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In this work, we investigate effects of strong correlation to quantum transport from atomic first principles. In order to accomplish this task, we use a well established state-of-the-art formalism of quantum transport where density functional theory (DFT) is carried out within the Keldysh non-equilibrium Green's functions (NEGF). To deal with certain strong correlation phenomenon, we integrated an local density approximation plus Hubbard U (LDA+U) exchange-correlation potential into the existing NEGF-DFT formalism. The LDA+U potential correctly accounts for the electronic structure of correlated material. We will present the theory and numerical implementation associated with the NEGF-DFT-(LDA+U) in detail. Extensive tests on the well known correlated material FeO crystal have been carried out and results compared with previous literature as well as to experimental data. / We then apply our NEGF-DFT-(LDA+U) technique to investigate transport physics of spin resolved tunnelling in Fe/MgO/Fe magnetic tunnel junctions (MTJ). We found that interfacial oxygen atoms are enough to localise the 3d electrons of infacial Fe atoms due to strong correlation. This surprising result substantially changes quantum transport properties of the MTJ, in particular it reduces magnetic resistance ratio by about 33%. This strongly correlated physics is absent if the conventional local spin density approximation (LSDA) is used in the NEGF-DFT analysis. Results of LSDA and LDA+ U exchange-correlation potential will be compared. Furthermore, through investigating contributions to scattering states by various atomic orbitals, we clearly identify the reason why LDA+U changes quantum transport in both quantitative and qualitative ways. Finally, we believe this strongly correlated physics should be general in other MTJs involving different oxides.

Mitochondria are eukaryotic organelles derived in evolution from within the ? subdivision of Proteobacteria. Although mitochondria are structurally and metabolically complex, modern-day mitochondrial genomes (mtDNA) encode only a small number of RNAs and proteins predominantly involved in adenosine triphosphate (ATP) formation through electron transport coupled to oxidative phosphorylation, as well as translation of mtDNA-encoded proteins. In humans, only 13 of the >1000 polypeptides that constitute the complete mitochondrial protein complement (proteome) are encoded in mtDNA; the remainder is encoded by nuclear DNA (nuDNA). It is therefore imperative to comprehensively catalog nuDNA-encoded mitochondrial proteins in order to understand holistically the evolution of mitochondria. Mitochondrial proteome investigations of animals, fungi and land plants have dramatically altered our conception of mitochondrial evolution: in contrast to mtDNA-encoded proteins, few nuDNA-encoded mitochondrial proteins are demonstrably derived from the eubacterial progenitor of mitochondria, and many are found only in eukaryotes. Notably, however, little is known about the mitochondria of eukaryotic microbes (protists), which constitute the bulk of biochemical and genetic diversity within the domain Eucarya. The proteomic characterization of protist mitochondria is therefore crucial to fully elucidating mitochondrial function and evolution. Employing tandem mass spectrometry (MS/MS), I have analyzed highly purified mitochondria from Acanthamoeba castellanii (Amoebozoa). In combination, nearly 750 nuDNA- and mtDNA-encoded proteins were identified. These data were used to catalog metabolic pathways and protein complexes, and to infer functional and evolutionary profiles of A. castellanii mitochondria. My analyses suggest that while A. castellanii mitochondria have many features in common with other eukaryotes, they possess several novel attributes and pronounced metabolic versatility. An analysis of the A. castellanii electron transport chain (ETC) was also performed, utilizing a combination of blue native polyacrylamide gel electrophoresis (BN-PAGE), MS/MS and bioinformatic queries. A significant proportion of A. castellanii ETC proteins was identified, yielding several insights into ETC evolution in eukaryotes. Lastly, I present two unusual cases of ‘split’ mitochondrial proteins: the iron-sulfur subunit SdhB of succinate:ubiquinone oxidoreductase (Complex II), in the phylum Euglenozoa and Cox1 of cytochrome c:O2 oxidoreductase (Complex IV) in various eukaryotes, including A. castellanii. Functional and evolutionary implications of these findings are discussed.

This thesis investigates the application of low energy electron irradiation to 1,3,5-trimethylbenzene films to test whether site-selective C–H bond cleavage can be achieved in a molecule presenting both aliphatic and aromatic target sites. IRRAS was used to characterize the orientation of vapour-deposited 1,3,5-trimethylbenzene on Au(111) and alkanethiolated gold under UHV and cryogenic conditions. On both substrates, the disordered as-deposited films were transformed by thermal treatment, producing two film structures – within the first 4-monolayers, aromatic rings lie nearly parallel to the metal surface, while molecules in additional layers are more upright. Low energy electron irradiation (0-10 eV) produced no dissociations in 1,3,5-trimethylbenzene; however, low energy electron transmission spectra indicate charge accumulates at interstitial sites in the mesitylene film, decelerating subsequent incident electrons. These decelerated electrons traverse the charged film and are reaccelerated, inducing dissociations in the underlying SAM. Contrary to literature claims, 1,3,5-trimethylbezene is a poor molecule for adsorption studies such as BET as the initial adsorption is disordered and thermodynamically unstable.

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