VictorJuiz/thesis huggingface dataset:
Magnetic Resonance Investigations of Adsorbate Dynamics in Metal-Organic Frameworks

Metal-organic frameworks (MOFs), a new class of porous materials, are crystalline networks of metal clusters or ions connected by organic linkers through coordination bonds. These frameworks exhibit a rich diversity of structures, chemistries, and topologies, as evidenced by the explosion of new MOF structures in the last decade. However, the nearly infinite number of possible network connectivities and framework compositions, as well as the significant impact of minor changes in reaction conditions on the structure obtained, impedes optimization. Although high-throughput synthesis can greatly accelerate the discovery of new materials, the speed of subsequent characterization, such as gas adsorption measurements, limits the rate of optimization. In response to this challenge, we describe the development of a high-throughput nuclear magnetic resonance (NMR) porosity screening tool that uses NMR relaxation times of adsorbed molecules to estimate porosity. The diffusion and exchange processes uncovered during the development of this NMR screening tool highlight the lack of a molecular understanding of how adsorbed molecules, or guests, move in metal-organic frameworks. Thus, we investigate adsorbate dynamics in detail using NMR relaxation and diffusion experiments. Our relaxation experiments, combined with molecular simulations, establish the presence of a new condensation phenomenon occurring in a model adsorbate-MOF system. Our diffusion studies explore the interplay between the adsorbate-adsorbent interaction energy and this new condensation phenomenon on adsorbate diffusion in MOFs. These fundamental investigations, as well as our more practical efforts in developing a porosity screening tool, provide detailed insight into molecular dynamics in confined systems, and this knowledge possesses broad implications for applications in separations and catalysis.

Advisor: Reimer, Jeffrey A
The Mechanism of Processivity and Directionality of Cytoplasmic Dynein

Cytoplasmic dynein is a dimeric motor that transports intracellular cargoes towards the minus-end of microtubules (MTs). In contrast to other processive motors, microtubule release of the dynein heads is not precisely coordinated and the mechanism of dynein processivity remains unclear. By engineering the mechanical and catalytic properties of the motor we show that dynein processivity minimally requires a single active motor domain (head) and a second inert MT binding domain. The AAA+ ring and the linker of the other head are dispensable, suggesting that processivity arises from a high ratio of MT bound to unbound time, and not from interhead communication. Additionally, nucleotide-dependent microtubule release is gated by tension on the linker domain./nWe find that dynein releases rapidly from the MT when force is applied in the forward direction (towards the minus-end), but remains bound under backward forces. This finding suggests that the asymmetric release properties of the microtubule binding domain (MTBD) control dynein directionality. Consistent with this hypothesis, replacing the MTBD with a catalytically inactive kinesin motor domain, which favors release towards the plus end, results in reversal of motor directionality. Furthermore, a dynein dimer maintains its minus-end directed motility when the released monomer is allowed to orient freely during the search for a new binding site. The results rule out directionality models based on a swinging mechanism of the linker domain. We propose that the mechanism of dynein directionality is fundamentally distinct from kinesin and myosin motors and determined by asymmetric release and binding properties of its MT binding interface. We develop a quantitative model for dynein stepping that reproduces the velocity and stepping characteristics of dynein motors and their response to chemical and mechanical perturbation.

Advisor: Yildiz, Ahmet
To Enter, to be entered, to merge: The role of religious experience in the traditions of Tantric Shaivism

The present work comprises a detailed study of specific terms of discourse in the pre-twelfth century sources of esoteric "Tantric" Shaivism, both scriptural and exegetical, some of which are still unpublished and others of which are published only in the original Sanskrit. As a dissertation in South Asian Studies using the philological method, the primary purpose of the study is to ascertain the range of meanings of certain technical terms of great importance to the theology and practice of the Shaiva religion, namely avesa, samavesa, and saktipata. The work focuses on both the independent meaning and the intersection of these key terms, incorporating also the terms diksa and vedha in the latter endeavor. The intersection of these terms constitutes a complex set of relationships, a nexus of ideas that lie at the very heart of the Shaiva tradition and which, due to the latter's widespread influence, came to be important in Tantric Buddhism and later forms of Hinduism as well. This thesis contends that samavesa--meaning the fusion or commingling of one's self with the energy of one's deity and/or the consciousness of one's guru--is the key term that distinguishes Tantric Shaivism from mainstream (esp. Vaidika) Indian religion. This constitutes a reinterpretation and overcoding of the earlier meaning of avesa, i.e. self-induced controlled possession by a deity./nSamavesa is important to all forms of Shaivism, whether dualistic and ritualized (the Siddhanta) or nondual subitist charismatic forms (the Kaula). This thesis further contends that a philological study of samavesa and related terms like saktipata demonstrates that religious experience (or evidence thereof) was considered central and indispensable to initiatory Shaivism throughout the medieval period. Saktipata was requisite to receive the basic level of initiation, and in the Kaula branch of the tradition, samavesa denoted forms of religious experience that were necessary for aspirants to demonstrate in order to receive higher-level initiations. The former term is still commonly used in many Hindu communities today to designate a "spiritual awakening" or initiatory experience that is transmitted by a qualified guru./nPart One of this work is a comprehensive overview of the nature and structure of the Shaiva religion, providing important context to what follows. Part Two studies the key terms of (sam)avesa, saktipata, etc. in a) early Sanskrit literature generally, b) Shaiva scriptures, and c) the abundant exegetical literature based on those scriptures.

Advisor: Goldman, Robert P.
Rospatt, Alexander von
Subsemble: A Flexible Subset Ensemble Prediction Method

Ensemble methods using the same underlying algorithm trained on different subsets of observations have recently received increased attention as practical prediction tools for massive data sets. We propose Subsemble, a general subset ensemble prediction method, which can be used for small, moderate, or large data sets. Subsemble partitions the full data set into subsets of observations, fits one or more user-specified underlying algorithm on each subset, and uses a clever form of V-fold cross-validation to output a prediction function that combines the subset-specific fits through a second user-specified metalearner algorithm. We give an oracle result that provides a theoretical performance guarantee for Subsemble. Through simulations, we demonstrate that Subsembles with randomly created subsets can be beneficial tools for small to moderate sized data sets, and often have better prediction performance than the same underlying algorithm fit just once on the full data set. We also describe how to include Subsembles as candidates in a SuperLearner library, providing a practical way to evaluate the performance of Subsembles relative to the same underlying algorithm fit just once on the full data set./nSince the final Subsemble estimator varies depending on the data within each subset, different strategies for creating the subsets used in Subsemble result in different Subsembles, which in turn have different prediction performance. To study the effect of subset creation strategies, we propose supervised partitioning of the covariate space to learn the subsets used in Subsemble. We highlight computational advantages of this approach, discuss applications to large-scale data sets, and develop a practical Supervised Subsemble method using regression trees to both create the covariate space partitioning, and select the number of subsets used in Subsemble. Through simulations and real data analysis, we show that this subset creation method can provide better prediction performance than the random subset version./nFinally, we develop the R package subsemble to make the Subsemble method readily available to both researchers and practitioners. We describe the subsemble function, discuss implementation details, and illustrate application of the Subsemble algorithm for prediction with subsemble through an example data set.

Advisor: van der Laan, Mark
Collecting Data With the Crowd

Hybrid human/machine database and search systems promise to greatly expand the usefulness of query processing by incorporating human knowledge and experience via "crowdsourcing" into existing systems for data gathering and other tasks. Of course, such systems raise many implementation questions. For example, how can we reason about query result quality in a hybrid system? How can we best combine the benefits of machine computation and human computation? In this thesis we describe how we attacked these challenges by developing statistical tools that enable users and systems developers to reason about query completeness in hybrid database systems, as well as combining human and automated processing in search engines. We present evaluations of these techniques using experiments run on a popular crowdsourcing platform, Amazon's Mechanical Turk.

Advisor: Franklin, Michael J
Virus Removal Mechanisms in Membrane Bioreactors and Implications For Water Reuse

Water reuse is a viable strategy to sustainably manage urban water resources. A clear understanding of the benefits and shortcomings of sophisticated treatment technologies is desirable in order to efficiently benefit from water reuse. A membrane bioreactor (MBR) is a wastewater treatment technology utilizing a membrane barrier. MBRs produce high quality effluent, although removal of viruses through the system has not been thoroughly characterized. There is a need to understand the physical mechanisms of virus removal in order to predict performance of MBRs to ensure consumer safety under water reuse scenarios. This dissertation outlines plausible mechanisms to explain virus removal within MBRs. Results of investigations at both the full-scale, as well as under more controlled laboratory conditions, are described. Additionally, the risk to consumers of potable water reuse is assessed for a range of treatment scenarios, comparing MBRs alongside other technologies, to provide a framework for decision-making. Through a better mechanistic understanding, we can determine the operational parameters and treatment train designs needed for reliable pathogen removal to protect the consumer, and expand potable water reuse.

Advisor: Nelson, Kara L
Design of Electrospun Hydrogel Fibers Containing Multivalent Peptide Conjugates for Cardiac Tissue Engineering

A novel material was designed using biomimetic engineering principles to recreate the chemical and physical environment of the extracellular matrix for cardiac tissue engineering applications. In order to control the chemical and specific bioactive signals provided by the material, a multivalent conjugate of a RGD-containing cell-binding peptide with hyaluronic acid was synthesized. These conjugates were characterized using in-line size exclusion chromatography with static multi-angle light scattering, UV absorbance, and differential refractive index measurements (SEC-MALS-UV-RI) to determine their molecular weight and valency, as well as the distributions of each. These conjugates were electrospun with poly(ethylene glycol) and poly(ethylene glycol) diacrylate to create a nanofibrous hydrogel material embedded with bioinstructive macromolecules. This electrospinning process was explored and optimized to create well-formed nanofibers. The diameter and orientation of the fibers was controlled to closely mimic the nanostructure of the extracellular matrix of the myocardium. Further characterization of the material was performed to ensure that its mechanical properties resemble those found in the myocardium. The availability of the peptides embedded in the hydrogel material was confirmed by measuring peptides released by trypsin incubation and was found to be sufficient to cause cell adhesion. This material was capable of supporting cell culture, maintaining the viability of cultured fibroblasts and cardiomyocytes, and preserving cardiomyocyte functionality. In this way, this material shows promise of serving as a biomimetic in vitro scaffold for generation of functional myocardial tissue, with possible applications as an in vivo cardiac patch for repair of the damage myocardium post-myocardial infarction.

Advisor: Healy, Kevin E
Studies to elucidate the molecular targets of two potent antimalarial benzoxaborole compounds in Plasmodium falciparum

With increasing resistance of malaria parasites to available drugs, there is a great need for new antimalarials, ideally with novel mechanisms of action. We are investigating the antimalarial activity and mechanisms of action of benzoxaboroles, a novel class of boron-containing compounds. Compounds 3661, 1467 and related compounds demonstrated good activity in vitro against chloroquine-resistant Plasmodium falciparum and in vivo against murine Plasmodium berghei infection (compound 3661: IC50 37 nM against W2-strain P. falciparum, ED90 0.3 mg/kg against murine P.berghei; compound 1467: IC50 196 nM, ED90 7.4 mg/kg). In an attempt to characterize mechanisms of action, we selected for parasites with decreased sensitivity to 3661 and 1467 by culturing with step-wise increases in concentration of the compounds followed by whole genome sequencing. Sequencing of parasites selected for resistance to 1467 showed several SNPs in the editing domain of a predicted leucyl tRNA synthetase (LeuRS) gene (PF3D7_0622800) and in another gene of unknown function (PF3D7_1218100). Additionally, both compounds were tested for stage-specificity by incubation with test compounds for 8 hour intervals across the parasite erythrocytic life cycle. Both compounds were most active against trophozoite stage parasites. To further understand the mechanism of action of 1467 and the related compound 1474, the incorporation of 14[C] leucine in parasite cultures or parasite extracts including exogenous tRNA was assessed in the presence or absence of the compounds. Dose-dependent inhibition of both protein synthesis and LeuRS activity was observed for 1467 and 1474, but not 3661 or the control artemisinin, supporting different mechanisms for the different benzoxaboroles. For 3661, in vitro resistance selection was also achieved by culturing parasites in step-wise increasing concentration and in a single high concentration of the compound. Cross-resistance was not seen between parasites selected with 3661 and those selected with 1467. Whole genome sequencing of multiple clones selected for resistance to 3661 revealed several SNPs in a gene that codes for a homolog of mammalian cleavage and polyadenylation specificity factor (CPSF; PF14_0364). In summary, we offer strong evidence for unique antimalarial mechanisms of action for two benzoxaboroles, identifying two potential novel antimalarial drug targets. Further investigation of these novel benzoxaborole mechanisms is underway.

Advisor: Harris, Eva
Rosenthal, Philip
New Developments in Semiconductor Nanowire Optoelectronics

Since the beginning of the new millennium, the nano-materials community has witnessed an exponential increase in the amount of research dedicated to inorganic semiconductor nanowires for optoelectronics. The prospect of miniaturized optoelectronics is enticing principally because they can enable new applications and scientific discoveries that are unattainable with traditional macroscopic devices. This potential has inspired academics to create nanowire-based devices such as gas and chemical sensors, photodetectors, light-emitting diodes, solar cells, waveguides, nanoscopic lasers, plasmonic lasers, and nonlinear optical converters. To continue the success of this field, it is critical to explore nanowires with improved functionalities for photonic applications. This work presents new developments for the next generation of nanowire optoelectronic devices./nThe unique boundary conditions of nanowires were explored to grow thermodynamically metastable materials directly onto bulk semiconductors. Using a single material, InGaN, single-crystalline nanowire light-emitting diodes that emit from blue to orange were fabricated without any evidence of phase separation, suggesting that the nanowire geometry relieves the significant lattice strain traditionally observed in macroscopic devices./nTo circumvent the lack of spectral control in nanowire lasers, a coupled cavity scheme was introduced into nanowire lasers to improve the laser performance at room-temperature. By axially coupling two nanowire cavities, spectral manipulation of the lasing modes in semiconductor nanowires were theoretically investigated and experimentally demonstrated. This compact architecture produced single-mode lasing with the added benefit of lowering the laser threshold with respect to the individual component cavities./nUsing these design principles for spectral manipulation, distributed Bragg reflectors (DBRs) integrated within semiconductor nanowires were explored to spatially and spectrally control specific longitudinal modes to demonstrate wavelength division, to improve laser performance, and to use as a platform to measure the effective refractive index of a waveguide made from a birefringent material. Using the results presented in this thesis, a discussion on the development of next-generation nanowire lasers is presented.

Advisor: Yang, Peidong
Tribe and State in Post-Ba`athist Iraq

In 2003, an erstwhile successful state apparatus - the security party-state of Ba`athist Iraq - collapsed as a result of the US-led Operation Iraqi Freedom. The breakdown of the state apparatus was then exacerbated by early occupational policy, which swept away the foundations of both the armed forces and the civil services. As a result, Iraq was faced with a condition of near-total anarchy, as US occupational institutions proved themselves unequal to replacing the state structures they had eliminated./nThat governance vacuum enabled non-state coercive actors to compete for authority in the shadow of the US occupation. In much of the country, the result was protracted, multi-sided struggle, but in al Anbar tribal leaders were able to establish themselves as the supreme authorities, carving out a tribal quasi-state in the governorate./nThis dissertation examines the process of state failure and the nature of politics in the absence of stable state structures, and in doing so concludes that the institutional configuration of the non-state coercive power competitors is the crucial deciding factor separating winners from losers. In al Anbar, it was two characteristics of the tribes - their hierarchical authority, forged out of long-term historical forces, and the more recent legacy of collusion with the Ba'athist state in the two decades prior to the US-led invasion. The central government in Iraq, like the proverbial stranger in the Alps, has been buffeted by blows from all directions, with unsure governance even in its core territories, while the tribes of western Iraq have only each other as significant rivals./nThe paper concludes with thoughts on generalizing this framework beyond al Anbar to the other regions of Iraq, and to other failed states.

Advisor: Zysman, John
Isotope-Specific Detection and Assay: Engineering Solution with Directional Nuclear Resonance Fluorescence

In this work we endeavor to engineer a new tool for isotope-specific assay and detection. We propose to utilize Nuclear Resonance Fluorescence (NRF) as the process that gives isotope-specific information about the object under investigation. Careful experimental and theoretical studies of angular dependencies of signal (NRF) and noise (other significant scattering channels) are presented. These studies motivate engineering design of detector array exploiting signal vs. noise discrepancies in angular distributions. User-defined materials of interest, detection / assay times and accuracy requirements inform the design yielding optimal performance.

Advisor: Morse, Edward C
Seismic Response of a Soft, High Plasticity, Diatomaceous Naturally Cemented Clay Deposit

The influence of diatoms on clayey soils behavior has been shown to be important through studies of these soil deposits in Japan, Mexico, Thailand, among others. In Guayaquil city, the presence of diatom assemblages in soil samples was identified in the deltaic estuarine deposition found throughout the urban area./nA new geotechnical characterization scheme for the Guayaquil soils was proposed based on geological studies, historical data of geotechnical explorations, in situ microtemor measurements, and Spectral Analysis of Surface Waves (SASW) tests performed at representative sites. Geotechnical parameters, such as plasticity, sensitivity, and void ratio, depend on the amount of cementation in the soils. This influences the static behavior of Guayaquil soils by producing an apparent overconsolidation ratio and high anisotropy ratio in some areas, which in turns, affect the seismic response of these deposits. Accordingly, some correlations were developed between geotechnical parameters and seismic response properties such as shear wave velocity for each geotechnical zone to characterize the Guayaquil soil deposits for dynamic analyses. The Construction Ecuadorian Norm requires that site-specific geotechnical investigations and seismic response analyses be performed for the high plasticity deltaic estuarine clays, which are the predominant soils in Guayaquil./nSelect soil constitutive models can capture the Guayaquil clay behavior as reflected in the results of advanced monotonic and cyclic test performed as part of this study. The analysis of these results provides a framework for understanding the mechanical behavior of the estuarine-deltaic, high plasticity, diatomaceous, naturally cemented clay in Guayaquil. Seismic response analyses using non-linear and linear equivalent models were also performed that provided useful insights./nBased on the calculated elastic and inelastic responses of the Guayaquil soils, a seismic zonation for the city was proposed where the appropriate seismic demand for a structure can be developed. In addition, a detailed procedure for estimating a design site response spectrum for Guayaquil City's prevalent soil conditions was developed. The experimental results and numerical procedures presented in this research provide key information for the design of engineered systems in Guayaquil and provide insights for cities worldwide, with similar geomorphological, seismic, and geotechnical characteristics

Advisor: Pestana, Juan M
Bray, Jonathan D