Recent Submissions

  • Decision and Inhibitory Trees for Decision Tables with Many-Valued Decisions

    Azad, Mohammad (2018-06-06)
    Decision trees are one of the most commonly used tools in decision analysis, knowledge representation, machine learning, etc., for its simplicity and interpretability. We consider an extension of dynamic programming approach to process the whole set of decision trees for the given decision table which was previously only attainable by brute-force algorithms. We study decision tables with many-valued decisions (each row may contain multiple decisions) because they are more reasonable models of data in many cases. To address this problem in a broad sense, we consider not only decision trees but also inhibitory trees where terminal nodes are labeled with “̸= decision”. Inhibitory trees can sometimes describe more knowledge from datasets than decision trees. As for cost functions, we consider depth or average depth to minimize time complexity of trees, and the number of nodes or the number of the terminal, or nonterminal nodes to minimize the space complexity of trees. We investigate the multi-stage optimization of trees relative to some cost functions, and also the possibility to describe the whole set of strictly optimal trees. Furthermore, we study the bi-criteria optimization cost vs. cost and cost vs. uncertainty for decision trees, and cost vs. cost and cost vs. completeness for inhibitory trees. The most interesting application of the developed technique is the creation of multi-pruning and restricted multi-pruning approaches which are useful for knowledge representation and prediction. The experimental results show that decision trees constructed by these approaches can often outperform the decision trees constructed by the CART algorithm. Another application includes the comparison of 12 greedy heuristics for single- and bi-criteria optimization (cost vs. cost) of trees. We also study the three approaches (decision tables with many-valued decisions, decision tables with most common decisions, and decision tables with generalized decisions) to handle inconsistency of decision tables. We also analyze the time complexity of decision and inhibitory trees over arbitrary sets of attributes represented by information systems in the frameworks of local (when we can use in trees only attributes from problem description) and global (when we can use in trees arbitrary attributes from the information system) approaches.
  • Numerical Computation of Detonation Stability

    Kabanov, Dmitry (2018-06-03)
    Detonation is a supersonic mode of combustion that is modeled by a system of conservation laws of compressible fluid mechanics coupled with the equations describing thermodynamic and chemical properties of the fluid. Mathematically, these governing equations admit steady-state travelling-wave solutions consisting of a leading shock wave followed by a reaction zone. However, such solutions are often unstable to perturbations and rarely observed in laboratory experiments. The goal of this work is to study the stability of travelling-wave solutions of detonation models by the following novel approach. We linearize the governing equations about a base travelling-wave solution and solve the resultant linearized problem using high-order numerical methods. The results of these computations are postprocessed using dynamic mode decomposition to extract growth rates and frequencies of the perturbations and predict stability of travelling-wave solutions to infinitesimal perturbations. We apply this approach to two models based on the reactive Euler equations for perfect gases. For the first model with a one-step reaction mechanism, we find agreement of our results with the results of normal-mode analysis. For the second model with a two-step mechanism, we find that both types of admissible travelling-wave solutions exhibit the same stability spectra. Then we investigate the Fickett’s detonation analogue coupled with a particular reaction-rate expression. In addition to the linear stability analysis of this model, we demonstrate that it exhibits rich nonlinear dynamics with multiple bifurcations and chaotic behavior.
  • Exploiting Data Sparsity In Covariance Matrix Computations on Heterogeneous Systems

    Charara, Ali (2018-05-24)
    Covariance matrices are ubiquitous in computational sciences, typically describing the correlation of elements of large multivariate spatial data sets. For example, covari- ance matrices are employed in climate/weather modeling for the maximum likelihood estimation to improve prediction, as well as in computational ground-based astronomy to enhance the observed image quality by filtering out noise produced by the adap- tive optics instruments and atmospheric turbulence. The structure of these covariance matrices is dense, symmetric, positive-definite, and often data-sparse, therefore, hier- archically of low-rank. This thesis investigates the performance limit of dense matrix computations (e.g., Cholesky factorization) on covariance matrix problems as the number of unknowns grows, and in the context of the aforementioned applications. We employ recursive formulations of some of the basic linear algebra subroutines (BLAS) to accelerate the covariance matrix computation further, while reducing data traffic across the memory subsystems layers. However, dealing with large data sets (i.e., covariance matrices of billions in size) can rapidly become prohibitive in memory footprint and algorithmic complexity. Most importantly, this thesis investigates the tile low-rank data format (TLR), a new compressed data structure and layout, which is valuable in exploiting data sparsity by approximating the operator. The TLR com- pressed data structure allows approximating the original problem up to user-defined numerical accuracy. This comes at the expense of dealing with tasks with much lower arithmetic intensities than traditional dense computations. In fact, this thesis con- solidates the two trends of dense and data-sparse linear algebra for HPC. Not only does the thesis leverage recursive formulations for dense Cholesky-based matrix al- gorithms, but it also implements a novel TLR-Cholesky factorization using batched linear algebra operations to increase hardware occupancy and reduce the overhead of the API. Performance reported of the dense and TLR-Cholesky shows many-fold speedups against state-of-the-art implementations on various systems equipped with GPUs. Additionally, the TLR implementation gives the user flexibility to select the desired accuracy. This trade-off between performance and accuracy is, currently, a well-established leading trend in the convergence of the third and fourth paradigm, i.e., HPC and Big Data, when moving forward with exascale software roadmap.
  • Optical and Temporal Carrier Dynamics Investigations of III-Nitrides for Semiconductor Lighting

    Ajia, Idris A. (2018-05-22)
    III-nitride semiconductors suffer significant efficiency limitations; ‘efficiency’ being an umbrella term that covers an extensive list of challenges that must be overcome if they are to fulfil their vast potential. To this end, it is imperative to understand the underlying phenomena behind such limitations. In this dissertation, I combine powerful optical and structural characterization techniques to investigate the effect of different defects on the carrier dynamics in III-nitride materials for light emitting devices. The results presented herein will enhance the current understanding of the carrier mechanisms in such devices, which will lead to device efficiency improvements. In the first part of this dissertation, the effects of some important types of crystal defects present in III-nitride structures are investigated. Here, two types of defects are studied in two different III-nitride-based light emitting structures. The first defects of interest are V-pit defects in InGaN/GaN multiple quantum well (MQW) blue LEDs, where their contribution to the high-efficiency of such LEDs is discussed. In addition, the effect of these defects on the efficiency droop phenomenon in these LEDs is elucidated. Secondly, the optical effects of grain boundary defects in AlN-rich AlGaN/AlGaN MQWs is studied. In this study, it is shown that grain boundary defects may result in abnormal carrier localization behavior in these deep ultraviolet (UV) structures. While both defects are treated individually, it is evident from these studies that threading dislocation (TD) defects are an underlying contributor to the more undesirable outcomes of the said defects. In the second part, the dissertation reports on the carrier dynamics of III-nitride LED structures grown on emerging substrates—as possible efficiency enhancing techniques—aimed at mitigating the effects of TD defects. Thus, the carrier dynamics of GaN/AlGaN UV MQWs grown, for the first time, on (2̅01) – oriented β-Ga2O3 is studied. It is shown to be a candidate substrate for highly efficient vertical UV devices. Finally, results from the carrier dynamics investigation of an AlGaN/AlGaN MQW LED structure homoepitaxially grown on AlN substrate are discussed, where it is shown that its high-efficiency is sustained at high temperatures through the thermal redistribution of carriers to highly efficient recombination sites.
  • A Study of Schrödinger–Type Equations Appearing in Bohmian Mechanics and in the Theory of Bose–Einstein Condensates

    Sierra Nunez, Jesus Alfredo (2018-05-16)
    The Schrödinger equations have had a profound impact on a wide range of fields of modern science, including quantum mechanics, superfluidity, geometrical optics, Bose-Einstein condensates, and the analysis of dispersive phenomena in the theory of PDE. The main purpose of this thesis is to explore two Schrödinger-type equations appearing in the so-called Bohmian formulation of quantum mechanics and in the study of exciton-polariton condensates. For the first topic, the linear Schrödinger equation is the starting point in the formulation of a phase-space model proposed in [1] for the Bohmian interpretation of quantum mechanics. We analyze this model, a nonlinear Vlasov-type equation, as a Hamiltonian system defined on an appropriate Poisson manifold built on Wasserstein spaces, the aim being to establish its existence theory. For this purpose, we employ results from the theory of PDE, optimal transportation, differential geometry and algebraic topology. The second topic of the thesis is the study of a nonlinear Schrödinger equation, called the complex Gross-Pitaevskii equation, appearing in the context of Bose-Einstein condensation of exciton-polaritons. This model can be roughly described as a driven-damped Gross-Pitaevskii equation which shares some similarities with the complex Ginzburg-Landau equation. The difficulties in the analysis of this equation stem from the fact that, unlike the complex Ginzburg-Landau equation, the complex Gross-Pitaevskii equation does not include a viscous dissipation term. Our approach to this equation will be in the framework of numerical computations, using two main tools: collocation methods and numerical continuation for the stationary solutions and a time-splitting spectral method for the dynamics. After performing a linear stability analysis on the computed stationary solutions, we are led to postulate the existence of radially symmetric stationary ground state solutions only for certain values of the parameters in the equation; these parameters represent the “strength” of the driving and damping terms. Moreover, numerical continuation allows us to show, for fixed parameters, the ground and some of the excited state solutions of this equation. Finally, for the values of the parameters that do not produce a stable radially symmetric solution, our dynamical computations show the emergence of rotating vortex lattices.
  • Linear Analyses of Magnetohydrodynamic Richtmyer-Meshkov Instability in Cylindrical Geometry

    Bakhsh, Abeer (2018-05-13)
    We investigate the Richtmyer-Meshkov instability (RMI) that occurs when an incident shock impulsively accelerates the interface between two different fluids. RMI is important in many technological applications such as Inertial Confinement Fusion (ICF) and astrophysical phenomena such as supernovae. We consider RMI in the presence of the magnetic field in converging geometry through both simulations and analytical means in the framework of ideal magnetohydrodynamics (MHD). In this thesis, we perform linear stability analyses via simulations in the cylindrical geometry, which is of relevance to ICF. In converging geometry, RMI is usually followed by the Rayleigh-Taylor instability (RTI). We show that the presence of a magnetic field suppresses the instabilities. We study the influence of the strength of the magnetic field, perturbation wavenumbers and other relevant parameters on the evolution of the RM and RT instabilities. First, we perform linear stability simulations for a single interface between two different fluids in which the magnetic field is normal to the direction of the average motion of the density interface. The suppression of the instabilities is most evident for large wavenumbers and relatively strong magnetic fields strengths. The mechanism of suppression is the transport of vorticity away from the density interface by two Alfv ́en fronts. Second, we examine the case of an azimuthal magnetic field at the density interface. The most evident suppression of the instability at the interface is for large wavenumbers and relatively strong magnetic fields strengths. After the shock interacts with the interface, the emerging vorticity breaks up into waves traveling parallel and anti-parallel to the magnetic field. The interference as these waves propagate with alternating phase causing the perturbation growth rate of the interface to oscillate in time. Finally, we propose incompressible models for MHD RMI in the presence of normal or azimuthal magnetic field. The linearized equations are solved numerically using inverse Laplace transform. The incompressible models show that the magnetic field suppresses the RMI, and the mechanism of this suppression depends on the orientation of the initially applied magnetic field. The incompressible model agrees reasonably well with compressible linear simulations.
  • Band Alignment Determination of Two-Dimensional Heterojunctions and Their Electronic Applications

    Chiu, Ming-Hui (2018-05-09)
    Two-dimensional (2D) layered materials such as MoS2 have been recognized as high on-off ratio semiconductors which are promising candidates for electronic and optoelectronic devices. In addition to the use of individual 2D materials, the accelerated field of 2D heterostructures enables even greater functionalities. Device designs differ, and they are strongly controlled by the electronic band alignment. For example, photovoltaic cells require type II heterostructures for light harvesting, and light-emitting diodes benefit from multiple quantum wells with the type I band alignment for high emission efficiency. The vertical tunneling field-effect transistor for next-generation electronics depends on nearly broken-gap band alignment for boosting its performance. To tailor these 2D layered materials toward possible future applications, the understanding of 2D heterostructure band alignment becomes critically important. In the first part of this thesis, we discuss the band alignment of 2D heterostructures. To do so, we firstly study the interlayer coupling between two dissimilar 2D materials. We conclude that a post-anneal process could enhance the interlayer coupling of as-transferred 2D heterostructures, and heterostructural stacking imposes similar symmetry changes as homostructural stacking. Later, we precisely determine the quasi particle bandgap and band alignment of the MoS2/WSe2 heterostructure by using scan tunneling microscopy/spectroscopy (STM/S) and micron-beam X-ray photoelectron spectroscopy (μ-XPS) techniques. Lastly, we prove that the band alignment of 2D heterojunctions can be accurately predicted by Anderson’s model, which has previously failed to predict conventional bulk heterostructures. In the second part of this thesis, we develop a new Chemical Vapor Deposition (CVD) method capable of precisely controlling the growth area of p- and n-type transition metal dichalcogenides (TMDCs) and further form lateral or vertical 2D heterostructures. This method also allows p- and n-type TMDCs to separately grow in a selective area in one step. In addition, we demonstrate a first bottom-up 2D complementary inverter based on hetero-TMDCs.
  • Solution-Processed Molecular Organic Solar cell: Relationship between Morphology and Device Performance

    Babics, Maxime (2018-05-09)
    In the last decade, organic photovoltaics (OPV) have gained considerable attention with a rapid improvement of power conversion efficiency (PCE) from 5% to more than 13%. At the origin of the gradual efficiency improvements are (i) the rationalization of material design and (ii) systematic optimization of film processing condition. OPV can have a key role in markets such as building-integrated photovoltaics (BIPV). The main advantages of organic solar cells are semitransparency, low weight, good performance at low light intensity, flexibility and potential low-cost module manufacture through solution processed-based technologies. In solution processed OPV, the active layer that converts photons into electric charges is a composite of two organic compounds, a donor (D) and an acceptor (A) where the best morphology is achieved via the so-called bulk heterojunction (BHJ): an interpenetrating phase-separated D-A network. Historically, research has been focused on polymer donors and guidelines about morphology and film processing have been established. However recent studies have shown that small-molecule (SM) donors can rival their polymer counterparts in performance. The advantages of SM are a defined molecular weight, the ease of purification and a good batch-to-batch reproducibility. Using this class of material the existing guidelines have to be adjusted and refined. In this dissertation, using new SM synthesized in our laboratory, solution-processed organic solar cells are fabricated in which the morphology of the active layer is controlled by thermal annealing, the use of additive or solvent vapor annealing. In-depth analyses of the morphology are correlated to charge generation, recombination and extraction inferred from device physics. In the first part of the dissertation, using a small amount of 1,8-Diiodooctane additive that acts as a plasticizer, it is found that the D-A domains do not necessarily need to be pure and that mixed domains can also result in high performing devices. In the second part of the dissertation, the effect of solvent vapor annealing, particularly effective for SM:PCBM BHJ, is discussed where excellent control of the morphology is achieved. In the last part of the dissertation, efficient organic solar cells with open circuit voltage of >1.05V are made via fine-tuning of the morphology.
  • Hyperbranched Polyethylenebased Macromolecular Architectures: Synthesis, Characterization, and Selfassembly

    Al-Sulami, Ahlam (2018-05)
    "Chain walking” catalytic polymerization CWCP is a powerful tool for the one-pot synthesis of a unique class of hyperbranched polyethylene HBPE-based macromolecules with a controllable molecular weight, topology, and composition. This dissertation focuses on new synthetic routes to prepare HBPE-based macromolecular architectures by combining the CWCP technique with ring opening polymerization ROP, atom–transfer radical polymerization ATRP, and “click” chemistry. Taking advantage of end-functionalized HBPE, and a new ethynyl-soketal star-shape agent, we were able to synthesize different types of the HBPE-based architectures including hyperbranched-on-hyperbranched core-shell nanostructure, and miktoarm-star-HBPE-based block copolymers. The first part of the dissertation provides a general introduction to the synthesis of polyethylene types with controllable structures. Well-defined polyethylene with different macromolecule architectures were synthesized either for academic or industrial purposes. In the second part, the HBPE with different topologies was synthesized by CWCP, using a α-diimine Pd (II) catalyst. The effect of the temperature and pressure on the catalyst activity and polymer properties, including branch content, molecular weight, distribution, and thermal properties were studied. Two series of samples were synthesized: a) serial samples (A) under pressures of 1, 5, and 27 atm at 5˚C, and b) serial samples (B) at temperatures of 5, 15, and 35 ˚C under 5 atm. Proton nuclear magnetic resonance spectroscopy, 1H NMR, and gel permeation chromatography, GPC, analysis were used to calculate the branching content, molecular weight, and distribution, whereas differential scanning calorimetry, DSC, was used to record the melting and glass transition temperatures as well as the degree of the crystallinity. Well-defined HBPE-based core diblock copolymers with predictable amphiphilic properties are studied in the third part of the project. Hyperbranched polyethylene-b-poly(N-isopropylacrylamide), HBPE-b-PNIPAM, and hyperbranched polyethylene-b-poly(solketal acrylate), HBPE-b-PSA, were successfully synthesized by combining CWCP and ATRP. The synthetic methodology includes the following steps; a) synthesis of multifunction hyperbranched polyethylene initiators HBPE-MI by direct copolymerization of ethylene with 2-(2-bromoisobutyryloxy)ethyl acrylate BIEA in the presence of a α-diimine Pd(II) catalyst, and b) HBPE-MI with α-bromoester groups used as initiation sites for ATRP. Proton nuclear magnetic resonance spectroscopy, 1H NMR, gel permeation chromatography,GPC, and Fourier transform infrared, FT-IR, spectroscopy, were used for determining the molecular and composition structures. Also, differential scanning calorimetry, DSC, and thermogravimetric analysis, TGA, were used to record the melting temperature and to study the thermal stability, respectively. In the fourth part, a well-defined 3-miktoarm star copolymer 3μ-HBPE(PCL)2 (HBPE: hyperbranched polyethylene, PCL: poly(ε-caprolactone) was synthesized by combining CWCP, ring opening polymerization, ROP, and “click” chemistry. The synthetic methodology includes the following steps: a) synthesis of azido-functionalized hyperbranched polyethylene HBPE-N3 by CWCP of ethylene with the α-diimine Pd(II) catalyst, followed by quenching with an excess of 4-vinylbenzyl chloride and transformation of –Cl to the azido group with sodium azide, b) synthesis of in-chain ethynyl-functionalized poly(ε-caprolactone), (PCL)2-C≡CH by ROP of ε-CL with ethynylfunctionalized solketal [3-(prop-2-yn-1-yloxy) propane-1,2-diol] as a bifunctional initiator, in the presence of P2-t-Bu phosphazene super base, and c) “clicking” HBPE-N3 and (PCL)2-C≡CH using the copper(I)-catalyzed alkyne–azide cycloaddition CuAAC. Proton nuclear magnetic resonance spectroscopy, 1H NMR, gel permeation chromatography, GPC, and Fourier transform infrared, FT-IR, spectroscopy, were used to determine the molecular and composition structures. Also, the differential scanning calorimetry, DSC, was used to record the melting point temperature. The fifth part illustrates the self-assembly behavior of the HBPE-based block copolymers of poly(N-isopropylacrylamide), NIPAM, and poly(ε-caprolactone), PCL, at room temperature in water and a petroleum ether-selective solvent for NIPAM and PCL respectively. The synthesized copolymers HBPE-b-NIPAM and 3μ-HBPE(PCL)2 revealed either core-shell nanostructure in vesicles or worms and worm-likes branches, as confirmed by combining the analysis of dynamic light scattering, DLS, transmission electron microscopy, TEM, and atomic force spectroscopy, AFM. All the findings presented in this dissertation emphasize the utility of "living" CWCP to synthesize end-functionalized HBPE, and new star-linkage HBPE-based complex architectures. The summary and future works concerning predictable properties and applications are discussed in the sixth part.
  • Thermal Limits and Thresholds of Red Sea Biota

    Chaidez, Veronica (2018-05)
    As ocean temperatures continue to rise, the effect of temperature on marine organisms becomes highly relevant. The Red Sea is the warmest sea and is rapidly warming with current surface temperatures (28 – 34 °C) already exceeding those of most tropical systems. This has major consequences for organisms that may already find themselves at their thermal limits. The aim of this project was to define the thermal limits and thresholds of certain Red Sea species. Firstly, to better understand the thermal regimes of the Red Sea, we looked at decadal trends in maximum sea surface temperature across the basin. Then, we tested the thermal capacities of Red Sea mangroves and zooplankton, two key ecological groups, by performing thermal stress experiments in the laboratory. We found that the Red Sea basin is warming faster than the global average (0.17 °C decade-1), the thermal limit of mangrove propagules is between 33 and 35 °C, and the limits among the most common zooplankton groups range from 30 to 36 °C. This project gives us a better understanding of how organisms respond to extreme temperatures and how they may be affected in a future, warmer, ocean.
  • Parameterization analysis and inversion for orthorhombic media

    Masmoudi, Nabil (2018-05)
    Accounting for azimuthal anisotropy is necessary for the processing and inversion of wide-azimuth and wide-aperture seismic data because wave speeds naturally depend on the wave propagation direction. Orthorhombic anisotropy is considered the most effective anisotropic model that approximates the azimuthal anisotropy we observe in seismic data. In the framework of full wave form inversion (FWI), the large number of parameters describing orthorhombic media exerts a considerable trade-off and increases the non-linearity of the inversion problem. Choosing a suitable parameterization for the model, and identifying which parameters in that parameterization could be well resolved, are essential to a successful inversion. In this thesis, I derive the radiation patterns for different acoustic orthorhombic parameterization. Analyzing the angular dependence of the scattering of the parameters of different parameterizations starting with the conventionally used notation, I assess the potential trade-off between the parameters and the resolution in describing the data and inverting for the parameters. In order to build practical inversion strategies, I suggest new parameters (called deviation parameters) for a new parameterization style in orthorhombic media. The novel parameters denoted ∈d, ƞd and δd are dimensionless and represent a measure of deviation between the vertical planes in orthorhombic anisotropy. The main feature of the deviation parameters consists of keeping the scattering of the vertical transversely isotropic (VTI) parameters stationary with azimuth. Using these scattering features, we can condition FWI to invert for the parameters which the data are sensitive to, at different stages, scales, and locations in the model. With this parameterization, the data are mainly sensitive to the scattering of 3 parameters (out of six that describe an acoustic orthorhombic medium): the horizontal velocity in the x1 direction, ∈1 which provides scattering mainly near the zero offset in the x1-x3 vertical plane, and ∈d, which is the ratio of the horizontal velocity squared in the x1 and x2 direction. Since, with this parameterization, the radiation pattern for the horizontal velocity is azimuth independent, we can perform an initial VTI inversion for two parameters (velocity and ∈1), then use ∈d to fit the azimuth variation in the data. This can be done at the reservoir level or any region of the model.
  • Identification and Characterization of Novel Plant Adenylate Cyclases – The Arabidopsis Thaliana Potassium Uptake Permeases

    Al-Younis, Inas (2018-05)
    Adenylyl Cyclases (ACs) catalyze the formation of the key universal second messenger adenosine 3’, 5’-cyclic monophosphate (cAMP) from adenosine 5’- triphosphate. Cyclic AMP participates in several signal transduction pathways and is present in bacteria and higher and lower eukaryotes including higher plants. Previous studies in plants have shown a role for cAMP in signal transduction during e.g. the cell cycle, elongation of the pollen tube and stimulation of protein kinase activity. More recently cAMP has been shown to play a role in stress responses. Interestingly, cAMP has also been shown to regulate ion transport in plant cells. Here we used a similar strategy that led to the discovery of the first guanylyl cyclase in plants that was based on the alignment of conserved and functionally assigned amino acids in the catalytic centre of annotated nucleotide cyclases from lower and higher eukaryotes, to identify a novel candidate ACs in Arabidopsis (Arabidopsis thaliana K+ Uptake 5 and 7). ATKUP5 and 7 are homologous to K+ uptake permeases (KUPs) from bacteria and high-affinity K+ transporters (HAKs) from fungi. The AC activity was investigated by recombinantly expressing the ATKUP5 and 7 AC domain in vitro and by complementation of an E. coli AC mutant (cyaA). Furthermore, ATKUP5 was tested for its ability to functionally complement a yeast mutant deficient in Trk1 and Trk2 high affinity potassium uptake transporters. Site-mutagenesis in the AC domain was used to test the effect of both functions in each other. Furthermore, ATKUP5 was characterized electrophysiologically in HEK-293 cells to characterize the nature of this transporter. The localization of the ATKUP5 in Arabidopsis was examined using a Green Fluorescent Protein (GFP) fusion with the ATKUP5 to determine whether ATKUP5 is expressed at the plasma or tonoplast membrane. Arabiodpsis thaliana of the wild type, overexpressing ATKUP5 and atkup5 mutant lines were used to examine phenotypic differences.
  • Estimation Methods for Infinite-Dimensional Systems Applied to the Hemodynamic Response in the Brain

    Belkhatir, Zehor (2018-05)
    Infinite-Dimensional Systems (IDSs) which have been made possible by recent advances in mathematical and computational tools can be used to model complex real phenomena. However, due to physical, economic, or stringent non-invasive constraints on real systems, the underlying characteristics for mathematical models in general (and IDSs in particular) are often missing or subject to uncertainty. Therefore, developing efficient estimation techniques to extract missing pieces of information from available measurements is essential. The human brain is an example of IDSs with severe constraints on information collection from controlled experiments and invasive sensors. Investigating the intriguing modeling potential of the brain is, in fact, the main motivation for this work. Here, we will characterize the hemodynamic behavior of the brain using functional magnetic resonance imaging data. In this regard, we propose efficient estimation methods for two classes of IDSs, namely Partial Differential Equations (PDEs) and Fractional Differential Equations (FDEs). This work is divided into two parts. The first part addresses the joint estimation problem of the state, parameters, and input for a coupled second-order hyperbolic PDE and an infinite-dimensional ordinary differential equation using sampled-in-space measurements. Two estimation techniques are proposed: a Kalman-based algorithm that relies on a reduced finite-dimensional model of the IDS, and an infinite-dimensional adaptive estimator whose convergence proof is based on the Lyapunov approach. We study and discuss the identifiability of the unknown variables for both cases. The second part contributes to the development of estimation methods for FDEs where major challenges arise in estimating fractional differentiation orders and non-smooth pointwise inputs. First, we propose a fractional high-order sliding mode observer to jointly estimate the pseudo-state and input of commensurate FDEs. Second, we propose a modulating function-based algorithm for the joint estimation of the parameters and fractional differentiation orders of non-commensurate FDEs. Sufficient conditions ensuring the local convergence of the proposed algorithm are provided. Subsequently, we extend the latter technique to estimate smooth and non-smooth pointwise inputs. The performance of the proposed estimation techniques is illustrated on a neurovascular-hemodynamic response model. However, the formulations are efficiently generic to be applied to a wide set of additional applications.
  • Versatile High-Performance Regenerated Cellulose Membranes Prepared using Trimethylsilyl Cellulose as a Precursor

    Puspasari, Tiara (2018-05)
    Cellulose has emerged as an indispensable membrane material due to its abundant availability, low cost, fascinating physiochemical properties and environment benignancy. However, it is believed that the potential of this polymer is not fully explored yet due to its insolubility in the common organic solvents, encouraging the use of derivatization-regeneration method as a viable alternative to the direct dissolution in exotic or reactive solvents. In this work, we use trimethylsilyl cellulose (TMSC), a highly soluble cellulose derivative, as a precursor for the fabrication of cellulose thin film composite membranes. TMSC is an attractive precursor to assemble thin cellulose films with good deposition behavior and film morphology; cumbersome solvents used in the one step cellulose processing are avoided. This derivative is prepared from cellulose by the known silylation reaction. The complete transformation of TMSC back into cellulose after the membrane formation is carried out by vapor-phase acid treatment, which is simple, scalable and reproducible. This process along with the initial TMSC concentration determines the membrane sieving characteristics. Unlike the typical regenerated cellulose membranes with meso- or macropores, membranes regenerated from TMSC display micropores suitable for the selective separation of nanomolecules in aqueous and organic solvent nanofiltration. The membranes introduced in this thesis represent the first polymeric membranes ever reported for highly selective separation of similarly sized small organic molecules based on charge and size differences with outstanding fluxes. Owing to its strong hydrophilic and amorphous character, the membranes also demonstrate excellent air-dehumidification performance as compared to previously reported thin film composite membranes. Moreover, the use of TMSC enables the creation of the previously unfeasible cellulose–polydimethylsiloxane (PDMS) and cellulose–polyethyleneimine (PEI) blend membranes with a good compatibility. The cellulose–PDMS membranes demonstrate attractive performance in ethanol-water pervaporation as compared to the commercial PDMS membrane, and allow nanofiltration of a wide range of solvents with different polarity. The cellulose-PEI membranes exhibit anomalous performance improvement in nanofiltration as compared to the corresponding pure membranes. This study has opened up many great opportunities for cellulose to continuously contribute to sustainable and economical membrane processes.
  • Interface Effects Enabling New Applications of Two-Dimensional Materials

    Sattar, Shahid (2018-05)
    Interface effects in two-dimensional (2D) materials play a critical role for the electronic properties and device characteristics. Here we use first-principles calculations to investigate interface effects in 2D materials enabling new applications. We first show that graphene in contact with monolayer and bilayer PtSe2 experiences weak van der Waals interaction. Analysis of the work functions and band bending at the interface reveals that graphene forms an n-type Schottky contact with monolayer PtSe2 and a p-type Schottky contact with bilayer PtSe2, whereas a small biaxial tensile strain makes the contact Ohmic in the latter case as required for transistor operation. For silicene, which is a 2D Dirac relative of graphene, structural buckling complicates the experimental synthesis and strong interaction with the substrate perturbs the characteristic linear dispersion. To remove this obstacle, we propose solid argon as a possible substrate for realizing quasi-freestanding silicene and argue that a weak van der Waals interaction and small binding energy indicate the possibility to separate silicene from the substrate. For the silicene-PtSe2 interface, we demonstrate much stronger interlayer interaction than previously reported for silicene on other semiconducting substrates. Due to the inversion symmetry breaking and proximity to PtSe2, a band gap opening and spin splittings in the valence and conduction bands of silicene are observed. It is also shown that the strong interlayer interaction can be effectively reduced by intercalating NH3 molecules between silicene and PtSe2, and a small NH3 discussion barrier makes intercalation a viable experimental approach. Silicene/germanene are categorized as key materials for the field of valleytronics due to stronger spin-orbit coupling as compared to graphene. However, no viable route exists so far to experimental realization. We propose F-doped WS2 as substrate that avoids detrimental effects and at the same time induces the required valley polarization. The behavior is explained by proximity effects on silicene/germanene due to the underlying substrate. Broken inversion symmetry in the presence of WS2 opens a substantial band gap in silicene/germanene. F doping of WS2 results in spin polarization, which, in conjunction with proximity-enhanced spin orbit coupling, creates sizable spin-valley polarization. For heterostructures of silicene and hexagonal boron nitride, we show that the stacking is fundamental for the details of the dispersion relation in the vicinity of the Fermi energy (gapped, non-gapped, linear, parabolic) despite small differences in the total energy. We also demonstrate that the tightbinding model of bilayer graphene is able to capture most of these features and we identify the limitations of the model.
  • Solution-Processed Smart Window Platforms Based on Plasmonic Electrochromics

    Abbas, Sara (2018-04-30)
    Electrochromic smart windows offer a viable route to reducing the consumption of buildings energy, which represents about 30% of the worldwide energy consumption. Smart windows are far more compelling than current static windows in that they can dynamically modulate the solar spectrum depending on climate and lighting conditions or simply to meet personal preferences. The latest generation of smart windows relies on nominally transparent metal oxide nanocrystal materials whose chromism can be electrochemically controlled using the plasmonic effect. Plasmonic electrochromic materials selectively control the near infrared (NIR) region of the solar spectrum, responsible for solar heat, without affecting the visible transparency. This is in contrast to conventional electrochromic materials which block both the visible and NIR and thus enables electrochromic devices to reduce the energy consumption of a building or a greenhouse in warm climate regions due to enhancements of both visible lighting and heat blocking. Despite this edge, this technology can benefit from important developments, including low-cost solution-based manufacturing on flexible substrates while maintaining durability and coloration efficiency, demonstration of independent control in the NIR and visible spectra, and demonstration of self-powering capabilities. This thesis is focused on developing low-temperature and all-solution processed plasmonic electrochromic devices and dual-band electrochromic devices. We demonstrate new device fabrication approaches in terms of materials and processes which enhance electrochromic performance all the while maintaining low processing temperatures. Scalable fabrication methods are used to highlight compatibility with high throughput, continuous roll-to-roll fabrication on flexible substrates. In addition, a dualband plasmonic electrochromic device was developed by combining the plasmonic layer with a conventional electrochromic ion storage layer. This enables independent control of the transmittance of NIR and visible spectra and is done without time- and energyintensive synthesis and processing methods. We have fabricated self-powered smart windows by integrating the plasmonic and dual-band devices with organic photovoltaic mini-modules and introduced static color bias with the help of photonic crystals to explore a few possibilities of multi-platform building integration.
  • Device Strategies Directed to Improving the Efficiency of Solution-Processed Organic Solar Cells

    Liang, Ru-Ze (2018-04-18)
    In the last decade, organic photovoltaics (OPVs) have been attracting much attention for their low cost, and feasibility of mass production in large-area modules. Reported power conversion efficiencies (PCE) of organic solar cells have reached more than 10%. These promising PCEs can be realized by uncovering important principles: (1) rational molecular design, (2) matching of the material energy level, (3) favorable morphology of donor-acceptor (D/A) network, (4) higher carrier mobilities, and (5) suppression of charge recombination within the bulk heterojunction (BHJ). Though these key properties are frequently stated, the relationships between these principles remain unclear, which motivates us to fill these gaps. In the beginning, we show that changing the sequence of donor and acceptor units of the benzodithiophene-core (BDT) SM donors critically impacts molecular packing and charge transport in BHJ solar cells. Moreover, we find out that by adding small amount of the external solvent additive, the domain size of the SMFQ1 become relatively smaller, resulting in the FF enhancement of ~70% and thus pushing PCE to >6.5%. To further improve the device performance, we utilize another technique of device optimization: Solvent Vapor Annealing (SVA). Compared with solvent additive, the SVA creates a solvent-saturated environment for SMs to re-arrange and crystalize, leading to PCE of >8%, with nearly-free bimolecular recombination. When the systems are shifted from fullerene acceptors to nonfullerene acceptors, using solvent additives in indacenodithiophene-core (IDT) systems significantly reduces the domain size from >500nm to <50nm and also allows the SM donors to orderly packed, rising the PCE from <1% to 4.5%. Furthermore in a similar IDT-based system, it shows unexpectedly high VOC and low energy loss, and high PCE > 6% can be reached by employing the dimethyl disulfide (DMDS) as the SVA solvent to re-organize the morphology from excessive mixing to ordered phase-separated D/A network. Lastly, taking advantage of the distinct and complementary absorption of fullerene and nonfullerene acceptors, we show that the SM ternary system successfully realizes the high PCE of 11%, good air stability, and scalable property.
  • Towards Real-Time Distributed Planning in Multi-Robot Systems

    Abdelkader, Mohamed (2018-04)
    Recently, there has been an increasing interest in robotics related to multi-robot applications. Such systems can be involved in several tasks such as collaborative search and rescue, aerial transportation, surveillance, and monitoring, to name a few. There are two possible architectures for the autonomous control of multi-robot systems. In the centralized architecture, a master controller communicates with all the robots to collect information. It uses this information to make decisions for the entire system and then sends commands to each robot. In contrast, in the distributed architecture, each robot makes its own decision independent from a central authority. While distributed architecture is a more portable solution, it comes at the expense of extensive information exchange (communication). The extensive communication between robots can result in decision delays because of which distributed architecture is often impractical for systems with strict real-time constraints, e.g. when decisions have to be taken in the order of milliseconds. In this thesis, we propose a distributed framework that strikes a balance between limited communicated information and reasonable system-wide performance while running in real-time. We implement the proposed approach in a game setting of two competing teams of drones, defenders and attackers. Defending drones execute a proposed linear program algorithm (using only onboard computing modules) to obstruct attackers from infiltrating a defense zone while having minimal local message passing. Another main contribution is that we developed a realistic simulation environment as well as lab and outdoor hardware setups of customized drones for testing the system in realistic scenarios. Our software is completely open-source and fully integrated with the well-known Robot Operating System (ROS) in hopes to make our work easily reproducible and for rapid future improvements.
  • Unearthing Bacillus endophytes from desert plants that enhance growth of Arabidopsis thaliana under abiotic stress conditions

    Bokhari, Ameerah (2018-04)
    Here, we embarked a bioprospecting project that focuses on the isolation and characterization of plant root endophytes, collected from the Thar Desert. A total of 381 endophytes were isolated and based on their 16S rRNA gene sequences, genus Bacillus (58 strains) was identified as the major taxon and only endophytes from this genus were isolated from all plant types. Of the 58 Bacillus strains, only 16 strains were selected for screening of plant growth promotion traits such as P and Zn solubilization, indole-3-acetic acid and siderophore production, and antimicrobial activity. Based on the presence of specific plant growth promotion traits 10 strains were shortlisted for further in vitro screening with A. thaliana; to confirm that these bacteria can confer resilience to plants under salt stress conditions. B. circulans (PK3-15 and PK3-109), B. cereus (PK6-15) B. subtilis (PK3-9) and B. licheniformis (PK5-26) displayed the ability to increased the fresh weight of A. thaliana under salt stress conditions by more than 50 % compared to the uninoculated control. An interesting observation was that B. circulans (PK3-109) (shown to produce IAA exopolysaccharide) and B. circulans (PK3-138) (shown to produce IAA) in vitro results were substantially different as B. circulans (PK3-138) decreased the total fresh weight of A. thaliana by 47 %, whilst B. circulans (PK3-109) was one of the best performing strains. Thus, the genomes of these two strains were sequences to unravel the molecular versatility of B. circulans strains, specifically with respect to their interaction with plants. Most of the genome of these strains is identical but the most interesting feature was the presence of 1/ the DegS–DegU two-component system that is known to mediate the salt stress response and DegU also represses toxin wapA similar to antitoxin wapI, and 2/ YxiG, a gene in the unique orthogroup of PK3-109 was found to be linked to WapI. Thus, PK3-138 substantially decreasing the total fresh weight of A. thaliana under salt stress conditions suggests that the toxic activity of a toxin such as WapA is not effectively ameliorated by the antitoxin such as WapI in the absence of a functional YxiG gene.
  • Investigating the Role of the Arabidopsis Homologue of the Human G3BP in RNA Metabolism, Cellular Stress Responses and Innate Immunity

    Abulfaraj, Aala A. (2018-04)
    Mitogen-activated protein kinases (MAPKs) belong to the most conserved signaling pathways and are found in all eukaryotes, including humans where they play important roles in various diseases and cancer. Stimulation of this signal transduction pathway by microbe-associated molecular patterns (MAMP) results in a multitude of events to regulate innate immune responses in Arabidopsis thaliana stimulating large-scale changes in gene expression. Starting from a phosphoproteomic screen in Arabidopsis thaliana wild type and mpk3, mpk4 and mpk6 mutants following microbe-associated molecular pattern (MAMP) treatment, several novel chromatin-associated proteins were identified that are differentially phosphorylated by stress-induced protein kinases. Arabidopsis Ras GTPase-activating protein SH3-domain-binding protein (AtG3BP-1) is a downstream putative substrate of the MAMP-stimulated MAPK pathway that is phosphorylated by MPK3, 4 and 6 in in vitro kinase assays. AtG3BP1 belongs to a highly conserved family of RNA-binding proteins in eukaryotes that link kinase receptormediated signaling to RNA metabolism. Here, we report the characterization of the Arabidopsis homolog of human G3BP1 in plant innate immunity. AtG3BP1 negatively regulates plant immunity and defense immune responses. Atg3bp1 mutant lines show constitutive stomata closure, expression of a number of key defense marker genes, and accumulate salicylic acid but not jasmonic acid. Furthermore, Atg3bp1 plants exhibit enhanced resistance to the biotrophic pathogen Pseudomonas syringae pv. tomato. Pathogen resistance was mediated by stomatal and apoplastic immunity in Atg3bp1. More generally, our data reinforce that AtG3BP1 is a key mediator of plant defense responses and transient expression of AtG3BP1 delivered striking disease resistance in the absence of yield penalty, highlighting a potential application of this gene in crop protection.

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