A detailed study of modern washover fan (fan) morphologies will clarify common fan geometries, lead to a better model for a “typical” fan, identify the preservation potential and probable geometries of fan facies in subsurface datasets and outcrops, and ultimately improve hydrocarbon recovery in barrier island reservoir systems. This study uses satellite imagery to conduct a spatial analysis of 118 modern fans to quantify geomorphologic attributes of fans. A new classification scheme for fans is proposed that refines the current fan model, dividing fans into channelized and non-channelized fans. Channelized fans are subdivided according to the location of primary deposition: barrier depo-center or lagoonal depo-center. Non-channelized fans are subdivided based on morphology: dissipative, lobate, or apron-sourced. Quantitative cross-plots of morphologic relationships are analyzed to define trends in fan morphologies. The most common type of fan encountered in our study is a non-channelized, line-sourced, lobate washover fan with an area of less than 1 km2 that is fully contained on a barrier and exhibits no subaqueous deposition in back-barrier waters. The Lower Cretaceous McMurray Formation is the primary reservoir of the Athabasca Oil Sands in Alberta, Canada. The upper McMurray is commonly interpreted as deposits of embayed coastal systems. Our location is in an under-studied area located 80 km northwest of Fort McMurray. Lateral and vertical facies changes, sedimentary structures, key surfaces, trace fossils, and bitumen saturation were documented in eight cores located along a 20 km transect situated paleo-landward of a Devonian paleo-high acting as a bedrock-barrier. Our data indicate that a flood tidal delta complex prograded landward into a back-barrier embayment through the stable, bedrock-controlled inlet. This system overlies middle McMurray fluvial sands and Devonian basement and was transgressed by marine waters prior to deposition of the overlying Wabiskaw Formation. Flood tidal delta sandbodies are bitumen saturated and therefore make good reservoirs; however, heavily bioturbated tidal flats can act as a barrier to flow where they encase flood tidal deltas, as encased sands were devoid of bitumen. This complex coastal paleogeography produced back-barrier deposits that contain a slightly more diverse, marine trace fossil assemblage than might otherwise be expected. / text

Cilia are evolutionarily conserved microtubule-based organelles projecting from nearly all vertebrate cells, and ciliary defects result in a variety of human disorders known as ciliopathies. Recent studies have shown that several planar cell polarity (PCP) proteins are essential for cilia functions. Here, we focused on Fritz, known as a novel PCP effector protein in Drosophila, in multi-ciliated cells in the epidermis of Xenopus laevis embryos. To investigate the role of Fritz, using confocal and scanning electron microscopy, we discovered that Fritz localizes along the ciliary axonemes and that knockdown of Fritz causes severe reductions in both axoneme length and number. Then, using pull-downs and mass-spectrometry, we identified Chaperonin Containing T-complex polypeptide 1 (CCT) and septin as interacting partners of Fritz. CCT is the key chaperonin interacting with septins, and both have been implicated in ciliogenesis. Using tagged CCT subunit constructs, we found that the tagged CCTα and CCTε co-localize with Fritz along the ciliary axonemes of multi-ciliated cells. Knockdown of Fritz resulted in the accumulation of CCT at the apical cytoplasm of multi-ciliated cells; however, it was confirmed that Fritz does not affect the CCT holoenzyme assembly. Septins, another interacting partner of Fritz, are novel cytoskeletal elements. Using septin antibodies, we found that endogenous septins also localize along the ciliary axonemes and accumulate in the apical cytoplasm of multi-ciliated cells in Fritz morphants. Similar ciliary defects were observed in septin morphants. Our results reveal that Fritz is essential for ciliogenesis, and that CCT and septin interact with Fritz to control ciliogenesis in Xenopus multi-ciliated cells. Additionally, tubulin acetylation is markedly reduced by Fritz knockdown, suggesting that Fritz affects tubulin acetylation.

The packing density of microelectronic devices has increased exponentially over the past four decades. Continuous enhancements in device performance and functionality have been achieved by the introduction of new materials and fabrication techniques. This thesis summarizes the thin film materials and metallization processes by chemical vapor deposition (CVD) developed during my graduate study with Professor Gordon at Harvard University. These materials and processes have the potential to build future generations of microelectronic devices with higher speeds and longer lifetimes. Manganese Silicate Diffusion Barrier: Highly conformal, amorphous and insulating manganese silicate \((MnSi_xO_y)\) layers are formed along the walls of trenches in interconnects by CVD using a manganese amidinate precursor vapor that reacts with the surfaces of the insulators. These \((MnSi_xO_y)\) layers are excellent barriers to diffusion of copper, oxygen and water. Manganese Capping Layer: A selective CVD manganese capping process strengthens the interface between copper and dielectric insulators to improve the electromigration reliability of the interconnects. High selectivity is achieved by deactivating the insulator surfaces using vapors containing reactive methylsilyl groups. Manganese at the Cu/insulator interface greatly increases the strength of adhesion between the copper and the insulator. Bottom-up Filling of Copper and Alloy in Narrow Features: Narrow trenches, with widths narrow than 30 nm and aspect ratios up to 9:1, can be filled with copper or copper-manganese alloy in a bottom-up fashion using a surfactant-catalyzed CVD process. A conformal manganese nitride \((Mn_4N)\) layer serves as a diffusion barrier and adhesion layer. Iodine atoms chemisorb on the \(Mn_4N\) layer and are then released to act as a catalytic surfactant on the surface of the growing copper layer to achieve void-free, bottom-up filling. Upon post-annealing, manganese in the alloy diffuses out from the copper and forms a self-aligned barrier in the surface of the insulator. Conformal Seed Layers for Plating Through-Silicon Vias: Through-silicon vias (TSV) will speed up interconnections between chips. Conformal, smooth and continuous seed layers in TSV holes with aspect ratios greater than 25:1 can be prepared using vapor deposition techniques. \(Mn_4N\) is deposited conformally on the silica surface by CVD to provide strong adhesion at Cu/insulator interface. Conformal copper or Cu-Mn alloy seed layers are then deposited by an iodine-catalyzed direct-liquid-injection (DLI) CVD process. / Chemistry and Chemical Biology

Polymers films and membranes with immobile and irreversible reactive sites can provide significant barrier properties for packaging materials. There is a need to develop mathematical models to understand the behavior of these reactive materials and to confidently extrapolate experimental data. Due to mechanical and optical requirements, barrier films may consist of composites, such as polymer blends and multilayer films with alternating reactive and inert layers. The reactive term that consumes the mobile species in the governing transport equations for such materials is a function of both the mobile species and the immobilized reactive sites, leading to non-linear partial differential equations that typically have to be solved numerically. Composite structures add to the complexity of the model. For the polymer blend, a multiscale model was developed, incorporating the reactive details within the particle into the bulk transport equation. For the multilayer film, initial conditions and diffusion coefficients were assigned independently for reactive or inert layers. The models developed for the three configurations were solved numerically over a wide parameter space. Three regimes were identified, namely early times characterized by an initial flux plateau, and intermediate regime, and long times, characterized by the time lag. Asymptotic analysis of the homogeneous model was used to develop analytical predictions for the three regimes, obviating the need to numerically solve the model’s non-linear equations. These predictions were generalized to polymer blends. For multilayer films, predictions for early and long times were developed. Results for polymer blends and multilayer composites were compared and discussions of the most suitable configuration for different scenarios were presented. The reactive barrier configurations studied require the knowledge of parameters such as reaction rates and coefficients of diffusion and solubility of the reactive polymer. Model and predictive equations have been developed to describe the transient mass uptake in reactive homogeneous films, enabling the extraction of these parameters from sorption experiments. / text

Utilization of amorphous metallic alloy has received much attention for use in numerous microelectronic and electrochemical devices since they provide unique electrical, thermal conductivity, and magnetic properties. To develop these functional properties, it is essential to understand the amorphous structure and the property relationships. First principles calculations provide insight into the structure, thermodynamic stability, electronic and magnetic properties of amorphous alloys. For Ru- and Co-based alloys, the thermodynamic stability was examined by calculating the mixing energy along with those of crystalline counterparts. The amorphous RuP, CoP, RuB, and CoB alloys, become energetically more favorable than their crystalline counterparts at moderate P(B) content. The atomistic structures have well-defined local structures depending on the atomic size ratio and electronic interactions between constituent elements. Their local ordering is attributed to strong p-d hybridization, which contributes to stabilizing the Ru(Co)-P(B) alloys. Surface segregation of P(B) and interfacial adhesion with copper were also studied. Li-X (X: Si, Ge, and Sn) were examined when 1 or 2 Li atoms are inserted into the interstitial sites. Li insertion in the tetrahedral site, which is the most preferable site in the diamond matrix, causes outward displacement and charge localization around the X neighbors, thereby weakening of the covalent bonds leading to destabilization of the host matrix. We present the energetics, structure, electronic and mechanical properties of crystalline and amorphous Li-X (X: Si, Ge, Sn, and Si+Sn) alloys. Our calculations show that the incorporation of Li leads to disintegration of the tetrahedrally-bonded X network into small clusters of various shapes. Electronic structure analysis highlights that the charge transfer leads to weakening or breaking of X bonds with the growing splitting between s and p states, and consequently the Li-X alloys softens with increasing Li content. / text

published_or_final_version / Architecture / Master / Master of Architecture

published_or_final_version / Architecture / Master / Master of Architecture

published_or_final_version / Physics / Doctoral / Doctor of Philosophy

The immune-reactive sperm are kept separate from the body by epithelial barriers such as the blood-testis barrier (BTB). While these barriers are beneficial for the protection of sperm from toxicants, they can make treating these areas difficult due to preventing the entry of pharmacological agents. This is especially an issue in the treatment of HIV and Ebola infection based on the ample evidence that these viruses are able to survive and spread from within the male genital tract (MGT), but only a few antiviral drugs are known to access the MGT. Transporters that line the epithelial barriers of the MGT, especially the BTB, are important for determining whether or not a drug is able to penetrate into the MGT through transepithelial transport. Several nucleoside analogs (NSA), which are used to treat HIV infection and leukemias, are known to be able to accumulate in seminal plasma, which makes them a useful tool for understanding transepithelial transport for the BTB. The purpose of these studies is to characterize the transport profile for the MGT, in particular the BTB, to gain a better understanding of how xenobiotics, especially ones based on nucleosides, can access the MGT. The chief finding of this work is the discovery of a transepithelial transport pathway expressed by Sertoli cells that allows for the entry of nucleosides (necessary for germ cell development) and NSA into the MGT. This pathway depends on equilibrative nucleoside transporter (ENT) 1 uptake and ENT2 efflux and occurs in both rats and humans. These studies provide the foundation for being able to predict the penetration of novel drugs into the MGT.

Habitat fragmentation and destruction caused by linear infrastructure, including roads, railways, and power line corridors, are recognized as major threats to biodiversity around the world. Roads can act as barriers by impeding animal movement and restricting animal space use. An understanding of factors that influence barrier effects is important to discern the impacts of habitat fragmentation and to develop appropriate mitigation. The barrier effects of roads are driven by several distinct but not mutually exclusive mechanisms that include traffic, edge, and gap avoidance. We used an endangered forest obligate, the Mount Graham red squirrel (Tamiasciurus hudsonicus grahamensis), as our study organism to assess effects of traffic noise on animal occurrence and demonstrated that traffic noise had spatially extensive and negative effects on site occupancy after accounting for effects of distance from roads and the environment. We investigated barrier effects of forest roads and assessed effects of traffic, road edges, and canopy gaps on space use of Mt. Graham red squirrels and compared to the response of introduced, edge-tolerant Abert's squirrels (Sciurus aberti). Forest roads acted as partial barriers for red squirrels regardless of traffic volume likely due to avoidance of canopy gap created by roads, whereas Abert's squirrels showed no avoidance of roads. Therefore, roads restricted movement and space use of a native forest-dependent species while creating habitat preferred by an introduced, edge-tolerated species. Through a meta-analysis of studies that quantified road crossing behavior by mammals, we found that all types of roads, from major highways to narrow forest roads, can impede movement for certain species of mammals. Magnitude of barrier effects of roads decreased as species body mass increased, and was affected positively by increasing road width. We suggest that the species-specific magnitude of barrier effects of roads may be anticipated with basic information from life history traits and road characteristics that are readily accessed through open resources or easily measured.