• 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.
    • Experimental study on the viscosity effects on the bubbly flow dynamics inside a large Hele-Shaw cell

      Al Brahim, Ahmed (2018-09)
      We study experimentally the gravity-driven bubbly flow inside a large Hele-Shaw cell. The bubbles and foam were created by a series of upside-down overturns of the half-filled cell about its horizontal axis. When the liquid flows down it entraps a large number of bubbles, which remain stable as the liquid contains surfactant molecules. The total number and sizes of these bubbles slowly asymptote to a steady state after dozens of overturns. It takes longer to reach this asymptote when the viscosity of the liquid is larger. The bubbles also become more monodisperse with more cell over-turns. The number and distribution of the bubbles in turn affects the average motion of the liquid phase, which is characterized by the downwards motion of the liquid center of mass. We use high-resolution 6k video-camera to track the trajectories of thousands of bubbles. This required the development of software codes to identify individual bubbles and follow them between video frames. Successful thresholding algorithm required a machine-learning component, which was integrated into the program. This program also needed to account for possible splitting or coalescence of adjacent bubbles. The program can also find the velocities along the trajectories. In this way we can find the vertical velocity of bubbles as a function of their sizes. The smaller bubbles are sometimes observed to move downwards against their buoyancy. This occurs when the viscous stress from the surrounding liquid phase overcomes the upwards buoyancy force. Bubbles with similar sizes were often found to be stacking together and having worm-like rising movement that is faster than their individual rising velocity. The occurrence of the bubble stacking was dependent on the distance between the bubbles, their sizes and their wakes. Clusters of tiny bubbles that are much smaller than the gap of the Hele-Shaw cell were observed to form layers which can severely hinder the overall liquid motion.
    • Weekly variation of viruses and heterotrophic nanoflagellates and their potential impact on bacterioplankton in a Red Sea shallow ecosystem

      Sabbagh, Eman I. (2018-09)
      Heterotrophic bacterioplankton plays a pivotal role in marine food webs and biogeochemical cycling. However, their temporal dynamics and underlying factors are still poorly understood in many regions, including the tropical waters of the Red Sea. The main goal of the MS project was to describe the seasonality and assess the impact of top-down controls (viruses and heterotrophic nanoflagellates) in parallel to bottom-up controls (substrate availability) on coastal bacterioplankton on a weekly basis. To that end, we monitored the abundance of the different planktonic groups by flow cytometry together with a set of environmental variables including temperature, salinity, dissolved organic carbon (DOC) and nitrogen (DON) and chlorophyll a concentration. We analyzed a weekly dataset collected over 2017 at the surface water of KAUST Harbor. The abundance of heterotrophic bacteria ranged from 1.55 to 4.97 x 105 cells ml-1, with that of autotrophic bacteria 4 to 14 fold less on average and presents 1 x 104 to 1.19x105 cells ml-1, while viruses ranged from 1.30 x 106 to 1.59 x 107 particles ml-1, and heterotrophic nanoflagellates (HNF) ranged from 8.62 x 10 to 1.63 x 103 cells ml-1. We distinguished between five groups of heterotrophic bacteria depending on the relative nucleic acid content, membrane state and cell-specific metabolic activity, two groups of Synechococcus, as well as three groups of viruses based on relative nucleic acid content. We found unexpected inverse relationship between viruses and HNFs. Based on a strong negative correlation, the results suggest that viruses controlled heterotrophic bacteria during summer until early winter period. HNFs showed a selective grazing behavior based their apparent preference to prey on both high (HNA) and low nucleic acid bacteria (LNA). Our results demonstrates that top-down control are key agents of heterotrophic bacterioplankton mortality and more important than bottom-up control in governing heterotrophic bacterioplankton abundances in the coastal tropical waters of the Red Sea.
    • 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.
    • Reconfigurable Electronics Platform: Concept, Mechanics, Materials and Process

      Damdam, Asrar N. (2018-08)
      Electronic platforms that are able to re-shape and assume different geometries are attractive for the advancing biomedical technologies, where the re-shaping feature increases the adaptability and compliance of the electronic platform to the human body. In this thesis, we present a serpentine-honeycomb reconfigurable electronic platform that has the ability to reconfigure into five different geometries: quatrefoil, ellipse, diamond, star and one irregular geometry. We show the fabrication processes of the serpentine-honeycomb reconfigurable platform in a micro-scale, using amorphous silicon, and in a macro-scale using polydimethylsiloxane (PDMS). The chosen materials are biocompatible, where the silicon was selected due to its superior electrical properties while the PDMS was selected due to its unique mechanical properties. We study the tensile strain for both fabricated-versions of the design and we demonstrate their reconfiguring capabilities. The resulting reconfiguring capabilities of the serpentine-honeycomb reconfigurable platform broaden the innovation opportunity for wearable electronics, implantable electronics and soft robotics.
    • Experimental Investigation on The Influence of Liquid Fuels Composition on The Operational Characteristics of The Liquid Fueled Resonant Pulse Combustor

      Qatomah, Mohammad (2018-07)
      In this study, the response of a liquid-fueled resonant pulse combustor to changes in liquid fuel composition was investigated. Experiments were performed with gasoline- ethanol, gasoline-diesel, and gasoline-heptane mixtures selected to produce meaningful variations in the ignition delay time. A review of ignition quality tester (IQT) data provided an expected increase in the overall delay for gasoline-ethanol mixtures with increasing ethanol concentrations, and a decrease for gasoline-diesel mixtures with increasing diesel concentrations in the mixture. By taking the phase of the ion signal as an indicator of heat release timing, the experimental results showed an agreement of gasoline-ethanol cases with the IQT data with a near linear increase with increasing ethanol concentrations. However, for gasoline-diesel, there exit no linear relation with the IQT data. For the case of gasoline-heptane mixtures, the results showed a linear decrease in delay with increasing heptane concentrations. Furthermore, it was shown that small changes in the physical properties of the fuel can significantly in sequence the cold-start operation of the combustor and alter the coupling between the unsteady heat release and resonant acoustic pressure wave during resonant operation. Dynamic combustion chamber pressure, stagnation temperature and pressure are recorded after a fixed warm-up time to characterize the performance and operation of the device. Results are interpreted in the context of fuel sensitivity and performance optimization of a resonant pulse combustor for pressure gain turbine applications.
    • Investigation of the Effect of Operational Parameters on the Fouling Development and Control in an Algal Membrane Photobioreactor for the Treatment of Simulated Secondary Wastewater

      Lamprea Cala, Andres (2018-07)
      The release of water effluents rich in nutrients such as nitrogen and phosphorus without adequate treatment represents environmental and human health concerns. Growing concerns about these impacts have resulted in increasingly stringent water quality regulations that encouraged the adoption of advanced treatment processes. Microalgae-based advanced wastewater treatment has gained momentum owing to its well-known advantages for advanced wastewater treatment, including the recovering of nutrients for the production of fertilizers, biofuels and fine chemical from microalgal biomass. Nevertheless, the progressive membrane fouling and permeate flux declining hamper the large-scale commercialization of membrane photobioreactors (MPBRs) in the wastewater sector. In order to get a further understanding of the fouling mechanisms and antifouling control strategies, this study investigated the effect of the hydraulic retention time on the fouling development, and the effect of different physical fouling control strategies in the fouling mitigation. A synthetic secondary effluent was continuously fed to three MPBRs operated at different HRTs (12, 24 and 36 hours). Different fouling behaviors were found as the HRT changed, which was confirmed by continuously monitoring the transmembrane pressure (TMP) and by measurements in the biomass and its algal organic matter (AOM) properties. Lowering the HRT resulted in higher fouling rates due to changes in the biomass and AOM properties. Higher HRTs led to lower fouling rates and to a lower organic rejection across the membrane. The retention of small-MW organics in SMPBR12h was found to exacerbate the fouling resistance, whereas the accumulation of large-MW biopolymers enhanced the rejection of organics, despite of not imparting significant resistance in SMPBR24h. In order to assess the impact of different physical fouling control strategies, namely relaxation, backwash and air scouring, OCT in-situ monitoring was employed in MPBR12h to provide real-time information of the fouling layer properties (thickness and relative roughness) and its interaction with the membrane surface. Different fouling mechanisms were observed under different fouling control strategies. MPBRRLX and MPBRBW presented similar fouling rates despite of the lower permeate productivities of the latter. The lowest fouling rates were observed in MPBRSC, where stronger interactions between the membrane and small-MW organics and particles was observed.
    • Mechanism Design for Virtual Power Plant with Independent Distributed Generators

      Kulmukhanova, Alfiya (2018-07)
      We discuss a model of a virtual power plant (VPP) that provides market access to privately-owned distributed generations (DGs). The VPP serves passive loads, processes bids from generators, and trades in the wholesale market. The generators can be renewable or thermal, and they act strategically to maximize their own profit. The VPP establishes the rules of the internal market to minimize the cost of energy and the cost of balancing while ensuring generator participation and load balancing. We derive a heuristic mechanism for internal market and propose a dynamic programming approach for minimizing the VPP cost. We present illustrative simulations for both single and multistage market bidding and then compare the resulting performance to the centralized VPP model, where the DGs are assumed to be owned by the VPP. We show that the proposed design incentivizes the DG agents to behave the same as in the centralized case, but the optimal cost paid by VPP is higher due to the payments to the DG owners.
    • Indoor Localization Using Three dimensional Multi-PDs Receiver Based on RSS

      Liu, Yinghao (2018-07)
      In modern life, there are many applications where positioning plays an important role. People have developed the global positioning system (GPS) to locate world wide position with error in decameter scales, which brings people much convenience. However, the accuracy of GPS is too low for indoor localization. The signals will drop down due to the signal attenuation caused by construction materials. With the well-developed GPS being indispensable for outdoor activities, many researchers have been also devoted to seeking an indoor positioning system to realize indoor localization with acceptable error. Indoor localization can be very useful in different situations, like locating, tracking, navigation and identification. For example, in the mall, locating the exact goods for customers can provide much convenience and benefits. Locating and tracking in the airport can greatly help passengers save their time and energy in reaching the destination. In another general scenario of identification, the population of observed targets is usually larger than just one. Hence, only with small error, indoor localization system (ILS) can be able to identify the targets despite the neighbors. Due to the emerging and urging demands of increasing the accuracy of indoor localization, we propose a novel design of three dimensional (3-D). optical receiver for visible light communication (VLC) indoor positioning system. First, we model the optical wireless channel. Then we utilize modified triangulation method to obtain more robust receiver position by using at least two light-emitting diodes (LEDs) and one receiver consisting of nine photodetectors (PDs). Finally, the improved algorithm is implemented and the results are shown under our three dimensional multiple photodetectors (multi-PDs) structure receiver. In the simulation, we take the parameters of Lambertian radiation pattern, LEDs and PDs as those shown in [1] . To be noticed, our design of multi-PDs receiver is fully expanded into three dimensions compared with the pyramid receiver (PR), which allows indoor positioning with our receiver structure to be more robust to the higher or corner positions. The details will be explained in the following sections. Based on Multiple-Photodiodebased Indoor Positioning algorithm [1], the indoor positioning algorithm is improved by redefining the optimization problem of obtaining the direction from receiver to LED and using weighted triangulation method to locate receiver position. We admit the solution under the redefined problem is not optimal to the actual problem. Yet, our given solution is better to that in [1] due to the existence of noise, which is reasonable and has been verified.
    • Entropy Stability of Finite Difference Schemes for the Compressible Navier-Stokes Equations

      AlSayyari, Mohammed (2018-07)
      In this thesis, we study the entropy stability of the compressible Navier-Stokes model along with a modification of the model. We use the discretization of the inviscid terms with the Ismail-Roe entropy conservative flux. Then, we study entropy stability of the augmentation of viscous, heat and mass diffusion finite difference approximations to the entropy conservative flux. Additionally, we look at different choices of the diffusion coefficient that arise from combining the viscous, heat and mass diffusion terms. Lastly, we present numerical results of the discretizations comparing the effects of the viscous terms on the oscillations near the shock and show that they preserve entropy stability.
    • 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.
    • Design of a Hydraulic Variable Compression Ratio Piston for a Heavy Duty Internal Combustion Engine

      Al Mudraa, Sultan (2018-07)
      A High percentage of fuel consumption worldwide is in internal combustion engines which has led environmental organizations and authorities to put further pressure on the engine industries to reduce CO2 emissions and enhance engine efficiency. However, historically, the effect of the compression ratio on increasing thermal efficiency of the engine is well known, hence; numerous technical solutions have been proposed to implement a variable compression ratio concept. A new first-class engineering solution to use a hydraulic piston was initially patented by BICERA (British Internal Combustion Engine Research Association) , then improved by Continental and Daimler Benz. A Hydraulic variable compression ratio piston is a hydraulically actuated piston that provides a practical method of obtaining a variable compression ratio piston. In this literature, a hydraulic variable compression ratio piston for a Volvo D13 diesel engine was designed, analyzed, modeled and discussed. This analysis was accomplished by first performing kinematic and dynamic analyses for the piston motion and acceleration based on the crank-slider mechanism. Following this the oil flow characteristics were defined in every mechanical element transferring the oil in its journey from the engine pump to the piston. Moreover, two different designs were proposed in an attempt to predict the compression ratio by modeling the hydraulic, dynamic and engine execution simultaneously. Additionally, stress on the piston was analyzed using Finite Element Analysis (FEA) to assure piston sustainment and rigidity against the harsh combustion chamber environment. In conclusion, the best design was successfully selected and finalized to reach a wide compression ratio range under a boosted inlet pressure based on the selected design, dimensions, check valves and relief valves.
    • Synthesis and Application of PN3P Cobalt Pincer Complex for Selective Hydrogenation of Nitriles to Secondary Imines and α -Alkylation of Nitriles with Alcohols

      Al Dakhil, Abdullah (2018-07)
      Pincer complexes moieties have attracted much attention in the past years. They have been proved that they are highly active catalysts in many different known transition metal-catalyzed organic reaction and some unpredictable organic transformation. In this thesis, we will use PN3P Cobalt pincer complex in two different applications. The first application is the unpresented Cobalt-catalyzed hydrogenation of nitriles to secondary imines. The selective hydrogenation of nitriles into secondary imines is a very challenging task and the catalysts play a very important role in the reaction and the selectivity. Herein in the thesis, we report the first selective hydrogenation of nitriles to secondary imines catalyzed by a well-defined and accessible PN3P cobalt pincer complex. Our results show different selectivity compared with the known PNP cobalt catalytic system during the nitriles hydrogenation. A set of aliphatic and aromatic nitriles are hydrogenated to the secondary imine under relatively mild conditions. The second application is the alkylation of nitriles with alcohols using PN3P cobalt pincer complex. The alcohol is being used here as alkylating agent in state of using toxic alkyl halides or excess amount of base to avoid any salt waste. The cobalt pincer complex work as catalyst for transformation that undergoes alkylation via hydrogen transfer pathways. The beauty of this reaction that it is delver water as the only byproduct. A different nitriles and alcohol are tolerated in this reaction.
    • Host-Guest Chemistry of Inorganic Porous Platforms

      Alsufyani, Maryam (2018-07)
      Complexes made by hosts that completely surround their guests provide a mean to stabilize reactive chemical intermediates, transfer biologically active cargo to a diseased cell, and construct molecular scale devices. By the virtue of inorganic host‐guest self‐assembly, the nucleation processes in the cavity of a {P8W48}‐archetype phosphotungstate has afforded a nanoscale 16‐GaIII‐32‐oxo cluster that contain the largest number of GaIII ions yet found in polyoxometalate chemistry. Catalytic activity via thus “Metal-Oxo Cluster within Cluster” Assembly has been preliminarily investigated. Besides, the hybrid aggregates composed of the inorganic {P8W48} and orgainc cyclic moiety has been studied.
    • Airborne Prokaryote and Virus abundance over the Red Sea

      Yahya, Razan (2018-07)
      Aeolian dust exerts a notable influence on atmospheric and oceanic conditions and human health, particularly in arid and semi-arid regions like Saudi Arabia. Dust is often characterized by its mineral and chemical composition, but there is a microbiological component of natural aerosols which has received comparatively little attention. Moreover, the amount of materials suspended in the atmosphere is highly variable from day to day. Thus, knowing the loads of dust and suspended microbes and its variability over the year is essential to understand the possible effects of dust on the Red Sea ecosystem. Here, we present the first estimates of dust and microbial loads at a coastal side on the Red Sea over a two-year period supplemented with information from dust samples collected along the Red Sea in offshore water and their variability. Weekly average dust loads ranged from 4.63 to 646.11 μg m-3, while the abundance of airborne prokaryotic cells and viral particles ranged from 31,457 to 608,333 cells m-3 and from 69,615.5 to 3,104,758 particles m-3, respectively. These are the first estimates of airborne microbial abundance that we are aware of in this region. The large number of dust particles and suspended microbes found in the air indicates that airborne microbes may have a large impact on our health and that of the Red Sea ecosystem.
    • Numerical Investigation of Shock Bubble Interaction using Wavelet Adaptive Multi-Resolution Method

      Dhopeshwar, Rahul (2018-07)
      When a shock interacts with a bubble having a different density than the environment or medium, the interaction causes compression and deformation of the bubble and generation of a vortex pair. Later, secondary vortices appear causing enhanced mixing. The enhanced mixing induced by the shock bubble interactions is particularly of interest in supersonic combustion and detonation. The Wavelet Adaptive Multi-resolution Representation (WAMR) method is particularly suitable for challenging continuum physics problems like shock bubble interaction, which has strong multi-scale character. This method provides an efficient strategy to create a dynamically adaptive spatial grid and to obtain a verified solution. Since the wavelet amplitude provides a first-hand estimate of the local error at each point, the method is able to efficiently capture a wide spectrum of spatial scales by dynamically changing the adaptive grid. Highly resolved computations are done only in the regions where abrupt transition occurs. In this work a detailed investigation of Shock Bubble Interaction (SBI) is carried out using shocks having Mach numbers from 1.2 to 3 for helium, nitrogen and krypton bubbles. Simulations carried out using WAMR method were used to analyze the effects of Mach number and density contrast on the shape, location and velocity of the bubble as well as vorticity and pressure in the flow field.
    • Fabrication and Characterization of Geometrically Confined Fe3Sn2 Skyrmion-based Devices

      GONG, CHEN (2018-06-27)
      Skyrmion is a topologically protected nanometer-sized spin configuration, which makes it a promising candidate for future memory devices. All skyrmion applications are based on the formation and manipulation of spin textures in nanostructured elements. Therefore, fabrication of geometrically confined skyrmion-based nanodevices is an essential step in the investigation of skyrmion properties. In this study, my research mainly focuses on the fabrication of high-quality Fe3Sn2 nanostripes with different geometric parameters for Lorentz transmission electron microscopy (LTEM) by a focused ion beam (FIB) system. The observation of the skyrmions using LTEM was mainly performed by Dr. Qiang Zhang, although I have deeply involved the discussion on new samples to be fabricated based on the results obtained from LTEM and also performed some LTEM experiments. To investigate the formation process and thermal stability of skyrmions in a geometrically confined environment, I have fabricated more than fifty high-quality nanostripes with a width of 265-4,000 nm. Studying with LTEM, a distinct evolutionary path of stripe-skyrmion transformation is observed after gradually increasing the magnetic field (out-of-plane direction) and the critical magnetic field of skyrmion is found to decrease with an increasing strength of confinements. Moreover, a series of racetrack devices with controlled thicknesses (125-404 nm) is fabricated to study the effect of thickness in skyrmion formation. Overall, in order to obtain less damaged, flat skyrmion-based devices by FIB system, experimental parameters are optimized and fabrication skills are improved. This method develops the possible application of centrosymmetric frustrated magnet Fe3Sn2 in skyrmion-based racetrack devices.
    • Monitoring the effects of offshore aquaculture on water quality in the Red Sea

      Dunne, Aislinn (2018-06)
      The Saudi Arabian government has announced an economic development plan (Vision 2030) to invest in a range of industries across the Kingdom, one of which is the development of aquaculture. In the face of a likely increase in Red Sea fish farming, we investigated the impacts of offshore fish farms on the coastal water quality of the Red Sea by a) measuring the environmental impacts of an operational Red Sea fish farm, and b) testing whether an existing aquaculture modeling software can be used as a meaningful planning tool in the development of Red Sea aquaculture. Water quality parameters such as dissolved oxygen, nutrients, particulate matter, chlorophyll, ammonium, and bacterial abundance were measured seasonally over the course of a year around an offshore fish farm along the south-central coast of Saudi Arabia to determine the impacts of fish farm effluent on the surrounding waters. Bacteria, phosphate, inorganic nitrogen, and suspended particulate matter showed patterns of enrichment close to the fish farm. Additionally, dissolved oxygen has slightly lower concentrations close to and down current from the fish farms. Benthic sediments from a nearby coral reef were also assessed for organic enrichment, but concentrations of total organic carbon and total nitrogen were not significantly different from those at an offshore reef. The data from these sampling efforts were then used as input parameters for an aquaculture modeling software (AquaModel.net), however many of the input parameters required to run the model were unavailable and meaningful conclusions could not be drawn from the results. Through field studies and modeling, we assessed the current impact of a Red Sea fish farm on water quality with the goal of predicting the potential impacts of future offshore aquaculture development in Saudi Arabia.
    • A Study of Recurrent and Convolutional Neural Networks in the Native Language Identification Task

      Werfelmann, Robert (2018-05-24)
      Native Language Identification (NLI) is the task of predicting the native language of an author from their text written in a second language. The idea is to find writing habits that transfer from an author’s native language to their second language. Many approaches to this task have been studied, from simple word frequency analysis, to analyzing grammatical and spelling mistakes to find patterns and traits that are common between different authors of the same native language. This can be a very complex task, depending on the native language and the proficiency of the author’s second language. The most common approach that has seen very good results is based on the usage of n-gram features of words and characters. In this thesis, we attempt to extract lexical, grammatical, and semantic features from the sentences of non-native English essays using neural networks. The training and testing data was obtained from a large corpus of publicly available essays written by authors of several countries around the world. The neural network models consisted of Long Short-Term Memory and Convolutional networks using the sentences of each document as the input. Additional statistical features were generated from the text to complement the predictions of the neural networks, which were then used as feature inputs to a Support Vector Machine, making the final prediction. Results show that Long Short-Term Memory neural network can improve performance over a naive bag of words approach, but with a much smaller feature set. With more fine-tuning of neural network hyperparameters, these results will likely improve significantly.
    • Neural Inductive Matrix Completion for Predicting Disease-Gene Associations

      Hou, Siqing (2018-05-21)
      In silico prioritization of undiscovered associations can help find causal genes of newly discovered diseases. Some existing methods are based on known associations, and side information of diseases and genes. We exploit the possibility of using a neural network model, Neural inductive matrix completion (NIMC), in disease-gene prediction. Comparing to the state-of-the-art inductive matrix completion method, using neural networks allows us to learn latent features from non-linear functions of input features. Previous methods use disease features only from mining text. Comparing to text mining, disease ontology is a more informative way of discovering correlation of dis- eases, from which we can calculate the similarities between diseases and help increase the performance of predicting disease-gene associations. We compare the proposed method with other state-of-the-art methods for pre- dicting associated genes for diseases from the Online Mendelian Inheritance in Man (OMIM) database. Results show that both new features and the proposed NIMC model can improve the chance of recovering an unknown associated gene in the top 100 predicted genes. Best results are obtained by using both the new features and the new model. Results also show the proposed method does better in predicting associated genes for newly discovered diseases.