A Game-theoretic Implementation of the Aerial Coverage Problem(2020-09) [Thesis]
Advisor: Shamma, Jeff S.
Committee members: Laleg-Kirati, Taous-Meriem; Elhoseiny, Mohamed H.Game theory can work as a coordination mechanism in multi-agent robotic systems by representing each robot as a player in a game. In ideal scenarios, game theory algorithms guarantee convergence to optimal configurations and have been widely studied for many applications. However, most of the studies focus on theoretical analysis and lack the details of complete demonstrations. In this regard, we implemented a real-time multi-robot system in order to investigate how game-theoretic methods perform in non-idealized settings. An aerial coverage problem was modeled as a potential game, where each aerial vehicle is an independent decision-making player. These players take actions under limited communication, and each is equipped with onboard vision capabilities. Three game-theoretic methods have been modified and implemented to solve this problem. All computations are performed using onboard devices, independent of any ground entity. The performance of the system is analyzed and compared with different tests and configurations
High-Speed GaN-Based Distributed-Feedback Lasers and Optoelectronics(2020-09) [Thesis]
Advisor: Ooi, Boon S.
Committee members: Ohkawa, Kazuhiro; Baran, Derya; Kuo, Hao-ChungGallium nitride (GaN) is a semiconductor material highly regarded for visible light generation since it provides the most efficient platform for compact violet, blue, and green light emitters, and in turn, high-quality and ubiquitous white lighting. Despite this fact, the potential of the GaN platform has not been fully exploited. This potential must enable the precise control in the various properties of light, realizing functions beyond the conventional. Simultaneously, the field of the telecommunications is looking for candidate technologies fit for wireless transmission in the next generations of communication. Visible light communication (VLC) may play a significant role in the future of the last mile of the network by providing both a fast internet connection and a high-quality illumination. Hence, a variety of optoelectronic platforms, including distributed-feedback (DFB) lasers, superluminescent diodes (SLDs), and multi-section lasers, can be used to exploit the full potential of GaN while offering unprecedented solutions for VLC and other applications, such as atomic clocks, high-resolution fluorescence microscopy, and on-chip nonlinear processing at visible wavelengths. This dissertation demonstrates green and sky-blue DFB lasers based on GaN, with resolution-limited single-mode emission at wavelengths around 514 nm and 480 nm, side-mode suppression ratio as large as 42.4 dB, and application to up to 10.5 Gbit/s data transmission. Preliminary observations of DFB lasers with emission close to the Fraunhofer lines are presented, offering a pathway for low-background noise applications. Blue-emitting SLDs are used to demonstrate a 3.8 Gbit/s transmitter while achieving spectral efficiency of up 118.2 (mW・nm)/(kA/cm2) in continuous-wave operation. Visual quality is confirmed by coherence length and white light generation. Short-wavelength SLDs have the potential for higher resolution and fluorescence excitation in classical optical coherence tomography and fiber gyroscopes. The demonstration of a two-section green laser diode is presented, achieving coupled-cavity lasing at wavelengths of 514 nm based on an integrated green laser–absorber in self-colliding pulse configuration, operated in continuous-wave electrical injection. The integrated laser offer potential for mode- locked and Q-switched lasing. The integrated laser is suitable for reconfiguration where laser–modulator, laser–absorber, and laser–amplifier are proposed and investigated at green wavelengths.
The Umklapp Scattering and Spin Mixing Conductance in Collinear Antiferromagnets(2020-08-31) [Thesis]
Advisor: Manchon, Aurelien
Committee members: Schwingenschlögl, Udo; Wu, YingAntiferromagnetic spintronics is a new promising field in applied magnetism. Antiferromagnetic materials display a staggered arrangement of magnetic moments so that they exhibit no overall magnetization while possessing a local magnetic order. Unlike ferromagnets that possess a homogeneous magnetic order, the spin-dependent phenomena occur locally upon the interaction between the itinerant electron and the localized magnetic moments. In fact, unique spin transport properties such as anisotropic magnetoresistance, anomalous Hall effect, magnetooptical Kerr effect, spin transfer torque and spin pumping have been predicted and observed, proving that antiferromagnetic materials stand out as promising candidates for spin information control and manipulation, and could potentially replace ferromagnets as the active part of spintronic devices. As a matter of fact, owing to their vanishing net magnetization, they produce no parasite stray fields, hence, they are mostly insensitive to external magnetic fields perturbations and displaying ultrafast magnetic dynamics. When a spin current is sent into an antiferromagnet, it experiences spin-dependent scattering, a mechanism that controls the spin transfer torque as well as the spin transmission across the antiferromagnet. The fully compensated antiferromagnetic interfaces are full of intriguing properties. For example, itinerant electron impinging on such an interface experiences a spin-flip associated with the sub-lattices interchange. This process, associated with Umklapp scattering, gives rise to a non-vanishing spin mixing conductance that governs spin transfer torque, spin pumping, and spin transmission. The thesis explores the mechanism of Umklapp scattering at a staggered antiferromagnetic interface and its associated spin mixing conductance. In this project we consider two systems of bilayer and trilayer antiferromagnetic (L-type, G-type) heterostructures. We first study the scattering coeffcients at the interface implemented by adopting the tight-binding model and proper boundary conditions. Then, in the trilayer case, we study the spin mixing conductance and the dephasing length associated with the transition from ferromagnetic order to antiferromagnetic order.
Fundamental Molecular Communication Modelling(2020-08-25) [Thesis]
Advisor: Alouini, Mohamed-Slim
Committee members: Keyes, David E.; Parsani, MatteoAs traditional communication technology we use in our day-to-day life reaches its limitations, the international community searches for new methods to communicate information. One such novel approach is the so-called molecular communication system. During the last few decades, molecular communication systems become more and more popular. The main di erence between traditional communication and molecular communication systems is that in the latter, information transfer occurs through chemical means, most often between microorganisms. This process already happens all around us naturally, for example, in the human body. Even though the molecular communication topic is attractive to researchers, and a lot of theoretical results are available - one cannot claim the same about the practical use of molecular communication. As for experimental results, a few studies have been done on the macroscale, but investigations at the micro- and nanoscale ranges are still lacking because they are a challenging task. In this work, a self-contained introduction of the underlying theory of molecular communication is provided, which includes knowledge from di erent areas such as biology, chemistry, communication theory, and applied mathematics. Two numerical methods are implemented for three well-studied partial di erential equations of the MC eld where advection, di usion, and the reaction are taken into account. Numerical results for test cases in one and three dimensions are presented and discussed in detail. Conclusions and essential analytical and numerical future directions are then drawn.
Shale Reservoir Simulation in Basins with High Pore Pressure and Small Diﬀerential Stress(2020-08) [Thesis]
Advisor: Patzek, Tadeusz
Committee members: Hoteit, Hussein; Finkbeiner, Thomas; Klimkowski, LukaszHydrocarbon production from mudrock (“shale”) reservoirs is fundamental in the global energy supply. Extracting commercial amounts of hydrocarbons from shale plays requires a combination of horizontal well drilling, hydraulic fracturing, and multi-stage completions. This technology creates conductive hydrofractures that may interact with pre-existing natural fractures and bedding planes. Microseismic studies and ﬁeld pilots have uncovered evidence of complex hydrofracture geometries that can lead to unsatisfactory wellbore ﬂow performance. This study examines the eﬀects of three hydrofracture geometries (”scenarios”) on wellbore production in overpressured shale oil reservoirs using a commercial reservoir simulator (CMG IMEX). The ﬁrst scenario is our reference case. It comprises ideal ized and vertical hydrofractures. The second scenario has an orthogonal hydrofracture network made up of vertical hydrofractures with perpendicular secondary fractures. The third scenario has vertical hydrofractures with horizontal bedding plane frac tures. We generated additional simulation models that aim to capture the eﬀect on hydrocarbon production of diﬀerent fracture properties, such as natural fracture ori entation and spacing, number of hydrofractures per stage, number of perpendicular secondary fractures and horizontal fractures, and fracture closure mechanism. The results show that ideal planar fractures are an oversimpliﬁcation of the hydrofracture geometry in anisotropic shale plays. They fail to represent the complex geometry in reservoir simulation and lead to unexpected hydrocarbon production forecasting. They also show that the generation of unpropped horizontal fractures harms hydro carbon productivity, while perpendicular secondary fractures enhance initial reservoir 5 ﬂuid production. The generation of horizontal hydrofractures is a particular scenario that may occur in reservoirs with high pore pressure and transitional strike-slip to reverse faulting regime. These conditions have been reported in unconventional source rock plays, like the Marcellus shale in northeast Pennsylvania and southwest Virginia, and the Tuwaiq Mountain formation in the Jafurah Basin in Saudi Arabia. Our ﬁndings reveal that the presence of horizontal hydrofractures might reduce the cumulative hydrocarbon production by 20%, and the initial hydrocarbon production by 55% compared to the reference case. Our work shows unique reservoir simulations that enable us to assess the impact of diﬀerent variables on wellbore production performance and understand the eﬀects of varied hydrofracture geometries on hydrocarbon production.
Broadband Reflective Metalens in Visible Band Based on Bragg Reflector Multilayers for VECSEL Applications(2020-08) [Thesis]
Advisor: Li, Xiaohang
Committee members: Roqan, Iman S.; Salama, Khaled N.In conventional optics, curved lenses focus light rays to a focal point after light passes through them. These lenses have been designed to shape the wavefront of the incident beam as it emerges from the curved surface of the lens. Conventional lenses suffer from many limitations, such as limited optical quality for imaging and integration difficulties with other optical components due to their large size, huge thickness, as well as being difficult to manufacture. Using subwavelength structure, it is possible to fabricate flat, thin lenses (metalenses) with new optical properties not found in nature, in which many fundamental properties of light (like polarization, focal point, and phase) can be controlled with high accuracy. This results in high resolution and high quality of optical imaging. This thesis demonstrates a new design of reflective metalens, in which the metalens structure is integrated with another optical component: Distributed Bragg Reflector (DBR). The metalens planer is a two-dimensional ultrathin planer arranged as an array with subwavelength separation distance. In recent works, a metalens was integrated with (metal/dielectric)-mirrors to form reflective metalenses. Simulation results show that, high-focusing efficiency is obtained for the lens (> 60%) with the ability to reflect96% of total incident optical power. In comparison, the new metalens-DBR design - processes maintain the same high-focusing efficiency, but with a reflectance of 99.99%, which makes it promising for optoelectronic integration and perfectly suitable for integration with Vertical Cavity Surface Emitting Lasers (VCSEL) technology. This study of the optical properties: focal length; optical aberration; insensitivity to light polarization; and focusing efficiency of demonstrated metalens was done mainly by Finite Difference Time Domaine (FDTD) by using Lumerical FDTD solution.
An Investigation of the Stresses Causing the Spontaneous Delamination of Titanium-Platinum Bilayers Leading to The Formation of Nanogaps(2020-07-23) [Thesis]
Advisor: Anthopoulos, Thomas D.
Committee members: Laquai, Frédéric; Lubineau, GillesAdhesion lithography has been used to pattern nanogaps between two electrodes of the same or different metals onto a substrate. Patterning Al and Ti/Pt bilayer electrodes have been shown to form nanogaps leaving behind relatively consistent nanogaps of less than 12 nm between the electrodes. These nanogaps are formed without the need for adhesion lithography due to the bilayer spontaneously delaminating from the aluminum electrodes, In this study, the stresses in the Ti/Pt bilayer are investigated to determine the amount of stress required for delamination and the properties causing it. The goal is to recreate this stress mechanism in other patterned metals such as Au and Al. Heat cycling is used to induce high stress in other metal electrode combinations in an attempt to induce spontaneous delamination in Al and Au but fails up to 310°C annealing temperature. Theoretical methods are used to determine the stress: searching for an appropriate mathematical model and using finite element analysis in ABAQUS software to create a simulation of the delaminating Ti/Pt bilayer. The stress is found to be caused by the residual stresses in platinum and the high energy e-beam deposition method. An experimental value for the stress and the ability to recreate it in other metals remains elusive.
Stochastic Geometry-based Analysis of LEO Satellite Communication Systems(2020-07-21) [Thesis]
Advisor: Alouini, Mohamed-Slim
Committee members: Gomes, Diogo A.; Park,Ki-Hong; Kishk, Mustafa AbdelsalamWireless coverage becomes one of the most signi cant needs of modern society because of its importance in various applications such as health, distance educa- tion, industry, and much more. Therefore, it is essential to provide wireless coverage worldwide, including remote areas, rural areas, and poorly served locations. Recent advances in Low Earth Orbit (LEO) satellite communications provide a promising solution to address these issues in poorly served locations. The thesis studies the performance of a multi-level LEO satellite communication system. More precisely, we model the LEO satellites' location as Binomial Point Process (BPP) on a spherical surface at n di erent altitudes given that the number of satellites at each altitude ak is Nk where 1 k n and study the distance distribution. The distance distribution is characterized in two categories depending on the location of the observation point: contact distance and the nearest neighbor distance. For that proposed model, we study the user coverage probability by using tools from stochastic geometry for a scenario where satellite earth stations (ESs) with two antennas are deployed on the ground where one of the antennas communicates with the user while the other communicates with LEO satellite. Additionally, we consider a practical use case where satellite communication systems are deployed to increase coverage in remote and rural areas. For that purpose, we compare the coverage probability of the satellite-based communication system in such regions with the coverage probability in case of relying on the nearest anchored base station (ABS), which is usually located at far distances from rural and remote areas
Development of High-Mobility Low-Temperature Solution-Processed Metal-Oxide Thin Film Transistors Grown by Spray Pyrolysis(2020-07-08) [Thesis]
Advisor: Anthopoulos, Thomas D.
Committee members: Tung, Vincent; Shamim, AtifIn today’s electronics, transistors are the main building blocks of the vast majority of electronic devices and integrated circuits. Types of transistors vary depending on the device structure and operation principle. Metal-oxide-based thin film transistors (MO TFTs), in particular, are an emerging technology that has a promising future in many applications, such as large-area display and wearable electronics. It exhibits unique features that make it superior to the existing Si-based technology, such as optical transparency and mechanical flexibility. However, some technical challenges in MO TFTs limit their emplyoment in today’s applications, such as low carrier mobility and high processing temperature. Solution-processed MO TFT based on spray pyrolysis combined with a carefully engineered TFT structure offers a dramatically enhance carrier mobility at low processing temperature. In this work, we are utilizing spray pyrolysis to grow In2O3 and ZnO based TFTs at low processing temperature. The structural effects of the channel layer on the electrical performance is investigated in two parts. The first part highlights the impact of thickness of the channel layer on the device performance of both In2O3 and ZnO, while the second part explores In2O3/ZnO heterojunction-based active layer. The results showed that increasing the channel thickness of both In2O3 and ZnO based TFTs enhanced the carrier mobility due to a reduced surface-roughness scattering effect. In addition, evidence showed that the electron transport mechanism in In2O3/ZnO heterojunction transitioned from trap-limited conduction (TLC) to percolation conduction (PC) process. Thanks to the existence of a 2D-confined electron sheet at the atomically sharp In2O3/ZnO heterointerface, the electron mobility was dramatically enhanced.
Control and Optimization of Chemical Reactors with Model-free Deep Reinforcement Learning(2020-07) [Thesis]
Advisor: Sarathy, Mani
Committee members: Shamma, Jeff S.; Pinnau, IngoAbstract: Model-based control and optimization is the predominant paradigm in process systems engineering. The performance of model-based methods, however, rely heavily on the accuracy of the process model, which declines over the operation cycle due to various causes, such as catalyst deactivation, equipment aging, feedstock variability, and others. This work aims to tackle this challenge by considering two alternative approaches. The first approach replaces existing control and optimization methods with model-free reinforcement learning (RL). We apply a state-of-the-art reinforcement learning algorithm to a network of reactions, evaluate the performance of the RL controller in terms of setpoint tracking, disturbance rejection, and robustness to parameter uncertainties, and optimize the reward function to achieve the desired control and optimization performance. The second approach presents a novel framework for integrating Economic Model Predictive Control (EMPC) and RL for online model parameters estimation. In this framework, EMPC optimally operates the closed-loop system while maintaining closed-loop stability and recursive feasibility. At the same time, the RL agent continuously compares the measured state of the process with the model’s predictions, and modifies the model parameters accordingly to optimize the process. The performance of the proposed framework is illustrated on a network of reactions with challenging dynamics and practical significance.
Blind Estimation of Central Blood Pressure Waveforms from Peripheral Pressure Signals(2020-07) [Thesis]
Advisor: Al-Naffouri, Tareq Y.
Committee members: Al-Naffouri, Tareq Y.; Laleg-Kirati, Taous-Meriem; Gao, XinThe central aortic blood pressure signal is an important source of information that contains cues about the cardiovascular system condition. Measuring this pulse wave clinically is burdensome as it can be only measured invasively with a catheter. As a result, many mathematical tools have been proposed in the past few decades to reconstruct the aortic pressure signal from the peripheral pressure signals that are usually easier to obtain noninvasively. At the distal level, the blood pressure signal is not directly useful since factors, such as length and stiffness of the arteries, play roles in changing the shape of the pressure signal significantly. In this thesis, multi-channel blind system identification techniques are proposed to estimate the central pressure waveform which vary in their accuracy and complex- ity. First, a simple linear method is applied by approximating the nonlinear arterial system as a linear time-invariant system and applying the cross-relation approach. Next, a more complicated nonlinear Wiener system is proposed to model the nonlinear arterial tree. Along with the channel’s coefficients, the nonlinear functions are estimated using cross-relation and kernel methods. Data-driven machine learning methods are tested to estimate the aortic pressure signals. In many cases, they suffer from underfitting problems. As a remedy, a hybrid machine learning and cross-relation approach is also proposed to add more robustness to the machine learning models. This hybrid approach is implemented by combining the cross-relation with any machine learning method, including deep learning approaches. The various methods are tested using pre-validated virtual databases. The results show that the linear method produces root mean squared errors between 3.40 mmHg and 6.24 mmHg depending on the cross-relation constraint and the equalization tech- nique. On the other hand, the root mean squared errors associated with the nonlinear methods are between 3.76 mmHg and 4.22 mmHg and hence more stable. For the hybrid machine learning and cross-relation approach, applying the cross-relation and the dictionary learning reduce the root mean squared errors up o 67% comparing with the pure machine learning models.
Synthesis and Characterization of Electroactive Vinylidene Fluoride Based Block Copolymers via Iodine Transfer Polymerization(2020-07) [Thesis]
Advisor: Hadjichristidis, Nikos
Committee members: Pinnau, Ingo; Nunes, Suzana PereiraAbstract: Poly (vinylidene fluoride) (PVDF), thanks to its versatile properties, finds many applications ranging from water purification membranes (thermal and chemical stability) to electronic devices (piezoelectric, pyroelectric and ferroelectric properties). Block copolymers of PVDF with other polymers further expand its properties and, consequently, its applications. Toward this line, my thesis investigates the synthesis, molecular characterization and properties of novel PVDF-based copolymers mainly with poly(tert-butyl acrylate) (PtBuA), poly(methyl methacrylate) (PMMA) and polystyrene (PSt). To prepare the block copolymers a living polymerization is needed, which is compatible with the VDF and the comonomer (tBuA, MMA, St). For this purpose, we used iodine transfer polymerization (ITP) with the difunctional chain transfer agent (CTA) C4F8I2. Difunctional macroinitiator (I-PVDF-I) was first obtained by ITP of VDF monomer with C4F8I2, followed by addition of the comonomer tBuA, MMA or St to afford the triblock copolymers poly(tert-butyl acrylate)-block-poly(vinylidene fluoride)-block-poly(tert-butyl acrylate) (PtBuA-b-PVDF-b-PtBuA), poly(methyl methacrylate)-block-poly(vinylidene fluoride)-block-poly(methyl methacrylate) (PMMA-b-PVDF-b-PMMA) and polystyrene-block-poly(vinylidene fluoride)-block-polystyrene (PSt-b-PVDF-b-PSt). The structure of all intermediates and final products were characterized by Nuclear Magnetic Resonance (NMR) and Gel Permeation Chromatography (GPC). The microstructure and polymorphism of all triblock copolymers, characterized by XRD, shown that the PVDF in the first two copolymers exhibits the electroactive β-phase, while in the third copolymer there is the coexistence of α- and γ-phases. Linear PVDF homopolymers, using the free radical and IT polymerizations, were prepared for comparison purposes. All linear polymers possess the α-phase. The thesis is divided into the following five chapters: 1. Introduction, where the scope of this thesis is given with a brief background on PVDF; 2. Literature Review, where a summary of previously published works on PVDF synthesis and polymorphism is presented; 3. Experimental Section, where detailed procedures and characterization methods are given; 4. Results and Discussion, where outcomes of successful experiments are discussed; and 5. Conclusion and Perspective, where the outcomes of this work are summarized and perspective are discussed.
A Comparative DNA Binding Study of the Human MAPK ERK2 and the Plant MAPK MPK4(2020-07) [Thesis]
Advisor: Arold, Stefan T.
Committee members: Hirt, Heribert; Al-Babili, SalimMitogen-activated protein kinases (MAPKs) are an important subfamily of protein kinases that are well conserved in all eukaryotes. MAPKs are the final component of a three-tiered signaling module that regulates the activation of various essential cellular responses. They activate most of their substrates through catalyzing their phosphorylation. However, emerging evidence reveals that some MAPKs also possess non-catalytic functions. In particular, the human MAPK ERK2 can bind to DNA directly and mediate gene expression. The mechanism by which ERK2 binds to DNA is still unclear. In this work, we combined structural, biophysical and biochemical methods to confirm DNA binding by ERK2 and to investigate whether ERK2’s closest plant homolog MPK4 also binds to DNA. First, we identified a possible ERK2-like DNA consensus motif in plant MAPKs. We found that several plant MAPKs, including MPK4, harbor a basic motif (KARK/R or ARR/K) in a region corresponding to the ERK2 KAR motif reported to mediate DNA binding. Next, we determined the DNA binding affinity of ERK2 and MPK4 to different DNA fragments and found that MPK4 associated directly with DNA in vitro, albeit with a significantly lower affinity than did ERK2. Moreover, we observed that ERK2 and MPK4 showed preferred binding to different DNA sequences. Site-directed mutagenesis on the proposed DNA binding region of MPK4 greatly weakened DNA binding, confirming that MPK4 and ERK2 use the same structural elements to associate with DNA. Phosphorylation of the MAPKs through an upstream MKK affected the DNA binding capacity for both ERK2 and MPK4, although the effects differed. Lastly, we observed that a MPK4 mutant with a constitutively increased catalytic affinity displayed a markedly stronger DNA binding affinity compared to wild type MPK4 and phosphorylated MPK4. By demonstrating that the plant MPK4 associated with DNA in vitro, and that this association can be modified by phosphorylation and mutations, we open the possibility of additional kinase-independent functions in plant MAPKs.
A Numerical Investigation of Pre-chamber Combustion Engines(2020-07) [Thesis]
Advisor: Im, Hong G.
Committee members: Bengt, Johansson; Keyes, David E.This work aims to enhance fundamental and practical understanding of pre-chamber (PC) combustion engines, using computational fluid dynamics (CFD) simulations conducted with the software CONVERGE employing the Reynolds-averaged Navier-Stokes turbulence closure and the well-stirred reactor combustion model for methane oxidation. First, to help the design of the KAUST pre-chamber, the simulations were conducted to assess the impact of design parameters such as throat and nozzle diameters, and nozzle length in a passively operated pre-chamber at lean conditions. The geometrical parameters showed to affect the pre-chamber combustion characteristics, such as pressure build-up, radical formation, heat release, and the composition of the jets penetrating and igniting the main chamber charge. It was found that the narrow-throat pre-chamber is strongly influenced by the throat diameter, but weakly influenced by nozzle length. A flow reversal pattern was observed, promoting the accumulation of intermediate species in the PC, leading to a secondary heat release. Subsequently, the validation of the actively fueled pre-chamber systems was assessed under different fueling strategy and validated against experimental data. The last chapter analyzes the impact of enrichment and stratification of the pre-chamber on the main chamber combustion. An open-cycle simulation was conducted to describe the full interaction between both chambers. The influence of fuel enrichment in the PC was compared to the passive mode operation and found to greatly impact in the overall system performance. It was found that the excessively rich PC does not yield the optimal results; instead, a pre-chamber with stoichiometric composition at spark timing does. Although the fuel distribution inside the PC 5 was not homogeneous, the active control of the PC was shown to enable a command of the pressure response. It was found that the upstream flame propagation forces part of the PC mixture to leak to the main chamber, creating localized fuel rich regions, which enhances the combustion of the MC charge. The overall MC combustion is found to be complex, influenced by the turbulent mixing and local cooling, and possibly local quenching events. The detailed interaction of mixing and combustion in the MC is not fully understood and is subject of future studies.
Analyzing Germline-Specific Expression in Caenorhabditis elegans(2020-07) [Thesis]
Advisor: Jensen, Christian Froekjaer
Committee members: Blilou, Ikram; Mahfouz, Magdy M.Maintaining cells in an undifferentiated totipotent state is essential for initiating developmental programs that lead to a fully formed organism in each generation and for maintaining immortal germ cells across generations. Caenorhabditis elegans is a powerful genetic model organism to study early germ cell development due to the animal’s transparency and the ability to screen for mutant phenotypes. However, our ability to use standard techniques to study gene expression using fluorescent reporter genes has been limited due to germline-specific silencing mechanisms that repress transgenes. Therefore, we lack even basic knowledge of how expression is regulated in C. elegans germ cells. In this study, we develop methods to overcome these silencing mechanisms by using a class of noncoding DNA, called Periodic An/Tn Clusters (PATCs), to prevent transgene silencing in the germline. We use these improved tools to test the proposed role of putative germline-specific regulatory DNA motifs and the role a periodic TT signal within germline promoters. We fused GFP to the promoter of a germline expressed gene (pcn-1), which is enriched for PATCs and contains a germline-specific motif (TTAAAG). Our results show that despite enrichment and phylogenetic conservation, the TTAAAG motif is not required for germline expression. To test additional motifs and periodic TTs, we have designed a system that will allow us to test synthetic gene fragments for bi-directional germline expression. These tools will allow us to rapidly test motif redundancy, motif spacing, and TT periodicity using gfp and rfp signals in the germline and will enable experiments aimed at understanding the role of germline regulatory elements.
Modeling of Sulfur Removal from Heavy Fuel Oil Using Ultrasound-Assisted Oxidative Desulfurization(2020-07) [Thesis]
Advisor: Roberts, William L.
Committee members: Sarathy, Mani; Dibble, Robert W.Growing environmental concerns, such as global warming, are giving rise to new regulations imposed by the International Maritime Organization (IMO) on sulfur content for marine fuels, thus, constraining refining processes. Oxidative desulfurization (ODS) is an appealing desulfurization method with some advantages over traditional processes like hydrodesulfurization (HDS), such as mild operating conditions and no-hydrogen consumption. ODS could be employed as a complementary or alternative process for HDS. During the oxidative desulfurization, the organo-sulfur compounds are oxidized to polar sulfones. Then, such sulfones are separated from the treated fuel oil using techniques such as liquid-liquid extraction. In the present work, the separation of oxidized sulfur-containing compounds of heavy fuel oil using ultrasound-assisted technology has been investigated and simulated in Aspen Plus. The oxidant selected was hydrogen peroxide, while the catalyst was acetic acid. The chosen solvent for the sulfone separation was acetonitrile. The primary goal of this work is to successfully emulate the operation performed by an oxidative desulfurization pilot plant-scale apparatus designed by Tecnoveritas®, which will later allow the analysis of the parameters on the overall sulfur removal efficiency.
Nanostructured Gold-Modified Laser Scribed Graphene Biosensor Based on Molecularly Imprinted Polymers(2020-07) [Thesis]
Advisor: Salama, Khaled N.
Committee members: Salama, Khaled N.; Ooi, Boon S.; Inal, SahikaRecently, laser scribed graphene (LSG) technology has shown great potential for the development of a plethora of sensing platforms due to its high sensitivity, 3D porous structure, and flexibility. Molecularly imprinted polymers (MIPs) have shown high potential as recognition elements for many applications such as biosensing. Hence, we report in this thesis a novel biosensing platform that utilizes nanostructured gold to enhance the performance of LSG sensors coupled with a biomimetic MIP biosensor. To the best of our knowledge, this is the first report of a nanostructured gold modified MIP based LSG biosensor to detect HER-2, which is an important breast cancer biomarker. HER-2 positive breast cancer is more aggressive and does not respond to the same treatment as standard breast cancer. As such, a simple and accurate sensing approach is highly needed for early detection of this type of cancer biomarkers. The LSG sensor platform was fabricated by irradiation of polyimide substrates using a CO2 laser under optimized conditions. Nanostructured gold was electrodeposited onto LSG to enhance its sensitivity and active surface area. Deposition parameters such as deposition voltage, deposition time, and gold chloride (HAuCl4) concentration were optimized to yield complete nanostructured gold coverage and enhanced electrical conductivity of LSG-Au electrodes. A deposition voltage of -0.9 V at 50 mM HAuCl4 for 4 minutes proved to be the optimal condition for gold deposition to yield a 150% peak current enhancement. To fabricate our MIP biosensor, 3,4- ethylenedioxythiophene (EDOT) was chosen from several functional monomers to form PEDOT due to its high conductivity and synergy with nanostructured gold. Electropolymerization of EDOT is performed after adsorbing 0.4mg/mL of HER-2 on the LSG-Au electrode for 20 min. The efficiency of LSG-Au-MIP was optimized by choosing an appropriate extraction agent and HER-2 concentration to be adsorbed on gold. The developed sensing strategy could differentiate between three rebinding concentrations of 10 ng/mL, 100ng/mL, and 200 ng/mL, which is sufficient to determine the HER-2 status of breast cancer since the clinical cut-off is 30.5ng/mL. The developed sensing strategy showed a high degree of novelty and could be useful for the non-invasive detection of cancer biomarkers.
Atom Transfer Radical Polymerization in Aqueous Media Using Different Water-Soluble Initiators and Ligands(2020-07) [Thesis]
Advisor: Hadjichristidis, Nikos
Committee members: Nunes, Suzana Pereira; Cavallo, LuigiAbstract: Styrene and methyl methacrylate have been polymerized successfully through atom transfer radical polymerization (ATRP) in aqueous dispersed media (emulsion ATRP). The thesis is divided into four experimental parts. In the first part, a water-soluble initiator was prepared for emulsion ATRP and utilized under various conditions in the presence of two ligands N, N, N’, N’’, N’’-Pentamethyldiethylenetriamine and 2,2’-bipyridine to attain activation/deactivation only in the oil phase with Tween 20 as a non-ionic surfactant. The initiator was synthesized by the reaction of diethanolamine with α-Bromoisobutyryl bromide in anhydrous tetrahydrofuran. 1H NMR spectroscopy (500 MHz, deuterium oxide, or chloroform-d) was performed to confirm the successful synthesis of the initiator and polystyrenes. In the second and third parts, two commercial initiators were used, poly(ethylene glycol) methyl ether 2-bromoisobutyrate (Mn= 2000 g/mol), and 2-hydroxyethyl 2-bromoisobutyrate (Mn= 211.05 g/mol). BPY, tris(2-pyridylmethyl) amine and 4, 4’-dinonyl -2, 2’-dipyridyl were used as the ligands with various molar ratios. Polyoxyethylene (80) sorbitan monooleate, and polyoxyethylene (20) oleyl ether were used as non-ionic surfactants. In the fourth part, a macroinitiator was synthesized by the reaction of polyoxyethylene (20) stearyl ether with α-Bromoisobutyryl bromide. The formation of the macroinitiator as well as the successful synthesis of poly(ethylene glycol)-b-polystyrene, and poly(ethylene glycol)-b-poly(methyl methacrylate) block copolymers were confirmed by Fourier transform infrared and 1H NMR spectroscopies. The molecular weight of the resulting polymers, as well as the stability of the emulsion systems, were evaluated by gel permeation chromatography and dynamic light scattering, respectively.
AC ELECTROHYDRODYNAMICS PHENOMENON IN 2D AND 3D MICROELECTRODES(2020-07) [Thesis]
Advisor: Salama, Khaled N.
Committee members: Salama, Khaled N.; Ooi, Boon S.; Thoroddsen, Sigurdur TAlternating current electrohydrodynamics (ac-EHD) has been reported as a promising technique for enhancing sensor performance by the intimate mixing of the analyte solution at the electrode surface. The lateral fluid motion created by the ac-EHD phenomenon can be tuned by changing the frequency, voltage, and electrode geometry. To date, various studies have been conducted on the use of 2D electrodes based ac- EHD devices for sensor applications. However, the use of 3D electrodes may provide better fluid mixing as compared to the 2D electrodes due to the high surface area of the electrodes. To test this hypothesis, 2D and 3D microelectrodes with different sizes were designed and fabricated for ac-EHD studies using standard lithography and etching processes. Previous methods to achieve 3D microstructures and common issues faced during fabrication are also discussed. The lateral fluid motion created by the 2D and 3D electrodes after the application of different voltages and frequencies was analyzed by tracking the motion of fluorescent beads present in the mixing fluid. Fluorescence microscopy technique was used to capture videos of the movement of fluorescent beads in the fluid. The videos were analyzed using ImageJ to calculate the speed of fluorescent beads in the case of 2D and 3D electrodes. Furthermore, a different pattern of the fluid motion was observed in the case of 3D electrodes, which highlights the complex fluid movement in the case of 3D electrodes as compared to the 2D electrodes.
3D Printed Micro-Optics for Biophotonics(2020-07) [Thesis]
Advisor: Liberale, Carlo
Committee members: Habuchi, Satoshi; Ooi, Boon S.; Moser, Christophe3D printing, also known as "additive manufacturing", indicates a set of fabrication techniques that build objects by adding material, typically layer by layer. The main advantages of 3D printing are unlimited shapes and geometry, fast prototyping, and cost-e ective small scale production. Two-photon lithography (TPL) is a laserbased 3D printing technique with submicron resolution, that can be used to create miniaturized structures. One of the most compelling applications of TPL is the 3D printing of miniaturized optical elements with unprecedented complexity, small-scale and precision. This could be potentially bene cial in biophotonics, a multidisciplinary research eld in which light-based techniques are used to study biological processes. My research has been aimed at demonstrating novel applications of 3D printing based on TPL to di erent biophotonic applications. In particular, here we show 3D printed micro-optical structures that enhance and/or enable novel functions in advanced biophotonics methods as two-photon microendoscopy, optical trapping and Stimulated Raman Scattering microscopy. Remarkably, the micro-optical structures presented in this thesis enable the implementation of advanced techniques in existing or simpler microscopy setups with little to no modi cation to the original setup. This possibility is essentially allowed by the unique miniaturization and in-situ 3D printing capabilities o ered by TPL.