ANALYSIS AND VISUALIZATION OF FLOW FIELDS USING INFORMATION-THEORETIC TECHNIQUES AND GRAPH-BASED REPRESENTATIONS

Three-dimensional flow visualization plays an essential role in many areas of science and engineering, such as aero- and hydro-dynamical systems which dominate various physical and natural phenomena. For popular methods such as the streamline visualization to be effective, they should capture the underlying flow features while facilitating user observation and understanding of the flow field in a clear manner. My research mainly focuses on the analysis and visualization of flow fields using various techniques, e.g. information-theoretic techniques and graph-based representations. Since the streamline visualization is a popular technique in flow field visualization, how to select good streamlines to capture flow patterns and how to pick good viewpoints to observe flow fields become critical. We treat streamline selection and viewpoint selection as symmetric problems and solve them simultaneously using the dual information channel [81]. To the best of my knowledge, this is the first attempt in flow visualization to combine these two selection problems in a unified approach. This work selects streamline in a view-independent manner and the selected streamlines will not change for all viewpoints. My another work [56] uses an information-theoretic approach to evaluate the importance of each streamline under various sample viewpoints and presents a solution for view-dependent streamline selection that guarantees coherent streamline update when the view changes gradually. When projecting 3D streamlines to 2D images for viewing, occlusion and clutter become inevitable. To address this challenge, we design FlowGraph [57, 58], a novel compound graph representation that organizes field line clusters and spatiotemporal regions hierarchically for occlusion-free and controllable visual exploration. We enable observation and exploration of the relationships among field line clusters, spatiotemporal regions and their interconnection in the transformed space. Most viewpoint selection methods only consider the external viewpoints outside of the flow field. This will not convey a clear observation when the flow field is clutter on the boundary side. Therefore, we propose a new way to explore flow fields by selecting several internal viewpoints around the flow features inside of the flow field and then generating a B-Spline curve path traversing these viewpoints to provide users with closeup views of the flow field for detailed observation of hidden or occluded internal flow features [54]. This work is also extended to deal with unsteady flow fields. Besides flow field visualization, some other topics relevant to visualization also attract my attention. In iGraph [31], we leverage a distributed system along with a tiled display wall to provide users with high-resolution visual analytics of big image and text collections in real time. Developing pedagogical visualization tools forms my other research focus. Since most cryptography algorithms use sophisticated mathematics, it is difficult for beginners to understand both what the algorithm does and how the algorithm does that. Therefore, we develop a set of visualization tools to provide users with an intuitive way to learn and understand these algorithms.

Climatological study of transport to the PICO-NARE site using atmospheric backward trajectories

This study developed a transport climatology to the PICO-NARE station, in the central North Atlantic Ocean, using a 40-year set of atmospheric back trajectories. The trajectory set was subjected to a cluster analysis in order to group trajectories into six flow patterns, or clusters. An air flow probability analysis was conducted in conjunction with the cluster analysis in order to determine the source regions for flow to the site. Seasonal differences in the flow patterns were found, which included enhanced westerly flow in the winter, decreased westerly flow in the summer, and spring and fall having moderate westerly flow. The North Atlantic Oscillation had a significant impact on the winter and fall seasons and less significant impacts during spring and summer. The results of the climatology can be used in conjunction with measurements of ozone, CO, NOx, and NOy, which are currently being measured at the site, to develop a long-term, seasonal climatology of transport of pollutants to the central North Atlantic.

Recurrent voluminous sector collapses at Volcán Barú, Panama

Two volcanic debris avalanche deposits (VDADs), both attributed to sector collapse at Volcán Barú, Panama, have been identified after an investigation of deposits that covered more than a thousand square kilometers. The younger Barriles Deposit is constrained by two radiocarbon ages that are ~9 ka; the older Caisán Deposit is at or beyond the radiocarbon range, >43,500 ybp. The total runout length of the Caisán Deposit was ~50 km and it covers 1190 km2. The Barriles Deposit extended to about 45 km and covered an area of 966 km2, overlapping most of the Caisán. The VDADs are blanketed by pyroclastic deposits and contain a predominance of andesitic material likely representing volcanic dome rock which accumulated above the active vent at Barú before collapsing. Despite heavy vegetation in the field area, over 4000 individual hummocks were digitized from aerial photography. Statistical analysis of hummock locations and geometries depict flow patterns of highly- fragmented material reflecting the effects of underlying topography and also help to define the limit of Barriles’ shorter termination. Barriles and Caisán are primarily unconfined, subaerial volcanic deposits that are among the world’s most voluminous. Calculated through two different geospatial processes, thickness values from field measurements and inferences yield volumes >30 km23 for both deposits. VDADs of comparable scale come from Mount Shasta, USA; Socompa, Chile/Argentina; and Shiveluch, Russia. Currently, the modern edifice is 200-400m lower than the pre-collapse Barriles and Caisán summits and only 16-25% of the former edifice has been replaced since the last failure.

DEVELOPMENT AND APPLICATIONS OF GENOMIC RESOURCES FOR TWO NORTH AMERICAN HARDWOOD TAXA

Hardwoods comprise about half of the biomass of forestlands in North America and present many uses including economic, ecological and aesthetic functions. Forest trees rely on the genetic variation within tree populations to overcome the many biotic, abiotic, anthropogenic factors which are further worsened by climate change, that threaten their continued survival and functionality. To harness these inherent genetic variations of tree populations, informed knowledge of the genomic resources and techniques, which are currently lacking or very limited, are imperative for forest managers. The current study therefore aimed to develop genomic microsatellite markers for the leguminous tree species, honey locust, Gleditsia triacanthos L. and test their applicability in assessing genetic variation, estimation of gene flow patterns and identification of a full-sib mapping population. We also aimed to test the usefulness of already developed nuclear and gene-based microsatellite markers in delineation of species and taxonomic relationships between four of the taxonomically difficult Section Lobatae species (Quercus coccinea, Q. ellipsoidalis, Q. rubra and Q. velutina. We recorded 100% amplification of G. triacanthos genomic microsatellites developed using Illumina sequencing techniques in a panel of seven unrelated individuals with 14 of these showing high polymorphism and reproducibility. When characterized in 36 natural population samples, we recorded 20 alleles per locus with no indication for null alleles at 13 of the 14 microsatellites. This is the first report of genomic microsatellites for this species. Honey locust trees occur in fragmented populations of abandoned farmlands and pastures and is described as essentially dioecious. Pollen dispersal if the main source of gene flow within and between populations with the ability to offset the effects of random genetic drift. Factors known to influence gene include fragmentation and degree of isolation, which make the patterns gene flow in fragmented populations of honey locust a necessity for their sustainable management. In this follow-up study, we used a subset of nine of the 14 developed gSSRs to estimate gene flow and identify a full-sib mapping population in two isolated fragments of honey locust. Our analyses indicated that the majority of the seedlings (65-100% - at both strict and relaxed assignment thresholds) were sired by pollen from outside the two fragment populations. Only one selfing event was recorded confirming the functional dioeciousness of honey locust and that the seed parents are almost completely outcrossed. From the Butternut Valley, TN population, pollen donor genotypes were reconstructed and used in paternity assignment analyses to identify a relatively large full-sib family comprised of 149 individuals, proving the usefulness of isolated forest fragments in identification of full-sib families. In the Ames Plantation stand, contemporary pollen dispersal followed a fat-tailed exponential-power distribution, an indication of effective gene flow. Our estimate of δ was 4,282.28 m, suggesting that insect pollinators of honey locust disperse pollen over very long distances. The high proportion of pollen influx into our sampled population implies that our fragment population forms part of a large effectively reproducing population. The high tendency of oak species to hybridize while still maintaining their species identity make it difficult to resolve their taxonomic relationships. Oaks of the section Lobatae are famous in this regard and remain unresolved at both morphological and genetic markers. We applied 28 microsatellite markers including outlier loci with potential roles in reproductive isolation and adaptive divergence between species to natural populations of four known interfertile red oaks, Q. coccinea, Q. ellpsoidalis, Q. rubra and Q. velutina. To better resolve the taxonomic relationships in this difficult clade, we assigned individual samples to species, identified hybrids and introgressive forms and reconstructed phylogenetic relationships among the four species after exclusion of genetically intermediate individuals. Genetic assignment analyses identified four distinct species clusters, with Q. rubra most differentiated from the three other species, but also with a comparatively large number of misclassified individuals (7.14%), hybrids (7.14%) and introgressive forms (18.83%) between Q. ellipsoidalis and Q. velutina. After the exclusion of genetically intermediate individuals, Q. ellipsoidalis grouped as sister species to the largely parapatric Q. coccinea with high bootstrap support (91 %). Genetically intermediate forms in a mixed species stand were located proximate to both potential parental species, which supports recent hybridization of Q. velutina with both Q. ellipsoidalis and Q. rubra. Analyses of genome-wide patterns of interspecific differentiation can provide a better understanding of speciation processes and taxonomic relationships in this taxonomically difficult group of red oak species.

Stilling Basin Scour Remediation Using Air Injection and Flat Plate Extension

The South Florida Water Management District (SFWMD) is responsible for managing over 2500 miles of waterways and hundreds of water control structures. Many of these control structures are experiencing erosion, known as scour, of the sediment downstream of the structure. Laboratory experiments were conducted in order to investigate the effectiveness of two-dimensional air diffusers and plate extensions (without air injection) on a 1/30 scale model of one of SFWMD gated spillway structures, the S65E gated spillway. A literature review examining the results of similar studies was conducted. The experimental design for this research was based off of previous work done on the same model. Scour of the riverbed downstream of gated spillway structures has the potential to cause serious damage, as it can expose the foundation of the structure, which can lead to collapse. This type of scour has been studied previously, but it continues to pose a risk to water control structures and needs to be studied further. The hydraulic scour channel used to conduct experiments contains a head tank, flow straighteners, gated spillway, stilling basin, scour chamber, sediment trap, and tailwater tank. Experiments were performed with two types of air diffusers. The first was a hollow, acrylic, triangular end sill with air injection holes on the upstream face, allowing for air injection upstream. The second diffuser was a hollow, acrylic rectangle that extended from the triangular end sill with air injection holes in the top face, allowing for vertical air injection, perpendicular to flow. Detailed flow and bed measurements were taken for six trials for each diffuser ranging from no air injection to 5 rows of 70 holes of 0.04" diameter. It was found that with both diffusers, the maximum amount of air injection reduced scour the most. Detailed velocity measurements were taken for each case and turbulence statistics were analyzed to determine why air injection reduces scour. It was determined that air injection reduces streamwise velocity and turbulence. Another set of experiments was performed using an acrylic extension plate with no air injection to minimize energy costs. Ten different plate lengths were tested. It was found that the location of deepest scour moved further downstream with each plate length. The 32-cm plate is recommended here. Detailed velocity measurements were taken after the cases with the 32-cm plate and no plate had reached equilibrium. This was done to better understand the flow patterns in order to determine what causes the scour reduction with the extension plates. The extension plate reduces the volume of scour, but more importantly translates the deepest point of scour downstream from the structure, lessening the risk of damage.

A REMOTE SENSING APPROACH TO CHARACTERIZE THE HYDROGEOLOGY OF MOUNTAINOUS AREAS: APPLICATION TO THE QUITO AQUIFER SYSTEM (QAS), ECUADOR

Climate change, intensive use, and population growth are threatening the availability of water resources. New sources of water, better knowledge of existing ones, and improved water management strategies are of paramount importance. Ground water is often considered as primary water source due to its advantages in terms of quantity, spatial distribution, and natural quality. Remote sensing techniques afford scientists a unique opportunity to characterize landscapes in order to assess groundwater resources, particularly in tectonically influenced areas. Aquifers in volcanic basins are considered the most productive aquifers in Latin America. Although topography is considered the primary driving force for groundwater flows in mountainous terrains, tectonic activity increases the complexity of these groundwater systems by altering the integrity of sedimentary rock units and the overlying drainage networks. Structural controls affect the primary hydraulic properties of the rock formations by developing barriers to flow in some cases and zones of preferential infiltration and subterranean in others. The study area focuses on the Quito Aquifer System (QAS) in Ecuador. The characterization of the hydrogeology started with a lineament analysis based on a combined remote sensing and digital terrain analysis approach. The application of classical tools for regional hydrogeological evaluation and shallow geophysical methods were useful to evaluate the impact of faulting and fracturing on the aquifer system. Given the spatial extension of the area and the complexity of the system, two levels of analysis were applied in this study. At the regional level, a lineament map was created for the QAS. Relationships between fractures, faults and lineaments and the configuration of the groundwater flow on the QAS were determined. At the local level, on the Plateaus region of the QAS, a detailed lineament map was obtained by using high-spatial-resolution satellite imagery and aspect map derived from a digital elevation model (DEM). This map was complemented by the analysis of morphotectonic indicators and shallow geophysics that characterize fracture patterns. The development of the groundwater flow system was studied, drawing upon data pertaining to the aquifer system physical characteristics and topography. Hydrochemistry was used to ascertain the groundwater evolution and verify the correspondence of the flow patterns proposed in the flow system analysis. Isotopic analysis was employed to verify the origin of groundwater. The results of this study show that tectonism plays a very important role for the hydrology of the QAS. The results also demonstrate that faults influence a great deal of the topographic characteristics of the QAS and subsequently the configuration of the groundwater flow. Moreover, for the Plateaus region, the results demonstrate that the aquifer flow systems are affected by secondary porosity. This is a new conceptualization of the functioning of the aquifers on the QAS that will significantly contribute to the development of better strategies for the management of this important water resource.

Speciation with gene-flow in eastern North American red oaks (Quercus section Lobatae)

As foundational species, oaks (Quercus : Fagaceae) support the activities of both humans and wildlife. However, many oaks in North America are declining, a crisis exacerbated by the previous disappearance of other hard mast-producing trees. In addition, the economic demands placed on this drought-tolerant group may intensify if climate change extirpates other, relatively mesophytic species. Genetic tools can help address these management challenges. To this end, we developed a suite of 27 microsatellite markers, of which 22 are derived from expressed sequence tags (ESTs). Many of these markers bear significant homology to known genes and may be able to directly assay functional genetic variation. Markers obtained from enriched microsatellite libraries, on the other hand, are typically located in heterochromatic regions and should reflect demographic processes. Considered jointly, genic and genomic microsatellites can elucidate patterns of gene-flow and natural selection, which are fundamental to both an organism's evolutionary ecology and conservation biology. To this end, we employed the developed markers in an FST-based genome scan to detect the signature of divergent selection among the red oaks (Quercus section Lobatae). Three candidate genes with putative roles in stress responses demonstrated patterns of diversity consistent with adaptation to heterogeneous selective pressures. These genes may be important in both local genetic adaptation within species and divergence among them. Next, we used an isolation-with-migration model to quantify levels of gene-flow among four red oaks species during speciation. Both speciation in allopatry and speciation with gene-flow were found to be major drivers of red oak biodiversity. Loci playing a key role in speciation are also likely to be ecologically important within species