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Title: PROBING THE PAN-GENOME OF LISTERIA MONOCYTOGENES
Creator: Deng, Xiangyu
Date: 2011-04-26, 2011-05
Description: Bacterial pathogens often show significant intra-species variations in ecological fitness, host preference and pathogenic potential to cause...
Show moreBacterial pathogens often show significant intra-species variations in ecological fitness, host preference and pathogenic potential to cause infectious disease. The species of Listeria monocytogenes, a facultative intracellular pathogen and the causative agent of human listeriosis, consists of at least three distinct genetic lineages. Two of these lineages predominantly cause human sporadic and epidemic infections, whereas the third lineage has never been implicated in human disease outbreaks despite its overall conservation of many known virulence factors. The genomes of 26 L. monocytogenes strains representing the three lineages are compared based on both in silico comparative genomic analysis and high-density, pan-genomic DNA microarray hybridizations. We uncover 86 genes and 8 small regulatory RNAs that likely make L. monocytogenes lineages differ in carbohydrate utilization and stress resistance during their residence in natural habitats and passage through the host gastrointestinal tract. We also identify 2,330 to 2,456 core genes that define this species along with an open pan-genome pool that contains more than 4,052 genes. Phylogenomic reconstructions based on 3,560 homologous groups allowed robust estimation of phylogenetic relatedness among L. monocytogenes strains. The pan-genome approach enables accurate co-analysis of DNA sequence and hybridization array data for both core gene estimation and phylogenomic reconstruction. Application of our method to the pan-genome of L. monocytogenes sheds new insights into the intra-species genomic diversification, niche expansion and evolution of this important foodborne pathogen.
Ph.D. in Biology, May 2011
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Title: Relationship of Executive Fuction Patterns and Academic Achievement Across DSM-IV Subtypes of Attention-Deficit/Hyperactivity Disorder
Creator: Young, Crystal
Date: 2012-07-18, 2012-07
Description: The aim of this study was to expand our understanding of the impact of executive function skills on academic achievement in children with ADHD...
Show moreThe aim of this study was to expand our understanding of the impact of executive function skills on academic achievement in children with ADHD, as well as investigate trends in executive functioning and academic achievement between ADHD subtypes in an adolescent sample. Each participant completed neuropsychological assessments including a measure of intelligence and academic functioning as well as several measures of executive functioning. Results suggested that children with ADHD – Combined Type do not significantly differ from children with ADHD – Inattentive Type on tasks of academic or executive functioning. Issues regarding outcomes associated with ADHD as well as diagnostic procedures are discussed.
Ph.D. in Psychology, July 2012
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Title: EFFECT OF TEMPERATURE, MOISTURE CONTENT AND SOIL SURFACE AREA ON THE BIOLOGICAL DEGRADATION OF BIOSOLIDS ADDED TO SOIL
Creator: Wen, Dongqi
Date: 2016, 2016-05
Description: The objective is to develop and apply an organic matter degradation model (OMDM) that predicts changes in the biological degradation of...
Show moreThe objective is to develop and apply an organic matter degradation model (OMDM) that predicts changes in the biological degradation of organic matter added to soils as a function of soil temperature, moisture content and mineral surface area using data from field and laboratory measurements. A one year long laboratory study was conducted to determine biosolids microbial degradation rates (21 ˚C and 20% moisture content) for soils from eight different fields Biosolids microbial degradation rates were also determined for the eight soils under field condition (10 ˚C and 10% moisture content) by applying a degradation rate model (DRM). The total mineral surface areas for 27 soil samples were also determined. Regression analysis revealed that the degradation rate was positively associated with mineral soil surface area (R2=0.85) and that the biosolids application rate is not significantly associated with the biosolids degradation rate (p value =0.35>0.01). The OMDM determines a decomposition rate of 1.04 yr-1 at 30 ˚C, 20% moisture content, and 10 m2/g soil and provides correction factors for changes in soil temperature, moisture, and mineral surface area. The model predicted in changes of the biological degradation rate of biosolids added to soils with mineral surface areas that vary from 1 to 10 m2/g soil under laboratory and field conditions. A comparison of the measured and simulated degradation rates for eight different soils produced R2 = 0.87 for field data. The model was also able to predict the degradation rate of biosolids for 19 additional soils under field conditions (R2=0.89). The model was also applied to agricultural plant litter. The estimated degradation rates are 0.45 yr-1 corn stover, 0.35 yr-1 oats, 0.26 yr-1 wheat, and 0.13 yr-1 millet at 30 ˚C, 20% moisture content and 10 m2/g. This study demonstrates that the effects of environmental conditions and soil mineral surface area have a significant impact on degradation rates of organic matter and must be considered when assessing degradation rates for organic matter added to soil. Higher temperatures and moisture content and finer soils are related to larger degradation rates.
Ph.D. in Environmental Engineering, May 2016
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Title: INSTANTANEOUS DETECTION OF SPATIAL GRADIENT ERRORS IN DIFFERENTIAL GNSS
Creator: Jing, Jing
Date: 2014, 2014-12
Description: Differential GNSS (Global Navigation Satellite System) is currently being ex- tended using a high integrity Ground Based Augmentation System ...
Show moreDifferential GNSS (Global Navigation Satellite System) is currently being ex- tended using a high integrity Ground Based Augmentation System (GBAS) to enable civil aircraft precision approach and landing. Differential GPS carrier phase measure- ments between ground-based GBAS reference antennas can provide the means to de- tect and isolate certain signal-in-space (SIS) failures and anomalies that are hazardous to aircraft, most notably ionospheric anomalies and ephemeris failures, which can be characterized as spatial range error gradients. In this research, we develop a monitor capable of instantaneously detecting multi-dimensional spatial gradient faults. The existence of large gradients, while rare, has prompted the development of numerous ground monitors for their detection. One drawback of previously proposed monitors is that their performance for a given ground antenna con guration is de- pendent on how antennas are paired to form measurement differences. In contrast, in this work a new monitor approach is developed to provide consistent detection performance, regardless of how the antennas are paired, by combining measurements from multiple, spatially separated ground antennas through a null space transforma- tion. It is shown that the `null space' monitor signi cantly improves the detection performance over existing fault detection algorithms and enables GBAS to support Category III precision approach and landing. The instantaneous carrier phase monitor cannot detect all gradients due to the presence of integer cycle ambiguities. These ambiguities cannot be resolved because the gradient magnitude is unknown a priori. Furthermore, it has been shown that the performance of such monitors is highly dependent on the reference antenna topol- ogy. The range of detectable gradients for all carrier phase monitors depends on two factors: the number of antennas and their con guration. One can always expand the detection range by using many antennas, but only at greatly increased operational cost. Optimizing antenna con guration has been overlooked as a means to improve performance; simple, heuristic arguments typically prevail in the associated siting decisions. For example, when given four antennas it is generally assumed that they should be sited in a square arrangement to balance performance in all directions. However, such heuristics do not provide the maximum detectable range of gradients, and exploiting the freedom to choose the antenna topology can dramatically expand the detectable range. Due to the presence of carrier phase cycle ambiguities, the re- sulting optimization problem is a constrained, mixed integer nonlinear programming problem. By solving the nonlinear program, the optimal GBAS antenna topology that maximizes the range of detectable gradients can be found for any number of antennas. For ionospheric fronts, the magnitude of the resulting gradient is bounded. However, orbit ephemeris faults can be arbitrarily large. The monitor must be able to detect all large gradients. To detect gradients beyond the capability of the car- rier phase monitor, code phase measurements are integrated into the monitor. Al- though we show this allows for the detection of all gradients, the number and spacing of ground antennas may not be suitable for all ground stations. Therefore, dual frequency carrier phase measurements are also considered to reduce the number of antennas required to achieve the desired detection performance. Finally, a search algorithm is developed to nd the antenna topology that enables the null space mon- itor to detect all hazardous gradients using code and dual frequency carrier phase measurements.
Ph.D. in Mechanical and Aerospace Engineering, December 2014
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Title: COMPUTATION AND ANALYSIS OF TUMOR GROWTH
Creator: Turian, Emma
Date: 2016, 2016-05
Description: The ability of tumors to metastasize is preceded by morphological instabilities such as chains or fingers that invade the host environment....
Show moreThe ability of tumors to metastasize is preceded by morphological instabilities such as chains or fingers that invade the host environment. Parameters that control tumor morphology may also contribute to its invasive ability. In this thesis, we investigate tumor growth using a two-phase Stokes model. We first examine the morphological changes using the surface energy of the tumor-host interface and investigate its nonlinear dynamics using a boundary integral method. In an effort to understand the interface stiffness, we then model the tumor-host interface as an elastic membrane governed by the Helfrich bending energy. Using an energy variation approach, we derive a modified Young-Laplace condition for the stress jump across the interface, and perform a linear stability analysis to evaluate the effects of viscosity, bending rigidity, and apoptosis on tumor morphology. Results show that increased bending rigidity versus mitosis rate contributes to a more stable growth. On the other hand, increased tumor viscosity or apoptosis may lead to an invasive fingering morphology. Comparison with experimental data on glioblastoma spheroids shows good agreement especially for tumors with high adhesion and low proliferation. Next, we evaluate tumor regression during cancer therapy by a combined modality involving chemotherapy and radiotherapy. The goal is to address the complexities of a vascular tumor (e.g. apoptosis and vascularization) during treatment. We introduce an apoptotic time delay and study its impact on tumor regression using numerical and asymptotic techniques. In particular, we implement the linear-quadratic model and identify two extreme sets of parameter data, namely the slow, and fast tumor response to therapy. Numerical simulations for the slow response set show good agreements with data representing non-small cell lung carcinoma. Using the evolution equation for tumor radius with time delay, we find that tumors with shorter time interval to the onset of apoptosis shrink faster.
Ph.D. in Applied Mathematics, May 2016
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Title: CORROSION-RESISTANT ELECTRO-CATALYSTS AND SUPPORTS FOR ELECTROCHEMICAL ENERGY CONVERSION
Creator: Wang, Guanxiong
Date: 2016, 2016-12
Description: Polymer electrolyte fuel cells (PEFCs) convert chemical energy of fuels (eg. Hydrogen) directly to electrical energy with excellent power...
Show morePolymer electrolyte fuel cells (PEFCs) convert chemical energy of fuels (eg. Hydrogen) directly to electrical energy with excellent power density, high efficiency, and zero emissions. Several challenges have delayed the commercialization of fuel cells with one being the high cost and durability of the carbon-supported-platinum-based (Pt/C) electrocatalysts. The lifetime/durability issue is critical as insufficient durability/reliability of the catalysts affects the lifetime and economical viability of these devices. Carbon support corrosion is a major durability issue since the corrosion reaction is thermodynamically favorable but kinetically sluggish under normal operating conditions. The potential transients that occur during start and stop in automotive applications can lead to electrode potential excursions of up to 1.5 V and contribute to carbon corrosion. The best way to mitigate support corrosion in PEFCs is to replace the carbon supports with alternatives having high electronic conductivity, surface area and porosity. This dissertation investigates the following carbon alternatives: (i) tin doped indium oxide (ITO) and (ii) 1:1 mixed oxides of ruthenia and silica (RSO). Microstructure characterization and electrochemical evaluations, including accelerated stress tests (start-up/shut-down and load cycling protocols) were performed to evaluate ORR activity, fuel cell performance, and electrochemical stability under PEFC operating conditions. The ITO support and 40%Pt/ITO catalysts demonstrated exceptional electrochemical stability (and reasonable ORR activity) in rotating disk electrode (RDE) experiments under accelerated potential cycling that mimicked automotive drive cycles. However, Pt/ITO exhibited poor performance and stability during MEA evaluation in a PEFC. X-ray photoelectron spectroscopy (XPS) was employed to reveal the degradation modes of Pt/ITO during PEFC operation and it was found that the increase in the surface hydroxide concentration generates a passivating In(OH)3 layer that increases electrode resistance and undermines PEFC performance. The influence of the catalyst support on PEM degradation during PEFC operation was also studied. Rotating ring-disk electrode (RRDE) experiments were employed to estimate the fraction of H2O2 generated during the ORR on the supports (C and RSO) and catalysts (benchmark Pt/C and Pt/RSO). The percentage of H2O2 generated on C and Pt/C was 50% higher than that on RSO and Pt/RSO thus explaining the observed oxidative degradation resistance of the PEM with the latter supports/catalysts.
Ph.D. in Chemical Engineering, December 2016
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Title: AUTOMATIC SUMMARIZATION OF CLINICAL ABSTRACTS FOR EVIDENCE-BASED MEDICINE
Creator: Summerscales, Rodney L.
Date: 2013, 2013-12
Description: The practice of evidence-based medicine (EBM) encourages health professionals to make informed treatment decisions based on a careful analysis...
Show moreThe practice of evidence-based medicine (EBM) encourages health professionals to make informed treatment decisions based on a careful analysis of current research. However, after caring for their patients, medical practitioners have little time to spend reading even a small fraction of the rapidly growing body of medical research literature. As a result, physicians must often rely on potentially outdated knowledge acquired in medical school. Systematic reviews of the literature exist for speci c clinical questions, but these must be manually created and updated as new research is published. Abstracts from well-written clinical research papers contain key information regarding the design and results of clinical trials. Unfortunately, the free text nature of abstracts makes it di cult for computer systems to use and time consuming for humans to read. I present a software system that reads abstracts from randomized controlled trials, extracts key clinical entities, computes the e ectiveness of the proposed interventions and compiles this information into machine readable and human readable summaries. This system uses machine learning and natural language processing techniques to extract the key clinical information describing the trial and its results. It extracts the names and sizes of treatment groups, population demographics, outcome measured in the trial and outcome results for each treatment group. Using the extracted outcome measurements, the system calculates key summary measures used by physicians when evaluating the e ectiveness of treatments. It computes absolute risk reduction (ARR) and number needed to treat (NNT) values complete with con dence intervals. The extracted information and computed statistics are automatically compiled into XML and HTML summaries that describe the details and results of the trial. xiii Extracting the necessary information needed to calculate these measures is not trivial. While there have been various approaches to generating summaries of medical research, this work has mostly focused on extracting trial characteristics (e.g. population demographics, intervention/outcome information). No one has attempted to extract all of the information needed, nor has anyone attempted to solve many of the tasks needed to reliably calculate the summary statistics.
PH.D in Computer Science, December 2013
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Title: OIL RECOVERY IN SINGLE CAPILLARIES AND POROUS MEDIA USING WETTING NANOFLUIDS
Creator: Zhang, Hua
Date: 2016, 2016-05
Description: Recent experiments and modeling conducted in our laboratory have demonstrated that the spreading of nanofluids, liquid suspensions of...
Show moreRecent experiments and modeling conducted in our laboratory have demonstrated that the spreading of nanofluids, liquid suspensions of nanosized particles, on solids are enhanced due to self-structuring of nanoparticles in the confined three-phase oil-nanofluid-solid contact region. Nanofluids have recently been proposed as agents for enhanced oil recovery (EOR). Despite recently widely conducted research using nanofluids for EOR, the underlying operating mechanism is not well understood. In this thesis, we attempt to understand the mechanism of nanofluid based EOR and evaluate its performance from reservoir core samples and model systems (glass capillary and sintered bead-pack). To visualize how oil displacement in the rock pores by nanofluid, we conducted model study using hexadecane and single glass capillary and showed the oil film dynamics in air and nanofluid after oil was displaced in the capillary. Based on the understanding of the role of nanofluid on oil displacement in capillaries, we conducted imbibition tests using Berea sandstones and flooding experiments in sintered glass-beads. X-ray microtomography was used to visualize and analyze fluid distribution and to see the effect of nanofluid in EOR. We finally considered fractured media by fabricating such structures. The dynamics of a cylindrical hexadecane layer deposited inside glass capillaries after the oil/air displacement was studied experimentally and by modeling. The oil layer subject to surface perturbation becomes unstable forming uniform, regularly-spaced double concave menisci across the capillary that are bridged with dimples (collars). In order to reveal the phenomena of the film thinning and stability between the double concave meniscus and the dimple, we monitored an air bubble approaching a flat glass surface in hexadecane. We found that the oil film thinning in a cylindrical glass capillary and on a flat glass substrate were similar; We adapted the model proposed by Gauglitz and Radke for our system (oil-air displacement) and solved it numerically. The numerical result shows a stable film between the liquid bridge and the dimple, which is consistent with our experimental observations. We also estimated the meniscus-film-dimple thickness profile and found it was in fair agreement with the model prediction. The dynamics of cylindrical hexadecane film after displacement by a nanofluid in a glass capillary was studied. We found the thick hexadecane film is unstable, and over time it breaks and forms a thin film. Once the thick film ruptures, it retracts and forms an annular rim (liquid ridge) that collects liquid. As the volume of the annular rim increases over time, it forms a double concave meniscus across the capillary and dewetting stops. The thin film on the right side of the double concave meniscus then breaks and the contact angle increases. The process repeats until droplets build along the capillary wall. Finally, the droplets are displaced from the capillary wall by the nanofluid and spherical droplets appear inside the capillary. This is a novel phenomenon not observed during dewetting by a solution without nanoparticles. The theoretical model based on the lubrication approximation using the capillary pressure gradient was developed to estimate the annular rim dewetting velocity. The predicted dewetting velocity is found to be in fair agreement with the experimental value. We conducted imbibition tests using a reservoir crude oil and a reservoir brine solution with a high salinity and a suitable nanofluid that displaces crude oil from Berea sandstone and single glass capillaries. We present visual evidence of the underlying mechanism based on the structural disjoining pressure for the crude oil displacement using a polymeric nanofluid (our definition of such a fluid means a suspension of polymeric particles in an aqueous substrate) in high salinity brine. The polymeric nanofluid is specially formulated to survive in a high salinity environment and is found to result in an increased efficiency of 50% for Berea sandstone compared to 17% using the brine alone at a reservoir temperature of 55 oC. These results aid our understanding of the role of the nanofluid in displacing crude oil from the rock especially in a high salinity environment containing Ca++ and Mg++ ions. Results are also reported using Berea sandstone and a nanofluid containing silica nanoparticles. We conducted a series of flooding experiments at different capillary numbers to quantify the performance of a polymeric nanofluid compared to brine using the sintered glass-beads. A high resolution X-ray microtomography (microCT) was used to visualize oil and brine distribution in a sintered bead-pack before and after nanofluid flooding. The results of flooding experiments showed that an additional oil recovery of approximately 15% is possible with nanofluids compared to brine at low capillary numbers, and is as effective as high capillary number brine flooding. Nanofluid induced additional oil recovery decreases as we increase the capillary number and the total oil recovered shows a marginal decrease. At first glance, these results are opposite of what one expects in the conventional EOR, where oil recovery is known to increase progressively with increasing capillary number. These results cannot be explained based on mobilization theories due to the reduced capillarity. Our results however are consistent with the mechanism of wettability alteration caused by structural disjoining pressure leading to the formation of the wetting nanofluid film between oil and substrate.We presented experimental studies of nanofluid flooding in fractured porous media formed with sintered glass-beads. The nanofluid injection is conducted at a rate where structural disjoining pressure driven recovery is operational. We found an additional 23.8% oil can be displaced using nanofluid after brine injection with an overall displacement efficiency of 90.4% provided the matrix was in its native wettability state. In summary, nanofluids are excellent EOR agents and their economic viability needs to be examined.
Ph.D. in Chemical Engineering, May 2016
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Title: COVERAGE AND CONNECTIVITY IN WIRELESS NETWORKS
Creator: Xu, Xiaohua
Date: 2012-04-25, 2012-05
Description: The limited energy resources, instability, and lacking central control in wireless networks motivates the study of connected dominating set ...
Show moreThe limited energy resources, instability, and lacking central control in wireless networks motivates the study of connected dominating set (CDS) which serves as rout- ing backbone to support service discovery, and area monitoring and also broadcasting. The construction of CDS involves both coverage and connectivity. We ¯rst study sev- eral problems related to coverage. Given are a set of nodes and targets in a plane, the problem Minimum Wireless Cover (MWC) seeks the fewest nodes to cover the targets. If all nodes are associated with some positive prices, the problem Cheapest Wireless Cover (CWC) seeks a cheapest set of nodes to cover the targets. If all nodes have bounded lives, the problem Max-Life Wireless Cover (MLWC) seeks wireless coverage schedule of maximum life subject to the life constraints of individ- ual nodes. We present a polynomial time approximation scheme (PTAS) for MWC, and two randomized approximation algorithms for CWC and MLWC respectively. Given a node-weighted graph, the problem Minimum-Weighted Dominating Set (MWDS) is to ¯nd a minimum-weighted vertex subset such that, for any vertex, it is contained in this subset or it has a neighbor contained in this set. We will propose a (4+²)-approximation algorithm for MWDS in unit disk graphs. Meanwhile, for the connecting part, given a node-weighted connected graph and a subset of terminals, the problem Node-Weighted Steiner Tree (NWST) seeks a lightest tree connecting a given set of terminals in a node-weighted graph. We present three approximation algorithms for NWST restricted to UDGs. This dissertation also explores the applications of CDS, and develops e±cient algorithms for the applications such as real-time aggregation scheduling in wireless networks. Given a set of periodic aggregation queries, each query has its own period , and the subset of source nodes Si containing the data, we ¯rst propose a family of e±cient and e®ective real-time scheduling protocols that can answer every job of each query task within a relative delay under resource constraints by addressing the following tightly coupled tasks: routing, transmission plan constructions, node activity scheduling, and packet scheduling. Based on our protocol design, we further propose schedulability test schemes to e±ciently and e®ectively test whether, for a set of queries, each query job can be ¯nished within a ¯nite delay. We also conduct extensive simulations to validate the proposed protocol and evaluate its practical performance. The simulations corroborate our theoretical analysis.
Ph.D. in Computer Science, May 2012
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Title: AN INTEGRATED DATA ACCESS SYSTEM FOR BIG COMPUTING
Creator: Yang, Xi
Date: 2016, 2016-07
Description: Big data has entered every corner of the fields of science and engineering and becomes a part of human society. Scientific research and...
Show moreBig data has entered every corner of the fields of science and engineering and becomes a part of human society. Scientific research and commercial practice are increasingly depending on the combined power of high-performance computing (HPC) and high-performance data analytics. Due to its importance, several commercial computing environments have been developed in recent years to support big data applications. MapReduce is a popular mainstream paradigm for large-scale data analytics. MapReduce-based data analytic tools commonly rely on underlying MapReduce file systems (MRFS), such as Hadoop Distributed File System (HDFS), to manage massive amounts of data. In the same time, conventional scientific applications usually run on HPC environments, such as Message Passing Interface (MPI), and their data are kept in parallel file systems (PFS), such as Lustre and GPFS, for high-speed computing and data consistency. As scientific applications become data intensive and big data applications become computing hungry, there is a surging interest and need to integrate HPC power and data processing power to support HPC on big data, the so-called big computing. A fundamental issue of big computing is the integration of data management and interoperability between the conventional HPC ecosystem and the newly emerged data processing/analytic ecosystem. However, data sharing between PFS and MRFS is limited currently, due to semantics mismatches, lacking communication middleware, and the diverged design philosophies and goals, etc. Also, challenges also exist in cross-platform task scheduling and parallelism. At the application layer, the data model mismatch between the raw data kept on file systems and the data management software of an application impedes cross-platform data processing as well. To support cross-platform integration, we propose and develop the Integrated Data Access System (IDAS) for big computing. IDAS extends the accessibilities of programming models and integrates the HPC environment with the data processing MapReduce/Hadoop environment. Under IDAS, MPI applications and MapReduce applications can share and exchange data under PFS and MRFS transparently and efficiently. Through this sharing and exchange, MPI and MapReduce applications can collaboratively provide both high-performance computing and data processing power for a given application. IDAS achieves its goal with several steps. First, IDAS enhances MPI-IO so that MPI-based applications can access data stored in HDFS efficiently. Here the term efficient means that HDFS is enhanced to support MPI-based applications. For instance, we have enhanced HDFS to transparently support N-to-1 file write for better write concurrency. Second, IDAS enhances Hadoop framework to enable MapReduce-based applications process data that resides on PFS transparently. Please notice that we have carefully chosen the term “enhance” here. That is MPI-based applications not only can access data stored on HDFS but also can continue access data stored on PFS. The same is for MapReduce-based applications. Through these enhancements, we achieve seamless data sharing. In addition, we have integrated data accessing with several application tools. In particular, we have integrated image plotting, query, and data subsetting within one application, for Earth Science data analysis. Many data centers prefer erasure-coding rather than triplication to achieve data durability, which trades data availability for lower storage cost. To this end, we have also investigated performance optimization of the erasure coded Hadoop system, to enhance Hadoop system in IDAS.
Ph.D. in Computer Science, July 2016
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Title: DYNAMIC COHERENT ACCEPTABILITY INDICES AND THEIR APPLICATIONS IN FINANCE
Creator: Zhang, Zhao
Date: 2011-05-02, 2011-05
Description: This thesis presents a unified framework for studying coherent acceptability indices in a dynamic setup. We study dynamic coherent...
Show moreThis thesis presents a unified framework for studying coherent acceptability indices in a dynamic setup. We study dynamic coherent acceptability indices and dynamic coherent risk measures. In particular, we establish a duality between them. We derive representation theorems for both dynamic coherent acceptability indices and dynamic coherent risk measures in terms of so called dynamically consistent sequence of sets of probability measures. In addition, we present an alternative approach to study dynamic coherent acceptability indices and the representation theorem. Finally, we provide examples and counterexamples of dynamic coherent acceptability indices, and their applications in portfolio management.
Ph.D. in Applied Mathematics, May 2011
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Title: ENVIRONMENTAL PERFORMANCE VS. FINANCIAL PERFORMANCE, MARKET INEFFICIENCY AND INVESTMENTS
Creator: He, Chaohua
Date: 2014, 2014-07
Description: It is challenging to de ne corporate environmental performance or corporate nancial performance. In this study, a company is considered to...
Show moreIt is challenging to de ne corporate environmental performance or corporate nancial performance. In this study, a company is considered to have good environmental performance (namely, be green, environment-friendly or environmentally responsible) if it is among the Top 100 of the 500 US greenest companies ranked by Newsweek, or has environmental strength(s) and no environmental concern in terms of the KLD ratings. A company is regarded to have good nancial performance if it has a high raw return, Sharpe ratio, and excess (or abnormal) return over various benchmarks. Preference will be given to excess return estimated using the Carhart four-factor model [14]. A previous published longitudinal study, co-authored with my advisor [13], unveils that: 1) environmentally responsible companies tend to experience signi cantly positive abnormal performance in the long horizon (e.g. from the fourth to seventh year after being selected); 2) the value-adding e ect and the market's upward price adjustments on undervalued intangible environmental strength(s) might have resulted in the long-term outperformance. Would environmentally responsible companies still outperform during shorter horizons, such as the event period of an environmental disclosure? Using event study methodologies, this paper investigates market responses to independent Newsweek environmental disclosures by analyzing cross-sectional and time-series abnormal security returns. Results suggest that the Top 100 greenest companies tend to display signi cant abnormal returns within 4 days after a disclosure, and the signi cant abnormal returns generally persist for no more than 3 trade days. e.g., the Carhart four-factor abnormal return, with statistical signi cance, is averaged at 0.50% per day over the four disclosure events. The ndings are robust to di erentmodels of normal return, removal of outliers, elimination of confounding e ects, controlling for characteristic factors, and adjusting for cross-sectional correlation and volatility shift on test statistics using BMP-adjusted technology[56]. Signi cant abnormal returns over the event period may indicate ine ciency of the nancial market. Fama-Macbeth regressions further reveal that short-horizon abnormal returns could be explained by a spectrum of characteristic variables, green investing, arbitrage trading, and/or various psychological biases. Complementing the cited longitudinal study, a portfolio-level comparison reveals that an actively managed green portfolio outperforms an actively managed nongreen portfolio in terms of raw return and risk-adjusted measures such as Sharpe ratio, Jensen's alpha and Fama-French alpha in the long horizon. The results are robust to di erent portfolio weighting technologies and the consideration of turnover costs. In addition, the green portfolio's outperformance is driven by a bunch of small, aggressive and relatively inactive stocks that have better performance than the market predicts. No evidence shows that the ever-increasing demand on green securities leads to the green portfolio's outperformance, because green stocks are actually less actively traded. Panel regressions further indicate that long-horizon corporate economic performance positively correlates to historical corporate environmental performance.
Ph.D. in Management Science, July 2014
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Title: QUALITY-OF-SERVICE AWARE SCHEDULING AND DEFECT TOLERANCE IN REAL-TIME EMBEDDED SYSTEMS
Creator: Li, Zheng
Date: 2015, 2015-05
Description: For real-time embedded systems, such as control systems used in medical, automotive and avionics industry, tasks deployed on such systems...
Show moreFor real-time embedded systems, such as control systems used in medical, automotive and avionics industry, tasks deployed on such systems often have stringent real-time, reliability and energy consumption constraints. How to schedule real-time tasks under various QoS constraints is a challenging issue that has drawn attention from the research community for decades. In this thesis, we study task execution strategies that not only minimize system energy consumption but also guarantee task deadlines and reliability satisfaction. We first consider the scenario when all tasks are of the same criticality. For this case, two task execution strategies, i.e. checkpointing based and task re-execution based strategies are developed. Second, considering the scenario when tasks are of different criticalities, a heuristic search based energy minimization strategy is also proposed. When tasks are of different criticalities, a commonly used approach to guaranteeing high-criticality task deadlines is to remove low-criticality tasks whenever the system is overloaded. With such an approach, the QoS provided to low-criticality tasks is rather poor, it can cause low-criticality tasks to have high deadline miss rate and less accumulated execution time. To overcome this shortcoming, we develop a time reservation based scheduling algorithm and a two-step optimization algorithm to meet high-criticality task deadlines, while minimizing low-criticality task deadline miss rate and maximizing their accumulated execution time, respectively. As many-core techniques mature, many real-time embedded systems are built upon many-core platforms. However, many-core platforms have high wear-out failure rate. Hence, the last issue to be addressed in the thesis is how to replace defective cores on many-core platforms so that deployed applications’ real-time properties can be maintained. We develop an offline and an online application-aware system reconfiguration strategy to minimize the impact of the physical layer changes on deployed real-time applications. All the developed approaches are evaluated through extensive simulations. The results indicate that the developed approaches are more effective in addressing the identified problems compared to the existing ones in the literature.
Ph.D. in Computer Science, May 2015
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Title: UNDERSTANDING REACTION MECHANISMS AND CONTROLLING REACTIVE SURFACE SPECIES DURING ATOMIC LAYER DEPOSITION OF METAL CHALCOGENIDES
Creator: Weimer, Matthew S.
Date: 2016, 2016-07
Description: Atomic layer deposition (ALD) is a thin film growth technique that relies on self-limiting reactions between vapor precursors and a surface....
Show moreAtomic layer deposition (ALD) is a thin film growth technique that relies on self-limiting reactions between vapor precursors and a surface. Significant progress has been made in the scope of materials grown by ALD, enabled by precursor development and investigation of surface reaction mechanisms; progress is still necessary. This dissertation has two portions. The first is the development of organometallic compounds to engender new material growth by ALD. Second is the development of X-ray absorption spectroscopy (XAS) tools and techniques for observations of the metal coordination environment during ALD. One material that can be difficult to make is doped materials. Composition of a doped material determines the film properties. One example is vanadium doped indium sulfide. This material was purposed as an intermediate bandgap solar absorbing material which can absorb multiple ranges of light. Two new precursors were developed for the growth of indium sulfide and vanadium sulfide. The indium sulfide material grown has shown superior film photocurrent qualities and doping of vanadium into indium sulfide with fine control over atomic placement was achieved. Films were grown that showed secondary absorptions which aligned with theoretical calculations. The flexibility of the V(III) precursor is shown by a short study on the control of the difficult vanadium-oxygen system in the deposition of stoichiometric oxides. To illustrate how XAS can be used in conjunction with other techniques tin dioxide growth from a stannylene precursor and hydrogen peroxide was studied. From ex situ XAS measurements nucleation, growth and termination reaction mechanism were discovered. Next, a mobile ALD reactor allowed for in situ XAS measurements to be performed on “flat” substrates for the first time. Specifically, the local coordination environment and surface reactions were followed while erbium was doped into alumina and coordination environment of manganese was investigated in the growth of manganese-doped zinc oxide, with the ability to probe in-plane versus out-of-plane bonds. These unique in situ XAS experiments allow for greater understand of metal and non-metal precursors as they interact with surfaces. This enhanced understanding enables new precursor development which leads to better control over surface chemistry and new materials.
Ph.D. in Chemistry, July 2016
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Title: ECONOMIC BASED CONTROL SYSTEM DESIGN
Creator: Omell, Benjamin Peter
Date: 2013, 2013-12
Description: EMPC differs from traditional MPC by directly utilizing a profit based function as the objective as opposed to a quadratic function that...
Show moreEMPC differs from traditional MPC by directly utilizing a profit based function as the objective as opposed to a quadratic function that minimizes the distance from a set point that is predetermined. However, implementation of EMPC can result in unexpected and at times pathological closed-loop behavior, including inventory creep, bang-bang actuation and instability. To address these issues, an infinite-horizon version of EMPC is developed and shown to avoid many of the performance issues observed in the finite-horizon version. First, modifications to the EMPC problem will be used for the conceptual development of the Economic Linear Optimal Controller (ELOC), which is a statistically constrained linear feedback controller. Then, pointwise- in-time constraints can be reintroduced using one of two methods; Constrained ELOC or Infinite-Horizon EMPC (IH-EMPC). We also investigate the impact of problem formulation modifications on the ELOC. The first issue is that of disturbance modeling and the second is the impact of controller sample-time. The third topic concerns incorporation of computational delay in the feedback-loop, using both full and partial state information structures. Finally an illustration of the impact of plant-model mismatch is presented. The Constrained ELOC formulation is further modified to allow for market responsive smart grid applications. In particular an Integrated Gasification Combined Cycle (IGCC) process with hydrogen storage will be used to demonstrate the Constrained ELOC for such applications. The ELOC will be used as a vehicle to exploit dispatch capabilities by pursuing directly the objective of maximizing revenue. The idea being that process modifications to enable dispatch capabilities will allow for a time-shift of power production away from periods of low energy value to periods of high value. An in depth discussion is provided on how energy value forecasts are incorporated into the design of the constrained ELOC. Finally, an extension of the ix ELOC to the controller embedded equipment design is provided. The work concludes with a discussion of the computational aspects of solving the ELOC problem. In particular, the impact of reverse-convex constraints inherent to the ELOC problem are discussed along with existing solution methods. The main contribution of this final chapter is a novel application of the Generalized Bender’s Decomposition (GBD) algorithm to the ELOC problem. This new approach is shown to retain global optimality, reduce computational effort (by orders of magnitude) and expand the class of problems one can solve.
PH.D in Chemical Engineering, December 2013
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Title: BIOPHYSICAL AND BIOCHEMICAL STUDY OF NATIVE AND EDITED DYSTROPHIN ROD REGION
Creator: Mangat, Khushdeep
Date: 2014, 2014-12
Description: Duchenne Muscular Dystrophy (DMD) is a severe X-linked recessive disease affecting 1 in 3500 boys that is characterized by the degeneration of...
Show moreDuchenne Muscular Dystrophy (DMD) is a severe X-linked recessive disease affecting 1 in 3500 boys that is characterized by the degeneration of muscle function and strength. The cause of this disease lies in gene defects that eliminate expression of the protein dystrophin. Becker Muscular Dystrophy, BMD is a milder form of disease that has a later onset and much longer survival (up to the 7th decade of life, compared to median survival of 25 years for DMD patients) because of the presence of low levels of modified dystrophin protein. BMD is very heterogeneous, however, and many cases are nearly as severe as DMD. A major therapy for DMD involves exon skipping, which produces modified forms of dystrophin that are very similar to BMD. However, how these edits impact the function of dystrophin, and how they are linked to the severity of BMD or the BMD-like state produced in DMD exon skip therapy is unknown. We investigated this in two specific cases involving a specific panel of BMD defects linked to a major cause of death, dilated cardiomyopathy (DCM). We also investigated the contribution of various exons to interaction with a signaling partner of dystrophin, neuronal nitric oxide synthetase (nNOS).
Ph.D. in Biological and Chemical Sciences, December 2014
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Title: PHYSICS-PRESERVING FINITE DIFFERENCE SCHEMES FOR THE POISSON-NERNST-PLANCK EQUATIONS
Creator: Flavell, Allen
Date: 2014, 2014-07
Description: The Poisson-Nernst-Planck equations are a system of nonlinear di erential equations that describe ow of charged particles in solution. This...
Show moreThe Poisson-Nernst-Planck equations are a system of nonlinear di erential equations that describe ow of charged particles in solution. This dissertation is about the design of numerical schemes to solve this system which preserves global properties exhibited by the system. There are two major advances presented. The rst is the design of schemes that conserve mass globally when the system is coupled with no- ux boundary conditions. Most notably, a scheme using central di erencing and TR-BDF2 achieves second order accuracy in both space and time, while also conserving global mass is presented. The second is the design of a more general scheme that preserves the time-varying properties of the free energy of the system. One such a scheme uses central di erencing in space and trapezoidal integration in time to achieve second order accuracy in both space and time, while also preserving the energy dynamics, but at the cost of requiring positivity of the solution. There is also a discussion of solution methods: the classic Newton iteration scheme is compared with a modi ed Gummel iteration scheme for the purpose of solving the transient equations. The intended application of this work is the modeling of ion channels, and many of the simulations presented use parameters consistent with models of ion channels.
Ph.D. in Applied Mathematics, July 2014
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Title: HYBRID TO SOCIAL CONDENSER: COMPETING APPROACHES TO MIXED-USE DEVELOPMENT
Creator: Zagow, Maged
Date: 2016, 2016-12
Description: In the last two decades, mixed use has taken center stage in urban planning development in the United States. The research frequently cites...
Show moreIn the last two decades, mixed use has taken center stage in urban planning development in the United States. The research frequently cites this development as a model that can address a variety of socioeconomic problems. Also, it has enjoyed a recent surge in popularity in redeveloping cities by providing more affordable housing opportunities, ensuring safety, reducing auto-dependency, and for providing a sense of place and community. However, its affordability, physical design, and outcomes are highly variable. This study is particularly interested in whether and how mixed use affects the socioeconomics configuration of the built environment. This study uses multilevel data from the county level to the zip code level that represents all US neighborhoods. I use different implementation methods of mixed-use development and different cultural and historical backgrounds to examine the data. The study adopts six mixed-use models that present different methodological interactions between socioeconomic spatial metrics and urban forms. These models represent the realistic constraints of urban geometry and of the socioeconomic structure that comprises the charateristics of race, income, accessibility, safety, adjacency, accessibility, environment, and density. This study finds that the built environment produces a rich landscape of information that appears to guide the opportunities for facilities. The analysis shows that mixed-use development may have certain effects on the number of facilities, housing, income, diversity, crime rate, employment, health, and environment. The analysis of this research works in two dimensions. First, urban models (Hybrid and Social Condenser in general and under two categories Metropolis and Neighborhood Community). The second dimension is the urban characteristics (zoning programming, land use mix, streets fabric), socioeconomics variables (Population density, occupied housing, median age, diversity of race, income, and employment rates), and location variation (states, and cities). The results confirm that mixing the facilities in hybrid communities create more jobs opportunities but limit the affordability of housing, social cohesion and the race diversity. But in Social Condenser models, there are more race diversity safety and healthy environment. These results reflect complexity demands more than mixed-use developments, beyond Jane Jacobs' requirements, and beyond the designation of selected mixed-use zones. This study contributes to the study of how mixed-use development models shift because of various social and economic conditions. The findings from this study can inform architects, investors, policymakers, economists, and planners about factors that sustain mixed-use neighborhoods in the United States and beyond. Urban designers will be able to inform how the seemingly necessary act of laying out mixed-use development can affect the socioeconomic structure of a city. Thus, this study is a useful source for more accurate planning ideas than generic abstract theories or slogans.
Ph.D. in Architecture, December 2016
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Title: STUDIES ON SYNTHETIC APPLICATIONS OF STEREOSELECTIVE AND REGIOSELECTIVE RING OPENING REACTIONS OF AZIRIDINIUM IONS
Creator: Chen, Yunwei
Date: 2014, 2014-12
Description: Aziridinium ions are valuable reactive intermediates in organic synthesis. Regioselective and stereoselective ring opening reactions of...
Show moreAziridinium ions are valuable reactive intermediates in organic synthesis. Regioselective and stereoselective ring opening reactions of aziridinium ions can provide various useful building blocks including optically active vincinal amines, amino alcohols and amino esters. Aziridinium ions are also involved in the biological process of anti-cancer agents. However, aziridinium ions are under-utilized in organic synthesis. In this thesis, we utilize stereoselective and regioselective ring opening reactions of aziridinium ions for synthesis of enantiomerically enriched compounds. Ring opening reactions of aziridinium ions were utilized in intramolecular Friedel-Crafts (FC) reactions for stereoselective and regioselective synthesis of 4-substituted tetrahydroisoquinoline. A series of β-haloamine were prepared as precuresors of aziridinium ions. The reaction conditions for ring opening of aziridinium ions for the FC reactions including temperature, catalysts, and solvents were optimized. Further, the reaction mechanism was studied to prove that the aziridinium ions were formed as the key intermediates during the intramolecular FC reaction. Intermolecular nucleophilic ring opening reaction of aziridinium ions was studied as a convenient method of carbon-carbon formation. Regioselective and stereoselective nucleophilic substitution reactions of aziridinium ions with indole analogues were carried out for the synthesis of optically active tryptamine analogues. The reactions proceeded smoothly to provide the tryptamine analogues in high yield in the presence of halo-sequestering agents, while the reaction provided the tryptamine products in significantly low yield in the absence of halo-sequestering agents. Ring opening reactions of aziridinium ions with malonic esters and Grignard reagents were carried out for the respective synthesis of optically active tryptamine analogues, γ-aminobuyric acid (GABA), and α-amine derivatives. The regiospecific ring opening reactions of aziridinium ions was directly applied for the synthesis of bifunctional ligands which have a potential use in targeted therapy and imaging of cancers. The novel bifunctional chelates with a shorter alkyl spacer C-NETA and 2E-C-NETA as well as the chelates with a longer alkyl spacer 5p-C-NETA were prepared. 5p-C-NETA was conjugated to a cyclic peptide c(RGDyK) as a targeting moiety for use in targeted radiation therapy. In addition, 2E-C-NETA was conjugated to a fluorescent dye Cy5.5 for theranostic applications. The experimental results indicated that the new bifunctional ligands have promising applications in the biomedical field. In summary, stereoselective and regioselective ring opening reactions of aziridinium ions have been successfully applied for the synthesis of optically active compounds such as 4-substituted tetrahydroisoquinolines, tryptamines, γ-aminobuyric acid, α-amine derivatives and the bifunctional chelators. We demonstrated that ring opening of versatile aziridinium intermediates is a strightforward and convenient method for the synthesis of various optically active compounds.
Ph.D. in Chemistry, December 2014
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Title: ELIASHBERG ANALYSIS OF CUPRATE OXIDE SUPERCONDUCTORS
Creator: Ahmadi, Omid
Date: 2011-11, 2011-12
Description: In this thesis, evidence for antiferromagnetic spin uctuations as the pairing glue in high temperature superconductors is presented through a...
Show moreIn this thesis, evidence for antiferromagnetic spin uctuations as the pairing glue in high temperature superconductors is presented through a modi ed Eliashberg analysis of experimental tunneling data of Bi2212 over a wide range of doping. In particular, the normalized conductance data of the junctions, from optimal to overdoped, will be tted at T=0K using d-wave Eliashberg equations where the spectral function is modeled after spin uctuation spectra seen in experiments. The corresponding real and imaginary diagonal and anomalous self-energy curves are extracted and compare well to photoemission experiments. This is followed by a temperature dependent Eliashberg analysis where the spectral function is now temperature dependent, based on trends seen in inelastic neutron scattering experiments. New results for temperature dependent self energy curves are also compared to experiment with slight deviations. Finally, the Josephson product is calculated as an independent check of the tunneling matrix used in tting the data.
Ph.D. in Physics, December 2011
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