Hydro-mechanical characterization of unsaturated clays using centrifuge technology

A number of experimental techniques and analytical methods, with emphasis in centrifuge testing, were implemented in this research to characterize the hydro-mechanical behavior of unsaturated clays. In particular, experimental procedures and back-analysis methods were developed to determine the Soil Water Retention Surface (SWRS) and the unsaturated hydraulic conductivity (k-function) of clays, both of low and high plasticity. New experimental devices and non-intrusive sensors were developed to expressly incorporate four key variables that control unsaturated flow processes: moisture content, suction, volumetric changes, and hydraulic conductivity. The new equipment and sensors are capable of monitoring all relevant variables without interfering with the flow process or the volumetric changes. Specifically, two nonintrusive sensor systems were implemented to upgrade the capabilities of the centrifuge permeameter for unsaturated soils (CPUS): a water content sensor, the GTDR, based on Time Domain Reflectometry, and an image-analysis tool to quantify soil deformation inflight. When combined, both systems combined allowed continuously monitoring the volumetric and water content changes in-flight. These tools allowed generating experimental data for the SWRS and hydraulic conductivity of clays, using steady-state and transient procedures. In addition, a new workbench equipment, the ATX Cell, was developed to facilitate the characterization of the hydro-mechanical behavior of unsaturated clays by simultaneously monitoring the void ratio, matric suction, and water content. It allows testing clays under different imposed stresses, a feature that was particularly relevant when testing on expansive clays. The hydraulic properties of an unsaturated low plasticity clay (RMA soil) were evaluated using centrifuge (N.g) testing with the implementation of the new sensors, as well as other standard (1.g) experimental techniques. RMA’s SWRS was determined over a wide range of void ratio values with samples compacted at optimum water content. Although volumetric changes measured in the ATX Cell were negligible, the level of deformation in RMA soil samples measured during centrifuge testing was found to depend on the initial conditions and stresses imposed during testing A comparison between destructive and non-destructive measurement revealed that destructive measurements result in changes that affect the measured volumetric water content and degree of saturation profiles. Non-intrusive sensors were found to solve this problem improving the definition of the SWRS. RMA k-function was evaluated using both, steady-state and transient methods. Gardner’s outflow method was applied to the transient measurements obtained from the ATX Cell, and Hydrus 1-D code was implemented to determine the k-function using transient information from centrifuge tests. Hydrus-1D overestimate the saturated hydraulic conductivity, however, the k-function was found to show good agreement with the hydraulic conductivity values obtained using steady-state (imposed flow) approach The hydro-mechanical behavior of an unsaturated high plasticity clay, Eagle Ford was characterized implementing all the sensors, devices and testing approaches previously developed in this research. Special focus was placed on the hydraulic properties, as well as on the swelling characteristics of this clay implementing centrifuge technology. The inclusion of the void ratio as an additional variable was found to be particularly relevant when interpreting the experimental data and defining the SWRS and k-function of the clay. The ATX Cell was used to evaluate the hydro-mechanical characteristics of Eagle Ford clay by monitoring the void ratio and water changes through different suction stages under different values of imposed stresses. The volume changes and changes in water content were found to depend on the initial void ratio and the stresses imposed. A coupled behavior was identified between the swelling and the inflow rates. In addition, a series of filter paper and chilled mirror hygrometer test were carried out. The experimental data generated with standard (1.g) methods incorporating the void ratio as an additional variable allowed defining the SWRS. The results from centrifuge tests in Eagle Ford clay showed that volume changes occur as a result of the coupled effect of the imposed stresses (due to the gravitational forces) and water content changes (wetting and drying phases). Image analysis was found to successfully detect the swelling and contraction of the soil in-flight. The volumetric water content measured with the GTDR’s was found to match the values measured using semi-destructive techniques. The use of the GTDR and image analysis techniques allowed obtaining experimental data to define the SWRS of Eagle Ford clay using centrifuge testing. A comparison between two centrifuge (hydrostatic) tests performed at 100g and 200g respectively showed that the void was reduced as a result of the higher imposed stresses, and in consequence a larger portion of the sample remained saturated despite of the higher suction imposed. Despite the higher hydraulic gradient, the flow velocity was smaller in the second test due to a possible reduction in the hydraulic conductivity. While steady-state techniques were successful implemented for low plasticity clays, this approach was time-consuming for high plasticity clays. The interpretation of transient information was found to become useful at determining the hydraulic conductivity. Swelling tests performed in the centrifuge showed that volumetric water content increased rapidly during primary swelling stage, while secondary swelling occurred under an approximately constant degree of saturation. The image analysis tools allowed defining volumetric changes along the sample, providing additional information to generate the swell-stress curve. The representation of the swelling test in the -e or Sr-e revealed that for samples compacted at different water contents but tested at the same vertical stress final equilibrium state after fully wetting was similar. Although this representation of the swelling test data eliminates the variable time it could be used to provide a method to evaluate the expansion in a soil profile under partial wetting conditions if the swelling is calculated using the void ratio values for a selected initial and final water content. A comparison in the [θ, e] plane of the results obtained from an ATX Cell test and a swelling tests performed at the same vertical stress in samples compacted at different water contents revealed that the final equilibrium achieved by both samples after fully wetting are similar.Civil, Architectural, and Environmental Engineerin

Doctor of Philosophy

dissertationSparse matrix codes are found in numerous applications ranging from iterative numerical solvers to graph analytics. Achieving high performance on these codes has however been a significant challenge, mainly due to array access indirection, for example, of the form A[B[i]]. Indirect accesses make precise dependence analysis impossible at compile-time, and hence prevent many parallelizing and locality optimizing transformations from being applied. The expert user relies on manually written libraries to tailor the sparse code and data representations best suited to the target architecture from a general sparse matrix representation. However libraries have limited composability, address very specific optimization strategies, and have to be rewritten as new architectures emerge. In this dissertation, we explore the use of the inspector/executor methodology to accomplish the code and data transformations to tailor high performance sparse matrix representations. We devise and embed abstractions for such inspector/executor transformations within a compiler framework so that they can be composed with a rich set of existing polyhedral compiler transformations to derive complex transformation sequences for high performance. We demonstrate the automatic generation of inspector/executor code, which orchestrates code and data transformations to derive high performance representations for the Sparse Matrix Vector Multiply kernel in particular. We also show how the same transformations may be integrated into sparse matrix and graph applications such as Sparse Matrix Matrix Multiply and Stochastic Gradient Descent, respectively. The specific constraints of these applications, such as problem size and dependence structure, necessitate unique sparse matrix representations that can be realized using our transformations. Computations such as Gauss Seidel, with loop carried dependences at the outer most loop necessitate different strategies for high performance. Specifically, we organize the computation into level sets or wavefronts of irregular size, such that iterations of a wavefront may be scheduled in parallel but different wavefronts have to be synchronized. We demonstrate automatic code generation of high performance inspectors that do explicit dependence testing and level set construction at runtime, as well as high performance executors, which are the actual parallelized computations. For the above sparse matrix applications, we automatically generate inspector/executor code comparable in performance to manually tuned libraries

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected

Percolation-based compiling for evaluation of parallelism and hardware design trade-offs

This thesis investigates parallelism and hardware design trade-offs of parallel and pipelined architectures. To explore these trade-offs we developed a retargetable compiler based on a set of powerful code transformations called Percolation Scheduling (PS) that map programs with real-time constraints and/or massive time requirements onto synchronous, parallel, high-performance or semi-custom architectures.High-performance is achieved through extraction of application inherent fine-grain parallelism and the use of a suitable architecture. Exploiting fine-grain parallelism is a critical part of exploiting all of the parallelism available in a given program, particularly since highly irregular forms of parallelism are often not visible at coarser levels and since the use of low-level parallelism has a multiplicative effect on the overall performance.To extract substantial parallelism from both the hardware and the compiler, we use a clean, highly parallel VLIW-like architecture that is synchronous, has multiple functional units and has a single program counter. The use of a hazard-free and homogeneous architecture does not result only in a better VLSI design but also considerably increases the compiler's ability to produce better code. To further enhance parallelism we modified the uni-cycle VLIW model and extended the transformations such that pipelined units that provide extra parallelism are used.Another approach presented is of resource constrained scheduling (RCS). Since the RCS problem is known to be NP-hard, in practice it may be solved only by a heuristic approach. We argue that using the heuristic after extraction of the unlimited-resources schedule may yield better results than if the heuristic has been applied at the beginning of the scheduling process.Through a series of benchmarks we evaluate hardware design trade-offs and show that speed-ups on average of one order of magnitude are feasible with sufficient functional units. However, when resources are limited we show that the number of functional units needed may be optimized for a particular suite of application programs

EFFECTS OF HYDROLOGIC VARIATIONS ON HYDRAULIC AND DEFORMATIONAL CHARACTERISTICS OF UNSATURATED SOILS

Constitutive models that can provide useful insight into the deformational mechanism induced by hydrologic variations are vital for design and analysis of structures where unsaturated regime predominates. An accurate description of unsaturated soils’ behavior not only requires a vigorous constitutive model, but essentially is achievable using real-time mechanical (e.g. small-strain shear modulus) and hydrologic data sets. The main objective of this research was to develop a robust constitutive scheme that is compatible to quick fluctuations in hydrologic conditions. The first step towards accomplishing this aim involved proposing a novel methodology to estimate the small-strain shear modules with respect to the variations in net normal stress and matric suction. Fundamental of the proposed scheme was established on the inverse relationship between the small-strain shear modulus and soil-water characteristic curve (SWCC). The model proved to be highly reliable in estimating real-time values of the small-strain shear modulus along several loading and hydrologic scenarios. Furthermore, a dependable and robust constitutive scheme, identified as SFG model was selected and further modified to simulate hydraulic characteristics and elastoplastic deformations of the unsaturated soils as direct responses to isotropic/triaxial loads and hydrological variations. The modifications involved reformation of hysteresis and elastic shear strain components of the original model. The modified-SFG model was fitted against several case studies representing various hydrologic conditions. The model successfully reproduced hydro-mechanical characteristics of the studied soils. More significantly, the modified-SFG model offers possibility of a real-time simulating of hydro-mechanical behavior of unsaturated soils with respect to rainfall and evapotranspiration events. Likewise, in this dissertation, long-term hydrologic variations within the soil’s body was simulated under transient infiltration framework. Correlation between various parts of hydrologic data was used to estimate different components of hydrological dataset. The transient infiltration model was subsequently coupled with the modified-SFG scheme and hydro-mechanical behaviors of an unsaturated hillslope was incrementally simulated with respect to hydrologic variations. The outcome of this study provides geotechnical engineers with a capability of estimating the deformational behavior of unsaturated soils, particularly stability of hillslopes, under various real-time rainfall and evapotranspiration conditions, and thus aids effectual risk assessments and construction managements

Suitability of Intelligent Compaction for Relatively Smaller-Scale Projects in Vermont

Intelligent Compaction (IC) is considered to be an innovative technology intended to address some of the problems associated with conventional compaction methods of earthwork (e.g. stiffness-based measurements instead of density-based measurements). IC typically refers to an improved compaction process using rollers equipped with an integrated measurement system that consists of a global positioning system (GPS), accelerometers, onboard computer reporting system, and infrared thermometers IC determines the compacted material’s stiffness/modulus simultaneously while compacting based on measured frequency and amplitude of excitation. The overarching objective of this research was to investigate the suitability of IC technology for comparatively smaller-scale embankment, subgrade, and base material construction that are typical for Vermont. The specific objectives were to: perform a literature review of IC technology; assess the accuracy and reliability of IC measured values (e.g. stiffness); investigate the influence of relevant parameters (i.e. density, soil type, moisture content, etc.) on these measurements; investigate different options for quality control (QC) and quality assurance (QA) specifications for IC; and make specific recommendations to the Agency. The literature review suggests that: (i) IC stiffness measurements near the surface are less reliable compared to deeper measurements; (ii) correlations between IC measured stiffness and modulus of spottest measurements vary considerably in layer and layered soil structures; and (iii) for asphalt, IC measured stiffness correlates well with nuclear density gauge measurements, only when the asphalt mix is hot. In addition, the existing quality control (QC) and quality assurance (QA) specifications for implementing IC need further improvements. It is suggested that to better investigate the reliability of implementing IC for both earthwork construction and asphalt pavement in Vermont’s harsh winter conditions, it would be necessary to conduct field experiments. In addition, preparing a new set of QC/QA specifications is an important step toward implementation of IC in Vermont projects, which can be accomplished in collaboration with other states and as some local experience in IC is gained. Also, it is recommended to evaluate the correlation between IC stiffness measurements and in-situ stiffness measurements in different seasons in Vermont

Large Genomes Assembly Using MAPREDUCE Framework

Knowing the genome sequence of an organism is the essential step toward understanding its genomic and genetic characteristics. Currently, whole genome shotgun (WGS) sequencing is the most widely used genome sequencing technique to determine the entire DNA sequence of an organism. Recent advances in next-generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. However, the assembly of NGS reads faces significant challenges due to short reads and an enormously high volume of data. Despite recent progress in genome assembly, current NGS assemblers cannot generate high-quality results or efficiently handle large genomes with billions of reads. In this research, we proposed a new Genome Assembler based on MapReduce (GAMR), which tackles both limitations. GAMR is based on a bi-directed de Bruijn graph and implemented using the MapReduce framework. We designed a distributed algorithm for each step in GAMR, making it scalable in assembling large-scale genomes. We also proposed novel gap-filling algorithms to improve assembly results to achieve higher accuracy and more extended continuity. We evaluated the assembly performance of GAMR using benchmark data and compared it against other NGS assemblers. We also demonstrated the scalability of GAMR by using it to assemble loblolly pine (~22Gbp). The results showed that GAMR finished the assembly much faster and with a much lower requirement of computing resources

Development of the engineering design integration (EDIN) system: A computer aided design development

The EDIN (Engineering Design Integration) System which provides a collection of hardware and software, enabling the engineer to perform man-in-the-loop interactive evaluation of aerospace vehicle concepts, was considered. Study efforts were concentrated in the following areas: (1) integration of hardware with the Univac Exec 8 System; (2) development of interactive software for the EDIN System; (3) upgrading of the EDIN technology module library to an interactive status; (4) verification of the soundness of the developing EDIN System; (5) support of NASA in design analysis studies using the EDIN System; (6) provide training and documentation in the use of the EDIN System; and (7) provide an implementation plan for the next phase of development and recommendations for meeting long range objectives