Recent Submissions

  • Ultrafast Spectroscopy of Polymer: Non-fullerene Small Molecule Acceptor Bulk Heterojunction Organic Solar Cells

    Alamoudi, Maha A (2019-01-07)
    Organic photovoltaics has emerged as a promising technology for electricity generation. The essential component in an organic solar cell is the bulk heterojunction absorber layer, typically a blend of an electron donor and an electron acceptor. Efforts have been made to design new materials such as donor polymers and novel acceptors to improve the power conversion efficiencies. New fullerene free acceptors providing low cost synthesis routes and tenability of their optoelectronic and electrochemical properties have been designed. Despite the efforts, still not much is known about the photopysical processes in these blends that limit the performance. In this respect, time-resolved spectroscopy such as transient absorption and time-resolved photoluminescence, can provide in-depth insight into the various (photo) physical processes in bulk heterojunction solar cell. In this thesis, PCE10 was used as donor and paired with different non fullerene acceptors. In the first part of this thesis the impact of the core structure (cyclopenta-[2, 1-b:3, 4-b’]dithiophene (CDT) versus indacenodithiophene (IDTT)) of malononitrile (BM)-terminated acceptors, abbreviated as CDTBM and IDTTBM, on the photophysical characteristics of BHJ solar cells is reported. The IDTT-based acceptor achieves power conversion efficiencies of 8.4%, higher than the CDT-based acceptor (5.6%), due to concurrent increase in short-circuit current and open-circuit voltage. Using (ultra)fast transient spectroscopy we demonstrate that reduced geminate recombination in PCE10: IDTTBM blends is the reason for the difference in short-circuit currents. External quantum efficiency measurements indicate that the higher energy of interfacial charge-transfer states observed for the IDTT-based acceptor blends is the origin of the higher open-circuit voltage. In the second part of this thesis, I report the impact of acceptor side chains on the photo-physical processes of BHJ solar cells using three different IDT-based acceptors, namely O-IDTBR, EH-IDTBR and O-IDTBCN blended with PCE10. Power conversion efficiencies as high as 10 % were achieved. The transient absorption spectroscopy experiments provide insight into sub-picosecond exciton dissociation and charge generation which is followed by nanosecond triplet state formation in PCE10:O-DTBR and PCE10:EH-IDTBR blends, while in O-IDTBCN triplets are not observed. Time delayed collection field experiments (TDCF) were performed to address the charge carrier generation and examine its dependence on the electric field.
  • Development of bismuth (oxy)sulfide-based materials for photocatalytic applications

    BaQais, Amal (2019-01-07)
    Technologies based on alternative and sustainable energy sources present a vital solution in the present and for the future. These technologies are strongly driven by the increased global energy demand and need to reduce environmental issues created by fossil fuel. Solar energy is an abundant, clean and free-access resource, but it requires harvesting and storage for a sustainable future. Direct conversion and storage of solar energy using heterogeneous photocatalysts have been identified as parts of a promising paradigm for generating green fuels from sunlight and water. This thesis focused on developing semiconductor absorbers in a visible light region for photocatalytic hydrogen production reaction. In addition, theoretical studies are combined with experimental results for a deep understanding of the intrinsic optoelectronic properties of the obtained materials. The study presents a novel family of oxysulfide BiAgOS, produced by applying a full substitution strategy of Cu by Ag in BiCuOS. I was interested to address how the total substitution of Cu by Ag in a BiCuOS system affects its crystal structure, optical and electronic properties using experimental characterizations and theoretical calculations. Single-phase bismuth silver oxysulfide BiAgOS was prepared via a hydrothermal method. Rietveld refinement of the powder confirmed that BiAgOS is an isostructural BiCuOS. The diffraction peak positions of BiAgOS, relative to those of BiCuOS, were shifted toward lower angles, indicating an increase in the cell parameters. BiCuOS and BiAgOS were found to have indirect bandgaps of 1.1 and 1.5 eV, respectively. The difference in the bandgap results from the difference in the valence band compositions. The hybrid level of the S and Ag orbitals in BiAgOS is located at a more positive potential than that of S and Cu, leading to a widened bandgap. Both materials possess high dielectric constants and low electron and hole effective masses, making them interesting for photoconversion applications. BiAgOS has a potential for photocatalytic hydrogen evolution reaction in the presence of sacrificial reagents; however, it is inactive toward water oxidation. BiCuOS and BiAgOS can be considered interesting starting compositions for the development of new semiconductors for PV or Z-scheme photocatalytic applications. The second study investigates the synthesis and characterization of NaBiS2, this contains Bi3+, which belongs to the p-block electronic configuration Bi3+ 6s26p0, and NaLaS2, which contains La3+ with electronic configuration 6s05d0. Solid-state reactions from oxide precursor starting materials were applied for synthesis the materials. The sulfurization process was conducted by pressurizing a saturated vapor of CS2. The obtained black material of NaBiS2 has an indirect transition with high absorption coefficients in the visible region of the spectrum and the absorption edge is determined at 1.21 eV. However, NaBiS2 did not show photocatalytic activity toward hydrogen production. NaLaS2 is characterized by an indirect transition with a bandgap in the UV region at 3.15 eV and can drive the photocatalytic hydrogen evolution reaction in Na2S/Na2SO3 solution. Utilizing the solid solution NaLa1-xBixS2 strategy, the absorption properties and band edge position for photocatalytic hydrogen evolution reaction were optimized. The results indicated that the bismuth content is critical parameter for maintaining the photocatalytic activity. The incorporation of low Bi content up to 6% in NaLaS2 leads to extending the photon absorption from the UV to the visible region and enhancing the photocatalytic activity of hydrogen production. In contrast, all the solid solutions that have Bi content of more than 12% present absorption edges close to that of pure NaBiS2, and they are inactive for photocatalytic hydrogen production. Combining the experimental measurements with density functional theory calculations, such behavior can be explained by the degree of overlapping of Bi and La states on the conduction band minimum (CBM). Finally, self-assembly of Bi2S3 nanorods were grown on FG or FTO substrates. Bi2S3 thin films were prepared by sulfurization of Bi metal layer using the hydrothermal method. The results show that Bi2S3 has absorption up to 1.3 eV and has a moderate absorption coefficient in the visible region. The ultraviolet photoelectron spectroscopy and photoelectron spectroscopy in air results showed that the conduction band minimum of Bi2S3 is located slightly above the hydrogen redox potential. However, Pt/Bi2S3 did not evolve a detectable amount of hydrogen, suggesting the presence of surface states that can hinder the hydrogen reduction reaction.
  • Communication Reducing Approaches and Shared-Memory Optimizations for the Hierarchical Fast Multipole Method on Distributed and Many-core Systems

    Abduljabbar, Mustafa (2018-12-06)
    We present algorithms and implementations that overcome obstacles in the migration of the Fast Multipole Method (FMM), one of the most important algorithms in computational science and engineering, to exascale computing. Emerging architectural approaches to exascale computing are all characterized by data movement rates that are slow relative to the demand of aggregate floating point capability, resulting in performance that is bandwidth limited. Practical parallel applications of FMM are impeded in their scaling by irregularity of domains and dominance of collective tree communication, which is known not to scale well. We introduce novel ideas that improve partitioning of the N-body problem with boundary distribution through a sampling-based mechanism that hybridizes two well-known partitioning techniques, Hashed Octree (HOT) and Orthogonal Recursive Bisection (ORB). To reduce communication cost, we employ two methodologies. First, we directly utilize features available in parallel runtime systems to enable asynchronous computing and overlap it with communication. Second, we present Hierarchical Sparse Data Exchange (HSDX), a new all-to-all algorithm that inherently relieves communication by relaying sparse data in a few steps of neighbor exchanges. HSDX exhibits superior scalability and improves relative performance compared to the default MPI alltoall and other relevant literature implementations. We test this algorithm alongside others on a Cray XC40 tightly coupled with the Aries network and on Intel Many Integrated Core Architecture (MIC) represented by Intel Knights Corner (KNC) and Intel Knights Landing (KNL) as modern shared-memory CPU environments. Tests include comparisons of thoroughly tuned handwritten versus auto-vectorization of FMM Particle-to-Particle (P2P) and Multipole-to-Local (M2L) kernels. Scalability of task-based parallelism is assessed with FMM’s tree traversal kernel using different threading libraries. The MIC tests show large performance gains after adopting the prescribed techniques, which are inevitable in a world that is moving towards many-core parallelism.
  • Spatio-Temporal Data Analysis by Transformed Gaussian Processes

    Yan, Yuan (2018-12-06)
    In the analysis of spatio-temporal data, statistical inference based on the Gaussian assumption is ubiquitous due to its many attractive properties. However, data collected from different fields of science rarely meet the assumption of Gaussianity. One option is to apply a monotonic transformation to the data such that the transformed data have a distribution that is close to Gaussian. In this thesis, we focus on a flexible two-parameter family of transformations, the Tukey g-and-h (TGH) transformation. This family has the desirable properties that the two parameters g ∈ R and h ≥ 0 involved control skewness and tail-heaviness of the distribution, respectively. Applying the TGH transformation to a standard normal distribution results in the univariate TGH distribution. Extensions to the multivariate case and to a spatial process were developed recently. In this thesis, motivated by the need to exploit wind as renewable energy, we tackle the challenges of modeling big spatio-temporal data that are non-Gaussian by applying the TGH transformation to different types of Gaussian processes: spatial (random field), temporal (time series), spatio-temporal, and their multivariate extensions. We explore various aspects of spatio-temporal data modeling techniques using transformed Gaussian processes with the TGH transformation. First, we use the TGH transformation to generate non-Gaussian spatial data with the Matérn covariance function, and study the effect of non-Gaussianity on Gaussian likelihood inference for the parameters in the Matérn covariance via a sophisticatedly designed simulation study. Second, we build two autoregressive time series models using the TGH transformation. One model is applied to a dataset of observational wind speeds and shows advantaged in accurate forecasting; the other model is used to fit wind speed data from a climate model on gridded locations covering Saudi Arabia and to Gaussianize the data for each location. Third, we develop a parsimonious spatio-temporal model for time series data on a spatial grid and utilize the aforementioned Gaussianized climate model wind speed data to fit the latent Gaussian spatio-temporal process. Finally, we discuss issues under a unified framework of modeling multivariate trans-Gaussian processes and adopt one of the TGH autoregressive models to build a stochastic generator for global wind speed.
  • Molybdenum Disulfide as an Efficient Catalyst for Hydrogen Evolution Reaction

    Alarawi, Abeer A. (2018-12-02)
    Hydrogen is a carrier energy gas that can be utilized as a clean energy source instead of oil and natural gas. Splitting the water into hydrogen and oxygen is one of the most favorable methods to generate hydrogen. The catalytic properties of molybdenum disulfide (MoS2) could be valuable in this role, particularly due to its unique structure and ability to be chemically modified, enabling its catalytic activity to be further enhanced or made comparable to that of Pt-based materials. In general, these modification strategies may involve either structural engineering of MoS2 or enhancing the kinetics of charge transfer, including by confining to single metal atoms and clusters or integrating with a conductive substrate. We present the results of synergetic integration of MoS2 films with a Si-heterojunction solar cell for generating H2 via the photochemical water splitting approach. The results of the photochemical measurements demonstrated an efficient photocurrent of 36. 3 mA cm-2 at 0 V vs. RHE and an onset potential of 0.56 V vs. RHE. In addition to 25 hours of continuous photon conversion to H2 generation, this study points out that the integration of the Si-HJ with MoS2 is an effective strategy for enhancing the internal conductivity of MoS2 towards efficient and stable hydrogen production. Moreover, we studied the effect of doping an atomic scale of Pt on the catalytic activity of MoS2. The electrochemical results indicated that the optimum single Pt atoms loading amount demonstrated a distinct enhancement in the hydrogen generating, in which the overpotential was minimized to -0.0505 V to reach a current density of 10 mA cm−2 using only 10 ALD cycles of Pt. The Tafel slopes of the ALD Pt/ML-MoS2 electrodes were in the range of 55–120 mV/decade, which indicates a fast improvement in the HER velocity as a result of the increased potential. Stability is another important parameter for evaluating a catalyst. The same (10 ALD cycles) Pt/ML-MoS2 electrode was able to continuously generate hydrogen molecules at for 150 hours. These superior results demonstrate that the low conductivity of semiconductive MoS2 can be enhanced by anchoring the film with Pt SAs and clusters, leading to sufficient charge transport and a decrease in the overpotential.
  • Unravelling the Metabolic Interactions of the Aiptasia-Symbiodiniaceae Symbiosis

    Cui, Guoxin (2018-12)
    Many omics-level studies have been undertaken on Aiptasia, however, our understanding of the genes and processes associated with symbiosis regulation and maintenance is still limited. To gain deeper insights into the molecular processes underlying this association, we investigated this relationship using multipronged approaches combining next generation sequencing with metabolomics and immunohistochemistry. We identified 731 high-confident symbiosis-associated genes using meta-analysis. Coupled with metabolomic profiling, we exposed that symbiont-derived carbon enables host recycling of ammonium into nonessential amino acids, which may serve as a regulatory mechanism to control symbiont growth through a carbon-dependent negative feedback of nitrogen availability to the symbiont. We then characterized two symbiosis-associated ammonium transporters (AMTs). Both of the proteins exhibit gastrodermis-specific localization in symbiotic anemones. Their tissuespecific localization consistent with the higher ammonium assimilation rate in gastrodermis of symbiotic Aiptasia as shown by 15N labeling and nanoscale secondary ion mass spectrometry (NanoSIMS). Inspired by the tissue-specific localization of AMTs, we investigated spatial expression of genes in Aiptasia. Our results suggested that symbiosis with Symbiodiniaceae is the main driver for transcriptional changes in Aiptasia. We focused on the phagosome-associated genes and identified several key factors involved in phagocytosis and the formation of symbiosome. Our study provided the first insights into the tissue specific complexity of gene expression in Aiptasia. To investigate symbiosis-induced response in symbiont and to find further evidence for the hypotheses generated from our host-focused analyses, we explored the growth and gene expression changes of Symbiodiniaceae in response to the limitations of three essential nutrients: nitrogen, phosphate, and iron, respectively. Comparisons of the expression patterns of in hospite Symbiodiniaceae to these nutrient limiting conditions showed a strong and significant correlation of gene expression profiles to the nitrogen-limited culture condition. This confirmed the nitrogen-limited growing condition of Symbiodiniaceae in hospite, and further supported our hypothesis that the host limits the availability of nitrogen, possibly to regulate symbiont cell density. In summary, we investigated different molecular aspects of symbiosis from both the host’s and symbiont’s perspective. This dissertation provides novel insights into the function of nitrogen, and the potential underlying molecular mechanisms, in the metabolic interactions between Aiptasia and Symbiodiniaceae.
  • Using single molecule fluorescence to study substrate recognition by a structure-specific 5’ nuclease

    Rashid, Fahad (2018-12)
    Nucleases are integral to all DNA processing pathways. The exact nature of substrate recognition and enzymatic specificity in structure-specific nucleases that are involved in DNA replication, repair and recombination has been under intensive debate. The nucleases that rely on the contours of their substrates, such as 5’ nucleases, hold a distinctive place in this debate. How this seemingly blind recognition takes place with immense discrimination is a thought-provoking question. Pertinent to this question is the observation that even minor variations in the substrate provoke extreme catalytic variance. Increasing structural evidence from 5’ nucleases and other structure-specific nuclease families suggest a common theme of substrate recognition involving distortion of the substrate to orient it for catalysis and protein ordering to assemble active sites. Using three single-molecule (sm)FRET approaches of temporal resolution from milliseconds to sub-milliseconds, along with various supporting techniques, I decoded a highly sophisticated mechanism that show how DNA bending and protein ordering control the catalytic selectivity in the prototypic system human Flap Endonuclease 1 (FEN1). Our results are consistent with a mutual induced-fit mechanism, with the protein bending the DNA and the DNA inducing a protein-conformational change, as opposed to functional or conformational selection mechanism. Furthermore, we show that FEN1 incision on the cognate substrate occurs with high efficiency and without missed opportunity. However, when FEN1 encounters substrates that vary in their physical attributes to the cognate substrate, cleavage happens after multiple trials During the course of my work on FEN1, I found a novel photophysical phenomena of protein-induced fluorescence quenching (PIFQ) of cyanine dyes, which is the opposite phenomenon of the well-known protein-induced fluorescence enhancement (PIFE). Our observation and characterization of PIFQ led us to further investigate the general mechanism of fluorescence modulation and how the initial fluorescence state of the DNA-dye complex plays a fundamental role in setting up the stage for the subsequent modulation by protein binding. Within this paradigm, we propose that enhancement and quenching of fluorescence upon protein binding are simply two different faces of the same process. Our observations and correlations eliminate the current inconvenient arbitrary nature of fluorescence modulation experimental design.
  • Molecular Basis for p85 Dimerization and Allosteric Ligand Recognition

    Aljedani, Safia (2018-12)
    The phosphatidylinositol-3-kinase α (PI3Kα) is a heterodimeric enzyme that is composed of a p85α regulatory subunit and a p110α catalytic subunit. PI3Kα plays a critical role in cell survival, growth and differentiation, and is the most frequently mutated pathway in human cancers. The PI3Kα pathway is also targeted by many viruses, such as the human immunodeficiency virus (HIV-1), the herpes simplex virus 1 (HSV-1) or the influenza A virus, to create favourable conditions for viral replication. The regulatory p85α stabilizes the catalytic p110α, but keeps it in an inhibited state. Various ligands can bind to p85α and allosterically activate p110α, but the mechanisms are still ill-defined. Intriguingly, p85α also binds to, and activates, the PTEN phosphatase, which is the antagonist of p110α. Previous studies indicated that only p85α monomers bind to the catalytic p110α subunit, whereas only p85α dimers bind to PTEN. These findings suggest that the balance of p85α monomers and dimers regulates the PI3Kα pathway, and that interrupting this equilibrium could lead to disease development. However, the molecular mechanism for p85α dimerization is controversial, and it is unknown why PTEN only binds to p85α dimers, whereas p110α only binds to p85α monomers. Here we set out to elucidate these questions, and to gain further understanding of how p85α ligands influence p85α dimerization and promote activation of p110α. We first established a comprehensive library of p85α fragments and protocols for their production and purification. By combining biophysical and structural methods such as small angle X-ray scattering, X-ray crystallography, nuclear magnetic resonance, microscale thermophoresis, and chemical crosslinking, we investigated the contributions of all p85α domains to dimerization and ligand binding. Contrarily to the prevailing thought in the field, we find that p85α dimerization and ligand recognition involves multiple domains, including those that directly bind to and inhibit p110α. This finding allows us to suggest a molecular mechanism that links p85α dimerization and allosteric p110α activation through ligands.
  • Cylindrical Magnetic Nanowires Towards Three Dimensional Data Storage

    Mohammed, Hanan (2018-12)
    The past few decades have witnessed a race towards developing smaller, faster, cheaper and ultra high capacity data storage technologies. In particular, this race has been accelerated due to the emergence of the internet, consumer electronics, big data, cloud based storage and computing technologies. The enormous increase in data is paving the path to a data capacity gap wherein more data than can be stored is generated and existing storage technologies would be unable to bridge this data gap. A novel approach could be to shift away from current two dimensional architectures and onto three dimensional architectures wherein data can be stored vertically aligned on a substrate, thereby decreasing the device footprint. This thesis explores a data storage concept based on vertically aligned cylindrical magnetic nanowires which are promising candidates due to their low fabrication cost, lack of moving parts as well as predicted high operational speed. In the proposed concept, data is stored in magnetic nanowires in the form of magnetic domains or bits which can be moved along the nanowire to write/read heads situated at the bottom/top of the nanowire using spin polarized current. Cylindrical nanowires generally exhibit a single magnetic domain state i.e. a single bit, thus for these cylindrical nanowire to exhibit high density data storage, it is crucial to pack multiple domains within a nanowire. This dissertation demonstrates that by introducing compositional variation i.e. multiple segments along the nanowire, using materials with differing values of magnetization such as cobalt and nickel, it is possible to incorporate multiple domains in a nanowire. Since the fabrication of cylindrical nanowires is a batch process, examining the properties of a single nanowire is a challenging task. This dissertation deals with the fabrication, characterization and manipulation of magnetic domains in individual nanowires. The various properties of are investigated using electrical measurements, magnetic microscopy techniques and micromagnetic simulations. In addition to packing multiple domains in a cylindrical nanowire, this dissertation reports the current assisted motion of domain walls along multisegmented Co/Ni nanowires, which is a fundamental step towards achieving a high density cylindrical nanowire-based data storage device.
  • Contributions to Computational Methods for Association Extraction from Biomedical Data: Applications to Text Mining and In Silico Toxicology

    Raies, Arwa B. (2018-11-29)
    The task of association extraction involves identifying links between different entities. Here, we make contributions to two applications related to the biomedical field. The first application is in the domain of text mining aiming at extracting associations between methylated genes and diseases from biomedical literature. Gathering such associations can benefit disease diagnosis and treatment decisions. We developed the DDMGD database to provide a comprehensive repository of information related to genes methylated in diseases, gene expression, and disease progression. Using DEMGD, a text mining system that we developed, and with an additional post-processing, we extracted ~100,000 of such associations from free-text. The accuracy of extracted associations is 82% as estimated on 2,500 hand-curated entries. The second application is in the domain of computational toxicology that aims at identifying relationships between chemical compounds and toxicity effects. Identifying toxicity effects of chemicals is a necessary step in many processes including drug design. To extract these associations, we propose using multi‐label classification (MLC) methods. These methods have not undergone comprehensive benchmarking in the domain of predictive toxicology that could help in identifying guidelines for overcoming the existing deficiencies of these methods. Therefore, we performed extensive benchmarking and analysis of ~19,000 MLC models. We demonstrated variability in the performance of these models under several conditions and determined the best performing model that achieves accuracy of 91% on an independent testing set. Finally, we propose a novel framework, LDR (learning from dense regions), for developing MLC and multi-target regression (MTR) models from datasets with missing labels. The framework is generic, so it can be applied to predict associations between samples and discrete or continuous labels. Our assessment shows that LDR performed better than the baseline approach (i.e., the binary relevance algorithm) when evaluated using four MLC and five MTR datasets. LDR achieved accuracy scores of up to 97% using testing MLC datasets, and R2 scores up to 88% for testing MTR datasets. Additionally, we developed a novel method for minority oversampling to tackle the problem of imbalanced MLC datasets. Our method improved the precision score of LDR by 10%.
  • Statistical characteristics and mapping of near-surface and elevated wind resources in the Middle East

    Yip, Chak Man Andrew (2018-11-28)
    Wind energy is expected to contribute to alleviating the rise in energy demand in the Middle East that is driven by population growth and industrial development. However, variability and intermittency in the wind resource present significant challenges to grid integration of wind energy systems. The first chapter addresses the issues in current wind resource assessment in the Middle East due to sparse meteorological observations with varying record lengths. The wind field with consistent space-time resolution for over three decades at three hub heights over the whole Arabian Peninsula is constructed using the Modern Era Retrospective-Analysis for Research and Applications (MERRA) dataset. The wind resource is assessed at a higher spatial resolution with metrics of temporal variations in the wind than in prior studies. Previously unrecognized locations of interest with high wind abundance and low variability and intermittency have been identified in this study and confirmed by recent on-site observations. The second chapter explores high-altitude wind resources that may provide alternative energy resources in this fossil-fuel-dependent region. This study identifies areas favorable to the deployment of airborne wind energy (AWE) systems in the Middle East and computes the optimal heights at which such systems would best operate. AWE potential is estimated using realistic AWE system specifications and assumptions about deployment scenarios and is compared with the near-surface wind generation potential concerning diurnal and seasonal variability. The results show the potential utility of AWE in areas in the Middle East where the energy demand is high. The third chapter investigates the potential for wind energy to provide a continuous energy supply in the region. We characterize the wind power variability at various time-scales of power operations to illustrate its effects across the Middle East via spectral analysis and clustering. Using a high-resolution dataset obtained from Weather Forecasting and Research (WRF) model simulations, this study showcases how aggregate variability may impact operation, and informs the planning of large-scale wind power integration in the Middle East in light of the scarcity of observational data.
  • Mechanisms of Enhanced Thermoelectricity in Chalcogenides

    Alsaleh, Najebah (2018-11-27)
    Thermoelectric materials can provide solutions to power generation and refrigeration challenges. Layered chalchogenides are of particular interest, with bismuth telluride and lead telluride being the most common compounds. Bismuth telluride is often used for room temperature applications, while its solid solutions with antimony or selenium as well as lead tellurides show better thermoelectric properties at elevated temperatures. Regrettably, the efficiency of the known thermoelectric materials is still low. Evidently, bringing thermoelectric energy harvesting to commercial viability is a materials challenge: How can we obtain materials with figure of merit above 3? This question drives the research community since the successes of nanoengineering in the 1990s. Nowadays, high-pressure technology is a promising frontier for making further advances in thermoelectric material performance. The main goal of this thesis is to understand the electronic and thermoelectric properties of selected materials using density functional theory and semi-classical Boltzmann transport theory. Bulk and monolayer CuSbS2 and CuSbSe2 are studied to clarify the role of the interlayer coupling for the thermoelectric properties. The calculated band gaps of the bulk compounds turn out to be in agreement with experiments and significantly higher than those of the monolayers, which thus show lower Seebeck coefficients. Since also the electrical conductivity is lower, the monolayers are characterised by lower power factors. Therefore, the interlayer coupling, even though it is weak, is found to be essential for the thermoelectric response. We study Cu (Sb,Bi)(S,Se)2 under hydrostatic pressure up to 8 GPa, considering the van der Waals interaction, as these compounds have layered structures. We find an indirect band gap that decreases monotonically with increasing hydrostatic pressure. Only CuBiS2 shows an indirect-indirect band gap transition around 3 GPa, leading to conduction band convergence with a concomitant 20% increase in the Seebeck co-efficient. This enhancement results from a complex interplay between multivalley and multiband effects as well as changes of the band effective masses. The variation of the electronic band structure of AB2Te4 (A = Pb, Sn and B = Bi, Sb) under hydrostatic pressure up to 8 GPa is analyzed in detail and its consequences for the material properties are explained.
  • Proximity Mechanisms in Graphene: Insights from Density Functional Theory

    Alattas, Maha H. (2018-11-27)
    One of the challenges in graphene fabrication is the production of large scale, high quality sheets. To study a possible approach to achieve quasi-freestanding graphene on a substrate by the intercalation of alkali metal atoms, Cs intercalation between graphene and Ni(111) is investigated. It is known that direct contact between graphene and Ni(111) perturbs the Dirac states. Cs intercalation restores the linear dispersion characteristic of Dirac fermions, which agrees with experiments, but the Dirac cone is shifted to lower energy, i.e., the graphene sheet is n-doped. Cs decouples the graphene sheet, while the spin polarization of Ni(111) does not extend through the intercalated atoms to the graphene sheet, for which we find virtually spin-degeneracy. In order to employ graphene in electronic applications, one requires a finite band gap. We engineer a band gap in metallic bilayer graphene by substitutional B and/or N doping. Specifically, the introduction of B-N pairs into bilayer graphene can be used to create a band gap that is stable against thermal fluctuations at room temperature. Introduction of B-N pairs into B and/or N doped bilayer graphene likewise hardly modifies the band dispersions, however, the size of the band gap is effectively tuned. We also study the influence of terrace edges on the electronic properties of graphene, considering bare edges and H, F, Cl, NH2 terminations. Periodic structural reconstruction is observed for the Cl and NH2 edge terminations due to interaction between the terminating atoms/groups. We observe that Cl edge termination p-dopes the terraces, while NH2 edge termination results in n-doping.
  • Towards Rational Design of Biosynthesis Pathways

    Alazmi, Meshari (2018-11-19)
    Recent advances in genome editing and metabolic engineering enabled a precise construction of de novo biosynthesis pathways for high-value natural products. One important design decision to make for the engineering of heterologous biosynthesis systems is concerned with which foreign metabolic genes to introduce into a given host organism. Although this decision must be made based on multifaceted factors, a major one is the suitability of pathways for the endogenous metabolism of a host organism, in part because the efficacy of heterologous biosynthesis is affected by competing endogenous pathways. To address this point, we developed an open-access web server called MRE (metabolic route explorer) that systematically searches for promising heterologous pathways by considering competing endogenous reactions in a given host organism. MRE utilizes reaction Gibbs free energy information. However, 25% of the reactions do not have accurate estimations or cannot be estimated. To address this issue, we developed a method called FC (fingerprint contribution) to provide a more accurate and complete estimation of the reaction free energy. To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. For a given pair of starting and desired compounds in a given chassis organism, MRE ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/. Accurate and wide-ranging prediction of thermodynamic parameters for biochemical reactions can facilitate deeper insights into the workings and the design of metabolic systems. Here, we introduce a machine learning method, referred to as fingerprint contribution (FC), with chemical fingerprint-based features for the prediction of the Gibbs free energy of biochemical reactions. From a large pool of 2D fingerprint-based features, this method systematically selects a small number of relevant ones and uses them to construct a regularized linear model. FC is freely available for download at http://sfb.kaust.edu.sa/Pages/Software.aspx.
  • Multilayer Dielectrics and Semiconductor Channels for Thin Film Transistor Applications

    Alshammari, Fwzah (2018-11-13)
    Emerging transparent conducting and semiconducting oxide (TCO) and (TSO) materials have achieved success in display markets. Due to their excellent electrical performance, TSOs have been chosen to enhance the performance of traditional displays and to evaluate their application in future transparent and flexible displays. This dissertation is devoted to the study ZnO-based thin film transistors (TFTs) using multilayer dielectrics and channel layers. Using multilayers to engineer transistor parameters is a new approach. By changing the thickness, composition, and sequence of the layers, transistor performance can be optimized. In one example, Al2O3/Ta2O5 bilayer gate dielectrics, grown by atomic layer deposition at low temperature were developed. The approach combined high dielectric constant of Ta2O5 and the excellent interface quality of Al2O3/ZnO, resulting in enhanced device performance. Using zinc oxide (ZnO)/hafnium oxide (HfO2) multilayer stack as a TFT channel with tunable layer thicknesses resulted in significant improvement in TFT stability. Atomic layer deposited SnO2 was developed as a gate electrode to replace ITO in thin film transistors and circuits. The SnO2 films deposited at 200 °C show low electrical resistivity of ~3.1×10-3 Ohm-cm with the high transparency of ~93%. TFT fabricated with SnO2 gate show excellent transistor properties. Using results from the above experiments, we have developed a novel process in which thin film transistors (TFTs) are fabricated using one binary oxide for all transistor layers (gate, source/drain, semiconductor channel, and dielectric). In our new process, by simply changing the flow ratio of two chemical precursors, C8H24HfN4 and (C2H5)2Zn, in an ALD system, the electronic properties of the binary oxide HZO were controlled from conducting, to semiconducting, to insulating. A complete study of HZO thin films deposited by (ALD) was performed. The use of the multi-layer (HfO2/ZnO) channel layer plays a key role in improving the bias stability of the devices. The low processing temperature of all materials at 160 °C is an advantage for the fabrication of fully transparent and flexible devices. After precise device engineering, including growth temperature, gate dielectric, electrodes (S/D&G) and semiconductor thickness, TFT with excellent device performance are obtained.
  • Statistical Analysis and Bayesian Methods for Fatigue Life Prediction and Inverse Problems in Linear Time Dependent PDEs with Uncertainties

    Sawlan, Zaid A (2018-11-10)
    This work employs statistical and Bayesian techniques to analyze mathematical forward models with several sources of uncertainty. The forward models usually arise from phenomenological and physical phenomena and are expressed through regression-based models or partial differential equations (PDEs) associated with uncertain parameters and input data. One of the critical challenges in real-world applications is to quantify uncertainties of the unknown parameters using observations. To this purpose, methods based on the likelihood function, and Bayesian techniques constitute the two main statistical inferential approaches considered here. Two problems are studied in this thesis. The first problem is the prediction of fatigue life of metallic specimens. The second part is related to inverse problems in linear PDEs. Both problems require the inference of unknown parameters given certain measurements. We first estimate the parameters by means of the maximum likelihood approach. Next, we seek a more comprehensive Bayesian inference using analytical asymptotic approximations or computational techniques. In the fatigue life prediction, there are several plausible probabilistic stress-lifetime (S-N) models. These models are calibrated given uniaxial fatigue experiments. To generate accurate fatigue life predictions, competing S-N models are ranked according to several classical information-based measures. A different set of predictive information criteria is then used to compare the candidate Bayesian models. Moreover, we propose a spatial stochastic model to generalize S-N models to fatigue crack initiation in general geometries. The model is based on a spatial Poisson process with an intensity function that combines the S-N curves with an averaged effective stress that is computed from the solution of the linear elasticity equations.
  • Synthesis and Characterization of Transition Metal Ion-based Hydrogels with Auxiliary Carboxylate Spacer Ligands for Selective Carbon Dioxide Separation and Other Potential Applications

    Al Dossary, Mona (2018-11)
    Metallo-supramolecular hydrogels have interesting dynamic properties for many applications. We report a simple method for synthesizing copper-based polymer hydrogels made from nontoxic poly(methyl vinyl ether-alt-maleic anhydride) (PVM-alt-MA) in the absence or presence of added dicarboxylates, such as adipate and terephthalate. We utilize metal-polycarboxylate backbone and carboxylate spacer ligands between polymers strands engineered via non-covalent metal ion coordination. Rheological measurements revealed that the mechanical stability of the hydrogels was enhanced by the addition of supplementary dicarboxylate ligands. The optimal ratio of polymer to dicarboxylate to Cu2+ was 10:4:2.5. Our scanning electron microscope (SEM) and Cryo-SEM imaging and physical adsorption measurements revealed the formation of pores. The Brunauer–Emmett–Teller (BET) surface area of the dried hydrogels increased from 177.96 m2 g−1 in a dried hydrogel without added dicarboxylate to 646.90 and 536.44 m2 g−1 with the addition of adipate and terephthalate, respectively. The pore volume increased as well. Separation of CO2 from post-combustion flue gases is important for environmental and economic sustainability. The PVM-alt-Na-MA:adipate:Cu2+ hydrogels are promising material for post-combustion CO2 separation. At normal conditions (298 K and 1 bar), the PVM-alt-Na-MA:adipate:Cu2+ hydrogel samples with 10:4:2.5 ratio, showed notable CO2/N2 selectivity of 78.46 and a high CO2/CH4 selectivity reaching 26.09 at 1 bar. Additionally, we investigated in detail the effect of transition metal ion on the rigidity and structure of hydrogels using Al3+, Fe3+, Cu2+, Ni2+, Zn2+, and Co2+. We also studied the effect of using tricarboxylate spacer ligands such as nitrilotriacetic (NTA) and trisodium citrate or tetracarboxylate such as ethylenediaminetetraacetic acid (EDTA). It is important to mention that one of the main advantages of our facile synthesis method is being simple and can be scaled up for commercial applications. For scaling up the synthesis of hydrogels, we utilized a filling machine that is able to increase the amount of hydrogel aliquots with variable volume. Silver-based hydrogels showed significant antibacterial activity, due to the presence of silver nanoparticles. We utilized a filling machine for application of amorphous wound dressing. The optimization of the conditions of the filling enabled us to scale up the synthesis and the filling process.
  • Synthesis of New Mixed Metal Chalcogenides: Crystal structure, Characterization and Properties Investigation

    Alahmary, Fatimah S. (2018-11)
    Metal chalcogenides are one of the most important class of compounds in the field of Inorganic Chemistry. A wide variety of chalco-anion building blocks provides excellent opportunities to synthesize new compounds with unique structure and properties, essential drives in maximizing technological impact. In this dissertation, the exploratory synthesis of new mixed-metal chalcogenide compounds is carried out. The novel phases were characterized using a wide spectrum of techniques, and their properties were investigated. The project started by investigating the synthesis of zeolite-like chalcogenides using a solid-state reaction. As a result, the thioaluminogermanate Na(AlS2)(GeS2)4 was synthesized with successful insertion of Al3+ cations into the chalcogenogermanate framework. This effectively extended the structural chemistry for this family of materials and approximated them to the aluminosilicate zeolites. The crystal structure of Na(AlS2)(GeS2)4 displayed a [(AlS2)(GeS2)4]1- 3D polyanionic framework, in which Al and Ge atoms share atomic positions and Na cations occupy the channels in-between. At room temperature and in a solvent medium, this compound exhibits a unique cation-exchange property with monovalent Ag+ and Cu+ ions, resulting in the formation of the isostructural compounds Ag(AlS2)(GeS2)4 and Cu(AlS2)(GeS2)4. The replacement of Na+ in the parent compound with Ag+ or Cu+ results in enhanced properties such as higher stability in air and narrower bandgap energies. The completeness of the ion-exchange reactions was confirmed using various analytical tools including single crystal XRD, EDX, and 23Na NMR. Following this initial success, a systematic study was carried out to synthesize unknown phases of transition and main group mixed-metal chalcogenides. As a result, the first example of an alkali/transition metal thioaluminate compound K2Cu3AlS4 was synthesized. For this, a solid-state reaction with K2S acting as a self-flux was used. The crystal structure of K2Cu3AlS4 consists of [Cu3AlS4]2- polyanionic anti-PbO type layers, in which Al and Cu atoms share the atomic positions, separated by K+ cations. The coordination environments of the Al and K cations were confirmed by solid-state 27Al and 39K NMR spectroscopies. The optical property and thermal stability of this new quaternary compound were also studied. The mixed-metal chalcogenides class is not restricted only to purely inorganic components; it can also be extended to inorganic-organic hybrid materials. In an attempt to synthesize main group chalcogenides mixed with transition metal complexes, the new compound [Ni(en)3]GeS2(OH)2•H2O was obtained. In the complex cation [Ni(en)3]2+, the ethylenediamine (en) ligands are bidentate to the Ni2+ through the N atoms resulting in a distorted octahedral geometry which is charge balanced by the rarely observed [GeS2(OH)2]2- tetrahedral anion. In agreement with single crystal data, the solid-state 1H NMR spectrum exhibits four signals corresponding to the -CH2 and NH2 protons of the (en) in addition to the H2O and -OH protons. This compound exhibits a paramagnetic response, studied by EPR spectroscopy and ZFC/FC magnetization measurements. The optical properties including UV-Vis absorption and photoluminescence emission were also measured. Knowing that it was possible to synthesize various types of mixed-metal chalcogenides, the focus was shifted to the production of those with interesting functional properties. In this way, Na2BiSbQ4 (Q = S, Se, Te) compounds were synthesized by reacting Bi and Sb in the corresponding Na2Q flux. The three phases obtained are isostructural and crystallize with NaCl-type structure. The unique feature of these structures is the existence of only one crystallographic metal site in the unit cell (where Bi, Sb and Na share the same atomic position). These mix of position sites provide the desirable lattice complexity with a totally random distribution of Na, Bi and Sb atoms. As expected, extremely low thermal conductivities at room temperature have been observed for the studied phases. The optical properties, solid-state 27Na NMR spectra, chemical and thermal stabilities are discussed.
  • Experiments on Turbulent Nonpremixed Flames at Elevated Pressures

    Boyette, Wesley (2018-11)
    Understanding reacting flows in conditions relevant to practical combustion devices is a challenging but critically important task. In such devices, combustion nearly always occurs in a turbulent flow field and at high pressure. The formation of soot is highly sensitive to these parameters. However, little research has been conducted in conditions that replicate the complex physics of such devices in simplified configurations. This body of work focuses on the development of a rig suitable for investigating turbulence-chemistry interactions in simple jet flames at high pressure and high Reynolds numbers and discusses results from the initial experiments in that rig. First, the flame structure of syngas flames at pressures up to 12 bar and at Reynolds numbers up to 83,500 is investigated using OH-PLIF. A corrugation factor is used to characterize the wrinkling of the flame fronts and PDFs of this factor show that the corrugation of the flame front is a very strong function of the Reynolds number, but in most cases, the pressure has no effect. Separations in the OH layers become less probable as the pressure increases if the Reynolds number remains constant. Next, the flame structure of nitrogen-diluted ethylene flames at pressures up to 5 bar and Reynolds numbers up to 50,000 are examined using OH-PLIF. Again, the corrugation factor is used to show that the flame fronts become more wrinkled as the Reynolds number increases. Further analysis shows that the extent of wrinkling is limited and further increases in turbulence result in more frequent breaks in the OH layer. Lastly, two soot studies on the ethylene flames are presented. The soot particle size distribution is characterized in two flames at atmospheric pressure. The time-averaged, mean particle diameter on the centerline increases as the distance from the nozzle increases. Soot volume fraction measurements are made with LII in three flames at different pressures and Reynolds numbers. Soot production is found to be much more sensitive to changes in pressure than changes in Reynolds number. Increases in the mean soot volume fraction as the pressure increases are due to higher instantaneous soot concentrations and lower soot intermittency.
  • Photo-physical Characterization of Donor-Acceptor Systems using Ultrafast Laser Spectroscopy

    Alsam, Amani A. (2018-11)
    In donor-acceptor systems, ultrafast interfacial charge transfer (CT), charge separation (CS) and charge recombination (CR), are among the key factors in determining the overall efficiency of the optoelectronic devices. In this regime, precise knowledge of the mechanisms of these processes on the femtosecond scale is urgently required. In this dissertation, using femtosecond transient absorption and mid-Infrared spectroscopies along with steady-state absorption and emission measurements, we are not only able to address the fundamental understanding of these ultrafast dynamical processes, but also control them at various inter- and intramolecular electron donor-electron acceptor systems. In the photoinduced intermolecular charge transfer systems, where donor and acceptor are separated from each other, three systems have been investigated; cationic poly[(9,9-di(3,3′-N,N′-trimethylammonium) propyl fluorenyl-2,7-diyl)-alt-co-(9,9-dioctyl-fluorenyl-2,7-diyl)] diiodide salt (PFN) conjugated polymer donor with 1,4-dicyanobenzene (DCB) acceptor, negatively charged porphyrin (POS) donor with positively charged (PFN) acceptor, and finally, positively charged (PFN) donor with negatively charged graphene carboxylate (GC) acceptor. Based on studying these three systems, we were able to explore some important factors and deriving forces including chemical structure, electrostatic interactions, energy band alignment, hydrogen bonding and solvents with different polarities and capabilities for hydrogen bonding that influence the rate and efficiency of the charge transfer at the interfaces of these donor-acceptor systems. For instance, unlike the conventional understanding of the key role of hydrogen bonding in promoting the charge-transfer process, our results reveal that the hydrogen-bonding increases the spacing between the donor and acceptor units which significantly hinders the charge-transfer process. On the other hand, in the photoinduced intramolecular charge transfer systems, where donor and acceptor are chemically attached to each other, we investigate the effects of conjugation length on photoinduced charge transfer in π-conjugated oligomers naphthalene diimide (NDI) end-capped oligo(phenylene ethynylene)s (PEn-NDI), and poly-(phenylene ethynylene) (PPE) donor backbone with (NDI) acceptor end-caps (PPE-NDI-n) systems. The results of femtosecond transient absorption and mid-IR spectroscopies show that the charge separation occurs on the 1-10 ps time scale with the rates decreasing as oligomer length increases in PEn-NDI system. In addition, in PPE-NDI-n system, the fluorescence quenching measurements indicate very efficient photoinduced electron transfer from the PPE backbone to the NDI end-groups, and the transfer efficiency increases with decreasing the number of units. Finally, the new physical insights reported in this thesis provide an understanding of several key variable components involved, thus paving the way toward the exploitation of efficient charge transfer at donor-acceptor interfaces, which is the key element and urgently required for optimal optoelectronic-device performance.

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