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  • Control of the CDC48A segregase by the plant UBX-containing (PUX) protein family

    Zhang, Junrui (2021-05) [Thesis]
    Advisor: Arold, Stefan T.
    Committee members: Blilou, Ikram; Jaremko, Lukasz
    In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest and most versatile family. However, few PUX proteins have been structurally or functionally characterized and how they participate in the substrate processing of CDC48A is not fully understood. Here, we first performed a comparative bioinformatic analysis, in which we found that the PUX proteins can be functionally divided into six types. We used this classification as a guide for our experimental efforts to elucidate how PUX proteins mediate client recognition and delivery for CDC48A-mediated unfolding. As a first step in this experimental analysis, we cloned and expressed a number of PUX protein constructs, we assessed their interaction features, and obtained crystals for several PUX domains. These bioinformatic and experimental results provide a basis for the in-depth structural and functional analysis of how PUX proteins control the CDC48A segregase.
  • Optimal policies for battery operation and design via stochastic optimal control of jump diffusions

    Rezvanova, Eliza (2021-04-26) [Thesis]
    Advisor: Tempone, Raul
    Committee members: Boffi, Daniele; Bolin, David
    To operate a production plant, one requires considerable amounts of power. With a wide range of energy sources, the price of electricity changes rapidly throughout the year, and so does the cost of satisfying the electricity demand. Battery technology allows storing energy while the electric power is lower, saving us from purchasing at higher prices. Thus, adding batteries to run plants can significantly reduce production costs. This thesis proposes a method to determine the optimal battery regime and its maximum capacity, minimizing the production plant's energy expenditures. We use stochastic differential equations to model the dynamics of the system. In this way, our spot price mimics the Uruguayan energy system's historical data: a diffusion process represents the electricity demand and a jump-diffusion process - the spot price. We formulate a corresponding stochastic optimal control problem to determine the battery's optimal operation policy and its optimal storage capacity. To solve our stochastic optimal control problem, we obtain the value function by solving the Hamilton-Jacobi-Bellman partial differential equation associated with the system. We discretize the Hamilton-Jacobi-Bellman partial differential equation using finite differences and a time splitting operator technique, providing a stability analysis. Finally, we solve a one-dimensional minimization problem to determine the battery's optimal capacity.
  • Depth Estimation Using Adaptive Bins via Global Attention at High Resolution

    Bhat, Shariq (2021-04-21) [Thesis]
    Advisor: Wonka, Peter
    Committee members: Hadwiger, Markus; Ghanem, Bernard
    We address the problem of estimating a high quality dense depth map from a single RGB input image. We start out with a baseline encoder-decoder convolutional neural network architecture and pose the question of how the global processing of information can help improve overall depth estimation. To this end, we propose a transformer-based architecture block that divides the depth range into bins whose center value is estimated adaptively per image. The nal depth values are estimated as linear combinations of the bin centers. We call our new building block AdaBins. Our results show a decisive improvement over the state-of-the-art on several popular depth datasets across all metrics. We also validate the e ectiveness of the proposed block with an ablation study.
  • Conductive Stretchable and 3D Printable Nanocomposite for e-Skin Applications

    Alsharif, Yasir (2021-04-21) [Thesis]
    Advisor: Baran, Derya
    Committee members: Lubineau, Gilles; Lanza, Mario
    Electronic skin (e-skin) materials have gained a wide range of attention due to their multiple applications in different areas, including soft robotics, skin attachable electronics, prosthetics, and health care. These materials are required to emulate tactile perceptions and sense the surrounding environments while maintaining properties such as flexibility and stretchability. Current e-skin fabrication techniques, such as photolithography, screen printing, lamination, and laser reducing, have limitations in terms of costs and manufacturing scalability, which ultimately preventing e-skin widespread usage. In this work, we introduce conductive stretchable 3D printable skin-like nanocomposite material. Our nanocomposite is easily 3D printed, cost-effective, and actively senses physical stimuli, such as strain and pressure, which gave them the potential to be used in prosthetics, skin-attachable electronics, and soft robotics applications. Using the conductive properties of carbon nanofibers, alongside a polymeric matrix based on Smooth-on platinum cured silicone and crosslinked PDMS, we can obtain a flexible and stretchable material that resembles human skin and can conduct electricity. A great advantage in our composite is the ability to tune its mechanical properties to fit the desired application area through varying PDMS's chain lengths and composition ratios in the nanocomposite. Also, the interconnecting network of micrometer-long nanofibers allows the measurement of resistivity changes upon physical stimuli, granting the nanocomposite sensing abilities. Moreover, we explored and optimized 3D printing of the nanocomposite material, which offering simplicity and versatility for fabricating complex 3D structures at lower costs.
  • Studies of Novel Small Molecule and Polymer blends for Application in Organic Light-Emitting Diodes

    Gkeka, Despoina (2021-04-20) [Thesis]
    Advisor: Anthopoulos, Thomas D.
    Committee members: Laquai, Frédéric; McCulloch, Iain; Tung, Vincent
    Display technology has become a vital and ubiquitous part of our daily life. Undoubtedly, today’s technologically minded society is living in the era of the digital image. After high resolution and efficiency could successfully be realized, the major trends in display technology now aim towards achieving high color purity for natural looking display colors. Organic light-emitting diodes (OLEDs), as one strong contender for high performance displays and lighting, have been undergoing tremendous industrial and commercial development. Despite the great progress, though, there is still space for improvement, especially in the case of blue light emitting devices. Blue OLEDs are always challenging, since they traditionally suffer from low efficiencies and lifetimes. Both, novel materials and device architectures, are driving ongoing developments while still always aiming to lower the overall costs. In a continual effort to search for robust materials for blue devices, small molecules (SMs) and polymers, are shown to be promising candidates. In this thesis is presented the results of the detailed study of photophysical and electroluminescence (EL) properties in the case of thin films based on blends of the conjugated polymer Poly(9,9-di-n-octylfluorenyl-2,7-diyl) (PFO) and the of novel SMs; 4,4'-(anthracene-9,10-diyl)bis(N,N-bis(4-methoxyphenyl)aniline) (TPAA) and 4,4'-(pyrene-1,6-diyl)bis(N,N-bis(4-methoxyphenyl)aniline) (TPAP). Finally, devices based on these systems are optimized step by step as a solution processable emissive layer (EML), for applications in sky blue OLEDs.
  • Toward Improving the Internet of Things: Quality of Service and Fault Tolerance Perspectives

    Alaslani, Maha S. (2021-04-13) [Dissertation]
    Advisor: Shihada, Basem
    Committee members: Alouini, Mohamed-Slim; Zhang, Xiangliang; Bessani, Alysson
    The Internet of Things (IoT) is a technology aimed at developing a global network of machines and devices that can interact and communicate with each other. Supporting IoT, therefore, requires revisiting the Internet's best e ort service model and reviewing its complex communication patterns. In this dissertation, we explore the unique characteristics of IoT tra c and examine IoT systems. Our work is motivated by the new capabilities o ered by modern Software De ned Networks (SDN) and blockchain technology. We evaluate IoT Quality of Service (QoS) in traditional networking. We obtain mathematical expressions to calculate end-to-end delay, and dropping. Our results provide insight into the advantages of an intelligent edge serving as a detection mechanism. Subsequently, we propose SADIQ, SDN-based Application-aware Dynamic Internet of things QoS. SADIQ provides context-driven QoS for IoT applications by allowing applications to express their requirements using a high-level SQL-like policy language. Our results show that SADIQ improves the percentage of regions with an error in their reported temperature for the Weather Signal application up to 45 times; and it improves the percentage of incorrect parking statuses for regions with high occupancy for the Smart Parking application up to 30 times under the same network conditions and drop rates. Despite centralization and the control of data, IoT systems are not safe from cyber-crime, privacy issues, and security breaches. Therefore, we explore blockchain technology. In the context of IoT, Byzantine fault tolerance-based consensus protocols are used. However, the blockchain consensus layer contributes to the most remarkable performance overhead especially for IoT applications subject to maximum delay constraints. In order to capture the unique requirements of the IoT, consensus mechanisms and block formation need to be redesigned. To this end, we propose Synopsis, a novel hierarchical blockchain system. Synopsis introduces a wireless-optimized Byzantine chain replication protocol and a new probabilistic data structure. The results show that Synopsis successfully reduces the memory footprint from Megabytes to a few Kilobytes with an improvement of 1000 times. Synopsis also enables reductions in message complexity and commitment delay of 85% and 99.4%, respectively.
  • Improving the Self-Consistent Field Initial Guess Using a 3D Convolutional Neural Network

    Zhang, Ziang (2021-04-12) [Thesis]
    Advisor: Schwingenschlögl, Udo
    Committee members: Laquai, Frédéric; Zhang, Xiangliang; Gao, Xin
    Most ab initio simulation packages based on Density Functional Theory (DFT) use the Superposition of Atomic Densities (SAD) as a starting point of the self-consistent fi eld (SCF) iteration. However, this trial charge density without modeling atomic iterations nonlinearly may lead to a relatively slow or even failed convergence. This thesis proposes a machine learning-based scheme to improve the initial guess. We train a 3-Dimensional Convolutional Neural Network (3D CNN) to map the SAD initial guess to the corresponding converged charge density with simple structures. We show that the 3D CNN-processed charge density reduces the number of required SCF iterations at different unit cell complexity levels.
  • Laser Based Pre-treatment of Secondary Bonded Composite T-joints for Improved Energy Dissipation

    Hashem, Mjed H. (2021-04-06) [Thesis]
    Advisor: Lubineau, Gilles
    Committee members: Anthopoulos, Thomas D.; Laquai, Frédéric; Wagih, Ahmed
    This study demonstrates an experimental investigation into the efficacy of a novel surface pre-treatment technique to improve the toughness and energy dissipation of composite CFRP T-joints. This novel technique optimizes CO2 laser irradiations to remove surface contaminations and modify the surface morphology of CFRP T-joint adherents. Pull-off tests were performed on T-joints that experienced peel-ply (PP) treatment and to those that were ablated with 10% (LC) and 30% (LA) laser power respectively. A further developed alternative pattern between LA and LC surface pre-treatment was examined. Two different quasi-isotropic stacking sequences have been studied by having surface fibers aligned in 0° and 45° direction. A series of surface roughness analysis, optical microscopy, SEM, CT scan and pictorial findings have been carried out to characterize the surface morphologies and failure modes prior to and after the failure. The patterning technique promoted non-local damage mechanisms which resulted in large improvements in the toughness and energy dissipation as compared to the other pre-treatment techniques. Up to ~12 times higher energy dissipation compared to peel-ply pre-treated T-joint were achieved with patterned T-joint structures that are stacked with a 0° surface fiber direction.
  • LITHIUM-SULFUR BATTERY DESIGN: CATHODES, SEPARATORS, AND LITHIUM METAL ANODES

    Guo, Dong (2021-04-04) [Dissertation]
    Advisor: Lai, Zhiping
    Committee members: Huang, Kuo-Wei; Alshareef, Husam N.; Li, Lain-Jong
    The shortage of energy sources and the global climate change crisis have become critical issues. Solving these problems with clean and sustainable energy sources (solar, wind, tidal, and so on) is a promising solution. In this regard, energy storage techniques need to be implemented to tackle with the intermittent nature of the sustainable energies. Among the next-generation energy storage systems, lithium sulfur batteries has gained prominence due to the low cost, high theoretical specific-capacity of sulfur. Extensive research has been conducted on this battery system. Nevertheless, several issues including the “shuttle effect” and the growth of lithium dendrites still exist, which could cause rapid capacity loss and safety hazards. Several methods are proposed to tackle the challenges in this dissertation, including cathode engineering, interlayer design, and lithium metal anode protection. An asymmetric cathode structure is first developed by a non-solvent induced phase separation (NIPS) method. The asymmetric cathode comprises a nanoporous matrix and ultrathin and dense top layer. The top-layer is a desired barrier to block polysulfides transport, while the sublayer threaded with cationic networks facilitate Li-ions transport and sulfur conversions. In addition, a conformal and ultrathin microporous membrane is electrodeposited on the whole surface of the cathode by an electropolymerization method. This strategy creates a close system, which greatly blocks the LiPS leakage and improves the sulfur utilization. A polycarbazole-type interlayer is deposited on the polypropylene (PP) separator via an electropolymerization method. This interlayer is ultrathin, continuous, and microporous, which defines the critical properties of an ideal interlayer that is required for advanced Li–S batteries. Meanwhile, a self-assembled 2D MXene based interlayer was prepared to offer abundant porosity, dual absorption sites, and desirable electrical conductivity for Li-ions transport and polysulfides conversions. A new 2D COF-on-MXene heterostructures is prepared as the lithium anode host. The 2D heterostructures has hierarchical porosity, conductive frameworks, and lithiophilic sites. When utilized as a lithium host, the MXene@COF host can efficiently regulate the Li+ diffusion, and reduce the nucleation and deposition overpotential, which results in a dendrite-free and safer Li–S battery.
  • Computation Offloading and Service Caching in Heterogeneous MEC Wireless Networks

    Zhang, Yongqiang (2021-04) [Thesis]
    Advisor: Alouini, Mohamed-Slim
    Committee members: Shihada, Basem; Kammoun, Abla; Zhang, Xiangliang
    Mobile edge computing (MEC) can dramatically promote the compu- tation capability and prolong the lifetime of mobile users by offloading computation- intensive tasks to edge cloud. In this thesis, a spatial-random two-tier heterogeneous network (HetNet) is modelled to feature random node distribution, where the small- cell base stations (SBSs) and the macro base stations (MBSs) are cascaded with resource-limited servers and resource-unlimited servers, respectively. Only a certain type of application services and finite number of offloaded tasks can be cached and processed in the resource-limited edge server. For that setup, we investigate the per- formance of two offloading strategies corresponding to integrated access and backhaul (IAB)-enabled MEC networks and traditional cellular MEC networks. By using tools from stochastic geometry and queuing theory, we derive the average delay for the two different strategies, in order to better understand the influence of IAB on MEC networks. Simulations results are provided to verify the derived expressions and to reveal various system-level insights.
  • Wireless Magnetic Sensors to Empower the Next Technological Revolution

    Almansouri, Abdullah S. (2021-04) [Dissertation]
    Advisor: Kosel, Jürgen
    Committee members: Salama, Khaled N.; Alshareef, Husam N.; Al Attar, Talal; Sonkusale, Sameer
    The next technological revolution, Industry 4.0, is envisioned as a digitally connected ecosystem where machines and gadgets are driven by artificial intelligence. By 2025, more than 75 billion devices are projected to serve this revolution. Many of which are to be integrated into the fabrics of everyday life in the form of smart wireless sensors. Still, two major challenges should be addressed to realize truly wireless and wearable sensors. First, the sensors should be flexible and stretchable, allowing for comfortable wearing. Second, the electronics should scavenge the energy it requires entirely from the environment, thus, eliminating the need for batteries, which are bulky, create ecological problems, etc. By addressing these two challenges, this dissertation paves the way for truly wearable sensors. The first part of the dissertation introduces a biocompatible magnetic skin with exceptional physical properties. It is highly-flexible, breathable, durable, and realizable in any desired shape and color. Attached to the skin of a user, the magnetic skin itself does not require any wiring, allowing to place the electronics and delicate components of the wireless sensor in a convenient nearby location to track the magnetic field produced by the magnetic skin. To demonstrate the performance of the magnetic skin, wearable systems are implemented as an assistive technology for severe quadriplegics, a touchless control solution for eliminating cross contaminations, and for monitoring blinking and eye movement for sleep laboratories. The second part of the dissertation is about wirelessly powering wireless sensors. In doing so, radio frequency (RF) rectifiers are a bottleneck, especially for ambient RF energy harvesting. Therefore, two RF rectifiers are introduced in standard CMOS technologies. The first architecture utilizes double-sided diodes to reduce the reverse leakage current, thus achieving a high dynamic range of 6.7 dB, -19.2 dBm sensitivity, and 86% efficiency. The second rectifier implements a dual-mode technique to lower the effective threshold voltage by 37%. Consequently, it achieves a 38% efficiency at −35 dBm input power and a 10.1 dB dynamic range while maintaining the same efficiency and sensitivity. Ultimately, combining these wireless powering techniques with the magnetic skin allows for truly wireless and wearable solutions.
  • Wireless Network Coding with Intelligent Reflecting Surfaces

    Kafizov, Amanat (2021-04) [Thesis]
    Advisor: Alouini, Mohamed-Slim
    Committee members: Shihada, Basem; Laleg-Kirati, Taous-Meriem; Kammoun, Abla
    Conventional wireless techniques are becoming inadequate for beyond fifth-generation (5G) networks due to latency and bandwidth considerations. To increase the wireless network throughput and improve wireless communication systems’ error performance, we propose physical layer network coding (PNC) in an Intelligent Reflecting Surface (IRS)-assisted environment. We consider an IRS-aided butterfly network, where we propose an algorithm for obtaining the optimal IRS phases. Also, analytic expressions for the bit error rate (BER) are derived. The numerical results demonstrate that the scheme proposed in this thesis significantly enhances the BER performance. The proposed scheme is compared to traditional network coding without IRS. For instance, at a target BER of 10−3, 28 dB and 0.75 dB signal to noise ratio (SNR) gains are achieved at the relay and destination node of the 32-element IRS-assisted butterfly network model.
  • Programmable materials for sensors, actuators and manipulators for soft robotics applications

    Chellattoan, Ragesh (2021-04) [Dissertation]
    Advisor: Lubineau, Gilles
    Committee members: Lacoste, Deanna; Blilou, Ikram; Leng, Jinsong
    This thesis describes the concept of programmable materials with tunable physical properties applicable to soft robots. We present these materials for three major applications in soft robotics: sensing, actuation, and robotic manipulation. The strain sensors recognize the internal stimuli in a soft robot, whereas the conductors collect the sensors’ signals to the control part. In the first part, we want to develop both stretchable strain sensors and conductors from a single material by programming a nanowire network’s electrical property, which we achieve through Electrical Welding (e-welding). We demonstrate the transformation of a Silver Nanowire (AgNW)-polymer sponge from a strain sensor to a stretchable conductor through e-welding. Using this method, we produced a soft hybrid e-skin having both a sensor and conductor from a single material. In the second part, we propose new active actuation solutions by obtaining quick, tunable pressure inside a soft material that we achieve through a liquid-gas phase transition of a stored liquid using an efficient electrode. We discuss the significant design variables to improve the performance and propose a new design for the electrodes, for enhancing actuation speed. We propose using low voltage equipment to trigger the phase transition to produce compact actuation technology for portable applications. Using this method, we produced a portable soft gripper. In the third and last part, we want to develop a simple robotic manipulation technology using a single-chambered soft body instead of a multi-chambered system. We propose using on-demand stiffness change in soft material to control the shape change of a single-chambered soft body. For this, we introduce a new concept of a stiffness tunable hybrid fiber: a fiber with stiff and soft parts connected in a series. We demonstrate a substantial change in membrane stiffness in the fiber through locking/unlocking of the soft part of the fiber. We integrated these fibers into a pneumatically operated single-chambered soft body to control its stiffness for on-demand shape change. If applied together, these three concepts could result in a fully printable, cheap, light, and easily controllable new generation soft robots with augmented functionalities.
  • Generation of Orbital Angular Momentum (OAM) Modes with a Spiral Phase Plate Integrated Laser Source

    Stegenburgs, Edgars (2021-04) [Dissertation]
    Advisor: Ooi, Boon S.
    Committee members: Alouini, Mohamed-Slim; Liberale, Carlo; Forbes, Andrew
    The objective of this work is to develop a near-infrared laser device capable of emitting orbital angular momentum (OAM) light. The prototyped device must be suitable for compact, energy-saving optical communication applications. Integrated OAM lasers will revolutionize high-capacity data transmission over any telecommuni- cation network environment, as OAM light can be guided and transmitted through kilometers of optical fibers and propagated in free space and underwater. Several methods for generating OAM light employing various complex monolithic and hybrid integration methods have been demonstrated. In this work, microscale integrated spiral phase plates (SPPs) are chosen to convert the laser beam output into an OAM mode. The concept and design fundamentals of SPPs are discussed, followed by the SPP fabrication process and their implementation in a high-speed communication setup and then integration with a semiconductor laser. SPPs are fabricated by a novel direct laser writing that provides the possibility to rapidly prototype 3D photonic structures via a two-photon polymerization pro- cess. After fabrication, SPPs are used in a fine-tuned free-space optical experimental setup that requires high-precision intercomponent alignment to test the high-speed OAM communication system and analyze the quality of OAM modes, resulting in high-purity OAM signals at data rates up to 1.8 Gbit/s – limited by the avalanche photodetector (APD) frequency response. The fabricated 20-μm-diameter SPPs were the smallest reported in the literature to date for optical characterization. A proof-of-concept monolithic light-emitting array, as a highly integrated OAM laser source, is further proposed for telecommunications and other applications. SPP-integrated 940-nm vertical-cavity surface-emitting laser (VCSEL) array chips that are relatively low-cost, have a small footprint, and are manufacturable in high volumes are developed. SPPs with topological charge modulus values from 1 to 3 are fabricated on the VCSEL arrays, demonstrating OAM modal purities up to ∼65%. The experimentally evaluated data rates in the OAM setup showed consistently sta- ble links up to 2.0 Gbit/s with a bit error ratio of ∼ 1.6 × 10−8 (APD-limited). The challenges of SPP-laser integration are summarized, with the conclusion that the widespread adoption of OAM is limited by the availability of practical integrated solutions for OAM generation and detection.
  • Experimental and theoretical study of PAH and incipient soot formation in laminar flames

    Li, Zepeng (2021-04) [Dissertation]
    Advisor: Roberts, William L.
    Committee members: Lacoste, Deanna; Chung, Suk Ho; Knio, Omar; Thomson, Murray J.
    Emissions of soot and polycyclic aromatic hydrocarbons (PAHs) from incomplete burning of hydrocarbon fuels pose a great threat to the environment and human health. To reduce such emissions, a comprehensive understanding of their evolution process is essential. In this work, a series of research studies were conducted to evaluate sooting tendencies and to experimentally and theoretically develop PAH mechanisms. The sooting tendencies of oxygenated fuels were quantitively investigated in counterflow diffusion flames. Sooting limits are described by critical fuel and oxygen mole fractions, measured with a laser scattering technique. The addition of dimethyl ether displays non-monotonic behavior on sooting tendencies at elevated pressures, which is attributed to the chemical effect from kinetic simulations. The tendency of incipient soot formation of other oxygenated fuels (e.g., alcohol, acid, ether, ketone, and carbonate ester) was also assessed, using a similar approach. As the precursor of soot, PAH measurement using laser induced fluoresecnce was implemented to track the evolution processes from PAHs to incipient soot. Developing a PAH mechanism is essential to the understanding of soot formation; however, PAH formation and its growth process are not well understood. Based on previous research, PAHs with 5-membered rings are abundant in flames. Therefore, the growth of PAHs with 5-membered rings was investigated, using acenaphthylene (A2R5) as the example. The density functional theory (DFT) and the transition state theory (TST) were adopted to calculate potential energy surfaces and reaction rate coefficients. The existence of 5-membered rings appreciably impacts PAH production by facilitating the formation of planar PAHs with C2H substitution, thereby improving existing PAH mechanisms. In PAH mechanisms, the thermochemistry properties are not all calculated, but are hypothesized to be equal to those of a similar structure. The simulation accuracy of the hypothesis is explored here by discussing the sensitivity of the thermochemistry parameters in flame simulations. The group additivity method utilizing THERM codes is used to calculate thermochemistry properties. PAH loading affects the sensitivity of thermochemistry properties to both flame temperature and product yields. These results show that either accurate thermochemistry properties, or reverse reaction rates should be provided in the mechanism to improve simulation accuracy.
  • Broadband Elastic Wave Propagation in Intact Rocks (Quasi-static to MegaHertz)

    Perbawa, Andika (2021-04) [Dissertation]
    Advisor: Santamarina, Carlos
    Committee members: Hoteit, Ibrahim; Santamarina, Carlos; Finkbeiner, Thomas; Lubineau, Gilles; Cascante, Giovanni
    Elastic wave propagation in saturated porous rocks reflects the fluid and mineral stiffness and their frequency-dependent interaction. Seismic imaging and borehole measurements in the field use low-frequency, long-wavelength signals (Hz-to-kHz), while standard laboratory-measurements operate in the MHz range. This thesis advances broadband elastic wave propagation methods (quasi-static, cyclic loading, first-mode resonance, and ultrasonic) to characterize intact rocks in order to gather laboratory data relevant to field conditions. Results show the critical effect of surface roughness at the specimen-endcap interfaces on stiffness measured under quasi-static conditions; local strain measurements using specimen-bonded strain gauges avoid seating effects. Multi-mode low-frequency resonant column testing provides the most reliable assessment of attenuation; attenuation increases and resonant frequency decreases with vibration amplitude for all vibration modes (longitudinal, torsional, and flexural). Ultrasonic P and S-wave velocities increase as a function of conf fining pressure and during early stages of deviatoric loading; trends follow a Hertzian power law. The corresponding -factors and -exponents exhibit a strong correlation with specimen type. The combination of ultrasonic measurement and coda wave analysis allows us to detect minute velocity changes during fluid invasion and damage evolution. Differences in P-wave velocity in specimens saturated with brine and supercritical CO2 are higher at seismic frequencies than in ultrasonic frequencies. 5 The new experimental methods implemented in this research and the comprehensive characterization studies provide new tools into intact rock characterization and contribute new insights on the physical properties of intact rocks and fluid-matrix interaction. Results highlight critical differences between field values and standard laboratory measurements
  • Performance comparison of Hierarchical Non-Terrestrial Networks for 6G

    Wang, Dengke (2021-04) [Thesis]
    Advisor: Alouini, Mohamed-Slim
    Committee members: Fariborzi, Hossein; Shihada, Basem; Park, Kihong
    This thesis investigates the fundamental performance of Hierarchical Non-Terrestrial Networks for the 6th generation (6G). 6G communication research is currently focus- ing on non-terrestrial networks (NTNs) to promote ubiquitous and ultra-high-capacity global connectivity. Specifically, multi-layered hierarchical networks, i.e., the orches- tration among different aerial/space platforms, including Unmanned Aerial Vehicles (UAVs), High Altitude Platforms (HAPs), and satellites co-operating at different al- titudes, currently represents one the most attractive technological options to solve coverage and latency constraints associated with the NTN paradigm. However, there are still several issues to be resolved for proper network design. In this thesis, we in- vestigate the propagation model in air/space links and then evaluate the performance of different multi-layered non-terrestrial configurations, and then provide guidelines on the optimal working point(s) for which it is possible to achieve a good compro- mise between improved system flexibility and network performance, with respect to a baseline standalone deployment.
  • Fish Movement in the Red Sea and Implications for Marine Protected Area Design

    Salinas-Akhmadeeva, Irene Antonina (2021-04) [Thesis]
    Advisor: Berumen, Michael L.
    Committee members: Green, Alison; Coker, Darren; Brainard, Rusty
    The Red Sea is valued for its biodiversity and the livelihoods it provides for many. It now faces overfishing, habitat degradation, and anthropogenic induced climate-change. Marine Protected Areas (MPAs) became a powerful management tool to protect vulnerable species and ecosystems, re-establish their balance, and enhance marine populations. For this, they need to be well designed and managed. There are 15 designated MPAs in the Red Sea but their level of enforcement is unclear. To design an MPA it is necessary to know if it will protect species of interest by considering their movement needs. In this thesis I aim at understanding fish movement in the Red Sea, specifically home range (HR) to inform MPA size designation. With not much empirical data available on HR for Red Sea fish, I used a Machine Learning (ML) classification model, trained with empirical literature HR measurements with Maximum Total Length (L Max), Aspect Ratio (AR) of the caudal fin, and Trophic Level as predictor variables. HR was classified into 5 categories: <.1 km, 0.1- 1.0 km, 2.0- 5.0 km, 5.0- 20 km, and >20 km. The model presents a 74.5% degree of accuracy. With it, I obtained the HR category for 337 Red Sea fish species. Having MPAs with a maximum linear dimension of at least 10km will meet the requirements of 90% of fish species evaluated in the model, which were small to medium size families (damselfishes, butterflyfishes, small wrasses, cardinalfishes, gobies and blennies). This percentage does not include larger species likely to move over much greater distances (10s, 100s or 1000s of km) (e.g., medium to large jacks, snappers,, groupers, sharks and rays). 60% of the Red Seas designated MPAs have the potential, if enforced as a No Take Area (NTA), to benefit more than 95% of reef fishes. However, larger MPAs will be required to protect more wide-ranging species. TRSP project in Al Wadj is proposing to close the entire SEZ to fishing. If they are successful in implementing and enforcing this fishing ban, TRSP will be the largest no take area in the Red Sea (~160 km long) that is likely to not only protect all of the species evaluated in the model, but also most wide-ranging species. Therefore, TRSP is not only likely to achieve and surpass its stated goal of increasing current fish biomass by 30%, but also to provide benefits to surrounding areas through the spillover of adults, juvenile and larvae to fished areas.
  • Expression, Purification and Characterization of Human DNA Polymerase Alpha

    Al-Amodi, Amani (2021-04) [Thesis]
    Advisor: Hamdan, Samir
    Committee members: Arold, Stefan T.; Mahfouz, Magdy M.
    DNA replication is a fundamental process in all living organisms. It is a semi- discontinuous process in which the leading strand is synthesized continuously and the lagging strand is synthesized discontinuously as short Okazaki fragments (OF). The initiation of DNA synthesis requires DNA polymerase α (Pol α/primase) in complex with the primase to form a complex of four subunits. Pol α/primase is the only enzyme that can perform de novo DNA synthesis on single-stranded DNA. The catalytic subunit of the primase (PRIM1) synthesizes RNA primers that are approximately nine nucleotides long. The synthesized RNA primers are then passed intramolecularly to the polymerase active site (POLA1), which is thought to be mediated by the C-terminal domain of the primase large subunit (PRIM2-C) to synthesize dNTPs of approximately 20 nucleotides. The aim of this project was to optimize the expression and purification of Pol α/primase. The insect codon optimized POLA1 was C-terminally Strep tagged and transposed into the baculovirus genome. The other subunits of Pol α/primase, POLA2, PRIM1 and PRIM2 were cloned and expressed in E. coli cells. The cell lysates from Sf9 insect cells and E. coli cells were then mixed and purified by immunoaffinity chromatography and size-exclusion chromatography. This helped us achieve a pure Pol α/primase containing all the four subunits with a good total yield. The identity of all the protein bands were verified by mass spectroscopy. Furthermore, the protein demonstrated primer extension activity on multiple primer/template substrates. We also characterized the effect of the human replication protein A (RPA) on the DNA polymerization activity of Pol α/primase.
  • Design and Implementation of Adaptive Morphology Feature for a Tetrahedron Shaped Drone

    Wali, Obadah (2021-04) [Thesis]
    Advisor: Feron, Eric
    Committee members: Younis, Mohammad I.; Park, Shinkyu
    In recent years, there has been an increase in the development of drone technologies. Furthermore a considerable interest in developing drones that utilizes platforms allowing for adaptive morphology has been growing steadily. In this work, we use a quadcopter to develop a drone with the feature of transforming its shape from a flat triangle to a tetrahedron. To achieve this property, two main features are considered. First, a controller for the propeller thrust force to control the movement of the triangular side facet. Second, a 60-degree angled bevel gear is used to ensure the positioning concurrency of the facets. In this study, we use MATLAB simulations to study the feasibility of the proposed concept. We use the simulations to determine the base requirement for the controller dynamics by simulating the output angle of the facets and to study the effect of the controllers on the angle reached by the facets. In addition, we perform an experimental analysis to validate our results from the simulations. We investigate the design limitations of the controllers and check the feasibility of the proposed drone design by studying the thrust force generated. The simulations and experiments showed that the presence of bevel gears can reduce the controller dynamics requirement to only a proportional controller. Furthermore, the thrust test for this drone design showed an estimated thrust force of approximately 1.7 times the thrust of a single motor. These results are promising and contribute to setting the foundation for more rigorous study of this design of drones, which have a noticeable impact on the ease of packaging and transportation applications.

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