Lattice Boltzmann Modeling of Fluid Flow and Solute Transport in Karst Aquifers

A novel modeling approach is applied to karst hydrology. Long-standing problems in karst hydrology and solute transport are addressed using Lattice Boltzmann methods (LBMs). These methods contrast with other modeling approaches that have been applied to karst hydrology. The motivation of this dissertation is to develop new computational models for solving ground water hydraulics and transport problems in karst aquifers, which are widespread around the globe. This research tests the viability of the LBM as a robust alternative numerical technique for solving large-scale hydrological problems. The LB models applied in this research are briefly reviewed and there is a discussion of implementation issues. The dissertation focuses on testing the LB models. The LBM is tested for two different types of inlet boundary conditions for solute transport in finite and effectively semi-infinite domains. The LBM solutions are verified against analytical solutions. Zero-diffusion transport and Taylor dispersion in slits are also simulated and compared against analytical solutions. These results demonstrate the LBM’s flexibility as a solute transport solver. The LBM is applied to simulate solute transport and fluid flow in porous media traversed by larger conduits. A LBM-based macroscopic flow solver (Darcy’s law-based) is linked with an anisotropic dispersion solver. Spatial breakthrough curves in one and two dimensions are fitted against the available analytical solutions. This provides a steady flow model with capabilities routinely found in ground water flow and transport models (e.g., the combination of MODFLOW and MT3D). However the new LBM-based model retains the ability to solve inertial flows that are characteristic of karst aquifer conduits. Transient flows in a confined aquifer are solved using two different LBM approaches. The analogy between Fick’s second law (diffusion equation) and the transient ground water flow equation is used to solve the transient head distribution. An altered-velocity flow solver with source/sink term is applied to simulate a drawdown curve. Hydraulic parameters like transmissivity and storage coefficient are linked with LB parameters. These capabilities complete the LBM’s effective treatment of the types of processes that are simulated by standard ground water models. The LB model is verified against field data for drawdown in a confined aquifer.

Tool cutting force modeling and wear estimation of micro-end-milling operations

The applications of micro-end-milling operations have increased recently. A Micro-End-Milling Operation Guide and Research Tool (MOGART) package has been developed for the study and monitoring of micro-end-milling operations. It includes an analytical cutting force model, neural network based data mapping and forecasting processes, and genetic algorithms based optimization routines. MOGART uses neural networks to estimate tool machinability and forecast tool wear from the experimental cutting force data, and genetic algorithms with the analytical model to monitor tool wear, breakage, run-out, cutting conditions from the cutting force profiles. The performance of MOGART has been tested on the experimental data of over 800 experimental cases and very good agreement has been observed between the theoretical and experimental results. The MOGART package has been applied to the micro-end-milling operation study of Engineering Prototype Center of Radio Technology Division of Motorola Inc.

A Modeling Approach to Determine the Impacts of Land Use and Climate Change Scenarios on the Water Flux of the Upper Mara River

With the flow of the Mara River becoming increasingly erratic especially in the upper reaches, attention has been directed to land use change as the major cause of this problem. The semi-distributed hydrological model Soil and Water Assessment Tool 5 (SWAT) and Landsat imagery were utilized in the upper Mara River Basin in order to 1) map existing field scale land use practices in order to determine their impact 2) determine the impacts of land use change on water flux; and 3) determine the impacts of rainfall (0%, ±10% and ±20%) and air temperature variations (0% and +5%) based on the Intergovernmental Panel on Climate Change projections on the water flux of the 10 upper Mara River. This study found that the different scenarios impacted on the water balance components differently. Land use changes resulted in a slightly more erratic discharge while rainfall and air temperature changes had a more predictable impact on the discharge and water balance components. These findings demonstrate that the model results 15 show the flow was more sensitive to the rainfall changes than land use changes. It was also shown that land use changes can reduce dry season flow which is the most important problem in the basin. The model shows also deforestation in the Mau Forest increased the peak flows which can also lead to high sediment loading in the Mara River. The effect of the land use and climate change scenarios on the sediment and 20 water quality of the river needs a thorough understanding of the sediment transport processes in addition to observed sediment and water quality data for validation of modeling results.

Sediment and pore water data of five cores from the continental slope off Uruguay

Assessing frequency and extent of mass movement at continental margins is crucial to evaluate risks for offshore constructions and coastal areas. A multidisciplinary approach including geophysical, sedimentological, geotechnical, and geochemical methods was applied to investigate multistage mass transport deposits (MTDs) off Uruguay, on top of which no surficial hemipelagic drape was detected based on echosounder data. Nonsteady state pore water conditions are evidenced by a distinct gradient change in the sulfate (SO4**2-) profile at 2.8 m depth. A sharp sedimentological contact at 2.43 m coincides with an abrupt downward increase in shear strength from approx. 10 to >20 kPa. This boundary is interpreted as a paleosurface (and top of an older MTD) that has recently been covered by a sediment package during a younger landslide event. This youngest MTD supposedly originated from an upslope position and carried its initial pore water signature downward. The kink in the SO4**2- profile approx. 35 cm below the sedimentological and geotechnical contact indicates that bioirrigation affected the paleosurface before deposition of the youngest MTD. Based on modeling of the diffusive re-equilibration of SO4**2- the age of the most recent MTD is estimated to be <30 years. The mass movement was possibly related to an earthquake in 1988 (approx. 70 km southwest of the core location). Probabilistic slope stability back analysis of general landslide structures in the study area reveals that slope failure initiation requires additional ground accelerations. Therefore, we consider the earthquake as a reasonable trigger if additional weakening processes (e.g., erosion by previous retrogressive failure events or excess pore pressures) preconditioned the slope for failure. Our study reveals the necessity of multidisciplinary approaches to accurately recognize and date recent slope failures in complex settings such as the investigated area.

Seismic reflection data, calcium/iron ratios, stable istopes, and magnetic susceptibility of sediment cores from the Pen Duick Escarpment, Gulf of Cadiz

Here we present a case study of three cold-water coral mounds in a juvenile growth stage on top of the Pen Duick Escarpment in the Gulf of Cadiz; Alpha, Beta and Gamma mounds. Although cold-water corals are a common feature on the adjacent cliffs, mud volcanoes and open slope, no actual living cold-water coral has been observed. This multidisciplinary and integrated study comprises geophysical, sedimentological and (bio)geochemical data and aims to present a holistic view on the interaction of both environmental and geological drivers in cold-water coral mound development in the Gulf of Cadiz. Coring data evidences (past or present) methane seepage near the Pen Duick Escarpment. Several sources and pathways are proposed, among which a stratigraphic migration through uplifted Miocene series underneath the escarpment. The dominant morphology of the escarpment has influenced the local hydrodynamics within the course of the Pliocene, as documented by the emplacement of a sediment drift. Predominantly during post-Middle Pleistocene glacial episodes, favourable conditions were present for mound growth. An additional advantage for mound formation near the top of Pen Duick Escarpment is presented by seepage-related carbonate crusts which might have offered a suitable substrate for coral settling. The spatially and temporally variable character and burial stage of the observed open reef frameworks, formed by cold-water coral rubble, provides a possible model for the transition from cold-water coral reef patches towards juvenile mound. These rubble "graveyards" not only act as sediment trap but also as micro-habitat for a wide range of organisms. The presence of a fluctuating Sulphate-Methane Transition Zone has an important effect on early diagenetic processes, affecting both geochemical and physical characteristics, transforming the buried reef into a solid mound. Nevertheless, the responsible seepage fluxes seem to be locally variable. As such, the origin and evolution of the cold-water coral mounds on top of the Pen Duick Escarpment is, probably more than any other NE Atlantic cold-water coral mound province, located on the crossroads of environmental (hydrodynamic) and geological (seepage) pathways.

Seawater carbonate chemistry and processes during experiments with Emiliania huxleyi, 2008

Ocean acidification in response to rising atmospheric CO2 partial pressures is widely expected to reduce calcification by marine organisms. From the mid-Mesozoic, coccolithophores have been major calcium carbonate producers in the world's oceans, today accounting for about a third of the total marine CaCO3 production. Here, we present laboratory evidence that calcification and net primary production in the coccolithophore species Emiliania huxleyi are significantly increased by high CO2 partial pressures. Field evidence from the deep ocean is consistent with these laboratory conclusions, indicating that over the past 220 years there has been a 40% increase in average coccolith mass. Our findings show that coccolithophores are already responding and will probably continue to respond to rising atmospheric CO2 partial pressures, which has important implications for biogeochemical modeling of future oceans and climate.

Multi-impurity adsorption model for modeling crystal purity and shape evolution during crystallization processes in impure media

Peer reviewed

Mathematical Modeling of Perifusion Cell Culture Experiments

In perifusion cell cultures, the culture medium flows continuously through a chamber containing immobilized cells and the effluent is collected at the end. In our main applications, gonadotropin releasing hormone (GnRH) or oxytocin is introduced into the chamber as the input. They stimulate the cells to secrete luteinizing hormone (LH), which is collected in the effluent. To relate the effluent LH concentration to the cellular processes producing it, we develop and analyze a mathematical model consisting of coupled partial differential equations describing the intracellular signaling and the movement of substances in the cell chamber. We analyze three different data sets and give cellular mechanisms that explain the data. Our model indicates that two negative feedback loops, one fast and one slow, are needed to explain the data and we give their biological bases. We demonstrate that different LH outcomes in oxytocin and GnRH stimulations might originate from different receptor dynamics. We analyze the model to understand the influence of parameters, like the rate of the medium flow or the fraction collection time, on the experimental outcomes. We investigate how the rate of binding and dissociation of the input hormone to and from its receptor influence its movement down the chamber. Finally, we formulate and analyze simpler models that allow us to predict the distortion of a square pulse due to hormone-receptor interactions and to estimate parameters using perifusion data. We show that in the limit of high binding and dissociation the square pulse moves as a diffusing Gaussian and in this limit the biological parameters can be estimated.

Elucidating the Space-Time Structure of Low Level Warm Season Precipitation Processes in the Southern Appalachian Mountains Using Models and Observations

Light rainfall is the baseline input to the annual water budget in mountainous landscapes through the tropics and at mid-latitudes. In the Southern Appalachians, the contribution from light rainfall ranges from 50-60% during wet years to 80-90% during dry years, with convective activity and tropical cyclone input providing most of the interannual variability. The Southern Appalachians is a region characterized by rich biodiversity that is vulnerable to land use/land cover changes due to its proximity to a rapidly growing population. Persistent near surface moisture and associated microclimates observed in this region has been well documented since the colonization of the area in terms of species health, fire frequency, and overall biodiversity. The overarching objective of this research is to elucidate the microphysics of light rainfall and the dynamics of low level moisture in the inner region of the Southern Appalachians during the warm season, with a focus on orographically mediated processes. The overarching research hypothesis is that physical processes leading to and governing the life cycle of orographic fog, low level clouds, and precipitation, and their interactions, are strongly tied to landform, land cover, and the diurnal cycles of flow patterns, radiative forcing, and surface fluxes at the ridge-valley scale. The following science questions will be addressed specifically: 1) How do orographic clouds and fog affect the hydrometeorological regime from event to annual scale and as a function of terrain characteristics and land cover?; 2) What are the source areas, governing processes, and relevant time-scales of near surface moisture convergence patterns in the region?; and 3) What are the four dimensional microphysical and dynamical characteristics, including variability and controlling factors and processes, of fog and light rainfall? The research was conducted with two major components: 1) ground-based high-quality observations using multi-sensor platforms and 2) interpretive numerical modeling guided by the analysis of the in situ data collection. Findings illuminate a high level of spatial – down to the ridge scale - and temporal – from event to annual scale - heterogeneity in observations, and a significant impact on the hydrological regime as a result of seeder-feeder interactions among fog, low level clouds, and stratiform rainfall that enhance coalescence efficiency and lead to significantly higher rainfall rates at the land surface. Specifically, results show that enhancement of an event up to one order of magnitude in short-term accumulation can occur as a result of concurrent fog presence. Results also show that events are modulated strongly by terrain characteristics including elevation, slope, geometry, and land cover. These factors produce interactions between highly localized flows and gradients of temperature and moisture with larger scale circulations. Resulting observations of DSD and rainfall patterns are stratified by region and altitude and exhibit clear diurnal and seasonal cycles.

A Molecular-scale Programmable Stochastic Process Based On Resonance Energy Transfer Networks: Modeling And Applications

While molecular and cellular processes are often modeled as stochastic processes, such as Brownian motion, chemical reaction networks and gene regulatory networks, there are few attempts to program a molecular-scale process to physically implement stochastic processes. DNA has been used as a substrate for programming molecular interactions, but its applications are restricted to deterministic functions and unfavorable properties such as slow processing, thermal annealing, aqueous solvents and difficult readout limit them to proof-of-concept purposes. To date, whether there exists a molecular process that can be programmed to implement stochastic processes for practical applications remains unknown.

In this dissertation, a fully specified Resonance Energy Transfer (RET) network between chromophores is accurately fabricated via DNA self-assembly, and the exciton dynamics in the RET network physically implement a stochastic process, specifically a continuous-time Markov chain (CTMC), which has a direct mapping to the physical geometry of the chromophore network. Excited by a light source, a RET network generates random samples in the temporal domain in the form of fluorescence photons which can be detected by a photon detector. The intrinsic sampling distribution of a RET network is derived as a phase-type distribution configured by its CTMC model. The conclusion is that the exciton dynamics in a RET network implement a general and important class of stochastic processes that can be directly and accurately programmed and used for practical applications of photonics and optoelectronics. Different approaches to using RET networks exist with vast potential applications. As an entropy source that can directly generate samples from virtually arbitrary distributions, RET networks can benefit applications that rely on generating random samples such as 1) fluorescent taggants and 2) stochastic computing.

By using RET networks between chromophores to implement fluorescent taggants with temporally coded signatures, the taggant design is not constrained by resolvable dyes and has a significantly larger coding capacity than spectrally or lifetime coded fluorescent taggants. Meanwhile, the taggant detection process becomes highly efficient, and the Maximum Likelihood Estimation (MLE) based taggant identification guarantees high accuracy even with only a few hundred detected photons.

Meanwhile, RET-based sampling units (RSU) can be constructed to accelerate probabilistic algorithms for wide applications in machine learning and data analytics. Because probabilistic algorithms often rely on iteratively sampling from parameterized distributions, they can be inefficient in practice on the deterministic hardware traditional computers use, especially for high-dimensional and complex problems. As an efficient universal sampling unit, the proposed RSU can be integrated into a processor / GPU as specialized functional units or organized as a discrete accelerator to bring substantial speedups and power savings.

Role of Vinculin in Regulating Force-Sensitive Dynamics of Adherens Junctions During Collective Cell Migration

Dynamic processes such as morphogenesis and tissue patterning require the precise control of many cellular processes, especially cell migration. Historically, these processes are thought to be mediated by genetic and biochemical signaling pathways. However, recent advances have unraveled a previously unappreciated role of mechanical forces in regulating these homeostatic processes in of multicellular systems. In multicellular systems cells adhere to both deformable extracellular matrix (ECM) and other cells, which are sources of applied forces and means of mechanical support. Cells detect and respond to these mechanical signals through a poorly understood process called mechanotransduction, which can have profound effects on processes such as cell migration. These effects are largely mediated by the sub cellular structures that link cells to the ECM, called focal adhesions (FAs), or cells to other cells, termed adherens junctions (AJs).

Overall this thesis is comprised of my work on identifying a novel force dependent function of vinculin, a protein which resides in both FAs and AJs - in dynamic process of collective migration. Using a collective migration assay as a model for collective cell behavior and a fluorescence resonance energy transfer (FRET) based molecular tension sensor for vinculin I demonstrated a spatial gradient of tension across vinculin in the direction of migration. To define this novel force-dependent role of vinculin in collective migration I took advantage of previously established shRNA based vinculin knock down Marin-Darby Canine Kidney (MDCK) epithelial cells.

The first part of my thesis comprises of my work demonstrating the mechanosensitive role of vinculin at AJ’s in collectively migrating cells. Using vinculin knockdown cells and vinculin mutants, which specifically disrupt vinculin’s ability to bind actin (VinI997A) or disrupt its ability to localize to AJs without affecting its localization at FAs (VinY822F), I establish a role of force across vinculin in E-cadherin internalization and clipping. Furthermore by measuring E-cadherin dynamics using fluorescence recovery after bleaching (FRAP) analysis I show that vinculin inhibition affects the turnover of E-cadherin at AJs. Together these data reveal a novel mechanosensitive role of vinculin in E-cadherin internalization and turnover in a migrating cell layer, which is contrary to the previously identified role of vinculin in potentiating E-cadherin junctions in a static monolayer.

For the last part of my thesis I designed a novel tension sensor to probe tension across N-cadherin (NTS). N-cadherin plays a critical role in cardiomyocytes, vascular smooth muscle cells, neurons and neural crest cells. Similar to E-cadherin, N-cadherin is also believed to bear tension and play a role in mechanotransduction pathways. To identify the role of tension across N-cadherin I designed a novel FRET-based molecular tension sensor for N-cadherin. I tested the ability of NTS to sense molecular tension in vascular smooth muscle cells, cardiomyocytes and cancer cells. Finally in collaboration with the Horwitz lab we have been able to show a role of tension across N-cadherin in synaptogenesis of neurons.

San Francisco Coastal System grain size and geochemical data for sand provenance study

Over 150 million cubic meter of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent widespread erosion of adjacent beaches, wetlands, and submarine environments. A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach sized-sand in the region, thereby identifying the activities and processes that directly limit supply to the outer coast. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, Bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., Foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry to robustly determine the provenance of beach-sized sand in the region.

Flux data of NU2_trap (Table A1)

Flux of bulk components, carbonate- and silicate-bearing skeleton organisms, and the d15N-isotopic signal were investigated on a 1-year time-series sediment trap deployed at the pelagic NU mooring site (Namibia Upwelling, ca. 29°S, 13°E) in the central Benguela System. The flux of bulk components mostly shows bimodal seasonality with major peaks in austral summer and winter, and moderate to low export in austral fall and spring. The calcium carbonate fraction dominates the export of particulates throughout the year, followed by lithogenic and biogenic opal. Planktonic foraminifera and coccolithophorids are major components of the carbonate fraction, while diatoms clearly dominate the biogenic opal fraction. Bulk d15N isotopic composition of particulate matter is positively correlated with the total mass flux during summer and fall, while negatively correlated during winter and spring. Seasonal changes in the intensity of the main oceanographic processes affecting the NU site are inferred from variations in bulk component flux, and in the flux and diversity patterns of individual species or group of species. Influence from the Namaqua (Hondeklip) upwelling cell through offshore migration of chlorophyll filaments is stronger in summer, while the winter flux maximum seems to reflect mainly in situ production, with less influence from the coastal and shelf upwelling areas. On a yearly basis, dominant microorganisms correspond well with the flora and fauna of tropical/subtropical waters, with minor contribution of near-shore organisms. The simultaneous occurrence of species with different ecological affinities mirrors the fact that the mooring site was located in a transitional region with large hydrographic variability over short-time intervals.

A suite of global, cross-scale topographic variables for environmental and biodiversity modeling, links to files in GeoTIFF format

Topographic variation, the spatial variation in elevation and terrain features, underpins a myriad of patterns and processes in geography and ecology and is key to understanding the variation of life on the planet. The characterization of this variation is scale-dependent, i.e. it varies with the distance over which features are assessed and with the spatial grain (grid cell resolution) of analysis. A fully standardized and global multivariate product of different terrain features has the potential to support many large-scale basic research and analytical applications, however to date, such technique is unavailable. Here we used the digital elevation model products of global 250 m GMTED and near-global 90 m SRTM to derive a suite of topographic variables: elevation, slope, aspect, eastness, northness, roughness, terrain roughness index, topographic position index, vector ruggedness measure, profile and tangential curvature, and 10 geomorphological landform classes. We aggregated each variable to 1, 5, 10, 50 and 100 km spatial grains using several aggregation approaches (median, average, minimum, maximum, standard deviation, percent cover, count, majority, Shannon Index, entropy, uniformity). While a global cross-correlation underlines the high similarity of many variables, a more detailed view in four mountain regions reveals local differences, as well as scale variations in the aggregated variables at different spatial grains. All newly-developed variables are available for download at http://www.earthenv.org and can serve as a basis for standardized hydrological, environmental and biodiversity modeling at a global extent.