• Sand temperature profiles at turtle nesting sites in the Red Sea: implications for hatchling sex ratios

      Tanabe, Lyndsey K. (2018-11)
      Climate change poses a serious threat to species that demonstrate temperature dependent sex determination (TDS), including marine turtles. Increased temperatures can result in highly female skewed sex ratios and decreased hatchling success. In situ sand temperature data was collected from the nesting depth of hawksbill and green turtles at five study sites along the coast of the Red Sea. The sand temperature profile at four of the sites exceeded the pivotal temperature of 29.2°C (commonly cited in literature) throughout the study duration, which suggests feminization of turtles could be occurring, but further studies need to identify the pivotal temperature in this region. The percentage of days exceeding the commonly cited maximum thermal threshold (33 and 35°C) was calculated for each site at 30 and 50 cm. Sand temperature recordings were as high as 36.0°C at 30 cm depth, and 35.3°C at 50 cm. This suggests that the turtle hatchlings in some areas of the Red Sea could already have high mortality rates due to high temperatures, unless they are locally adapted to these high temperatures. The Red Sea is home to five out of the seven extant species of marine turtles in the world, but not much is known about these populations. The Red Sea is an understudied region of the world, but it has the potential to provide insight on how species might adapt to future climate change due to its high and variable water temperatures (range of 20°C to 35°C) and high salinity (40 PSU). Sites with lower sand temperatures (and lower risk of feminization) may represent priority areas for conservation efforts, particularly in regions facing imminent coastal development.
    • Scheduling Broadcasts in a Network of Timelines

      Manzoor, Emaad A. (2015-05-12)
      Broadcasts and timelines are the primary mechanism of information exchange in online social platforms today. Services like Facebook, Twitter and Instagram have enabled ordinary people to reach large audiences spanning cultures and countries, while their massive popularity has created increasingly competitive marketplaces of attention. Timing broadcasts to capture the attention of such geographically diverse audiences has sparked interest from many startups and social marketing gurus. However, formal study is lacking on both the timing and frequency problems. In this thesis, we introduce, motivate and solve the broadcast scheduling problem of specifying the timing and frequency of publishing content to maximise the attention received. We validate and quantify three interacting behavioural phenomena to parametrise social platform users: information overload, bursty circadian rhythms and monotony aversion, which is defined here for the first time. Our analysis of the influence of monotony refutes the common assumption that posts on social network timelines are consumed piecemeal independently. Instead, we reveal that posts are consumed in chunks, which has important consequences for any future work considering human behaviour over social network timelines. Our quantification of monotony aversion is also novel, and has applications to problems in various domains such as recommender list diversification, user satiation and variety-seeking consumer behaviour. Having studied the underlying behavioural phenomena, we link schedules, timelines, attention and behaviour by formalising a timeline information exchange process. Our formulation gives rise to a natural objective function that quantifies the expected collective attention an arrangement of posts on a timeline will receive. We apply this formulation as a case-study on real-data from Twitter, where we estimate behavioural parameters, calculate the attention potential for different scheduling strategies and, using the method of marginal allocation, discover a new scheduling strategy that outperforms popular scheduling heuristics while producing fewer posts.
    • Sea Surface Height Variability and Eddy Statistical Properties in the Red Sea

      Zhan, Peng (2013-05)
      Satellite sea surface height (SSH) data over 1992-2012 are analyzed to study the spatial and temporal variability of sea level in the Red Sea. Empirical orthogonal functions (EOF) analysis suggests the remarkable seasonality of SSH in the Red Sea, and a significant correlation is found between SSH variation and seasonal wind cycle. A winding-angle based eddy identification algorithm is employed to derive the mesoscale eddy information from SSH data. Totally more than 5500 eddies are detected, belonging to 2583 eddy tracks. Statistics suggest that eddies generate over the entire Red Sea, with two regions in the central basin of high eddy frequency. 76% of the detected eddies have a radius ranging from 40km to 100km, of which both intensity and absolute vorticity decrease with eddy radius. The average eddy lifespan is about 5 weeks, and eddies with longer lifespan tend to have larger radius but less intensity. Different deformation rate exists between anticyclonic eddies (AEs) and cyclonic eddies (CEs), those eddies with higher intensity appear to be less deformed and more circular. Inspection of the 84 long-lived eddies suggests the AEs tend to move a little more northward than CEs. AE generation during summer is obviously lower than that during other seasons, while CE generation is higher during spring and summer. Other features of AEs and CEs are similar with both vorticity and intensity reaching the summer peaks in August and winter peaks in January. Inter-annual variability reveals that the eddies in the Red Sea are isolated from the global event. The eddy property tendencies are different from the south and north basin, both of which exhibit a two-year cycle. Showing a correlation coefficient of -0.91, Brunt–Väisälä frequency is negatively correlated with eddy kinetic energy (EKE), which results from AE activities in the high eddy frequency region. Climatological vertical velocity shear variation is identical with EKE except in the autumn, suggesting the vertical shear could convert the energy from baroclinic instability into eddy activity. Finally, numerical simulation results from the MIT general circulation model (MITgcm) are validated with previous studies and observations. The vertical structure of the simulated flux through Bab el Mandeb is successfully reproduced. Further validation with the 2010 cruise suggests that the thermocline occurs at ~200m, but the model vertical salinity gradient is lower than the observations. The model surface eddy variability is also examined, suggesting good agreement with satellite observations.
    • Seabed Filter Feasibility Study of Om Almisk Island

      Sesler, Kathryn (2012-06)
      Freshwater access has always been and is continuing to be a severe problem in desert coastal regions, despite the fact that they have an unlimited supply of easily accessible saline water. Water desalination plants are well established and heavily relied upon throughout the Middle East, Saudi Arabia in particular. However, water desalination tends to be a very expensive and energy intensive solution to the problem. The transition from using open water intake systems and all of the pretreatment processes that they require, to using seabed water filters as an intake, would potentially reduce the lifetime costs, energy consumption, and environmental impacts commonly associated with water desalination. This is because the filtration process that the seabed filter generates, serves as sufficient pretreatment for seawater as well as eliminating any risk of entrainment or impingement of marine organisms. The main objective of this research is to conduct a feasibility study on Om Almisk Island, an island off the coast of King Abdullah University of Science and Technology (KAUST), to determine if it would be a suitable location to construct a seabed water filter as a replacement for the current open water intake. The Om Almisk Island site was evaluated through collection of sand samples over a radial grid around Om Almisk Island and sample analysis using grain size distribution, porosity, and hydraulic conductivity. The lack of mud, high hydraulic conductivity, proximity to KAUST, and the shallow waters of the sandy apron surrounding Om Almisk Island make this an ideal location for a seabed water filter to be used as an intake and pretreatment for the KAUST desalination plant. This location also has low tide change and the presence of benthic macrofauna to create bioturbation in the sediments, which could inhibit the growth of a schmutzdecke. If this biological layer forms, it could drastically reduce the hydraulic conductivity of the system. Due to the high hydraulic conductivity of the native sand, a relatively small footprint is possible for the design of the filter. A design with an intake of 105,000 m3/day, using four active galleries and one standby gallery was generated.
    • Seismic Imaging and Velocity Analysis Using a Pseudo Inverse to the Extended Born Approximation

      Alali, Abdullah A. (2018-05)
      Prestack depth migration requires an accurate kinematic velocity model to image the subsurface correctly. Wave equation migration velocity analysis techniques aim to update the background velocity model by minimizing image residuals to achieve the correct model. The most commonly used technique is differential semblance optimization (DSO), which depends on applying an image extension and penalizing the energy in the non-physical extension. However, studies show that the conventional DSO gradient is contaminated with artifact noise and unwanted oscillations which might lead to local minima. To deal with this issue and improve the stability of DSO, recent studies proposed to use an inversion formula rather than migration to obtain the image. Migration is defined as the adjoint of Born modeling. Since the inversion is complicated and expensive, a pseudo inverse is used instead. A pseudo inverse formula has been developed recently for the horizontal space shift extended Born. This formula preserves the true amplitude and reduces the artifact noise even when an incorrect velocity is used. Although the theory for such an inverse is well developed, it has only been derived and tested on laterally homogeneous models. This is because the formula contains a derivative of the image with respect to a vertical extension evaluated at zero offset. Implementing the vertical extension is computationally expensive, which means this derivative needs to be computed without applying the additional extension. For laterally invariant models, the inverse is simplified and this derivative is eliminated. I implement the full asymptotic inverse to the extended Born to account for laterally heterogeneity. I compute the derivative of the image with respect to a vertical extension without performing any additional shift. This is accomplished by applying the derivative to the imaging condition and utilizing the chain rule. The fact that this derivative is evaluated at zero offset vertical extension, makes it possible to compute the derivative without applying the extension. I also verify the newly proposed inversion formula on a laterally variant velocity model. In addition, I test the effect of the computed derivative and compare its contribution with the full formula. This additional term has overall limited influence on conventional images. Its largest impact is on vertical reflectors such as salt flanks, granted the velocity is varying laterally in the background as often is in this case. Otherwise, for most applications, we can obtain good quality extended images without this additional term.
    • Self-recruitment in a coral reef fish population in a marine reserve

      Herrera Sarrias, Marcela (2014-12)
      Marine protected areas (MPAs) have proliferated in the past decades to protect biodiversity and sustain fisheries. However, most of the MPA networks have been designed without taking into account a critical factor: the larval dispersal patterns of populations within and outside the reserves. The scale and predictability of larval dispersal, however, remain unknown due to the difficulty of measuring dispersal when larvae are minute (~ cm) compared to the potential scale of dispersal (~ km). Nevertheless, genetic approaches can now be used to make estimates of larval dispersal. The following thesis describes self-recruitment and connectivity patterns of a coral reef fish species (Centropyge bicolor) in Kimbe Bay, Papua New Guinea. To do this, microsatellite markers were developed to evaluate fine-scale genetics and recruit assignment via genetic parentage analysis. In this method, offspring are assigned to potential parents, so that larval dispersal distances can then be inferred for each individual larvae. From a total of 255 adults and 426 juveniles collected only 2 parentoffspring pairs were assigned, representing less than 1% self-recruitment. Previous data from the same study system showed that both Chaetodon vagagundus and Amphiprion percula have consistent high self-recuitment rates (~ 60%), despite having contrasting life history traits. Since C. bicolor and C. vagabundus have similar characteristics (e.g. reproductive mode, pelagic larval duration), comparable results were expected. On the contrary, the results of this study showed that dispersal patterns cannot be generalized across species. Hence the importance of studying different species and seascapes to better understand the patterns of larval dispersal. This, in turn, will be essential to improve the design and implementation of MPAs as conservation and management tools.
    • Self-Recruitment in the Bumphead Parrotfish Under Different Levels of Fishing Pressure in the Solomon Islands

      Lozano-Cortés, Diego (2014-12)
      Knowledge in the spatial patterns of fish larval dispersal is crucial for the establishment of a sustainable management of fisheries and species conservation. Direct quantification of larval dispersal is a challenging task due to the difficulty associated with larval tracking in the vast ocean. However, genetic approaches can be used to estimate it. Here, I employed genetic markers (microsatellites) as a proxy to determine dispersal patterns and self-recruitment levels using parentage analysis in the bumphead parrotfish (Bolbometapon muricatum) in the Solomon Islands. Tissue samples of 3924 fish (1692 juveniles, 1121 males and 1111 females) were collected from a spear-fishery at the Kia District in Santa Isabel Island. The samples come from three distinct zones with different fishing pressure histories (lightly fished, recently fished, and heavily fished). The mean dispersal distance estimated for the bumphead parrotfish was 36.5 Km (range 4 – 78 Km) and the genetic diversity for the population studied was low in comparison with other reef fishes. The parentage analysis identified 68 parent–offspring relationships, which represents a self-recruitment level of almost 50 %. Most of the recruits were produced in the zone that recently started to be fished and most of these recruits dispersed to the heavily fished zone. Comparisons of genetic diversity and relatedness among adults and juveniles suggested the potential occurrence of sweepstakes reproductive success. These results suggest that management measures must be taken straightaway to assure the sustainability of the spear-fishery. These measures may imply the ban on juveniles fishing in the heavily fished zone and the larger adults in the recently fished zone. Overall, the population dynamics of the studied system seem to be strongly shaped by self-recruitment and sweepstakes reproduction events.
    • Semi-Supervised Half-Quadratic Nonnegative Matrix Factorization for Face Recognition

      Alghamdi, Masheal M. (2014-05)
      Face recognition is a challenging problem in computer vision. Difficulties such as slight differences between similar faces of different people, changes in facial expressions, light and illumination condition, and pose variations add extra complications to the face recognition research. Many algorithms are devoted to solving the face recognition problem, among which the family of nonnegative matrix factorization (NMF) algorithms has been widely used as a compact data representation method. Different versions of NMF have been proposed. Wang et al. proposed the graph-based semi-supervised nonnegative learning (S2N2L) algorithm that uses labeled data in constructing intrinsic and penalty graph to enforce separability of labeled data, which leads to a greater discriminating power. Moreover the geometrical structure of labeled and unlabeled data is preserved through using the smoothness assumption by creating a similarity graph that conserves the neighboring information for all labeled and unlabeled data. However, S2N2L is sensitive to light changes, illumination, and partial occlusion. In this thesis, we propose a Semi-Supervised Half-Quadratic NMF (SSHQNMF) algorithm that combines the benefits of S2N2L and the robust NMF by the half- quadratic minimization (HQNMF) algorithm.Our algorithm improves upon the S2N2L algorithm by replacing the Frobenius norm with a robust M-Estimator loss function. A multiplicative update solution for our SSHQNMF algorithmis driven using the half- 4 quadratic (HQ) theory. Extensive experiments on ORL, Yale-A and a subset of the PIE data sets for nine M-estimator loss functions for both SSHQNMF and HQNMF algorithms are investigated, and compared with several state-of-the-art supervised and unsupervised algorithms, along with the original S2N2L algorithm in the context of classification, clustering, and robustness against partial occlusion. The proposed algorithm outperformed the other algorithms. Furthermore, SSHQNMF with Maximum Correntropy (MC) loss function obtained the best results for most test cases.
    • Separation, Characterization and Fouling Potential of Sludge Waters from Different Biological Wastewater Treatment Processes

      Xue, Jinkai (2011-07)
      The major limitation, which hinders the wider application of membrane technology and increases the operating costs of membranes involved in wastewater treatment plants, is membrane fouling induced by organic matter. Extracellular polymeric products (EPS) and soluble microbial products (SMP) are the two most mentioned major foulants in publications, for which the debate on precise definitions seems to be endless. Therefore, a concept of sludge water, which conceptually covers both EPS and SMP, has been developed in this research. A standard procedure of sludge water separation, which is centrifugation at 4000g for 15 min followed by 1.2μm glass fiber filter filtration, was established based on separation experiments with membrane tank sludge from the KAUST MBR wastewater treatment plant. Afterwards, sludge waters from the KAUST MBR WWTP anoxic tank, aerobic tank and membrane tank as well as sludge waters from the Jeddah WWTP anoxic tank, aerobic tank and secondary effluent were produced through the previously developed standard procedure. The obtained sludge water samples were thereafter characterized with TOC/COD, LC-­‐OCD and F-­‐EEM, which showed that KAUST anoxic/ aerobic /membrane tank sludge waters had similar characteristics for all investigated parameters, yet the influent naturally had a higher DOC and biopolymer concentration. Moreover, lower TOC/COD, negligible biopolymers and low levels of humics were found in KAUST effluent. Compared with the KAUST MBR WWTP, the Jeddah WWTP’s sludge waters generally had higher DOC and biopolymer concentrations. To investigate sludge water fouling potential, the KAUST membrane tank sludge water as well as the Jeddah secondary effluent were filtrated through a membrane array consisting of an ultrafiltration (UF) Millipore RC10kDa at the first step followed by a nanofiltration (NF) KOCH Acid/Base stable NF200 at the second step. It was found that cake layer and standard blocking occurred simultaneously during both of these filtration processes. For the KAUST MBR membrane tank sludge water and the Jeddah WWTP effluent, the fouling potential of humic/building blocks was much higher than that of biopolymers. Compared with the KAUST MBR membrane tank sludge water, the Jeddah WWTP effluent had comparable biopolymer fouling potential and higher humic/building blocks fouling potential.
    • Sequential Optimization of Global Sequence Alignments Relative to Different Cost Functions

      Odat, Enas M. (2011-05)
      The purpose of this dissertation is to present a methodology to model global sequence alignment problem as directed acyclic graph which helps to extract all possible optimal alignments. Moreover, a mechanism to sequentially optimize sequence alignment problem relative to different cost functions is suggested. Sequence alignment is mostly important in computational biology. It is used to find evolutionary relationships between biological sequences. There are many algo- rithms that have been developed to solve this problem. The most famous algorithms are Needleman-Wunsch and Smith-Waterman that are based on dynamic program- ming. In dynamic programming, problem is divided into a set of overlapping sub- problems and then the solution of each subproblem is found. Finally, the solutions to these subproblems are combined into a final solution. In this thesis it has been proved that for two sequences of length m and n over a fixed alphabet, the suggested optimization procedure requires O(mn) arithmetic operations per cost function on a single processor machine. The algorithm has been simulated using C#.Net programming language and a number of experiments have been done to verify the proved statements. The results of these experiments show that the number of optimal alignments is reduced after each step of optimization. Furthermore, it has been verified that as the sequence length increased linearly then the number of optimal alignments increased exponentially which also depends on the cost function that is used. Finally, the number of executed operations increases polynomially as the sequence length increase linearly.
    • Sequential Optimization of Paths in Directed Graphs Relative to Different Cost Functions

      Mahayni, Malek A. (2011-07)
      Finding optimal paths in directed graphs is a wide area of research that has received much of attention in theoretical computer science due to its importance in many applications (e.g., computer networks and road maps). Many algorithms have been developed to solve the optimal paths problem with different kinds of graphs. An algorithm that solves the problem of paths’ optimization in directed graphs relative to different cost functions is described in [1]. It follows an approach extended from the dynamic programming approach as it solves the problem sequentially and works on directed graphs with positive weights and no loop edges. The aim of this thesis is to implement and evaluate that algorithm to find the optimal paths in directed graphs relative to two different cost functions ( , ). A possible interpretation of a directed graph is a network of roads so the weights for the function represent the length of roads, whereas the weights for the function represent a constraint of the width or weight of a vehicle. The optimization aim for those two functions is to minimize the cost relative to the function and maximize the constraint value associated with the function. This thesis also includes finding and proving the relation between the two different cost functions ( , ). When given a value of one function, we can find the best possible value for the other function. This relation is proven theoretically and also implemented and experimented using Matlab®[2].
    • Set-Up and Validation of a Dynamic Solid/Gas Bioreactor

      Lloyd-Randol, Jennifer D. (2012-05)
      The limited availability of fossil resourses mandates the development of new energy vectors, which is one of the Grand Challenges of the 21st Century [1]. Biocatalytic energy conversion is a promising solution to meet the increased energy demand of industrialized societies. Applications of biocatalysis in the gas-phase are so far limited to production of fine chemicals and pharmaceuticals. However, this technology has the potential for large scale biocatalytic applications [2], e.g. for the formation of novel energy carriers. The so-called solid/gas biocatalysis is defined as the application of a biocatalyst immobilized on solid-phase support acting on gaseous substrates [3]. This process combines the advantages of bio-catalysis (green chemistry, mild reaction conditions, high specicity & selectivity) and heterogeneous dynamic gas-phase processes (low diffusion limitation, high conversion, simple scale-up). This work presents the modifications of a PID Microactivity Reference reactor in order to make it suitable for solid/gas biocatalysis. The reactor design requirements are based on previously published laboratory scale solid/gas systems with a feed of saturated vapors [4]. These vapors are produced in saturation flasks, which were designed and optimized during this project. Other modifications included relocation of the gas mixing chamber, redesigning the location and heating mechanism for the reactor tube, and heating of the outlet gas line. The modified reactor system was verified based on the Candida antarctica lipase B catalyzed transesterication of ethyl acetate with 1-hexanol to hexyl acetate and ethanol and results were compared to liquid-phase model reactions. Products were analyzed on line by a gas chromatograph with a flame ionization detector. C. antarc- tica physisorbed on silica particles produced a 50% conversion of hexanol at 40 C in the gas-phase. A commercial immobilized lipase from Iris Biotech produced 99% and 97% conversions of hexanol in similar experiments. This project achieved its goal to design, establish and successfully verify a solid/- gas biocatalysis reactor. Future work will target optimization of the reactor's operating conditions and the development of whole cell catalysts for energy production reactions. Potential experiments include the study of hydrogenolytic carbon dioxide reduction to methanol by free enzymes or methanogenic organisms [5], and the investigation of hydrogen production by water splitting of algae or cyanobacteria.
    • Shape-Tailored Features and their Application to Texture Segmentation

      Khan, Naeemullah (2014-04)
      Texture Segmentation is one of the most challenging areas of computer vision. One reason for this difficulty is the huge variety and variability of textures occurring in real world, making it very difficult to quantitatively study textures. One of the key tools used for texture segmentation is local invariant descriptors. Texture consists of textons, the basic building block of textures, that may vary by small nuisances like illumination variation, deformations, and noise. Local invariant descriptors are robust to these nuisances making them beneficial for texture segmentation. However, grouping dense descriptors directly for segmentation presents a problem: existing descriptors aggregate data from neighborhoods that may contain different textured regions, making descriptors from these neighborhoods difficult to group, leading to significant errors in segmentation. This work addresses this issue by proposing dense local descriptors, called Shape-Tailored Features, which are tailored to an arbitrarily shaped region, aggregating data only within the region of interest. Since the segmentation, i.e., the regions, are not known a-priori, we propose a joint problem for Shape-Tailored Features and the regions. We present a framework based on variational methods. Extensive experiments on a new large texture dataset, which we introduce, show that the joint approach with Shape-Tailored Features leads to better segmentations over the non-joint non Shape-Tailored approach, and the method out-performs existing state-of-the-art.
    • Shilling Attack Prevention for Recommender Systems Using Social-based Clustering

      Lee, Tak (2011-06-06)
      A Recommender System (RS) is a system that utilizes user and item information to predict the feeling of users towards unfamiliar items. Recommender Systems have become popular tools for online stores due to their usefulness in confidently recommending items to users. A popular algorithm for recommender system is Collaborative Filtering (CF). CF uses other users' profiles to predict whether a user is interested in a particular object. This system, however, is vulnerable to malicious users seeking to promote items by manipulating rating predictions with fake user profiles. Profiles with behaviors similar to "victim" users alter the prediction of a Recommender System. Manipulating rating predictions through injected profiles is referred to as a shilling attack. It is important to develop shilling attack prevention frameworks for to protect the trustworthiness of Recommender Systems. In this thesis, we will demonstrate a new methodology that utilizes social information to prevent malicious users from manipulating the prediction system. The key element in our new methodology rests upon the concept of trust among real users, an element we claim absent among malicious profiles. In order to use trust information for shilling attack prevention, we first develop a weighting system which makes the system rely more on trustworthy users when making predictions. We then use this trust information to cluster out untrustworthy users to improve rating robustness. The robustness of the new and classic systems is then evaluated with data from a public commercial consumer RS, Epinions.com. Several complexity reduction procedures are also introduced to make implementing the algorithms mentioned possible for a huge commercial database.
    • Significance of Microbiology in Porous Hydrocarbon Related Systems

      Augsburger, Nicolas (2017-07)
      This thesis explores bio-mediated processes in geotechnical and petroleum engineering. Worldwide energy consumption is rapidly increasing as the world population and per-capita consumption rises. The US Energy Information Agency (EIA) predicts that hydrocarbons will remain the primary energy source to satisfy the surging energy demands in the near future. The three topics described in detail in this document aim to link microbiology with geotechnical engineering and the petroleum industry. Microorganisms have the potential to exploit residual hydrocarbons in depleted reservoirs in a technique known as microbial enhanced oil recovery, MEOR. The potential of biosurfactants was analyzed in detail with a literature review. Biosurfactant production is the most accepted MEOR technique, and has been successfully implemented in over 700 field cases. Temperature is the main limiting factor for these techniques. The dissolution of carbonates by microorganisms was investigated experimentally. We designed a simple, economical, and robust procedure to monitor diffusion through porous media. This technique determined the diffusion coefficient of H+ in 1.5% agar, 1.122 x 10-5 cm2 sec-1, by using bromothymol blue as a pH indicator and image processing. This robust technique allows for manipulation of the composition of the agar to identify the effect of specific compounds on diffusion. The Red Sea consists of multiple seeps; the nearby sediments are telltales of deeper hydrocarbon systems. Microbial communities associated with the sediments function as in-situ sensors that provide information about the presence of carbon sources, metabolites, and the remediation potential. Sediments seeps in the Red Sea revealed different levels of bioactivity. The more active seeps, from the southern site in the Red Sea, indicated larger pore sizes, higher levels of carbon, and bioactivity with both bacteria and archaeal species present.
    • The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

      Lardhi, Sheikha F. (2013-05)
      Surface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.
    • Simulating Coral Reef Connectivity in the Southern Red Sea

      Wang, Yixin (2018-05)
      Connectivity is an important component of coral reef studies for its role in the enhancement of ecosystem resilience. Previous genetic structure and physical circulation studies in the Red Sea reveal a homogeneity within the coral reef complexes in the central and northern parts of the basin. Yet, genetic isolation and relatively low connectivity has been observed in the southern Red Sea. Raitsos et al. (2017) recently hypothesized that coral reefs in the southern Red Sea are more connected with regions outside the basin, rather than with the central and northern Red Sea. Using a physical circulation approach based on a 3-D backward particle tracking simulation, we further investigate this hypothesis. A long-term (> 10 years), very high resolution (1km) MITgcm simulation is used to provide detailed information on velocity in the complex coastal regions of the Red Sea and the adjacent narrow Bab-El-Mandeb Strait. The particle tracking simulation results support the initial hypothesis that the coastal regions in the southern Red Sea exhibit a consistently higher connectivity with the regions outside the Bab-El-Mandeb Strait, than with the central and northern Red Sea. Substantially high levels of connectivity, facilitated by the circulation and eddies, is observed with the coastal regions in the Gulf of Aden. A strong seasonality in connectivity, related to the monsoon-driven circulation, is also evident with the regions outside of the Red Sea. The winter surface intrusion plays a leading role in transporting the particles from the Gulf of Aden and the Indian Ocean into the Red Sea, while the summer subsurface intrusion also supports the transport of particles into the Red Sea in the intermediate layer. In addition, the connectivity with the central and northern Red Sea is more affected by the intensity of the eddies. Evidence also suggests that potential connectivity exists between the coastal southern Red Sea and the coasts of Oman, Socotra, Somalia, Kenya, Tanzania and the north coast of the Madagascar.
    • Simulation of 2-D Compressible Flows on a Moving Curvilinear Mesh with an Implicit-Explicit Runge-Kutta Method

      AbuAlSaud, Moataz (2012-07)
      The purpose of this thesis is to solve unsteady two-dimensional compressible Navier-Stokes equations for a moving mesh using implicit explicit (IMEX) Runge- Kutta scheme. The moving mesh is implemented in the equations using Arbitrary Lagrangian Eulerian (ALE) formulation. The inviscid part of the equation is explicitly solved using second-order Godunov method, whereas the viscous part is calculated implicitly. We simulate subsonic compressible flow over static NACA-0012 airfoil at different angle of attacks. Finally, the moving mesh is examined via oscillating the airfoil between angle of attack = 0 and = 20 harmonically. It is observed that the numerical solution matches the experimental and numerical results in the literature to within 20%.
    • Simulation of CO2 Injection in Porous Media with Structural Deformation Effect

      Negara, Ardiansyah (2011-06-18)
      Carbon dioxide (CO2) sequestration is one of the most attractive methods to reduce the amount of CO2 in the atmosphere by injecting it into the geological formations. Furthermore, it is also an effective mechanism for enhanced oil recovery. Simulation of CO2 injection based on a suitable modeling is very important for explaining the fluid flow behavior of CO2 in a reservoir. Increasing of CO2 injection may cause a structural deformation of the medium. The structural deformation modeling in carbon sequestration is useful to evaluate the medium stability to avoid CO2 leakage to the atmosphere. Therefore, it is important to include such effect into the model. The purpose of this study is to simulate the CO2 injection in a reservoir. The numerical simulations of two-phase flow in homogeneous and heterogeneous porous media are presented. Also, the effects of gravity and capillary pressure are considered. IMplicit Pressure Explicit Saturation (IMPES) and IMplicit Pressure-Displacements and an Explicit Saturation (IMPDES) schemes are used to solve the problems under consideration. Various numerical examples were simulated and divided into two parts of the study. The numerical results demonstrate the effects of buoyancy and capillary pressure as well as the permeability value and its distribution in the domain. Some conclusions that could be derived from the numerical results are the buoyancy of CO2 is driven by the density difference, the CO2 saturation profile (rate and distribution) are affected by the permeability distribution and its value, and the displacements of the porous medium go to constant values at least six to eight months (on average) after injection. Furthermore, the simulation of CO2 injection provides intuitive knowledge and a better understanding of the fluid flow behavior of CO2 in the subsurface with the deformation effect of the porous medium.
    • Single-Copy Insertion of Split-GFP for the Restriction of Germline Expression in Caenorhabditis elegans

      Al Johani, Mohammed (2018-11)
      Gene regulation in C. elegans germ cells depend on transgenerational chromatin modification and small RNA pathways. Germline silencing mechanisms evolved to repress foreign DNA from compromising the transfer of genetic information to progeny. Effective genetic tools that circumvent the silencing machinery will facilitate studies using this model organism. Specifically, translation of heat-shock inducible transgenes is inhibited in the germline making it challenging to transiently express enzymes to modify the genome. Here, we describe a genetic screen design that can be used to identify pathways that prevent germline expression of heat-shock induced transgenes. We use split-GFP (GFP1-10 and GFP11) to confine a genetic screen to germ cells. Stable transgenic lines with germline expression of single-copy integrated GFP11 were produced using MosSCI. The insertion lines will be used in RNAi or chemical mutagenesis screens for the germline de-repression of GFP1-10 expressed under heat-shock promoters. The screen is likely to identify candidate RNAi or chromatin factors involved in repressing heat-shock expression in the germline, particularly from extrachromosomal arrays. Inducible high-level expression in the germline from extrachromosomal arrays would be a valuable tool for large-scale genome engineering.