are essential for understanding how structural disorder influences NMR results and how the oxidation state of transition metal impacts the Fermi contact shift. Experimental techniques, including solid-state NMR spectroscopy and diffraction methods, are applied to study the lithium-ion exchange process and structural evolution during electrochemical cycling. Selective inversion NMR experiments were used to quantify the exchange rates relative to lithiation levels, and in combination with diffraction methods and DFT calculations, enabled the development of a structure model that elucidates the corresponding phase changes in the material. Moreover, the thesis discusses the impact of structural modifications on the lithium-ion dynamics within Li1.71FeV2O7, revealing a direct link between specific crystallographic changes and enhanced lithium mobility. The integration of DFT calculations with experimental observations provides a comprehensive understanding of the material's behavior, paving the way for improvements in cathode design. Overall, this research contributes significantly to the field of LIBs, offering novel insights into the complex interplay between structure, dynamics, and electrochemical performance in cathode materials. / Thesis / Doctor of Science (PhD) / This thesis explores the lithium-ion dynamics and structural changes in the new cathode material LiFeV2O7 using solid-state NMR spectroscopy and density functional theory (DFT). As the demand for high-performance lithium-ion batteries (LIBs) grows, discovering cathode materials with better energy density, stability, and safety becomes crucial. LiFeV2O7 is particularly interesting due to its structure, which includes two transition metals that undergo redox processes. This study combines advanced DFT calculations with experimental techniques to understand how structural disorder and the oxidation state of transition metals affect NMR results. Solid-state NMR spectroscopy and diffraction methods are used to examine lithium-ion exchange and structural changes during battery cycling. The research identifies how specific crystallographic changes enhance lithium mobility, providing insights that can improve cathode design. This comprehensive study contributes to the development of more efficient and stable LIBs by revealing the complex interplay between structure, dynamics, and electrochemical performance.

Regulation of the actin cytoskeleton is key to cellular function and underlies processes including cell migration, mitosis and endocytosis. Motile cells send out dynamic actin protrusions that enable them to sense and interact with their environment, as well as generating physical forces. Linking of the actin cytoskeleton to the cell membrane is essential for the formation of these protrusions. The proteins that are thought to fulfil such a role have a membrane interacting domain (such as the PH domain in lamellipodin, or I-BAR protein in IRSp53) and a domain which interacts with actin regulatory proteins (such as the SH3 domain of IRSp53, which binds Ena and VASP). I investigated the contribution of the F-BAR protein Toca-1 in linking actin polymerisation to membranes, by characterising a new protein-protein interaction and the interaction of Toca-1 with giant unilamellar vesicles. FBP17, a homologue of Toca-1, can oligomerise to form 2D flat lattices and 3D tubules on membranes. Proteins of the Toca-1 family have previously been implicated in actin polymerisation in cell-free systems and during endocytosis. However, there is emerging evidence that Toca-1 family proteins could also be involved in the formation of outward facing protrusions, lamellipodia and filopodia. In an in vitro system that recapitulates the formation of filopodia-like structures (FLS) on supported lipid bilayers, Toca-1 is recruited early, suggesting a Toca-1 scaffolding mechanism could precede the recruitment of other actin regulators. One prediction of this model is that Toca-1 would bind proteins previously implicated in filopodia formation, such as formins. I found that extracts depleted of Toca-1 binding partners no longer forms filopodia-like structures and subsequently optimised pull-down assays to identify Toca-1 binding partners by mass-spectrometry. I identified four formins, Diaph1, Diaph3, FHOD1 and INF2, and as well as the actin elongation factors and filopodia proteins, Ena and VASP. I further characterised these interactions and found that Toca-1 binds Ena and VASP via its SH3 domain. The interaction is direct and is strongly reduced if the proline-rich region in Ena is deleted. VASP was still able to bind without its proline rich region, suggesting there could be additional binding sites. I discovered that the binding of Ena and VASP was dependent on the clustering state of Toca-1, whilst the binding of the previously identified Toca-1 binding partner N-WASP was not. This further supports the importance of Toca-1 oligomerisation in actin polymerisation. I tested these interactions in the FLS system and found that increasing Toca-1 concentration leads to increased recruitment of N-WASP, as well as the novel binding partner Ena to the structures, whereas an increase in VASP was not observed. SH3-domain mediated interactions are required for Toca-1 recruitment to FLS, suggesting that its membrane and protein binding activities act cooperatively. I showed that unlike N-WASP, which promotes the formation of branched actin, Ena and VASP are not required for actin polymerisation on supported lipid bilayers, suggesting that they are redundant with other factors in the elongation step of FLS formation. Ena and VASP are known to be important for the formation of neuronal filopodia and so I began to further test the role of these interactions in a cellular context using a neuronal cell culture system. As well as recruiting protein binding partners, F-BAR family proteins are implicated in stabilising lipid microdomains and can induce the clustering of phosphoinositides. I investigated the role of Toca-1 in actin polymerisation on PI(4,5)P2-rich giant unilamellar vesicles (GUVs). Actin-rich tails formed on the GUVs only when excess Toca-1 was supplemented into the extracts, and I propose that this is due to lipid organisation by Toca-1. In summary, my work suggests a model in which Toca-1 clusters, stabilises the membrane lipids and recruits regulators of actin polymerisation, such as Ena. This mechanism could be used to link actin polymerisation to the membrane in cellular protrusions, such as filopodia.

Dans le domaine du stockage de l'énergie, et en particulier celui des batteries Li-ion, comprendre les mécanismes Redox liés à l'insertion de Li+ dans les matériaux d'électrode est un défi majeur. Les pnictogénures de métaux de transition représentent une nouvelle classe d'électrodes négatives offrant une alternative intéressante, en termes de sécurité et de performances, à l'électrode de graphite actuellement commercialisées. Ils réagissent avec le lithium par des réactions de conversion qui transforment l'électrode MPy en un composite M ̊/yLi3P. Grâce aux outils de la chimie théorique et à des analyses locales de la liaison chimique, une modélisation ab-initio (DFT/DFT+U) de ces électrodes a permis de (i) comprendre les phénomènes microscopiques à l'origine de leurs performances, (ii) caractériser les phases intermédiaires stabilisées au cours des charges/décharges de la batterie, et (iii) proposer une méthodologie d'analyse simple et efficace, transférable à tous les matériaux de conversion.

First-principles calculations such as density functional theory (DFT) employ numerical approaches to solve the Schrodinger equation of a system. Standard functionals employed to determine the cohesive system energy, specifically the local density and generalized gradient approximations (LDA and GGA), underestimate the correlation of 5f electrons to their ions in AO₂ systems (A=U/Pu/Np). The standard correction, the "Hubbard +U," causes the multidimensional energy surface to develop a large number of local minima which do not correspond to the ground state (global minimum). Because all useful energy values derived from DFT calculations depend on small differences between relatively large cohesive energies, comparing systems wherein one or more of the samples are not in the ground state has the potential to introduce large errors. This work presents an analysis of the fundamental issues of metastable states in both pure and binary AO₂ systems, investigates novel methods of handling them, and describes why current literature approaches which appear to work well for the pure compounds are not well-suited for systems containing multiple actinide species.