VictorJuiz/thesis huggingface dataset:
Graph Algorithms in the Internet Age

This dissertation addresses a series of graph problems inspired by the computational issues with face with the Internet, a massive distributed network of autonomous agents. There are several levels to this problem. From a systems perspective, what can we do to facilitate computation over massive graphs? From a modeling perspective, what do natural graphs look like and what features are useful? From a game theoretic perspective, the graphs often represent individuals or systems with their own goals and agendas. Can we understand how these systems compete and when these competitions are fair or can be manipulated?/nThese questions are addressed. For the first, we consider the problem of streaming graph partitioning and show it is feasible. For the second, we study the joint degree distribution of a graph and show it is combinatorially easy to work with. Finally, we address questions about tournament design and manipulation.

Advisor: Rao, Satish B
Systematics and ecology of the moss genus Scleropodium (Brachytheciaceae)

Scleropodium is a genus of six species in the Brachytheciaceae. Although they are common in north temperate zones, they have not received monographic treatment in over a century. The aims of this study were to test species circumscriptions within the genus with molecular data, complete a thorough global taxonomic treatment of the genus, and to quantitatively investigate the ecological preferences of the species./nA molecular phylogenetic study was conducted using 104 individuals spanning the range of morphological variation and the geographic extent of the genus. Maximum Parsimony and Bayesian phylogenetic analyses and a statistical parsimony network analysis of ITS and the chloroplast rps4, bsbA2 and trnG regions were performed. Although slight differences were found among analyses, there were six clear molecular groups. Five of these corresponded directly to the species Scleropodium californicum, S. cespitans, S. julaceum, S. obtusifolium and S. touretii. The sixth species, S. occidentale, is new to science and is described here. It is similar in ecology and morphology to S. obtusifolium, but has several diagnostic features in both molecular markers and morphological characters. Molecular data also revealed that S. australe, previously recognized as an endemic species in Tasmania, is nested in phylogenetic analyses within European S. touretii./nFor the taxonomic treatment, specimens from across the global distribution of the genus were obtained and examined. Earlier taxonomic problems are resolved and new determinations of many herbarium specimens resulted in substantial changes in the known geographic distributions of the species. Nomenclatural problems are addressed, including lectotypification of S. cespitans, neotypification of S. touretii, and snynonymization of S. colpophyllum with S. cespitans and S. australe with S. touretii. Two Korean species, S. brachyphyllum and S. coreense, are excluded from Scleropodium./nA study of niche differences among five of the six species was conducted in the coast ranges of California. The study employed twenty-eight100m2 plots to investigate mesosite and microsite differences among species. Differences could be found in all species pairs except for S. obtusifolium and S. occidentale, both of which are restricted to seasonal drainages. Environmental factors that were important at broad spatial scales included slope and tree canopy cover. Finer scale differences at the scale of individual moss patches were found in distance of the moss patches from drainages, substrate type and shade. Although niche differences were observed and quantified, niche overlap was extensive and mixed moss patches with two species growing intertwined were common. Niche differences among sexes within species was also investigated, but results were mostly not significant. In the more common species, there were trends toward female sex ratio bias and restriction of male individuals to more mesic habitats, but these results were mostly confounded by numbers non-expressing individuals.

Advisor: Mishler, Brent D
Genome-Free Viral Capsids for Targeted Drug Delivery to Breast Cancer

A targeted drug delivery vehicle based on the bacteriophage MS2 viral capsid was constructed using site-selective bioconjugation reactions. A palladium-catalyzed tyrosine allylation reaction was evaluated for interior modification of intact MS2 capsids with water-insoluble drug molecules. Ultimately, a tri-functional linker was synthesized and used to attach multiple copies of the chemotherapeutic agent taxol to the interior surface of an MS2 mutant containing a uniquely modifiable cysteine. This virus-based vehicle was able to deliver and release taxol to breast cancer cells in vitro and effect cytotoxicity at comparable levels to that of the drug alone. We next utilized a sodium periodate mediated oxidative coupling reaction to attach multiple types of targeting groups to the exterior of the MS2 capsids. Targeting groups we evaluated include short peptides, DNA aptamers, and engineered proteins. The most effective of these targeting groups proved to be a class of engineered binding proteins called designed ankyrin repeat proteins (DARPins). MS2 capsids modified with anti-HER2 DARPins were found to preferentially bind in vitro to several breast cancer cell lines overexpressing HER2.

Advisor: Francis, Matthew B
Ultraproducts of O-Minimal Structures

There are three main parts to this thesis, all centred around ultraproducts of o-minimal structures./nIn the first part we investigate (for a fixed first-order language L) what we call the L-theory of o-minimality. It is the theory consisting of those L-sentences true in all o-minimal L-structures. We find that when L expands the language of real closed fields by at least one new function or relation symbol, the L-theory of o-minimality is not recursively axiomatizable. In particular, for any recursive list of/naxioms A which is consistent with the L-theory of o-minimality, we find that there are locally o-minimal, definably complete structures satisfying A which are not elementarily equivalent to an ultraproduct of o-minimal structures. We call the latter sort of structures pseudo-o-minimal./nIn the second part we investigate uniform finiteness and cell decomposition in the pseudo-o-minimal setting. To do this, we introduce the notion of a pseudo-o-minimal structure tallying a discrete definable set. Investigating this notion, we answer some questions of uniqueness and existence. Finally, we show that under certain assumptions about the discrete definable sets that a given pseudo-o-minimal structure can tally, we have a version of uniform finiteness, at least in the planar case. This is the first step towards a cell decomposition theorem in this setting./nIn the final section, we look into two classes of examples of ultraproducts of o-minimal structures. For the first class, we note the o-minimality of a certain subset of these structures, and show the non-o-minimality of another. In particular, we derive the o-minimality of a new structure related to the real field with the exponential function. The second class is relatively intractable, but we discuss its relation to an important open problem in o-minimality.

Advisor: Scanlon, Thomas
Curved String Topology and Tangential Fukaya Categories

For manifolds $M$ with a specific rational homotopy type, I study a non-commutative Landau-Ginzburg model whose underlying ring is the differential-graded algebra (dga) $B=C_*(\Omega(M))$, that is chains on the based loop space with Pontryagin product and with potential $W$ in $B$. For $M=\mathbb{C}P^{n_1}\times \mathbb{C}P^{n_2} \times \ldots \mathbb{C}P^{n_k}$ or $S^{n_1} \times S^{n_2} \times \ldots S^{n_k}$, we explain how the field theories we define have a Fukaya category interpretation.

Advisor: Teleman, Constantin
Regulatory Dynamics of Natural and Artificial Photosynthesis

The research presented in this dissertation focuses on understanding the regulation of excited states, both in natural photosynthesis and in artificial systems./nChapters 1, 2, and 3 contribute to the understanding of natural photosynthesis by describ- ing a mathematical model that quantifies a process by which plants protect themselves from damage due to excess absorbed energy. Chapter 1 contains a description of a mathematical model of photosynthetic processes that govern the rapid components of nonphotochemical quenching. Chapter 2 contains a manual describing a Graphical User Interface (GUI) for this model. Chapter 3 extends the model of nonphotochemical quenching and applies the model to understand the role of the specific pigments and proteins which are required for rapidly-reversible nonphotochemical quenching to take place./nChapters 4 and 5 are focused on experimental work done on artificial systems. Chapter 4 reports on the excited state dynamics of a pH-sensitive dye that has been used to regulated the excited state lifetime of an artificial antenna. Chapter 5 reports measurements of four molecular donor-bridge-acceptor triads where the bridge between the donor and acceptor is different in each triad, with the aim of understanding how the chemical bonding between donor and acceptor affects the timescales and yield of energy transfer and charge separation.

Advisor: Fleming, Graham R
Magnetism of Complex Oxide Thin Films and Heterostructures

Studies of magnetism at reduced scales have revealed new phenomena that are distinctly different from their bulk counterparts providing insight to the fundamental mechanisms that govern magnetism and other correlated properties. To this end, the use of heteroepitaxy and heterostructures is invaluable for investigating magnetism at reduced dimensions and at surfaces and interfaces. This dissertation is a compilation of investigations examining the magnetic properties of spinel-structure oxide thin films and heterostructures. Of particular interest are non-collinear spin systems as closely competing exchange interactions between magnetic moments give rise to a plethora of ground state degeneracies and phenomena inaccessible in the bulk./nThe first part of this dissertation highlights the use of heteroepitaxial lattice distortions as a method to tune spin functionality and potentially lift ground state degeneracies more broadly in frustrated magnets. It discusses the first synthesis of heteroepitaxial thin films of the frustrated canted-moment ferrimagnet, CuCr2O4, and demonstrates the modification of exchange interaction strengths which results in greater collinear spin ordering and enhanced magnetization compared to the bulk. The data illustrates the sensitivity of the strong competing exchange interactions suggesting that strain is a promising instrument for perturbing the delicate balance of the exchange interactions in frustrated materials./nThe second part of this dissertation probes magnetic proximity effects induced by interfaces and unconventional transport properties when CuCr2O4 is incorporated as a barrier layer in magnetic tunnel junctions comprised of ferromagnetic La0.7Sr0.3MnO3 and Fe3O4 electrodes. It is surprising that a heterostructure composed entirely of magnetic materials can achieve distinct magnetic and resistive switching given the complexities present at the two barrier-electrode interfaces. Studies of the CuCr2O4/Fe3O4 interface again illustrate the delicate balance between exchange interactions as proximity effects by Fe3O4 are believed to modulate alignment in the Cr moments. Additionally, the bias dependence of JMR displays a local minimum at zero bias which is believed to be the result of the Fe3O4 band structure and spin filtering properties of the CuCr2O4 barrier.

Advisor: Wu, Junqiao
New methods for the deoxygenation of 1,2-diols and epoxides

Abstract/nChapter 1 : Introduction./nOur chemical industry is currently capable of converting fossil fuel feedstocks (unsaturated hydrocarbons) into useful polymers and chemicals. Replacing those feedstocks with renewable sources is an important goal for sustainability. Our research focuses on the defunctionalization of heavily oxygenated biomass materials so they can be used in the chemical industry's current factories. Of particular interest are three and four carbon monomers which would be obtained from the defunctionalization of the simple alditols glycerol and erythritol./nChapter 2 : Formic Acid-Mediated Didehydroxylation of Vicinal Diols: Reaction Development and Mechanistic Studies/nWe developed a simple formic acid-mediated didehydroxylation of diols. Our substrate scope was limited to simple polyols. Isotope labeling studies suggested the intermediacy of a carbocation as well as an orthoformate ester. Attempts at isolating the carbocation intermediate were unsuccessful./nChapter 3 : CO2 Reduction - In situ Formation of Formic Acid with Concomitant Didehydroxylation of Vicinal Diols/nWe successfully reduced carbon dioxide with a heterogeneous rhodium catalyst to form a mixture of formic acid and amine. Attempts at didehydroxylation using the synthesized mixture were successful, though low yielding. Concomitant reduction of carbon dioxide and didehydroxylation was not achieved./nChapter 4 : Rhenium-Catalyzed Deoxygenation of Diols and Epoxides/nMany oxo-rhenium catalysts were synthesized and used for the deoxygenation of diols and epoxides. We were unable to obtain conclusive spectroscopic data of the reaction's progress, limiting our ability to propose a mechanism.

Advisor: Bergman, Robert G
First-principles studies of carbon nanostructures and spin-phonon and electron-phonon coupling in solids

This work presents first-principles theoretical studies on two topics of condensed matter physics. The first topic is the adsorption of metal adatoms on graphene. Graphene, a two-dimensional material made of carbon atoms arranged in a honeycomb lattice, has many outstanding properties that can be enhanced or tailored by adsorbing adatoms on its surface. The second topic involves the coupling of spins or electrons to phonons in a solid. The interaction between different degrees of freedom of a material complicates the study of its properties but also leads to fascinating phenomena, such as superconductivity, and potential device applications. This dissertation is organized into six chapters:/n· In Chapter One, we give an overview of this work and review the first-principles theory and methods used in our studies./n· Chapter Two focuses on structural, energetic, and electronic properties for a variety of adatom species adsorbed on the graphene surface. We classify different species as having mostly ionic or covalent character of bonding to graphene. For ionically bonded adatoms, charge transfer between the adatom and graphene is signficant. We find general trends relating the surface dipole moment, work function, and atomic ionization potential of the adatom species./n· In Chapter Three, we study the electronic structure of adatoms on graphene when a gate voltage is applied to control the number of electrons in the system. Lithium on graphene, a prototype system, and cobalt on graphene, an experimentally relevant case, are studied. We find that localized states on the adatom can be charged or discharged by the application of gate voltage, and we study the changes in potential and charge density of the system as electrons are added or removed./n· In Chapter Four, we extend the work in Chapter Three to consider the possibility of transforming the electronic structure of one species of adatom on graphene into that of another by applying a gate voltage. We find that within our model, such transformations are possible for certain adatom species./n· In Chapter Five, the zone-center phonons for the frustrated antiferromagnetic compound ZnCr2O4 are calculated. We find that the transition from nonmagnetic to antiferromagnetic ordering causes a splitting of certain degnerate phonon frequencies, in agreement with experimental results./n· In Chapter Six, the pressure dependence of electron-phonon coupling and the superconducting transition temperature (Tc ) in elemental arsenic is studied. We find that an experimentally observed peak in Tc as a function of pressure is related to a structural transition and can be explained mainly by changes in electronic structure and phonon frequencies with pressure.

Advisor: Cohen, Marvin L
Behavioral and Neural Effects of Reasoning Training

My thesis research has focused broadly on how the environment shapes the structure and function of prefrontal cortex, for better or worse. I am interested in understanding in how experience-dependent plasticity can be harnessed to boost, or in some cases, remediate prefrontal function. I focused on training reasoning, the ability to solve novel problems, for two reasons: 1) reasoning is highly predictive of academic outcomes, and 2) reasoning was originally conceptualized as a fixed trait, and many people, both in science and in the general public, still believe that reasoning is set in stone. I conducted two studies, one in children and one in adults, to test the predictions that reasoning ability is malleable, and that repeated practice with reasoning problems strengthens connectivity within the frontoparietal network that supports high-level cognition./nIn my first study, children from low socioeconomic status backgrounds participated in 8 weeks of training with computerized and non-computerized games that targeted either reasoning ability or cognitive speed. Training led to dissociable behavioral outcomes: children in the reasoning training group improved substantially on a matrix reasoning test, while children in the speed training group improved specifically on a measure of cognitive speed. Reasoning gains corresponded to roughly 10 points in performance IQ. These results indicated that reasoning is modifiable by training in this population./nIn my second study, I capitalized on the fact that adults are taught reasoning skills by courses aimed at improving performance on the Law School Admissions Test (LSAT). I recruited young adults who were enrolled in an LSAT preparation course, and age- and IQ-matched controls intending to take the LSAT in the future. Magnetic resonance imaging (MRI) measures were collected for all subjects during two scanning sessions separated by 90 days. I first tested whether reasoning training altered functional connectivity at rest. I found strengthened fronto-parietal and parietal-striatal functional connectivity, particularly between hemispheres. I next investigated whether structural connectivity, as measured by diffusion in white matter, had been altered by training. I found training-related radial diffusivity (RD) decreases in white matter connecting frontal cortices, and mean diffusivity (MD) decreases closer to cortex in white matter in left frontal lobe and right parietal lobe. In conclusion, my thesis research has demonstrated that training can improve reasoning ability and, in adults, alter functional and structural connectivity. These results provide evidence for neural plasticity in large-scale networks supporting high-level cognition.

Advisor: Bunge, Silvia A
Optimization of Protein Bioconjugation Reactions Using Combinatorial Peptide Libraries

The covalent attachment of chemical groups to proteins is an important tool for many areas of chemical biology, including the study of protein function and the creation of protein-based materials. In order to create well-defined protein bioconjugates, methods of site-specfic protein modification are required. We have developed a high-throughput method of optimizing protein bioconjugation reactions using a combinatorial peptide library in which short peptides serve as a model for protein reactivity. The library screening was achieved using a one-bead-one-compound peptide library, a colorimetric detection scheme to identify high-yielding sequences, and a deconvolution method using a built-in peptide truncation ladder for rapid mass spectrometry sequencing of hit beads. We applied this screening platform in the context of a pyridoxal 5'-phosphate (PLP)-mediated transamination reaction specific for the N-terminus, and were able to identify an N-terminal sequence with high reactivity towards this reaction that can be incorporated into proteins of interest to result in high levels of modification. The screening platform was also used for the discovery and optimization of new N-terminal protein modification reactions.

Advisor: Francis, Matthew B
Faint Coronal Hard X-rays From Accelerated Electrons in Solar Flares

Solar flares are huge explosions on the Sun that release a tremendous amount of energy from the coronal magnetic field, up to 1033 ergs, in a short time (100--1000 seconds), with much of the energy going into accelerated electrons and ions. An efficient acceleration mechanism is needed, but the details of this mechanism remain relatively unknown. A fraction of this explosive energy reaches the Earth in the form of energetic particles, producing geomagnetic storms and posing dangers to spaceborne instruments, astronauts, and Earthbound power grids. There are thus practical reasons, as well as intellectual ones, for wishing to understand this extraordinary form of energy release./nThrough imaging spectroscopy of the hard X-ray (HXR) emission from solar flares, the behavior of flare-accelerated electrons can be studied. The Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) spacecraft launched in 2002 with the goal of better understanding flare particle acceleration. Using rotation modulation collimators, RHESSI is able to cover a wide energy range (3 keV--17 MeV) with fine angular and energy resolutions. RHESSI's success in the last 10 years in investigating the relationship between energetic electrons and ions, the nature of faint sources in the corona, the energy distribution of flares, and several other topics have significantly advanced the understanding of flares./nBut along with the wealth of information revealed by RHESSI come some clear observational challenges. Very few, if any, RHESSI observations have come close to imaging the electron acceleration region itself. This is undoubtedly due to a lack of both sensitivity (HXRs from electron beams in the tenuous corona are faint) and dynamic range (HXR sources at chromospheric flare footpoints are much brighter and tend to obscure faint coronal sources). Greater sensitivity is also required to investigate the role that small flares in the quiet Sun could play in heating the corona./nThe Focusing Optics X-ray Solar Imager (FOXSI) is a developing project to address these observational difficulties. FOXSI is a sounding rocket payload developed under NASA's Low Cost Access to Space program. The project spearheads a shift to using direct imaging via focusing grazing-incidence HXR optics rather than the indirect Fourier techniques used by RHESSI and its predecessors. Such optics can attain higher sensitivity since photons are focused onto a small detector volume and have significantly better dynamic range than Fourier methods do. On November 2, 2012 the FOXSI rocket payload was flown for a 6-minute observation and successfully imaged a solar flare, providing the first focused HXR spectroscopic images of the Sun above 5 keV./nThe motivation, construction, testing, and flight of FOXSI will be described in this text, along with case studies on the use of FOXSI to analyze unique coronal HXR sources from two solar flares.

Advisor: Lin, Robert P.
Krucker, Sam