• A Tale of Two Aggregations: Kinship and Population Genetics of Whale Sharks (Rhincodon typus) at Shib Habil, Saudi Arabia, and Mafia Island, Tanzania.

      Hardenstine, Royale (2015-12)
      In a recent global study of whale shark population genetics, aggregations were found to belong to either the Indo-Pacific or Atlantic population. This overview included an aggregation found within the Red Sea near Al Lith, Saudi Arabia, however the Mafia Island, Tanzania, aggregation was not part of the study. Both aggregations have unique aspects with the Saudi Arabian individuals showing sexual parity with no segregation, while recent acoustic results have revealed cryptic residency at Mafia Island. Genetic analysis using 11 microsatellite markers was performed on whale sharks from both locations. A combination of primers sourced from previous studies and newly designed primers were used to compare both aggregations and the individuals within. Samples were collected in the Red Sea for 5 seasons spanning 6 years, and for 2 seasons in Tanzania. Analysis with STRUCTURE showed a lack of significant genetic differences between the two aggregations, confirming that whale sharks in Tanzania are part of the Indo-Pacific population. Kinship analysis using COLONY found two potential pairs of full siblings in Tanzania. One pair had a high probability (.993) of being a full sibling dyad while the other had a lower probability (.357). There were no sibling pairs identified from the Red Sea aggregation. Genetic diversity was investigated using allelic richness over the 6 seasons at Al Lith, with values showing no significant change. This is in contrast to results that showed a decline in genetic diversity at Western Australia’s Ningaloo reef. These differences, however, only highlight the need for genetic diversity studies over longer time periods and at other aggregations within the Indo-Pacific.
    • Testing the Feasibility of Using PERM to Apply Scattering-Angle Filtering in the Image-Domain for FWI Applications

      Alzahrani, Hani Ataiq (2014-09)
      ABSTRACT Testing the Feasibility of Using PERM to Apply Scattering-Angle Filtering in the Image-Domain for FWI Applications Hani Ataiq Alzahrani Full Waveform Inversion (FWI) is a non-linear optimization problem aimed to estimating subsurface parameters by minimizing the mis t between modeled and recorded seismic data using gradient descent methods, which are the only practical choice because of the size of the problem. Due to the high non-linearity of the problem, gradient methods will converge to a local minimum if the starting model is not close to the true one. The accuracy of the long-wavelength components of the initial model controls the level of non-linearity of the inversion. In order for FWI to converge to the global minimum, we have to obtain the long wavelength components of the model before inverting for the short wavelengths. Ultra-low temporal frequencies are sensitive to the smooth (long wavelength) part of the model, and can be utilized by waveform inversion to resolve that part. Un- fortunately, frequencies in this range are normally missing in eld data due to data- acquisition limitations. The lack of low frequencies can be compensated for by uti- lizing wide-aperture data, as they include arrivals that are especially sensitive to the long wavelength components of the model. The higher the scattering angle of a 5 recorded event, the higher the model wavelength it can resolve. Based on this prop- erty, a scattering-angle ltering algorithm is proposed to start the inversion process with events corresponding to the highest scattering angle available in the data, and then include lower scattering angles progressively. The large scattering angles will resolve the smooth part of the model and reduce the non-linearity of the problem, then the lower ones will enhance the resolution of the model. Recorded data is rst migrated using Pre-stack Exploding Re ector Migration (PERM), then the resulting pre-stack image is transformed into angle gathers to which an angle ltering process is applied to remove events below a certain cut-o angle. The ltered pre-stack image cube is then demigrated (forward modeled) to produce ltered surface data that can be used in waveform inversion. Numerical tests con rm the feasibility of the proposed ltering algorithm. However, the accuracy of the ltered section is limited by PERM's singularity for horizontally-traveling waves, which in turn is dependent on the velocity model used for migration and demigration
    • Theoretical Kinetic Study of the Unimolecular and H-Assisted Keto-Enol Tautomerism Propen-2-ol ↔Acetone. Pressure Effects and Implications in the Pyrolysis and Oxidation of tert- And 2-Butanol

      Grajales Gonzalez, Edwing Javier (2018-05)
      The need for renewable and cleaner sources of energy has made biofuels an interesting alternative to fossil fuels, especially in the case of butanol isomers, with their favorable blend properties and low hygroscopicity. Although C4 alcohols are prospective fuels, some key reactions governing their pyrolysis and combustion have not been adequately studied, leading to incomplete kinetic models. Butanol reactions kinetics is poorly understood. Specifically, the unimolecular and H-assisted tautomerism of propen-2-ol to acetone, which are included in butanol combustion kinetic models, are assigned rate parameters based on the analogous unimolecular tautomerism vinyl alcohol ↔ acetaldehyde and H addition to the double bound of iso-butene, respectively. In an attempt to update current kinetic models for tert- and 2-butanol, a theoretical kinetic study of the unimolecular and H-assisted tautomerism, i-C3H5OH⟺CH3COCH3 and i-C3H5OH+Ḣ⟺CH3COCH3+Ḣ, was carried out by means of CCSD(T,FULL)/aug-cc-pVTZ//CCSD(T)/6-31+G(d,p) and CCSD(T)/aug-cc-pVTZ//M062X/cc-pVTZ ab initio calculations, respectively. For H-assisted tautomerism, the reaction takes place in two consecutive steps: i-C3H5OH+Ḣ⟺CH3ĊOHCH3 and CH3ĊOHCH3⟺CH3COCH3+Ḣ. Multistructural torsional anharmonicity and variational transition state theory were considered in a wide temperature and pressure range (200 K – 3000 K, 0.1 kPa – 108 kPa). It was observed that decreasing pressure leads to a decrease in rate constants, describing the expected falloff behavior for both isomerizations. Results for unimolecular tautomerism differ from vinyl alcohol ↔ acetaldehyde analogue reactions, which shows lower rate constant values. Tunneling turned out to be important, especially at low temperatures. Accordingly, pyrolysis simulations in a batch reactor for tert- and 2-butanol with computed unimolecular rate constants showed important differences in comparison with previous results, such as larger acetone yield and quicker propen-2-ol consumption. In the combustion and pyrolysis batch reactor simulations, using all the rate constants computed in this work, H-assisted reactions are limited because H radicals become abundant once the propen-2-ol has been consumed by other reactions, such as the non-catalyzed tautomerism i-C3H5OH⟺CH3COCH3, which becomes one of the main source of acetone. The intermediate radical (CH3ĊOHCH3) is formed exclusively from tert-butanol, with its concentration in 2-butanol oxidation being smaller because the secondary alcohol is unable to produce the radical directly. In all cases, the intermediate is converted effectively to acetone.
    • Thermal Responses of Growth and Toxin Production in Four Prorocentrum Species from the Central Red Sea

      Aynousah, Arwa (2017-06)
      Harmful algae studies, in particular toxic dinoflagellates, and their response to global warming in the Red Sea are still limited. This study was aimed to be the first to characterize the identity, thermal responses and toxin production of four Prorocentrum strains isolated from the Central Red Sea, Saudi Arabia. Morphological and molecular phylogenetic analysis identified the strains as P. elegans, P. rhathymum and P. emarginatum. However, the identity of strain P. sp.6 is currently unresolved, albeit sharing close affinity with P. leve. Growth experiments showed that all species could grow at 24-32°C, but only P. sp.6 survived the 34°C treatment. The optimum temperatures (Topt) estimated from the Gaussian model corresponded to 27.17, 29.33, 26.87, and 27.64°C for P. sp.6, P. elegans, P. rhathymum and P. emarginatum, respectively. However, some discrepancy with the Topt derived from the growth performance were observed for P. elegans and P. emarginatum, as thermal responses differed from the typical Gaussian fit. The Prorocentrum species examined showed a sharp decrease after the optimum temperature resulting in very high activation energies for the fall slope, especially for P. elegans and P. emarginatum. The minimum critical temperature limit for growth was not detected within the range of temperatures examined. Subsequently, high performance liquid chromatography coupled with mass spectrometry (HPLC-MS) analysis revealed all species as non okadaic acid (OA, common toxin of the Prorocentrum genus) producers at any temperature treatment. However, other forms of toxin (i.e. fast acting toxins) not examined here could be produced. Therefore, further investigations are required. The results of this study provided significant contribution to our knowledge regarding the presence, thermal response and toxin production of four Prorocentrum species from the Central Red Sea, Saudi Arabia.
    • Three-dimensional Modeling and Simulation of a Tuning Fork

      Larisch, Lukas (2018-09-16)
      The mathematical characterization of the sound of a musical instrument still follows Schumann’s laws [1]. According to this theory, the resonances of the instrument body, “the formants”, filter the oscillations of the sound generator (e.g., strings) and produce the characteristic “timbre” of an instrument. This is a strong simplification of the actual situation. It applies to a point source and does not distinguish between a loudspeaker and a three-dimensional instrument. In this work we investigate Finite-Element-based numerical simulations of eigenfrequencies and eigenmodes of a tuning fork in order to capture the oscillation behavior of its eigenfrequencies. We model the tuning fork as an elastic solid body and solve an eigenvalue equation derived from a system of coupled equations from linear elasticity theory on an unstructured three-dimensional grid. The eigenvalue problem is solved using the preconditioned inverse iteration (PINVIT) method with an efficient geometric multigrid (GMG) preconditioner. The latter allows us to resolve the tuning fork with a high resolution grid, which is required to capture fine modes of the simulated eigenfrequencies. To verify our results, we compare them with measurement data obtained from an experimental modal analyses of a real reference tuning fork. It turns out that our model is sufficient to capture the first eight eigenmodes of a reference tuning fork, whose identification and reproduction by simulation is novel to the knowledge of the author.
    • Threshold Based Opportunistic Scheduling of Secondary Users in Underlay Cognitive Radio Networks

      Song, Yao (2011-12)
      In underlay cognitive radio networks, secondary users can share the spectrum with primary users as long as the interference caused by the secondary users to primary users is below a certain predetermined threshold. It is reasonable to assume that there is always a large pool of secondary users trying to access the channel, which can be occupied by only one secondary user at a given time. As a result, a multi-user scheduling problem arises among the secondary users. In this thesis, by manipulating basic schemes based on selective multi-user diversity, normalized thresholding, transmission power control, and opportunistic round robin, we propose and analyze eight scheduling schemes of secondary users in an underlay cognitive radio set-up. The system performance of these schemes is quantified by using various performance metrics such as the average system capacity, normalized average feedback load, scheduling outage probability, and system fairness of access. In our proposed schemes, the best user out of all the secondary users in the system is picked to transmit at each given time slot in order to maximize the average system capacity. Two thresholds are used in the two rounds of the selection process to determine the best user. The first threshold is raised by the power constraint from the primary user. The second threshold, which can be adjusted by us, is introduced to reduce the feedback load. The overall system performance is therefore dependent on the choice of these two thresholds and the number of users in the system given the channel conditions for all the users. In this thesis, by deriving analytical formulas and presenting numerical examples, we try to provide insights of the relationship between the performance metrics and the involved parameters including two selection thresholds and the number of active users in the system, in an effort to maximize the average system capacity as well as satisfy the requirements of scheduling outage probability and feedback load.
    • Tin (Sn) - An Unlikely Ally to Extend Moore's Law for Silicon CMOS?

      Hussain, Aftab M. (2012-12)
      There has been an exponential increase in the performance of silicon based semiconductor devices in the past few decades. This improvement has mainly been due to dimensional scaling of the MOSFET. However, physical constraints limit the continued growth in device performance. To overcome this problem, novel channel materials are being developed to enhance carrier mobility and hence increase device performance. This work explores a novel semiconducting alloy - Silicon-tin (SiSn) as a channel material for CMOS applications. For the first time ever, MOS devices using SiSn as channel material have been demonstrated. A low cost, scalable and manufacturable process for obtaining SiSn by diffusion of Sn into silicon has also been explored. The channel material thus obtained is electrically characterized by fabricating MOSCAPs and Mesa-shaped MOSFETs. The SiSn devices have been compared to similar devices fabricated using silicon as channel material.
    • TiO2/Cu2O composite based on TiO2 NTPC photoanode for photoelectrochemical (PEC) water splitting under visible light

      Shi, Le (2015-05)
      Water splitting through photoelectrochemical reaction is widely regarded as a major method to generate H2 , a promising source of renewable energy to deal with the energy crisis faced up to human being. Efficient exploitation of visible light in practice of water splitting with pure TiO2 material, one of the most popular semiconductor material used for photoelectrochemical water splitting, is still challenging. One dimensional TiO2 nanotubes is highly desired with its less recombination with the short distance for charge carrier diffusion and light-scattering properties. This work is based on TiO2 NTPC electrode by the optimized two-step anodization method from our group. A highly crystalized p-type Cu2O layer was deposited by optimized pulse potentiostatic electrochemical deposition onto TiO2 nanotubes to enhance the visible light absorption of a pure p-type TiO2 substrate and to build a p-n junction at the interface to improve the PEC performance. However, because of the real photocurrent of Cu2O is far away from its theoretical limit and also poor stability in the aqueous environment, a design of rGO medium layer was added between TiO2 nanotube and Cu2O layer to enhance the photogenerated electrons and holes separation, extend charge carrier diffusion length (in comparison with those of conventional pure TiO2 or Cu2O materials) which could significantly increase photocurrent to 0.65 mA/cm2 under visible light illumination (>420 nm) and also largely improve the stability of Cu2O layer, finally lead to an enhancement of water splitting performance.
    • Titanium Neopentyl supported on KCC-1 and Al-modified KCC-1 and its Catalytic Application for Ethylene polymerization

      Alrais, Lujain M. (2018-08)
      A new generation of Titanium based catalysts for ethylene polymerization has been developed through the Surface Organometallic Chemistry (SOMC) methodology using a novel type of silica support having a 3D fibrous morphology, KCC-1. The first type of Tibased catalyst was obtained by reacting isolated silanol surface groups, ≡SiOH of KCC-1 (dehydroxylated at 700 ⁰C under high vacuum, 10-5 bar) with titanium (IV) tetraneopentyl, Ti(CH2tBu)4 to produce [(≡SiO)Ti(CH2tBu)3]. The second type of Ti-based catalyst was generated by using an Al-modified KCC-1. The peculiarity of this support is due to the presence of tetra-coordinated aluminum-bound hydroxyl group, [(≡Si-O-Si≡)(≡SiO)2Al- OH] that can be used as a Lewis Acid anchor sites and generate new catalytic properties. The well-defined [(≡Si-O-Si≡)(≡SiO)2Al-OH] was obtained by reacting diisopropylaluminum hydride with KCC treated at 700 °C followed by a thermal treatment at 400 °C and oxidation with N2O. IR spectra of pyridine adsorbed on the Al sites show that these were strong Lewis acid sites (constituting 80% of the total Al sites). Thus, the highly electrophilic support surface was used to create a single well-defined surface organo-titanium fragment [(≡Si–O–Si≡)(≡Si–O–)2Al–O–Ti(CH2tBu)3] by the reaction of the surface [(≡Si–O–Si≡)(≡Si–O)2Al–OH]) groups with Ti(CH2-tBu)4 at room temperature for 4 h in dry pentane. The performance of each Ti-supported catalyst assessed for ethylene polymerization. It was found that Al-modified support (highly electrophilic) provide better activity compared to the unmodified one. Indeed, the productivity of the catalyst [(≡Si–O– Si≡)(≡Si–O–)2Al–O–Ti(CH2tBu)3] was found to be 67.8 g of PE/ 1mmol Ti/ 1h with molecular weight of 3208408 g/mol; polydispersity was found to be 2.3, and (HDPE) high-density polyethylene was obtained. In contrast, [(≡SiO)Ti(CH2tBu)3] (unmodified one) produces lower molecular weight polymer 989843 g/mol, higher polydispersity (PD) 6.7 and low-density polyethylene (LDPE) productivity was found to be 14.670 g PE/1mmol Ti /1h. These results demonstrate that modification of the oxide ligands on silica through a generation of Al Lewis acid site opens up new catalytic properties, markedly enhancing the catalytic performance of supported organotitanium species. We also demonstrate how the silica mesostructure (2D vs 3D ) affects the catalytic activity in ethylene polymerization. While SBA15 (2D) could limit the accessibility of the active sites resulting in lower yield. In contrast, KCC-1 (3D) are more active in ethylene polymerization, because the active sites reside on the external surface are fully accessible to the substrate.
    • TMAC: Timestamp-Ordered MAC Protocol for Wireless Mesh Networks

      Nawab, Faisal (2011-05)
      Wireless Mesh Networks (WMNs) have emerged to meet a need for a self-organized and self-configured multi-hop wireless network infrastructure. Low cost infrastructure and ease of deployment have made WMNs an attractive technology for last mile access. However, 802.11 based WMNs are subject to serious fairness issues. With backlogged TCP traffic, nodes which are two or more hops away from the gateway are subject to starvation, while the one-hop away node saturates the channel with its own local traffic. We study the interactions of TCP and IEEE 802.11 MAC in WMNs to aid us in understanding and overcoming the unfairness problem. We propose a Markov chain to capture the behavior of TCP sessions, particularly the impact on network throughput performance due to the effect of queue utilization and packet relaying. A closed form solution is derived to numerically derive the throughput. Based on the developed model, we propose a distributed MAC protocol called Timestamp-ordered MAC (TMAC), aiming to alleviate the unfairness problem in WMNs via a manipulative per-node scheduling mechanism which takes advantage of the age of each packet as a priority metric. Simulation is conducted to validate our model and to illustrate the fairness characteristics of TMAC. Our results show that TMAC achieves excellent resource allocation fairness while maintaining above 90% of maximum link capacity in parking lot and large grid topologies. Our work illuminates the factors affecting TCP fairness in WMNs. Our theoretical and empirical findings can be used in future research to develop more fairness-aware protocols for WMNs.
    • Tomographic Particle Image Velocimetry Using Colored Shadow Imaging

      Alarfaj, Meshal K. (2016-02)
      Tomographic Particle Image Velocimetry Using Colored Shadow Imaging by Meshal K Alarfaj, Master of Science King Abdullah University of Science & Technology, 2015 Tomographic Particle image velocimetry (PIV) is a recent PIV method capable of reconstructing the full 3D velocity field of complex flows, within a 3-D volume. For nearly the last decade, it has become the most powerful tool for study of turbulent velocity fields and promises great advancements in the study of fluid mechanics. Among the early published studies, a good number of researches have suggested enhancements and optimizations of different aspects of this technique to improve the effectiveness. One major aspect, which is the core of the present work, is related to reducing the cost of the Tomographic PIV setup. In this thesis, we attempt to reduce this cost by using an experimental setup exploiting 4 commercial digital still cameras in combination with low-cost Light emitting diodes (LEDs). We use two different colors to distinguish the two light pulses. By using colored shadows with red and green LEDs, we can identify the particle locations within the measurement volume, at the two different times, thereby allowing calculation of the velocities. The present work tests this technique on the flows patterns of a jet ejected from a tube in a water tank. Results from the images processing are presented and challenges discussed.
    • Towards an Efficient Artificial Neural Network Pruning and Feature Ranking Tool

      AlShahrani, Mona (2015-05-24)
      Artificial Neural Networks (ANNs) are known to be among the most effective and expressive machine learning models. Their impressive abilities to learn have been reflected in many broad application domains such as image recognition, medical diagnosis, online banking, robotics, dynamic systems, and many others. ANNs with multiple layers of complex non-linear transformations (a.k.a Deep ANNs) have shown recently successful results in the area of computer vision and speech recognition. ANNs are parametric models that approximate unknown functions in which parameter values (weights) are adapted during training. ANN’s weights can be large in number and thus render the trained model more complex with chances for “overfitting” training data. In this study, we explore the effects of network pruning on performance of ANNs and ranking of features that describe the data. Simplified ANN model results in fewer parameters, less computation and faster training. We investigate the use of Hessian-based pruning algorithms as well as simpler ones (i.e. non Hessian-based) on nine datasets with varying number of input features and ANN parameters. The Hessian-based Optimal Brain Surgeon algorithm (OBS) is robust but slow. Therefore a faster parallel Hessian- approximation is provided. An additional speedup is provided using a variant we name ‘Simple n Optimal Brain Surgeon’ (SNOBS), which represents a good compromise between robustness and time efficiency. For some of the datasets, the ANN pruning experiments show on average 91% reduction in the number of ANN parameters and about 60% - 90% in the number of ANN input features, while maintaining comparable or better accuracy to the case when no pruning is applied. Finally, we show through a comprehensive comparison with seven state-of-the art feature filtering methods that the feature selection and ranking obtained as a byproduct of the ANN pruning is comparable in accuracy to these methods.
    • Towards Controlling Latency in Wireless Networks

      Bouacida, Nader (2017-04-24)
      Wireless networks are undergoing an unprecedented revolution in the last decade. With the explosion of delay-sensitive applications in the Internet (i.e., online gaming and VoIP), latency becomes a major issue for the development of wireless technology. Taking advantage of the significant decline in memory prices, industrialists equip the network devices with larger buffering capacities to improve the network throughput by limiting packets drops. Over-buffering results in increasing the time that packets spend in the queues and, thus, introducing more latency in networks. This phenomenon is known as “bufferbloat”. While throughput is the dominant performance metric, latency also has a huge impact on user experience not only for real-time applications but also for common applications like web browsing, which is sensitive to latencies in order of hundreds of milliseconds. Concerns have arisen about designing sophisticated queue management schemes to mitigate the effects of such phenomenon. My thesis research aims to solve bufferbloat problem in both traditional half-duplex and cutting-edge full-duplex wireless systems by reducing delay while maximizing wireless links utilization and fairness. Our work shed lights on buffer management algorithms behavior in wireless networks and their ability to reduce latency resulting from excessive queuing delays inside oversized static network buffers without a significant loss in other network metrics. First of all, we address the problem of buffer management in wireless full-duplex networks by using Wireless Queue Management (WQM), which is an active queue management technique for wireless networks. Our solution is based on Relay Full-Duplex MAC (RFD-MAC), an asynchronous media access control protocol designed for relay full-duplexing. Compared to the default case, our solution reduces the end-to-end delay by two orders of magnitude while achieving similar throughput in most of the cases. In the second part of this thesis, we propose a novel design called “LearnQueue” based on reinforcement learning that can effectively control the latency in wireless networks. LearnQueue adapts quickly and intelligently to changes in the wireless environment using a sophisticated reward structure. Testbed results prove that LearnQueue can guarantee low latency while preserving throughput.
    • Towards macroscopic modeling of electro-thermo-mechanical couplings in PEDOT/PSS: Modeling of moisture absorption kinetics

      Zhanshayeva, Lyazzat (2018-07)
      Organic conducting polymer, poly(3,4-ethylene dioxythiophene)-poly(styrene sulfonate) (PEDOT:PSS), is widely recognized for its electro-actuation mechanism and is used in flexible electronics. Its high potential as actuator is based on a strong coupling between chemical, mechanical and electrical properties which directly depends on external stimuli. There is no model today to describe the interplay between moisture absorption, mechanical expansion and electrical stimulus. Elucidating the role of each component in the effective actuation properties is needed to further optimize and tailor such materials. The objective of this thesis is to develop a macroscopic model to describe water sorption kinetics of the PEDOT:PSS film. We used gravimetric analysis of pure PEDOT:PSS film of three different thicknesses to investigate absorption kinetics over a broad range of temperatures and relative humidity. Our results revealed that the moisture uptake of PEDOT:PSS film does not follow Fickian diffusion law due to the retained amount of water after desorption process. We used an existing diffusionreaction model to describe this behavior, and COMSOL Multiphysics and MATLAB software programs to implement it. We observed that the generic model we used in our work could predict polymer behavior with 95% accuracy. However, our model was not able to properly represent the data at very high relative humidity at low temperature, which was attributed to the excessive swelling of the film. Also, we examined a relation between the moisture content of PEDOT:PSS and its mechanical strain and electrical conductivity. The results presented here are the first step towards a general multiphysics electro-thermo-mechanical description of PEDOT:PSS based actuators.
    • Towards observing the encounter of the T7 DNA replication fork with a lesion site at the Single molecule level

      Shirbini, Afnan (2017-05)
      Single-molecule DNA flow-stretching assays have been a powerful approach to study various aspects on the mechanism of DNA replication for more than a decade. This technique depends on flow-induced force on a bead attached to a surface-tethered DNA. The difference in the elastic property between double-strand DNA (long) and single-strand DNA (short) at low regime force allows the observation of the beads motion when the dsDNA is converted to ssDNA by the replisome machinery during DNA replication. Here, I aim to develop an assay to track in real-time the encounter of the bacteriophage T7 replisome with abasic lesion site inserted on the leading strand template. I optimized methods to construct the DNA substrate that contains the abasic site and established the T7 leading strand synthesis at the single molecule level. I also optimized various control experiments to remove any interference from the nonspecific interactions of the DNA with the surface. My work established the foundation to image the encounter of the T7 replisome with abasic site and to characterize how the interactions between the helicase and the polymerase could influence the polymerase proofreading ability and its direct bypass of this highly common DNA damage type.
    • Towards The Generation of Functionalized Magnetic Nanowires to Target Leukemic Cells

      Alsharif, Nouf (2016-04)
      In recent years, magnetic nanowires (NWs) have been widely used for their therapeutic potential in biomedical applications. The use of iron (Fe) NWs combines two important properties, biocompatibility and remote manipulation by magnetic fields. In addition the NWs can be coated and functionalized to target cells of interest and, upon exposure to an alternating magnetic field, have been shown to induce cell death on several types of adherent cells, including several cancer cell types. For suspension cells, however, using these NWs has been much less effective primarily due to the free-floating nature of the cells minimizing the interaction between them and the NWs. Leukemic cells express higher levels of the cell surface marker CD44 (Braumüller, Gansauge, Ramadani, & Gansauge, 2000), compared to normal blood cells. The goal of this study was to functionalize Fe NWs with a specific monoclonal antibody towards CD44 in order to target leukemic cells (HL-60 cells). This approach is expected to increase the probability of a specific binding to occur between HL-60 cells and Fe NWs. Fe NWs were fabricated with an average diameter of 30-40 nm and a length around 3-4 μm. Then, they were coated with both 3-Aminopropyl-triethoxysilane and bovine serum albumin (BSA) in order to conjugate them with an anti-CD44 antibody (i.e. anti-CD44-iron NWs). The antibody interacts with the amine group in the BSA via the 1-Ethyl-3-3-dimethylaminopropyl-carbodiimide and N-Hydroxysuccinimide coupling. The NWs functionalization was confirmed using a number of approaches including: infrared spectroscopy, Nanodrop to measure the concentration of CD44 antibody, as well as fluorescent-labeled secondary antibody staining to detect the primary CD44 antibody. To confirm that the anti-CD44-iron NWs and bare Fe NWs, in the absence of a magnetic field, were not toxic to HL-60 cells, cytotoxicity assays using XTT (2,3-Bis-2-Methoxy-4-Nitro-5-Sulfophenyl-2H-Tetrazolium-5-Carboxanilide) were performed and resulted in a high level of biocompatibility. In addition, the internalization of the coated NWs have been studied by coating them with a pH dependent dye (pHrodoTM Red) that showed a signal once the NWs were internalized by the cell.
    • Transcription Activator-Like Effectors (TALEs) Hybrid Nucleases for Genome Engineering Application

      Wibowo, Anjar (2011-06-06)
      Gene targeting is a powerful genome engineering tool that can be used for a variety of biotechnological applications. Genomic double-strand DNA breaks generated by engineered site-specific nucleases can stimulate gene targeting. Hybrid nucleases are composed of DNA binding module and DNA cleavage module. Zinc Finger Nucleases were used to generate double-strand DNA breaks but it suffers from failures and lack of reproducibility. The transcription activator–like effectors (TALEs) from plant pathogenic Xanthomonas contain a unique type of DNA-binding domain that bind specific DNA targets. The purpose of this study is to generate novel sequence specific nucleases by fusing a de novo engineered Hax3 TALE-based DNA binding domain to a FokI cleavage domain. Our data show that the de novo engineered TALE nuclease can bind to its target sequence and create double-strand DNA breaks in vitro. We also show that the de novo engineered TALE nuclease is capable of generating double-strand DNA breaks in its target sequence in vivo, when transiently expressed in Nicotiana benthamiana leaves. In conclusion, our data demonstrate that TALE-based hybrid nucleases can be tailored to bind a user-selected DNA sequence and generate site-specific genomic double-strand DNA breaks. TALE-based hybrid nucleases hold much promise as powerful molecular tools for gene targeting applications.
    • Transcriptional Profiling of Chromera velia Under Diverse Environmental Conditions

      Tayyrov, Annageldi (2014-05)
      Since its description in 2008, Chromera velia has drawn profound interest as the closest free-­‐living photosynthetic relative of apicomplexan parasites that are significant pathogens, causing enormous health and economic problems. There-­‐ fore, this newly described species holds a great potential to understand evolu-­‐ tionary basis of how photosynthetic algae evolved into the fully pathogenic Apicomplexa and how their common ancestors may have lived before they evolved into obligate parasites. Hence, the aim of this work is to understand how C. velia function and respond to different environmental conditions. This study aims to reveal how C. velia is able to respond to environmental perturbations that are applied individually and simultaneously since, studying stress factors in separation fails to elucidate complex responses to multi stress factors and un-­‐ derstanding the systemic regulation of involved genes. To extract biologically significant information and to identify genes involved in various physiological processes under variety of environmental conditions (i.e. a combination of vary-­‐ ing temperatures, iron availability, and salinity in the growth medium) we pre-­‐ pared strand specific RNA-­‐seq libraries for 83 samples in diverse environmental conditions. Here, we report the set of significantly differentially expressed genes as a re-­‐ sponse to the each condition and their combinations. Several interesting up-­‐ regulated and down-­‐regulated genes were found and their functions and in-­‐ volved pathways were studied. We showed that the profound regulation of HSP20 proteins is significant under stress conditions and hypothesized that the-­‐ se proteins might be involved in their movements.
    • Transfer Hydrogenation: Employing a Simple, In Situ Prepared Catalytic System

      Ang, Eleanor Pei Ling (2017-04)
      Transfer hydrogenation has been recognized to be an important synthetic method in both academic and industrial research to obtain valuable products including alcohols. Transition metal catalysts based on precious metals, such as Ru, Rh and Ir, are typically employed for this process. In recent years, iron-based catalysts have attracted considerable attention as a greener and more sustainable alternative since iron is earth abundant, inexpensive and non-toxic. In this work, a combination of iron disulfide with chelating bipyridine ligand was found to be effective for the transfer hydrogenation of a variety of ketones to the corresponding alcohols in the presence of a simple base. It provided a convenient and economical way to conduct transfer hydrogenation. A plausible role of sulfide next to the metal center in facilitating the catalytic reaction is demonstrated.
    • Transformational Electronics: Towards Flexible Low-Cost High Mobility Channel Materials

      Nassar, Joanna M. (2014-05)
      For the last four decades, Si CMOS technology has been advancing with Moore’s law prediction, working itself down to the sub-20 nm regime. However, fundamental problems and limitations arise with the down-scaling of transistors and thus new innovations needed to be discovered in order to further improve device performance without compromising power consumption and size. Thus, a lot of studies have focused on the development of new CMOS compatible architectures as well as the discovery of new high mobility channel materials that will allow further miniaturization of CMOS transistors and improvement of device performance. Pushing the limits even further, flexible and foldable electronics seem to be the new attractive topic. By being able to make our devices flexible through a CMOS compatible process, one will be able to integrate hundreds of billions of more transistors in a small volumetric space, allowing to increase the performance and speed of our electronics all together with making things thinner, lighter, smaller and even interactive with the human skin. Thus, in this thesis, we introduce for the first time a cost-effective CMOS compatible approach to make high-k/metal gate devices on flexible Germanium (Ge) and Silicon-Germanium (SiGe) platforms. In the first part, we will look at the various approaches in the literature that has been developed to get flexible platforms, as well as we will give a brief overview about epitaxial growth of Si1-xGex films. We will also examine the electrical properties of the Si1-xGex alloys up to Ge (x=1) and discuss how strain affects the band structure diagram, and thus the mobility of the material. We will also review the material growth properties as well as the state-of-the-art results on high mobility metal-oxide semiconductor capacitors (MOSCAPs) using strained SiGe films. Then, we will introduce the flexible process that we have developed, based on a cost-effective “trench-protect-release-reuse” approach, utilizing the industry’s most used bulk Si (100) wafers, and discuss how it has been used for getting flexible and semi-transparent SiGe and Ge platforms. Finally, we examine the electrical characteristics of our materials through the fabrication of high-k/metal gate MOSCAPs with SiGe and Ge as channel material. We present their electrical performance on both non- flexible and flexible platform and discuss further improvement that has to be made in order to get better behaving devices for future MOSFET fabrication.