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HIV evolution: biogeography and intra-individual dynamics

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The entire history of HIV-1 is hidden in its ten thousand bases, where information regarding its evolutionary traversal through the human population can only be unlocked with fine-scale sequence analysis.

The entire history of HIV-1 is hidden in its ten thousand bases, where information regarding its evolutionary traversal through the human population can only be unlocked with fine-scale sequence analysis. Measurable footprints of mutation and recombination have imparted upon us a wealth of knowledge, from multiple chimpanzee-to-human transmissions to patterns of neutralizing antibody and drug resistance. Extracting maximum understanding from such diverse data can only be accomplished by analyzing the viral population from many angles. This body of work explores two primary aspects of HIV sequence evolution, point mutation and recombination, through cross-sectional (inter-individual) and longitudinal (intra-individual) investigations, respectively. Cross-sectional Analysis: The role of Haiti in the subtype B pandemic has been hotly debated for years; while there have been many studies, up to this point, no one has incorporated the well-known mechanism of retroviral recombination into their biological model. Prior to the use of recombination detection, multiple analyses produced trees where subtype B appears to have first entered Haiti, followed by a jump into the rest of the world. The results presented here contest the Haiti-first theory of the pandemic and instead suggest simultaneous entries of subtype B into Haiti and the rest of the world. Longitudinal Analysis: Potential N-linked glycosylation sites (PNGS) are the most evolutionarily dynamic component of one of the most evolutionarily dynamic proteins known to date. While the number of mutations associated with the increase or decrease of PNGS frequency over time is high, there are a set of relatively stable sites that persist within and between longitudinally sampled individuals. Here, I identify the most conserved stable PNGSs and suggest their potential roles in host-virus interplay. In addition, I have identified, for the first time, what may be a gp-120-based environmental preference for N-linked glycosylation sites.

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Date Created
  • 2013

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Efficiency-limiting recombination mechanisms in high-quality crystalline silicon for solar cells

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Recent technology advancements in photovoltaics have enabled crystalline silicon (c-Si) solar cells to establish outstanding photoconversion efficiency records. Remarkable progresses in research and development have been made both on the

Recent technology advancements in photovoltaics have enabled crystalline silicon (c-Si) solar cells to establish outstanding photoconversion efficiency records. Remarkable progresses in research and development have been made both on the silicon feedstock quality as well as the technology required for surface passivation, the two dominant sources of performance loss via recombination of photo-generated charge carriers within advanced solar cell architectures.

As these two aspects of the solar cell framework improve, the need for a thorough analysis of their respective contribution under varying operation conditions has emerged along with challenges related to the lack of sensitivity of available characterization techniques. The main objective of my thesis work has been to establish a deep understanding of both “intrinsic” and “extrinsic” recombination processes that govern performance in high-quality silicon absorbers. By studying each recombination mechanism as a function of illumination and temperature, I strive to identify the lifetime limiting defects and propose a path to engineer the ultimate silicon solar cell.

This dissertation presents a detailed description of the experimental procedure required to deconvolute surface recombination contributions from bulk recombination contributions when performing lifetime spectroscopy analysis. This work proves that temperature- and injection-dependent lifetime spectroscopy (TIDLS) sensitivity can be extended to impurities concentrations down to 109 cm-3, orders of magnitude below any other characterization technique available today. A new method for the analysis of TIDLS data denominated Defect Parameters Contour Mapping (DPCM) is presented with the aim of providing a visual and intuitive tool to identify the lifetime limiting impurities in silicon material. Surface recombination velocity results are modelled by applying appropriate approaches from literature to our experimentally evaluated data, demonstrating for the first time their capability to interpret temperature-dependent data. In this way, several new results are obtained which solve long disputed aspects of surface passivation mechanisms. Finally, we experimentally evaluate the temperature-dependence of Auger lifetime and its impact on a theoretical intrinsically limited solar cell. These results decisively point to the need for a new Auger lifetime parameterization accounting for its temperature-dependence, which would in turn help understand the ultimate theoretical efficiency limit for a solar cell under real operation conditions.

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Date Created
  • 2018