1,133 Works

Thesis Chapter 3 tables

Mariam Awlia
The dataset includes the IDs, phenotypic measurements, multivariate analysis and genome-wide association data collected from the Arabidopsis HapMap population that was used in a high-throughput phenotyping experiment under salt stress to identify the underlying genetic components.

Genome-wide Studies of Mycolic Acid Bacteria: Computational Identification and Analysis of a Minimal Genome

Frederick Kinyua Kamanu
The mycolic acid bacteria are a distinct suprageneric group of asporogenous Grampositive, high GC-content bacteria, distinguished by the presence of mycolic acids in their cell envelope. They exhibit great diversity in their cell and morphology; although primarily non-pathogens, this group contains three major pathogens Mycobacterium leprae, Mycobacterium tuberculosis complex, and Corynebacterium diphtheria. Although the mycolic acid bacteria are a clearly defined group of bacteria, the taxonomic relationships between its constituent genera and species are less...

Species-independent MicroRNA Gene Discovery

Timothy K. Kamanu
MicroRNA (miRNA) are a class of small endogenous non-coding RNA that are mainly negative transcriptional and post-transcriptional regulators in both plants and animals. Recent studies have shown that miRNA are involved in different types of cancer and other incurable diseases such as autism and Alzheimer’s. Functional miRNAs are excised from hairpin-like sequences that are known as miRNA genes. There are about 21,000 known miRNA genes, most of which have been determined using experimental methods. miRNA...

Nano-Micro Materials Enabled Thermoelectricity From Window Glasses

Salman Bin Inayat
With growing world population and decreasing fossil fuel reserves we need to explore and utilize variety of renewable and clean energy sources to meet the imminent challenge of energy crisis. Solar energy is considered as the leading promising alternate energy source with the pertinent challenge of off sunshine period and uneven worldwide distribution of usable sun light. Although thermoelectricity is considered as a reasonable energy harvester from wasted heat, its mass scale usage is yet...

Visual Workflows for Oil and Gas Exploration

Thomas Hollt
The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures to plan the path of the borehole, is crucial in order to minimize economic and ecological risks. Before that, the placement, as well as the operations of oil rigs need to be planned carefully, as off-shore oil exploration is vulnerable to hazards caused by...

Modeling the Performance of Fast Mulipole Method on HPC platforms

Huda Ibeid
The current trend in high performance computing is pushing towards exascale computing. To achieve this exascale performance, future systems will have between 100 million and 1 billion cores assuming gigahertz cores. Currently, there are many efforts studying the hardware and software bottlenecks for building an exascale system. It is important to understand and meet these bottlenecks in order to attain 10 PFLOPS performance. On applications side, there is an urgent need to model application performance...

An LTCC Based Compact SIW Antenna Array Feed Network for a Passive Imaging Radiometer

Hattan Abuzaid
Passive millimeter-wave (PMMW) imaging is a technique that allows the detection of inherent millimeter-wave radiation emitted by bodies. Since different bodies with varying properties emit unequal power intensities, a contrast can be established to detect their presence. The advantage of this imaging scheme over other techniques, such as optical and infrared imaging, is its ability to operate under all weather conditions. This is because the relatively long wavelengths of millimeter-waves, as compared to visible light,...

Mesoporous Carbon Produced from Tri-constituent Mesoporous Carbon-silica Composite for Water Purification

Yanjie Yu
Highly ordered mesoporous carbon-silica nanocomposites with interpenetrating carbon and silica networks were synthesized by the evaporation-induced tri-constituent co- assembly approach. The removal of silica by concentrated NaOH solution produced mesoporous carbons, which contained not only the primary large pores, but also the secondary mesopores in the carbon walls. The thus synthesized mesoporous carbon was further activated by using ZnCl2. The activated mesoporous carbon showed an improved surface area and pore volume. The synthesized mesoporous carbon...

Factors Affecting Detection Probability of Acoustic Tags in Coral Reefs

Edgar F. Bermudez
Acoustic telemetry is an important tool for studying the movement patterns, behaviour, and site fidelity of marine organisms; however, its application is challenged in coral reef environments where complex topography and intense environmental noise interferes with acoustic signals, and there has been less study. Therefore, it is particularly critical in coral reef telemetry studies to first conduct a long-term range test, a tool that provides informa- tion on the variability and periodicity of the transmitter...

A Density Functional Theory Study of Doped Tin Monoxide as a Transparent p-type Semiconductor

Danilo Bianchi Granato
In the pursuit of enhancing the electronic properties of transparent p-type semiconductors, this work uses density functional theory to study the effects of doping tin monoxide with nitrogen, antimony, yttrium and lanthanum. An overview of the theoretical concepts and a detailed description of the methods employed are given, including a discussion about the correction scheme for charged defects proposed by Freysoldt and others [Freysoldt 2009]. Analysis of the formation energies of the defects points out...

Exploring Archaeal Communities And Genomes Across Five Deep-Sea Brine Lakes Of The Red Sea With A Focus On Methanogens

Yue Guan
The deep-sea hypersaline lakes in the Red Sea are among the most challenging, extreme, and unusual environments on the planet Earth. Despite their harshness to life, they are inhabited by diverse and novel members of prokaryotes. Methanogenesis was proposed as one of the main metabolic pathways that drive microbial colonization in similar habitats. However, not much is known about the identities of the methane-producing microbes in the Red Sea, let alone the way in which...

On micro to mesoscale homogenization of electrical properties for damaged laminated composites (and their potential applications in electrical tomography)

Lakshmi Selvakumaran
Efficient and optimal use of composites in structures requires tools to monitor and capture the complex degradation that can occur within the laminates over time. Structural health monitoring (SHM) techniques uses sensors/actuators on the structure to progressively monitor the health of the structure with minimal manual intervention. Electrical tomography (ET) is a SHM technique that uses voltage measurements from the surface of the laminate to reconstruct a conductivity map of the structure. Since damage has...

Wireless Physical Layer Security: On the Performance Limit of Secret-Key Agreement

Marwen Zorgui
Physical layer security (PLS) is a new paradigm aiming at securing communications between legitimate parties at the physical layer. Conventionally, achieving confidentiality in communication networks relies on cryptographic techniques such as public-key cryptography, secret-key distribution and symmetric encryption. Such techniques are deemed secure based on the assumption of limited computational abilities of a wiretapper. Given the relentless progress in computational capacities and the dynamic topology and proliferation of modern wireless networks, the relevance of the...

Fabrication and Characterization of Micro-membrane GaN Light Emitting Diodes

Hsien-Yu Liao
Developing etching of GaN material system is the key to device fabrications. In this thesis, we report on the fabrication of high throughput lift-off of InGaN/GaN based micro-membrane light emitting diode (LED) from sapphire substrate using UV-assisted photoelectroless chemical (PEsC) etching. Unlike existing bandgap selective etching based on unconventional sacrificial layer, the current hydrofluoric acid based wet etching process enables the selective etching of undoped GaN layer already incorporated in standard commercial LED structures, thus...

ACCTuner: OpenACC Auto-Tuner For Accelerated Scientific Applications

Fatemah Alzayer
We optimize parameters in OpenACC clauses for a stencil evaluation kernel executed on Graphical Processing Units (GPUs) using a variety of machine learning and optimization search algorithms, individually and in hybrid combinations, and compare execution time performance to the best possible obtained from brute force search. Several auto-tuning techniques – historic learning, random walk, simulated annealing, Nelder-Mead, and genetic algorithms – are evaluated over a large two-dimensional parameter space not satisfactorily addressed to date by...

Reversibly Bistable Flexible Electronics

Nasir Alfaraj
Introducing the notion of transformational silicon electronics has paved the way for integrating various applications with silicon-based, modern, high-performance electronic circuits that are mechanically flexible and optically semitransparent. While maintaining large-scale production and prototyping rapidity, this flexible and translucent scheme demonstrates the potential to transform conventionally stiff electronic devices into thin and foldable ones without compromising long-term performance and reliability. In this work, we report on the fabrication and characterization of reversibly bistable flexible electronic...

Combating Impairments in Multi-carrier Systems: A Compressed Sensing Approach

Shamael Al-Shuhail
Multi-carrier systems suffer from several impairments, and communication system engineers use powerful signal processing tools to combat these impairments and keep up with the capacity/rate demands. Compressed sensing (CS) is one such tool that allows recovering any sparse signal, requiring only a few measurements in a domain that is incoherent with the domain of sparsity. Almost all signals of interest have some degree of sparsity, and in this work we utilize the sparsity of impairments...

Stimuli Responsive Self-Assembled Hybrid Organic-Inorganic Materials

Safaa Al-Rehili
Because of the latest developments in nanotechnology and the need to have new functions, a high demand for innovative materials is created. The technological requirements for new applications cannot be fulfilled by most of the well-developed materials like metals, plastics, or ceramics. Therefore, composite materials that can exhibit better properties in contrast to their single counterpart represents a valuable and interesting alternative for the development of new and more performing functional materials. In the past...

The Role of Chromatin Associated Proteins in Plant Innate Immunity and Jasmonic Acid Signaling

Mai Jarad
Pathogen-associated molecular pattern (PAMP) recognition occurs by plasma membrane located receptors that induce among other processes nuclear gene expression. The plant FLS2-BAK1 receptor complex binds the bacterial PAMP, flg22 and induces a series of defense responses. The resulting signal transduction events occur through the activation of two MAPK signaling cascades, which trigger a rapid and strong activation of MPK3, MPK4 and MPK6. Cellular responses to pathogens are regulated by the activated MAPKs, which lead to...

Work Function Tuning in Sub-20nm Titanium Nitride (TiN) Metal Gate: Mechanism and Engineering

Mehdi Hasan
Scaling of transistors (the building blocks of modern information age) provides faster computation at the expense of excessive power dissipation. Thus to address these challenges, high-k/metal gate stack has been introduced in commercially available microprocessors from 2007. Since then titanium nitride (TiN) metal gate’s work function (Wf) tunability with its thickness (thickness increases, work function increases) is a well known phenomenon. Many hypotheses have been made over the years which include but not limited to:...

Burning Characteristics of Premixed Flames in Laminar and Turbulent Environments

Ossama Mannaa
Considering the importance of combustion characteristics in combustion applications including spark ignition engines and gas turbines, both laminar and turbulent burning velocities were measured for gasoline related fuels. The first part of the present work focused on the measurements of laminar burning velocities of Fuels for Advanced Combustion Engines (FACE) gasolines and their surrogates using a spherical constant volume combustion chamber (CVCC) that can provide high-pressure high-temperature (HPHT) combustion mode up to 0.6 MPa, 395...

An Inverse Source Problem for a One-dimensional Wave Equation: An Observer-Based Approach

Sharefa M. Asiri
Observers are well known in the theory of dynamical systems. They are used to estimate the states of a system from some measurements. However, recently observers have also been developed to estimate some unknowns for systems governed by Partial differential equations. Our aim is to design an observer to solve inverse source problem for a one dimensional wave equation. Firstly, the problem is discretized in both space and time and then an adaptive observer based...

Identifying Regulatory Patterns at the 3'end Regions of Over-expressed and Under-expressed Genes

Ghofran K. Othoum
Promoters, neighboring regulatory regions and those extending further upstream of the 5’end of genes, are considered one of the main components affecting the expression status of genes in a specific phenotype. More recently research by Chen et al. (2006, 2012) and Mapendano et al. (2010) demonstrated that the 3’end regulatory regions of genes also influence gene expression. However, the association between the regulatory regions surrounding 3’end of genes and their over- or under-expression status in...

Analysis of gene and protein name synonyms in Entrez Gene and UniProtKB resources

Basil Arkasosy
Ambiguity in texts is a well-known problem: words can carry several meanings, and hence, can be read and interpreted differently. This is also true in the biological literature; names of biological concepts, such as genes and proteins, might be ambiguous, referring in some cases to more than one gene or one protein, or in others, to both genes and proteins at the same time. Public biological databases give a very useful insight about genes and...

Genetic variability of the whitefly Bemisia tabaci and its secondary endosymbionts in the Arabian Peninsula

Alaa I. Ragab
The whitefly Bemisia tabaci species complex has been well documented as one of the most economically important emergent plant virus vectors, through serious feeding damage to its broad range of plant hosts and transmission of plant viruses to important agricultural crops. It has been shown to have associations with endosymbionts which have significant effects on the insect fitness. The purpose of this study was to provide information for the biotype and secondary endosymbiont distribution for...

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  • King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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