Properties of molecules in tunnel junctions

Molecular tunnel junctions involve studying the behaviour of a single molecule sandwiched between metal leads. When a molecule makes contact with electrodes, it becomes open to the environment which can heavily influence its properties, such as electronegativity and electron transport. While the most common computational approaches remain to be single particle approximations, in this thesis it is shown that a more explicit treatment of electron interactions can be required. By studying an open atomic chain junction, it is found that including electron correlations corrects the strong lead-molecule interaction seen by the ΔSCF approximation, and has an impact on junction I − V properties. The need for an accurate description of electronegativity is highlighted by studying a correlated model of hexatriene-di-thiol with a systematically varied correlation parameter and comparing the results to various electronic structure treatments. The results indicating an overestimation of the band gap and underestimation of charge transfer in the Hartree-Fock regime is equivalent to not treating electron-electron correlations. While in the opposite limit, over-compensating for electron-electron interaction leads to underestimated band gap and too high an electron current as seen in DFT/LDA treatment. It is emphasised in this thesis that correcting electronegativity is equivalent to maximising the overlap of the approximate density matrix to the exact reduced density matrix found at the exact many-body solution. In this work, the complex absorbing potential (CAP) formalism which allows for the inclusion metal electrodes into explicit wavefunction many-body formalisms is further developed. The CAP methodology is applied to study the electron state lifetimes and shifts as the junction is made open.

Cognitive dysfunction in Duchenne muscular dystrophy: a possible role for neuromodulatory immune molecules

Duchenne muscular dystrophy (DMD) is an X chromosome-linked disease characterized by progressive physical disability, immobility, and premature death in affected boys. Underlying the devastating symptoms of DMD is the loss of dystrophin, a structural protein that connects the extracellular matrix to the cell cytoskeleton and provides protection against contraction-induced damage in muscle cells, leading to chronic peripheral inflammation. However, dystrophin is also expressed in neurons within specific brain regions, including the hippocampus, a structure associated with learning and memory formation. Linked to this, a subset of boys with DMD exhibit nonprogressing cognitive dysfunction, with deficits in verbal, short-term, and working memory. Furthermore, in the genetically comparable dystrophin-deficient mdx mouse model of DMD, some, but not all, types of learning and memory are deficient, and specific deficits in synaptogenesis and channel clustering at synapses has been noted. Little consideration has been devoted to the cognitive deficits associated with DMD compared with the research conducted into the peripheral effects of dystrophin deficiency. Therefore, this review focuses on what is known about the role of full-length dystrophin (Dp427) in hippocampal neurons. The importance of dystrophin in learning and memory is assessed, and the potential importance that inflammatory mediators, which are chronically elevated in dystrophinopathies, may have on hippocampal function is also evaluated.