X-ray computed tomography (CT) is a popular imaging technique used for reconstructing volumetric properties for a large range of objects. Compared to traditional optical means, CT is a valuable tool for analyzing objects with interesting internal structure or complex geometries that are not accessible with. In this thesis, a variety of applications in computer vision and graphics of inverse problems using tomographic imaging modalities will be presented: The first application focuses on the CT reconstruction...

Environmental gradients exist at global and local scales and the variable conditions they encompass allow the coexistence of different microbial assemblages. Studying gradients and the selection forces they enclose can reveal the spatial succession and interactions of microorganisms and, therefore, how they are assembled in functionally stable communities. By combining high-throughput sequencing technology and laboratory experimental approaches, I investigated the factors that influence the microbial community assemblages in two types of environmental gradients in the...

Defect passivation and surface modification of perovskite semiconductors play a key role in achieving highly efficient and stable perovskite solar cells (PSCs) and light-emitting diodes (LEDs). This dissertation describes three novel strategies for such defect passivation and surface modification. In the first strategy, we demonstrate a facile approach using inorganic perovskite quantum dots (QDs) to supply bulk- and surface-passivation agents to combine high power conversion efficiency (PCE) with high stability in CH3NH3PbI3 (MAPbI3) inverted PSCs....

Energy demand is driven by increasing population and quality of life. Fractures localize mechanical deformations and fluid flow, and they impede heat flow through the rock matrix. Therefore, fractures present a challenge to both the recovery of underground energy and long-term waste disposal solutions like carbon geological storage. Fracture are planar discontinuities that form when brittle rocks. The discrete element method can model the complex micromechanics of rock failure. In this thesis we present a...

In this thesis, we capitalize on the two-dimensional (2D) nature of MXenes by using them as precursors for the synthesis of 2D functional material. MXenes are easily intercalated with monovalent cations K, Na, Li due to their expanded d-spacing after etching. Based on these ideas, we have developed new synthesis processes of texture functional materials using MXenes as precursors. We have successfully synthesized two-dimensional Nb2C MXene based high aspect ratio ferroelectric potassium niobate (KNbO3) and...

Oviposition habitat is important to species with no protracted parental care. For sea turtles, nest site selection may affect offspring fitness through microenvironmental characteristics such as moisture, beach slope, temperature and grain size. Climate change and coastal development will result in changes of nest site characteristics. In particular in Saudi Arabia, with the advent of tourism, there will be development of giga-projects such as the crossborder city of NEOM and luxury tourist resort ‘The Red...

The process of full-waveform inversion (FWI) seeks a model of the Earth’s sub surface that produces simulated data to fit the observed data. The resolution of the model can be both complex and costly to meet such an objective. Resolving the reservoir is even more challenging as it requires an accurate representation of the physics throughout. Although FWI for diving waves has been successfully applied, the reservoir located at depth requires FWI to take advantage...

The use of quadratic discriminant analysis (QDA) or its regularized version (RQDA) for classification is often not recommended, due to its well-acknowledged high sensitivity to the estimation noise of the covariance matrix. This becomes all the more the case in unbalanced data settings for which it has been found that R-QDA becomes equivalent to the classifier that assigns all observations to the same class. In this paper, we propose an improved R-QDA that is based...

Electromagnetic (EM) imaging schemes are inherently non-linear and ill-posed. Albeit there exist remedies to these fundamental problems, more efficient solutions are still being sought. To this end, in this thesis, the non-linearity is tackled in- corporating a multitude of techniques (ranging from Born approximation (linear), inexact Newton (linearized) to complete nonlinear iterative Landweber schemes) that can account for weak to strong scattering problems. The ill-posedness of the EM inverse scattering problem is circumvented by formulating...

Identifying marine pollutant sources is essential in order to assess, contain and minimize their risk. We propose a Lagrangian Particle Tracking algorithm (LPT) to study the transport of passive tracers continuously released from fixed and moving sources and to identify their source in a backward mode. The LPT is designed to operate with uncertain flow fi elds, described by an ensemble of realizations of the sea currents. Starting from a region of high probability, re-...

Marine ecosystems are already threatened by the effects of climate change through increases in ocean temperatures and pCO2 levels due to increasing atmospheric CO2. Marine fish living close to their thermal maximum have been shown to be especially vulnerable to temperatures exceeding that threshold, and even relatively small increases in elevated pCO2 levels have led to behavioral impairments with amplified predation risks. These ongoing threats highlight the need for further understanding of how these changes...

The enclosed datasets have been generated by the internal spatial data generator tool included in the ExaGeoStat software (https://github.com/ecrc/exageostat). The datasets are univariate 2D spatial data spanning different correlation strengths between the geospatial locations with three different smoothness levels (0.6, 1.5, and 2.3). The main purpose of these datasets is to validate any exact or approximation geospatial modeling algorithm by providing the truth parameters used for generating each dataset. For certain data configurations that are...

Dataset of particulate scattering and backscattering coefficients, chlorophyll a, temperature, salinity and density from surface to 200 m depth for different stations in the Red Sea during different cruises. Particulate scattering and backscattering coefficient were obtained using a wetlabs ac-s sensor and a wetlabs BB9 sensor respectively. Temperature, salinity and density were obtained using a seabird CTD sensor. Chlorophyll a concentration was obtained by HPLC.

Recently, laser scribed graphene (LSG) technology has shown great potential for the development of a plethora of sensing platforms due to its high sensitivity, 3D porous structure, and flexibility. Molecularly imprinted polymers (MIPs) have shown high potential as recognition elements for many applications such as biosensing. Hence, we report in this thesis a novel biosensing platform that utilizes nanostructured gold to enhance the performance of LSG sensors coupled with a biomimetic MIP biosensor. To the...

Abstract: Styrene and methyl methacrylate have been polymerized successfully through atom transfer radical polymerization (ATRP) in aqueous dispersed media (emulsion ATRP). The thesis is divided into four experimental parts. In the first part, a water-soluble initiator was prepared for emulsion ATRP and utilized under various conditions in the presence of two ligands N, N, N’, N’’, N’’-Pentamethyldiethylenetriamine and 2,2’-bipyridine to attain activation/deactivation only in the oil phase with Tween 20 as a non-ionic surfactant. The...

Using machine learning, especially deep learning, to facilitate biological research is a fascinating research direction. However, in addition to the standard classi cation or regression problems, whose outputs are simple vectors or scalars, in bioinformatics, we often need to predict more complex structured targets, such as 2D images and 3D molecular structures. The above complex prediction tasks are referred to as structured prediction. Structured prediction is more complicated than the traditional classi cation but has...

Porous materials have exhibited some remarkable performances in wide range of applications such as in the field of catalysis, gas adsorption, water treatment, bio- imaging, drugs delivery and energy applications. This is due to the pore characteristic of these materials. In fact, their properties depend mainly on the pore size, pore morphology and pore size distribution. The knowledge of understanding the effect of chemical nature of porous materials on the heterogeneous catalysis has significantly increased...

Internet of Things (IoT) is an emerging paradigm about building a massive internet to link billions of non-living things to make smart decisions for humans and improve their quality of life. For many of IoT devices, such as wireless sensor nodes dispersed in the environment, there is not much control over their placements or orientations. Thus, there is a need to develop orientation insensitive antennas that ensure reliable data transmission irrespective of devices’ positions or...

The utilization of ammonia as a fuel is a pragmatic approach to pave the way towards a low-carbon economy. Ammonia compromises almost 18 % of hydrogen by mass and accepted as one of the hydrogen combustion enablers with existing infrastructure for transportation and storage. From an environmental and sustainability standpoint, ammonia combustion is an attractive energy source with zero carbon dioxide emissions. However, from a practical point of view, the direct combustion of ammonia is...

This is the supporting information for the article "El Niño/Southern Oscillation response to low-latitude volcanic eruptions depends on ocean pre-conditions and eruption timing". The archive includes all necessary files needed to reproduce the results - the modified source code of the CM2.1 climate model, input data, SATO1.8 volcanic dataset, and other data necessary to reproduce the simulations described in the paper.

Numerous short flapped DNA structures are created during the semi-discontinuous replication. These toxic intermediates are quickly resolved to produce a fully intact duplex of replicated DNA. Structure specific nuclease are key to resolving these structures, and show a high degree of specificity for their cognate substrate structures while being essentially insensitive to nucleotide sequence. Herein I demonstrate through confocal based single molecule experiments that the 5’ structure specific nuclease Flap Endonuclease 1 (FEN1) achieves its...

Cyclodipeptides (CDPs) are the smallest, most stable cyclic peptides that are synthesized as secondary metabolites by bacteria. The aim of this study was to investigate the effect of the Pseudomonas argentinensis (SA190) and four (CDPs), named as cis-cyclo-(Pro-Phe) (Cyclo2), cis-cyclo-(Pro-Leu) (Cyclo3), cis-cyclo-(Pro-Tyr) (Cyclo4) and cis-cyclo-(Pro-Val) (Cyclo5), with three concentrations (1µM, 100nM, and 10nM), on the growth of Arabidopsis thaliana under normal plant growth conditions [1/2MS media], salt conditions [125 mM NaCl] and drought conditions [25%...

Drone racing has recently became a topic of interest in research especially with the increase of power of mobile processors. There are many approaches of localizing (perception), planning, and strategizing against an adversarial agent online, with varying degrees of computational complexity and success. This thesis presents a game theoretic approach to solve this problem in the context of drone racing. The game theory planner strategizes against an opponent by using the “iterated best response” learning...

The advancement of both electronics and instrumentation technology has fostered the development of multi-physics platforms that can probe the earth’s subsurface. Remote, non-destructive testing techniques have led to the increased deployment of electromagnetic waves in sensor technology. Electromagnetic wave techniques are reliable and have the capacity to sense materials and associated properties with minimal perturbation. However, meticulous data analyses and mathematical derivations reveal inconsistencies in some formulations. Thus, revisiting the fundamental physics that underlies both...

Produced water (PW), or water associated with crude oil extraction, is the largest oily wastewater stream generated worldwide. The reuse and reclamation of these important water volumes are critical for more sustainable operation in the oilfield. Ceramic membrane filtration is a promising technology for PW treatment; however, fouling is the major drawback for a broader application. Fouling leads to higher resistance to flow, reducing membrane lifetime, and ultimately leading to higher capital expenditures and operating...