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Title: ENHANCED DEGRADATION AND PEPTIDE SPECIFICITY OF MMP-SENSITIVE SCAFFOLDS FOR NEOVASCULARIZATION OF ENGINEERED TISSUES
Creator: Sokic, Sonja
Date: 2013, 2013-07
Description: Biomaterial strategies for engineering tissues of clinically relevant size require the formation of rapid and stable neovascularization. The...
Show moreBiomaterial strategies for engineering tissues of clinically relevant size require the formation of rapid and stable neovascularization. The ability of an engineered scaffold to induce vascularization is highly dependent on its rate of degradation. During the process of material degradation, the scaffold should degrade in a manner allowing for cellular infiltration, lumen formation, and extracellular matrix (ECM) synthesis. Matrix metalloproteinases (MMPs) play a key role in mediating cell-induced proteolytic matrix degradation, remodeling, and controlled neovascularization. Poly (ethylene glycol) PEG hydrogels have been extensively investigated as scaffolds for tissue engineering applications due to their ease of chemical modification allowing for the recapitulation of key aspects of the neovascularization process. The goal of the work described in this thesis was to develop strategies to enhance and control the degradation of MMP-sensitive PEG diacrylate (PEGDA) hydrogels without inducing changes to the bulk physical and mechanical properties of the material and to further study the effect of the cleavage site concentration and MMP-sensitive peptide substrate specificity on the rate of neovascularization and tissue remodeling in vitro and in vivo. In the first part of this study, a detailed investigation was completed to investigate the effects of the mechanical and physical properties of the scaffolds as well as the role of proteolytically mediated hydrogel degradation on 3D fibroblast invasion within MMPsensitive PEGDA hydrogels. Initial studies focused on the use of a modified version of a previously published multistep conjugation method to generate degradable PEGDA macromer conjugates containing variations in the number of MMP-sensitive domains. Theoretical and experimental characterization of this multistep conjugation demonstrated xi that this method leads to the formation of multiple species that directly affect the compressive modulus and degradation rate of the scaffold making it difficult to control degradation independent of alterations in the bulk physical and mechanical hydrogel properties. After manipulation of multiple polymerization conditions, hydrogels with similar compressive moduli but different hydrogel degradation rates were synthesized. These initial studies showed that an increase in the incorporation of proteolytically sensitive domains in PEGDA hydrogels of similar modulus lead to enhanced degradation and 3D fibroblast invasion. In this study, the role of soluble FGF-1 on fibroblast invasion within these scaffolds was investigated and it was demonstrated that the inclusion of FGF-1 in the scaffolds results in further enhancement of fibroblast invasion in a dosedependent fashion. Further studies were necessary to develop a more controllable and robust approach in tuning scaffold degradation independent of alterations in the bulk physical and mechanical properties. In order to address this, a novel approach was developed to engineer protease-sensitive peptides with multiple proteolytic cleavage sites that could be covalently crosslinked into hydrogels without compromising the physical and mechanical biomaterial properties. This approach avoided the need for utilizing a multistep conjugation process as peptides could be incorporated into the backbone of PEG using a single step conjugation. Using this approach, hydrogels formed with the engineered peptides led to significantly enhanced degradation and neovascularization in vitro as compared to scaffolds with a single protease sensitive peptide between crosslinks. In addition, hydrogels with enhanced susceptibility to degradation promoted vascularization over a wider range of matrix properties. This approach allowed for controlled xii concentration of the proteolytic cleavage sites within the matrix and thus tuning of hydrogel degradation for tissue engineering applications. In the final study, MMP-sensitive peptide substrates specific to degradation by MMPs known to be expressed during neovascularization were screened for degradation and their role in neovascularization. MMP-sensitive PEGDA hydrogels (SSite and TriSite) were synthesized with peptide substrates sensitive to cleavage by MMP-2, MMP- 9, MMP-14, a mixed sequence of MMP-2, 9 and 14, and compared to the peptide substrate used in the previous studies, which is degraded by collagenase enzymes. The hydrogels were evaluated for their sensitivity and specificity to degradation by MMPs, in terms of cleavage site concentration, and for their role in neovascularization and tissue remodeling in vitro and in vivo. The presented approach allows for the incorporation of varying cleavage site concentration and MMP-sensitive peptide substrates into PEG hydrogels without alterations in the mechanical and physical properties of the hydrogels. Results showed that without the incorporation of growth factors in this scaffold, vascularization and tissue invasion was supported in all MMP-sensitive hydrogel groups regardless of the MMP-sensitive peptide substrate embedded in the matrix. In addition, the cleavage site concentration had a profound impact in enhancing vascularization in vitro and tissue invasion in vivo. These techniques can be used to tune the properties of polymer scaffolds for neovascularization and tissue remodeling. In addition, these studies provide insight into the effect of the physical, mechanical, and degradative properties of these systems and on the role of cleavage site concentration, and MMP substrate specificity on xiii neovascularization and tissue invasion within proteolytically degradable PEG hydrogel constructs.
PH.D in Biomedical Engineering, July 2013
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Title: HIGH PERFORMANCE, HIGH STABILITY AND LOW POWER SRAM DESIGN BY USING CARBON NANOTUBE FIELD EFFECT TRANSISTORS
Creator: Wang, Wei
Date: 2012-07-07, 2012-07
Description: As the feature size of silicon semiconductor devices scales down to nanometer range, planar bulk CMOS design and fabrication encounter...
Show moreAs the feature size of silicon semiconductor devices scales down to nanometer range, planar bulk CMOS design and fabrication encounter significant challenges. This situation is exacerbated when it comes to SRAM, as SRAM takes a large part of power consumption and area overhead in modern VLSI processor designs. To achieve higher performance, stability and lower power consumption, carbon nanotube (CNT) has been introduced to SRAM design as an alternative material. The semiconducting single-walled CNTs are promising candidates for the channel material of CMOS devices because of two advantages over the other semiconductor materials: high ON current, leading to high speed and low OFF current, leading to less leakage power. In this research work, characterizing work of technology parameters for 6T carbon nanotube field effect transistor (CNFET) SRAM cell is performed for basic understanding of the relationship between SRAM delay/power and CNFET technology parameters. Stability issue is studied by investigating the diameter and transistor ratio impacts on the SRAM static noise margin (SNM). A stability-optimized 6T CNFET SRAM cell achieves 38.88% reading delay reduction, 21.61% writing delay reduction, 85.65% reading power reduction, 5.88% writing power reduction, 97.80% leakage power reduction, 41.41% SNM increment, 91.23% reading power-delay product (PDP) reduction and 26.23% writing PDP reduction, compared with conventional silicon MOSFET SRAM cell. To mitigate major CNT imperfection impacts on CNFET circuits, a misalignment immune SRAM design method is proposed to eliminate CNT misalignment problem by using etching region defined in circuit layout; and a diameter variation sensing and compensating system is designed to mitigate the negative impacts of CNT diameter variation on SRAM delay and power consumption. A hybrid silicon/CNT 4T SRAM cell design is proposed for low-power high-density cache application, which is better than conventionally used 6T SRAM in terms of power consumption and circuit area. Finally, a design flow of high performance, high stability and low power SRAM is summarized.
Ph.D. in Electrical Engineering, July 2012
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Title: CONTROLLER DESIGN AND DISTRIBUTED CONTROL WITHIN MULTI-AGENT SYSTEMS
Creator: Shao, Quan Min
Date: 2013, 2013-12
Description: None
PH.D in Chemical and Biological Engineering, December 2013

Title: POLYMER ELECTROLYTE MEMBRANES FOR ELECTROCHEMICAL ENERGY CONVERSION AND STORAGE SYSTEMS: FUEL CELLS AND REDOX FLOW BATTERIES
Creator: Yun, Sukhwan
Date: 2014, 2014-12
Description: Direct methanol fuel cells (DMFCs) and redox flow batteries (RFBs) are well-known electrochemical energy conversion/storage systems that...
Show moreDirect methanol fuel cells (DMFCs) and redox flow batteries (RFBs) are well-known electrochemical energy conversion/storage systems that utilize redox reactions to convert or store electricity. Ion exchange membranes (IEMs) are used in DMFCs and RFBs as electrolyte separators. The critical requirements for IEMs in these applications are high ionic conductivity, low electrolyte permeability, high stability, and low cost. Silsesquioxane (SQO)-based sulfonated poly(etheretherketone) composite membranes were synthesized. Morphological changes in the composite membranes resulting from the introduction of SQO were studied using small-angle x-ray scattering. A sharp decrease in proton conductivity with SQO loading (> 20 wt%) was attributed to morphological changes in the membrane, including agglomeration and inhomogeneous dispersion of SQO particles within the ionic domains. Anion exchange membranes (AEMs) based on quaternized cardo-poly(etherketone) (QPEK-C) were prepared and evaluated for all-vanadium RFB (VRFB) applications. The QPEK-C AEMs with different degrees of functionalization (0.9–1.6) exhibited sulfate ion conductivities ranging between 5.6 and 15.2 mS cm-1 at 30 oC. The AEM had a lower VO2+ permeability (2.8×10-8 cm2 s-), compared to that of Nafion® 212 (2.9±0.2 ×10-7 cm2 s-1), which was attributed to the Donnan exclusion effect. The mechanical strength of QPEK-C AEM degraded by 35% after exposure to a 1.5 M VO2+ solution for 1500 hours due to the oxidation of aromatic rings. A single-cell VRFB employing the AEM separator yielded current and energy efficiencies (at 30 mA cm-2) of 97-99% and 80-82 %, respectively. Enhanced sulfate ion conductivity (8.4 ± 0.2 mS cm-1) and decreased VO2+ permeability (0.53×10-9 cm2 s-1) were achieved by incorporating 20 wt% of n-(trimethoxysilylpropyl)-n,n,n-trimethylammonium additives into QPEK-C, (the pristine QPEK-C AEM yielded corresponding values of 4.5 ± 0.5 mS cm-1 and 1.09×10-9 cm2 s-1). About 99% coulombic efficiency was achieved with the VRFBs employing the composite AEM. However, a rapid reduction of the ionic conductivity down to the value of the pristine membrane was observed when the composite AEM was immersed in 1.5 M VO2+ solution for 3 days. Vanadium-cerium RFBs (V-Ce RFBs) evaluated with QPEK-C AEM separators yielded identical energy efficiency (84%) to corresponding RFBs evaluated with Nafion® 212. However, after over 20 charge-discharge cycles, the V-Ce RFB with the AEM separator yielded unchanged efficiency and capacity, while a 50% loss of capacity was observed with the Nafion® separator. This suggested that QPEK-C AEMs are promising candidates for RFB separators when different cations are used in the two electrolyte solutions, in that they act as efficient barriers that preclude the intermixing of the cations due to the Donnan exclusion effect.
Ph.D. in Chemical Engineering, December 2014
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Title: MULTI-DIMENSIONAL BATCH SCHEDULING FRAMEWORK FOR HIGH-END SUPERCOMPUTERS
Creator: Zhou, Zhou
Date: 2016, 2016-05
Description: In the field of high performance computing (HPC), batch scheduling plays a critical role. They determine when and how to process the various...
Show moreIn the field of high performance computing (HPC), batch scheduling plays a critical role. They determine when and how to process the various jobs waiting for service. Conventional batch schedulers allocate user jobs solely based on their CPU footprints. However, for a given user job, it requires many different resources during its execution, such as power, network, I/O bandwidth, etc. Today’s job schedulers rarely take into account these resource requirements which sometimes turn out to be the Achilles’ heel of system-wide performance. In this research, we propose a multi-dimensional batch scheduling framework for high-end supercomputers. Our research aims to treat these common but often ignored resources (e.g., power, network, bandwidth) as schedulable resource and further transform each scheduling into a multi-objective optimization process. Our main contributions consist of a set of scheduling models and policies, aiming at addressing the issues in batch scheduling for large-scale production supercomputers. We evaluate our design by means of trace-based simulations using real workload and performance traces from production systems. Experimental results show our methods can effectively improve batch scheduling regarding user satisfaction, system performance and operating cost.
Ph.D. in Computer Science, May 2016
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Title: OPTIMAL SIGNAL TIMING DESIGN FOR URBAN STREET NETWORKS UNDER USER EQUILIBRIUM BASED TRAFFIC CONDITIONS
Creator: Liu, Yi
Date: 2015, 2015-05
Description: In the ever-growing travel demand, traffic congestion on freeways and expressways recurs more frequently at a higher number of locations and...
Show moreIn the ever-growing travel demand, traffic congestion on freeways and expressways recurs more frequently at a higher number of locations and for longer durations with added severity. This becomes especially true in large metropolitan areas. Particular to the urban areas, excessive crowdedness caused by inefficient traffic control also results in urban street networks operating in near or over-saturated conditions, leading to unpleasant travel experience due to long delays at intersections. As a consequence, the recurrent traffic congestion on roadway segments and vehicle delays at intersections inevitably compromise energy efficiency, traffic mobility improvement, safety enhancement, and environmental impacts mitigation. All too often, neither restraining travel demand nor expanding system capacity is desirable and practical. Conversely, effectively utilizing the capacity of the existing transportation system has been increasingly thought of as the solution to congestion relief. With respect to the urban street networks, developing effective means for urban intersection signal optimization becomes essential to reduce intersection delays. Conventional signal timing optimization methods use historical traffic data and assume that traffic flows will remains unchanged after the implementation of new signal timing plans. Traffic flows are assumed to be constant, but in fact, when signal timing plans change, travel times for some travel routes will alter, which requires drivers in the network to adjust their choice of travel routes to arrive at the destinations, and result in redistribution of traffic in the network. Therefore, the effects of interactions between signal timing plans and traffic flows need to be explicitly taken into consideration. This study introduces a new methodology that jointly considers signal timing optimization and traffic assignment in an overall analytical framework that contains model formulations under assumptions consistent with real world situations. Such a framework is well suited for applications in real world cases. Specifically, the overall optimization framework is formulated as a bilevel optimization problem. In the proposed basic model, at the upper level, a traffic signal timing optimization problem for urban network is introduced to minimize system total travel time by optimizing signal green splits. At the lower level, a static user equilibrium problem is formulated for networkwide traffic assignment. In the vehicle delay estimation, the time-dependent stochastic delay model in the 2010 Highway Capacity Manual (HCM 2010) is employed and formulated as Variational Inequality constraints, what allow the state-of-the-art MPEC solver, GAMS/NLPEC, to solve the problem for a local optimal effectively and efficiently. The bi-level optimization model is first tested using a small network (the test network) and a computational experiment using a subarea network in the Chicago central district is conducted to assess the practicality of the model formulation in real world applications. In order to import more reality to the basic model and also consider the potential system benefit that comes from different signal phasing design, an enhanced model is developed based on the basic model by employing integer and binary variables. Formulating the problem with binary variables allows for the selection of proper phasing design. Heuristic solution methods are proposed and tested using the test network.
Ph.D. in Civil Engineering, May 2015
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Title: DISRUPTION OF EPILEPTIC SEIZURES USING TARGETED MULTI-SITE ELECTRICAL STIMULATION
Creator: Sobayo, Tiwalade
Date: 2015, 2015-12
Description: Neuronal populations in the brain achieve levels of synchronous electrophysiological activity during both normal brain function and...
Show moreNeuronal populations in the brain achieve levels of synchronous electrophysiological activity during both normal brain function and pathological states such as epileptic seizures. Understanding how the dynamics of neuronal oscillators in the brain evolve from normal to diseased states is a critical component towards decoding such complex behaviors. In my studies, I assessed multi-site dynamics underlying seizure evolution in limbic epilepsy by analyzing oscillators in recordings of local field potentials from three brain structures (bilateral hippocampi and anteromedial thalamus) in a rat model of temporal lobe epilepsy extracted using the empirical mode decomposition (EMD) technique. The analysis revealed patterns of multi-site phase coherence during initiation and termination phases of seizures. The multi-site synchrony events as seizures naturally terminated were used to model electrical deep brain stimulation (DBS) protocols aimed at stopping ongoing epileptic seizures. The location and frequency of the natural termination synchrony varied between subjects but was stable in time within each animal. My studies reveal that DBS protocols were significantly more effective at rapidly stopping seizures when the frequency and location of multi-site stimulation reflected the endogenous synchrony dynamics observed in each subject. These results strongly suggest that tailoring DBS protocols to individual endogenous rhythms that may represent how brains naturally resolve epileptic seizures could play a critical role in vastly improving the overall efficacy of this important therapy.
Ph.D. in Biomedical Engineering, December 2015
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Title: NEUTRON PRODUCTION IN THE M2 MUON BEAM LINE AT CERN
Creator: Draeger, Emily
Date: 2014, 2014-05
Description: Spallation neutrons produced from cosmic ray muons are a major source of backgrounds in underground physics experiments. Experiments have been...
Show moreSpallation neutrons produced from cosmic ray muons are a major source of backgrounds in underground physics experiments. Experiments have been done to study spallation neutron production and yield, but our understanding of these processes is still limited. There are various interactions that can produce spallation neutrons. Most of these production mechanisms are fairly well understood; much of the uncertainty in our understanding of spallation neutrons lies in mechanisms such as virtual photon exchange and the assumptions used to calculate the photonuclear cross section. Even the experiments that have been carried out do not agree with each other or theoretical calculations. Spallation neutron production mechanisms are discussed, as well as a new experiment to study spallation neutrons. The impact of this study on current and future underground physics experiments is also explored.
PH.D in Physics, May 2014
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Title: NOVEL FAULT DIAGNOSTIC TECHNIQUE AND UNIVERSAL SENSOR FOR PERMANENT MAGNET ELECTRIC MACHINES USING SEARCH COILS
Creator: Da, Yao
Date: 2012-04-23, 2012-05
Description: Over the past decade, permanent magnet synchronous machines (PMSMs) have gained significant popularity in industry, such as wind turbines and...
Show moreOver the past decade, permanent magnet synchronous machines (PMSMs) have gained significant popularity in industry, such as wind turbines and electric vehicles, owing to their high efficiency, high output power to volume ratio, and high torque to current ratio. In these mission critical applications, an unexpected fault or failure of the machine could lead to very high repair or replacement cost, or even catastrophic system failure. Therefore a robust and reliable health monitoring and fault diagnostic approach is desired, which could help in scheduling preventive maintenance to lengthen their lifespan and avoid machine failure. This dissertation presents a novel multi-faults diagnostic approach using search coils. These search coils are wound around armature teeth, so they typically need to be installed during manufacturing. But its immunity to high frequency harmonics makes it suitable for inverter/rectifier fed motors or generators, such as wind turbines and automotive systems. In addition, this method does not require the knowledge of proprietary constructional details of the machine. Since the electromagnetic flux is directly measured in this method, it provides much more information than any other scheme: the direction of eccentricity and the location of shorted windings. Furthermore, this method is also capable of evaluating the severity of each fault, which is of significant importance in mission critical applications such as automotive, aerospace and military applications. In addition to these uses, the search coils can be used as a universal sensor to estimate phase current or rotor position, which are critical information in a PMSM close-loop control, which allow it to work as a backup sensor for fault tolerant operation. The proposed fault detection scheme and universal sensor concept have been tested under several scenarios with Finite Element Analysis and experimentally validated.
Ph.D. in Electrical Engineering, May 2012
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Title: CELL-MATRIX INTERACTIONS IN ADIPOSE TISSUE FUNCTION
Creator: Vaicik, Marcella K.
Date: 2015, 2015-07
Description: The overall goal of this work is to apply in vivo and in vitro models to study the basement membrane protein laminin α4 (lama4) in adipocyte...
Show moreThe overall goal of this work is to apply in vivo and in vitro models to study the basement membrane protein laminin α4 (lama4) in adipocyte function. Adipose tissue accumulation, lipogenesis, and structure were examined in mice with a null mutation of the lama4 gene (Lama4−/−) and compared to wild-type animals (Lama4+/+). The Lama4−/−mice phenotype was investigated to evaluate if the differences were due specifically to the adipose tissue function. Physical activity and food intake does not differ between Lama4+/+ and Lama4−/− mice. However, Lama4−/− mice have a significantly increased metabolic rate at 25°C and 16°C compared to Lama4+/+ mice. In contrast, in thermoneutral conditions at 30°C both Lama4+/+ and Lama4−/− mice exhibit equivalent metabolic rates. Interestingly, when room temperature housed mice fat pads were evaluated with immunohistochemistry, Lama4−/− mice exhibit significantly increased UCP-1 expression in subcutaneous adipose. These results suggest that beiging, white to brown adipocytes, in subcutaneous adipose tissue in Lama4−/− mice may lead to decreased adipose tissue accumulation and improved metabolic function. While animal models indicate the absence of lama4 results in more beiging in subcutaneous adipose tissue, an in vitro tissue engineered model was developed to study the adipocyte function in a controlled microenvironment. Primary cell spheroids developed from Lama4+/+ and Lama4−/− were incorporated into synthetic poly(ethylene glycol) (PEG) hydrogels within a range of stiffnesses. When the cells were given the same chemical cues their functions differed depending upon microenvironment stiffness. Beige function in adipocyte cells in 3D can be influenced by matrix stiffness. In conclusion, the laminin alpha 4 basement membrane protein absence in adipose tissue results in adipocyte functional changes in vivo. The Lama4−/− mice have resistance to diet induced weight gain and increased metabolic rate at room temperature and when cold challenged. The Lama4−/− mice had increased beiging in the subcutaneous depot. Additionally, a tissue engineered model was developed to further study cell-ECM interactions first identified in an animal model. These in vivo findings and the engineered model of adipose tissue have great potential for studying obesity and other adipose related diseases. Future work will require continued interdisciplinary collaboration towards the successful identification and screening of novel therapeutics using engineered tissue models.
Ph.D. in Biomedical Engineering, July 2015
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Title: DEVELOPMENT OF A HIGH ANGULAR RESOLUTION DIFFUSION IMAGING TEMPLATE AND PROBABILISTIC CONNECTIVITY-BASED ATLAS OF THE HUMAN BRAIN
Creator: Varentsova, Anna
Date: 2016, 2016-05
Description: Digital human brain atlases consisting of MRI-based templates and semantic labels delineating different brain regions serve a critical role in...
Show moreDigital human brain atlases consisting of MRI-based templates and semantic labels delineating different brain regions serve a critical role in neuroimaging, mainly facilitating spatial normalization and automated segmentation for the purposes of voxel-wise, region-of-interest, and network analyses. Diffusion MRI templates contain rich information about the microstructure of the brain, however the accuracy of templates constructed based on the diffusion tensor imaging (DTI) model is limited in regions with complex neuronal microarchitecture. High angular resolution diffusion imaging (HARDI) overcomes limitations of the DTI model and is capable of resolving intravoxel heterogeneity. In this work a method to develop artifact-free HARDI template of the human brain from low angular resolution data is presented. Existing white matter (WM) atlases have been generated either based on anatomical landmarks, thus mixing tracts with substantially different roles, or using DTI tractography, which fails in regions with crossing fibers. Connectivity-based atlases developed using HARDI templates and probabilistic tractography have potential to identify functionally distinct subregions of the brain. This work presents connectivity-based atlas of human brain WM created using HARDI template in ICBM-152 space and a set of FreeSurfer grey matter labels.
Ph.D. in Physics, May 2016
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Title: FIELD AND PHOTO-EMISSION IN A SHORT-PULSE, HIGH-CHARGE CESIUM TELLURIDE RF PHOTOINJECTOR
Creator: Wisniewski, Eric E.
Date: 2014, 2014-05
Description: A new high-charge RF gun is now operating at the Argonne Wakefield Accelerator (AWA) facility at Argonne National Laboratory (ANL). The 1.5...
Show moreA new high-charge RF gun is now operating at the Argonne Wakefield Accelerator (AWA) facility at Argonne National Laboratory (ANL). The 1.5 cell 1.3 GHz gun uses a Cesium telluride photocathode driven with a 248 nm laser to provide short-pulse, high charge electron beams for the new 75 MeV drive beamline. The high-gradient RF gun (peak field on the cathode > 80MV/m) is a key piece of the facility upgrade. The large Cs2Te photocathode (diameter > 30 mm) was fabricated in-house. The photo-injector will be used to generate high-charge, short pulse, single bunches (Q > 100 nC) and bunch-trains (Q>1000 nC) for wakefield experiments, typically involving dielectric-loaded accelerating structures. Details of the photocathode fabrication process and the results of associated diagnostic measurements are presented, including QE measurements and work function measurements performed with a Kelvin probe. Field-emitted dark current from the Cs2Te cathode was measured during RF conditioning and characterized. Fowler-Nordheim plots of the data are presented and compared to similar measurements made using a copper cathode in the initial phase of conditioning. The results for cesium telluride exhibited non-linear regions within the Fowler-Nordheim plots similar to previous experimental results for other p-type semiconductors. Results of quantum efficiency (QE) studies are presented with the cathode operating in both single and bunch-train modes. QE uniformity and lifetime studies are presented. During commissioning, the cesium telluride photocathode produced bunch-charge of 100 nC, breaking the previous record. No evidence of bunch-train position-dependence of QE was found when generating four-bunch trains with total charge up to 200 nC.
PH.D in Physics, May 2014
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Title: BIOLOGICAL STRATEGIES FOR ENHANCEMENT OF LIQUID FUELS: SULFUR REMOVAL FROM PETROLEUM AND BIOETHANOL PRODUCTION
Creator: Wang, Jia
Date: 2013, 2013-12
Description: Rhodococcus baikonurensis CW25 was transformed with the Rhodococcus erythropolis strain IGTS8 desulfurization operon (dszABC, which encodes...
Show moreRhodococcus baikonurensis CW25 was transformed with the Rhodococcus erythropolis strain IGTS8 desulfurization operon (dszABC, which encodes the enzymes of the “4S” desulfurization pathway) or this operon modified to contain a synthetic cysteine-methionine rich “sulpeptide” gene (S1) (dszAS1BC). The two CW25 derivatives were subjected to directed evolution to select faster growing cells using the key 4S pathway substrate dibenzothiophene (DBT) as the sole source of sulfur. Data of cell doubling times verified the success of selection of cultures with increasingly rapid growth. The desulfurization activities of resting cells of early passages demonstrated improvements, and the highest activity of the dszAS1BC-bearing CW25 derivative was 115% higher than that of the CW25 derivative without S1. In addition, a trend of initial high activity was followed by a decrease in subsequent passages. Rates of DBT metabolism of growing cells demonstrated a different trend, probably because the activity of growing cells concurrently reflects the activity of DszABC enzymes and the growth rates of the recombinants. Dry cell weights fluctuated during the evolution process, probably because of variations in the efficiency of the conversion of the sulfur in DBT into sulfite, then into sulfate or biomass, or, for the S1-bearing cells, because the secretion of the S1 peptide from cells might have variable efficiency. A mixed culture of two Paenibacillus species (“W” and “Y”) was isolated that can metabolize DBT at temperatures up to 54 ºC. Strain Y is the only one of the two with desulfurization activity, while strain W enhances the desulfurization ability of Y. The W-Y culture may be a useful starting point for selection of desulfurization cultures with even greater thermal stability. xiii Ethanologenic Escherichia coli strain FBR5 was compared with Vitreoscilla hemoglobin (VHb)-expressing FBR5 (TS3) regarding the concentrations of ATP, NAD+, NADH, NAD+/NADH ratio; and growth and ethanol production at various points during growth. The significant finding was that the NAD+/NADH ratio for TS3 was lower in early growth, but higher in later growth compared to that for FBR5. This is probably because more NADH was required by TS3 for its enhanced ethanol production and VHb-related increased respiration under microaeration conditions.
PH.D in Biology, December 2013
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Title: MATHEMATICAL MODELING OF POLY(ETHYLENE GLYCOL) DIACRYLATE HYDROGEL SYNTHESIS VIA VISIBLE LIGHT FREE-RADICAL PHOTOPOLYMERIZATION FOR TISSUE ENGINEERING APPLICATIONS
Creator: Lee, Chu-yi
Date: 2013, 2013-05
Description: Crosslinked hydrogels of poly(ethylene glycol) diacrylate (PEGDA) have been extensively used as scaffolds for applications in tissue...
Show moreCrosslinked hydrogels of poly(ethylene glycol) diacrylate (PEGDA) have been extensively used as scaffolds for applications in tissue engineering. In this thesis, PEGDA hydrogels are synthesized using visible light free-radical photopolymeriza- tion (λ = 514 nm) in the presence of the visible light photosensitive dye, EosinY, the co-initiator, triethanolamine (TEA), a comonomer, N-vinyl pyrrolidone (NVP), a crosslinking agent, PEGDA, and an optional PEG monoacrylate monomer that contains the cell adhesive ligand YRGDS. The incorporation level of the YRGDS lig- and as well as the physical and mechanical properties of these hydrogels dictate cell behavior and tissue regeneration. These hydrogel properties may be tuned through variations in polymerization conditions. The goal of this thesis was to develop a math- ematical model for PEGDA hydrogel formation which predicts the incorporation level of YRGDS and the crosslink density of hydrogel as a variety of polymerization con- ditions. This model provides insight into the process of hydrogel crosslinking and in effectively guiding the experimental design of these scaffolds for tissue engineering applications. To accomplish this task two major components comprised the studies of this thesis. The first component involved an investigation of the visible light photo- initiation mechanism of EosinY and TEA, and the second component involved the develop of a hydrogel synthesis model and its validation. Experiments and modeling were used to determine an expression for the rate of initiation of the EosinY/TEA initiation system and to propose a photoinitiation mechanism. In Chapter 2, exper- imental data and parameter fitting were utilized to obtain an empirical expression for the rate of initiation. However, this empirical expression did not consider the ef- fect of inhomogeneous light distribution which is present in this experimental system. The dynamics of light absorption during polymerization were measured under differ- xiv ent conditions in order to gain insight into the kinetic photoinitiation mechanism as well as the rate of initiation. In Chapter 3, a mechanism for this photo-initiation was proposed. Using this mechanism the light absorption dynamics accounting for inhomogeneous light distribution were simulated which were found to be in an agree- ment with the light absorption measurements shown in Chapter 2. Further validation of this proposed mechanism was achieved from polyNVP conversion measurements. This photo-initiation mechanism was implemented in the hydrogel model. In Chapter 4, the hydrogel synthesis model was developed based on the kinetic approach of the method of moments combined with the Numerical Fractionation technique. The model was used to predict the dynamics of hydrogel properties such as gel fraction, crosslink density, and RGD incorporation under various polymerization conditions. Model predictions were compared with experimental data. Three sets of experiments were conducted. In the first set of experiments where hydrogels were formed in the absence of Acryl-PEG-RGD, the total double bond concentration was kept constant while varying the compositions of NVP and PEGDA. The model and the experiments showed a maximum crosslink density for an acrylate to double bond ratio of 0.5 to 0.6. This is related to the synergistic cross-propagation between NVP and PEGDA, which results in an increase in the rate of polymerization leading to higher crosslink density. In the second set of experiments, hydrogels were formed in the presence of Acryl-PEG-RGD to investigate its incorporation as well as the hydrogel crosslink density. The model showed reasonable agreement with the experimental data and in some cases the predicted RGD deviated from the experimental measurements due to changes in volume upon swelling. The effect of swelling was not considered by the model. The calculated crosslink densities were compared with the inverse swelling ratios from the experiments. The reduction of free volume due to the space occupied xv by the unreacted pendant double bonds was not considered by the model. This reduc- tion of free volume affected the apparent swelling ratio obtained from experiments thus resulting in the observed mismatch between the experimental trends and the predicted crosslink density by the model. In the third set of experiments, additional crosslink density measurements were conducted using a PEGDA macromer of lower molecular weight (MW = 575 Da.). The experiments were performed in the absence of Acryl-PEG-RGD. Few cases were not accurately predicted since the model did not consider the reduction in the concentration of available pendant double bonds when gelation occurs. Among the three set of experiments, the hydrogel synthesis model offers reasonable predictions for most of the experimental cases. This model can be used as a guide for experimen- tally designing PEGDA hydrogels with the desired properties for tissue engineering applications.
PH.D in Chemical and Biological Engineering, May 2013
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Title: DEGRADATION RATE MODEL TO ESTIMATE SOIL CARBON SEQUESTRATION
Creator: Zhai, Wenjuan
Date: 2016, 2016-05
Description: Concern over climate change as a consequence of carbon dioxide (CO2) emissions from human activities has resulted in efforts to better...
Show moreConcern over climate change as a consequence of carbon dioxide (CO2) emissions from human activities has resulted in efforts to better understand potential mitigation measures such as carbon sequestration in soils. Processes shaping natural carbon sequestration may be used to remove excess CO2 from combustion and other anthropogenic sources of carbon, and, alleviate concerns over climate change. Land application of biosolids is a process that increases the amount of soil carbon sequestration and may produce carbon credits in accordance with the definition of UN Climate Change Convention. A dynamic degradation rate model (DRM) has been developed based on a mass balance and first order kinetics to describe the soil organic carbon (SOC) decomposition process, which provides insights on carbon sequestration due to microbial biomass, SOC, CO2 emission rates, residence time of sequestered carbon, and biomass to biosolids ratios. A curve fitting approach was used to produce a best fit average degradation rate for biosolids degradation and microbial biomass yield. This study employed a 34-year biosolids application database from the literature to determine the amount of carbon sequestered in 41 strip-mined Illinois fields. The DRM application identifies two SOC phases in soil. Soil organic carbon gain in phase one (first 10 yrs) is primarily due to biosolids C application remaining and accumulation while in phase two, SOC gain is due to biomass or C sequestration. Carbon sequestration changes with time relate to variations in biosolids application amounts (10 and 18 Mg ha-1 yr-1), different degradation rate constants (0.04yr-1 to 0.16yr-1), and biomass yields (35 to 40%). Additionally, comparison between model simulation results and laboratory resultsdetermine the amount of carbon sequestered in 41 strip-mined Illinois fields. The DRM application identifies two SOC phases in soil. Soil organic carbon gain in phase one (first 10 yrs) is primarily due to biosolids C application remaining and accumulation while in phase two, SOC gain is due to biomass or C sequestration. Carbon sequestration changes with time relate to variations in biosolids application amounts (10 and 18 Mg ha-1 yr-1), different degradation rate constants (0.04yr-1 to 0.16yr-1), and biomass yields (35 to 40%). Additionally, comparison between model simulation results and laboratory resultsdetermine the amount of carbon sequestered in 41 strip-mined Illinois fields. The DRM application identifies two SOC phases in soil. Soil organic carbon gain in phase one (first 10 yrs) is primarily due to biosolids C application remaining and accumulation while in phase two, SOC gain is due to biomass or C sequestration. Carbon sequestration changes with time relate to variations in biosolids application amounts (10 and 18 Mg ha-1 yr-1), different degradation rate constants (0.04yr-1 to 0.16yr-1), and biomass yields (35 to 40%). Additionally, comparison between model simulation results and laboratory resultsdetermine the amount of carbon sequestered in 41 strip-mined Illinois fields. The DRM application identifies two SOC phases in soil. Soil organic carbon gain in phase one (first 10 yrs) is primarily due to biosolids C application remaining and accumulation while in phase two, SOC gain is due to biomass or C sequestration. Carbon sequestration changes with time relate to variations in biosolids application amounts (10 and 18 Mg ha-1 yr-1), different degradation rate constants (0.04yr-1 to 0.16yr-1), and biomass yields (35 to 40%). Additionally, comparison between model simulation results and laboratory results provided by a yearlong study indicates that higher temperatures and moisture content and finer soils are related to larger degradation rates. To summarize, this study has the following contributions: (1) developed a degradation rate model which simulates the biosolids degradation process in soil and identifies two SOC phases in soil, and quantifies the biosolids degradation rate constant, biomass yield, and the C sequestered amount for multiple and long term soil application; (2) assessed the effect of changes in the amount of biosolids applied, soil type, and weather conditions on the C degradation rate by comparing model results to laboratory data; and (3) provides an easy quantitative method for predicting C sequestration from biosolids added to soil.
Ph.D. in Environmental Engineering, May 2016
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Title: SURFACE CHARACTERIZATION OF NIOBIUM FOR SUPERCONDUCTING RF CAVITIES
Creator: Cao, Chaoyue
Date: 2014, 2014-07
Description: Surface characterization techniques including point contact tunneling (PCT) spectroscopy and Raman spectroscopy have been employed to study...
Show moreSurface characterization techniques including point contact tunneling (PCT) spectroscopy and Raman spectroscopy have been employed to study the surface of niobium (Nb) superconducting radio frequency (SRF) cavities. PCT spectroscopy provides a direct means of measuring the surface superconductivity, which is closely correlated with the cavity’s performance characterized by the quality factor Q. Cavities with remarkably high Q show near ideal tunneling spectra with sharp coherent peaks and low zero bias conductance, consistent with the Bardeen-Cooper-Schrie↵er (BCS) density of states (DOS), and bulk gap parameter, " = 1.55 -1.6 meV. Cavities with Q-drop often exhibit strong non-uniform heating during RF operations, with high loss regions identified as hot spots. PCT spectra on hot spots reveal suppressed superconductivity, broadened DOS and Kondo tunneling, consistent with magnetic impurities on the surface. Raman spectra on hot spots indicate the presence of various impurities on the surface including amorphous carbon, C-H chain compounds and NbC, providing insights into the formation of hot spots. The origin of the impurities is unclear at present but it is suggested that particular processing steps in SRF cavity fabrication may be responsible.
Ph.D. in Physics, July 2014
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Title: BIG DATA SYSTEM INFRASTRUCTURE AT EXTREME SCALES
Creator: Zhao, Dongfang
Date: 2015, 2015-07
Description: Rapid advances in digital sensors, networks, storage, and computation along with their availability at low cost is leading to the creation of...
Show moreRapid advances in digital sensors, networks, storage, and computation along with their availability at low cost is leading to the creation of huge collections of data { dubbed as Big Data. This data has the potential for enabling new insights that can change the way business, science, and governments deliver services to their consumers and can impact society as a whole. This has led to the emergence of the Big Data Computing paradigm focusing on sensing, collection, storage, management and analysis of data from variety of sources to enable new value and insights. To realize the full potential of Big Data Computing, we need to address several challenges and develop suitable conceptual and technological solutions for dealing them. Today's and tomorrow's extreme-scale computing systems, such as the world's fastest supercomputers, are generating orders of magnitude more data by a variety of scienti c computing applications from all disciplines. This dissertation addresses several big data challenges at extreme scales. First, we quantitatively studied through simulations the predicted performance of existing systems at future scales (for example, exascale 1018 ops). Simulation results suggested that current systems would likely fail to deliver the needed performance at exascale. Then, we proposed a new system architecture and implemented a prototype that was evaluated on tens of thousands nodes on par with the scale of today's largest supercomputers. Micro benchmarks and real-world applications demonstrated the e ectiveness of the proposed architecture: the prototype achieved up to two orders of magnitude higher data movement rate than existing approaches. Moreover, the system prototype was incorporated with features that were not well supported in conventional systems, such as distributed metadata management, distributed caching, lightweight provenance, transparent compression, acceleration through GPU encoding, and parallel serialization. Towards exploring the proposed architecture at millions of node scales, simulations were conducted and evaluated with a variety of workloads, showing near linear scalability and orders of magnitude better performance than today's state-of-the-art storage systems.
Ph.D. in Computer Science, July 2015
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Title: BIO-COMPOSITE NANOMATERIALS; CHARACTERIZATION, MANIPULATION AND APPLICATION
Creator: Kim, Taeyoung
Date: 2013, 2013-05
Description: Biomaterials are any matter or material which interacts with biological system which were present on natural or synthetic nonviable materials....
Show moreBiomaterials are any matter or material which interacts with biological system which were present on natural or synthetic nonviable materials. An ideal biomaterial must physically and chemically compatible for biological applications to avoid toxicity and immune reaction. Collagen is a widely abundant, robust biopolymer that is found in the extracellular matrix (ECM) of many tissues. In terms of its structure and organization, collagen is a bio-nano material. The use of collagen in stem cell differentiation is particularly enticing since it is now evident that the extracellular matrix (ECM) proteins can regulate the cell’s fate and growth by their molecular and physical properties. In this thesis research, we have characterized the physical and structural properties of collagen and its composite materials. We found collagen interacts with NaCl and other nano-materials, such as carbon nanotube (CNT) and TiO2 nanotube, resulting in the modification of collagen structure and increase of its stiffness. In particular, CNT has changed collagen structure at both the molecular level and the higher organizational level. The effects of the matrices on cell growth and development were studied. It was found that collagen/CNT matrix specify and accelerate the stem cell differentiation toward neural cells. Since neurons form the foundation of biological circuit, manipulation of neurons in growth has the potential to form desired biological circuit. We also examined collagen in vaginal wall connective tissues, and found that alteration of collagen properties in clinical tissues is correlated to the onset of pelvic organ prolapse.
PH.D in Chemistry, May 2013
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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: OPTIMIZATION AND MARKET CLEARING IN THE POWER SYSTEMS WITH HIGH-LEVEL RENEWABLES
Creator: Ye, Hongxing
Date: 2016, 2016-05
Description: The increasing penetration of renewable energy source (RES), such as wind and solar power generation, in recent years to meet various...
Show moreThe increasing penetration of renewable energy source (RES), such as wind and solar power generation, in recent years to meet various renewable portfolio standards (RPS) has led to more uncertainties in power systems. The RES penetration level is expected to further increase in order to reduce emission and fight climate change. The growing uncertainties caused by RES pose new challenges in power and energy systems. Advanced models and technologies are urgent to provide secure, affordable and clean energy to customers. Security-Constrained Unit Commitment (SCUC) problem is one of the most important tools in the modern power system. It determines the optimal short-term generating planning. The electricity is priced and settled based on its solution. In order to manage the uncertainties caused by renewables, it is urgent to develop new SCUC models and solution approaches. SCUCs considering the uncertainties have become a focus of research in recent years. The proposed optimistic robust SCUC combines the idea of robust optimization and reserve concept in the electricity. The merit of the robust optimization is that its solution can be immunized against any uncertainties. It exactly meets the first priority, reliability, in power system operation. The robust optimization is attractive in theory. However, a solution is robust if and only if the system can survive in the worst case scenario. Hence, the key task is to identify the worst case scenario. Unfortunately, finding the worst case scenario in general is a non-deterministic polynomial-time hard (NP-hard) problem. This will create issue in satisfying the timeliness requirement that the optimal scheduling must be obtained quickly (e.g., within several hours) in the day-ahead electricity markets. This dissertation proposes a fast solution approach to finding the worst case scenario by exploring the special structure in the SCUC problem. This dissertation proposes a new market mechanism for managing uncertain ties caused by high-level RES based on the robust optimization. A new concept, Uncertainty Marginal Price (UMP), is proposed to charge uncertainty sources and to credit flexible sources. For the first time, explicit price signals are provided and utilized to manage any level uncertainties within a robust optimization framework. The proposed mechanism manages uncertainties from both the source side (uncertainty reduction) and resource side (uncertainty accommodation). In short term, it provides incentives for RES operators to improve forecasting accuracy (i.e. to reduce uncertainties) and existing flexible resources (e.g. storage) to participate the uncertainty accommodation. In long term, the proposed mechanism provides price signals for siting new flexible resources (e.g. energy storage) to accommodate uncertainties from increasing RES penetration.
Ph.D. in Electrical Engineering, May 2016
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