VictorJuiz/thesis huggingface dataset:
The development and characterization of the novel heavy element mass separator FIONA and the investigation of short-lived isomeric states in ^{255} Lr

A \ce{^{209}Bi}(\ce{^{48} Ca}, 2n)\ce{^{255} Lr} reaction was performed using the Berkeley Gas-filled separator (BGS) at the 88$''$ cyclotron in Lawrence Berkeley National Laboratory. This class of heavier actinide readily populates high angular momentum $K$-states with $>1$ms lifetimes, allowing for their separation and detection. The $K$-isomers of \Lr were identified by their conversion electron decays and their nuclear levels measured using coincident $\gamma$-ray spectroscopy. With a beam energy of 232 MeV, almost ten times the number of previous reported converted transitions were observed. From these higher statistics, the preliminary conclusions are presented, including the eight new low-lying rotational states observed in the de-excitation of \ce{^{255}Lr}. These isomeric studies provide a valuable view to the nuclear structure of the heaviest elements, testing the current explanations and models./nThe BGS is currently being upgraded with a secondary, mass sensitive secondary separator to improve detection sensitivity and expand research scope. For this separator, known as FIONA, simulations were used to investigate the effective separation and transport efficiency. Based on crossed electric and magnetic fields, the ion trajectories in a variety of configurations were modeled. The degree of mass separation was explored to determine this approach's viability with respect to heavy and superheavy element mass identification. A simulated mass resolution of $R = 784 ~ A/ \Delta A$ is reported, indicating the required mass sensitivity for superheavy elements is achievable./nA testing set-up of the FIONA mass separation scheme was built and characterized to verify the simulated behavior. Initially designed from an available 0.7 T dipole magnet and a custom electrode array, the independent beam-line and separator was built to record the ion trajectories and compare them to simulation. Using an off-line ${}^{nat}$Xe${}^{+}$ ion source, a 0.5~keV ion beam was delivered to the crossed field region with $\vec{B} = 0.3667$ T and $\vec{E} = 1240$ V. For the ${}^{nat}$Xe${}^{+}$ ions, which have a similar $m/q$ as a superheavy element, a mass resolution of $\bar{R} = ~ 628.6 A/ \Delta A$ is reported, well within the necessary predictions for superheavy element mass separation. Agreement with simulation and further prospect with the BGS is discussed.

Advisor: Cerny, Joseph
A Comprehensive Design of Quantum Dots for Imaging

Quantum dots (QDs) have proved to be invaluable fluorophores for single molecule imaging at high spatial and temporal resolution because they are brighter and more photostable than organic dyes or fluorescent proteins. However, use of QDs in biomolecular applications is limited by their large size, frequent blinking of their fluorescence signal, and challenges in their conjugation to the molecules of interest. QDs are often too large for confined or crowded systems due to their bulky passivating layer. QDs suffer a further increase in diameter during bioconjugation. QDs cannot withstand traditional bioconjugation methods that utilize small molecules, and other approaches require the use of large proteins. Therefore, a unifying strategy for small probe size, bioconjugation, and elimination of QD blinking has not yet been achieved./nIn this dissertation, I chronicle the design of a new system for the application of QDs to the study of biological systems. I utilize core/shell CdSe/CdS structures that blink less frequently and are brighter than conventional CdSe/ZnS structures. I characterize the difference between these two types of QDs at the single-molecule level and highlight the advantages for single-molecule imaging at accuracies on the nanometer scale that are present with CdSe/CdS QDs. I upgrade an existing small molecule-fusion protein system for bioconjugation (SNAP-tag) that improves the labeling of protein targets tenfold over the conventional system. I apply SNAP-functionalized CdSe/CdS QDs to the study of human kinesin-1, a motor protein responsible for directional transport of cargos along cytoskeletal tracks in the cell. I use these QDs to explore the role of interhead tension in coordinated motion using a mutant protein in a geometry previously inaccessible with commercial QDs. I show that these QDs can target kinesins for labeling in live cells. Our QD design strategy will likely extend their use to previously inaccessible systems such as small individual proteins or membrane-embedded complexes.

Advisor: Yildiz, Ahmet
Glassy Dynamics on a Lattice and in Nature

When a liquid is cooled below its melting temperature under conditions that prevent it from crystallizing, it forms an amorphous solid, or "glass." Glass-forming materials are ubiquitous, ranging from familiar silica glasses of which everyday windows are composed, to liquid water. While structurally indistinguishable from high-temperature liquids, supercooled liquids exhibit rich and complex dynamics. For instance, as the temperature is lowered, structural reorganization within supercooled liquids occurs over increasingly long time scales. Inspecting atomistic mobility over an interval of time reveals that dynamics is "heterogeneous," with distinct regions of mobility and immobility in space-time. In this dissertation, we characterize glassy dynamics in experimental systems and in coarse-grained lattice models. We show how the characteristic dynamics of atomistic glass-forming materials can be reproduced using a kinetically constrained lattice model referred to as the Arrow model, and thus present glassy dynamics "on a lattice." We then show that combining the Arrow model with a second lattice model that undergoes a thermodynamic phase transition captures the competition between crystallization and glass formation experienced by a material cooled below its melting temperature. With this combined model, we demonstrate how specific cooling protocols influence polycrystalline structure, and we qualitatively reproduce the non-monotonic temperature dependence of crystallization time scales. Finally, we explore glassy dynamics "in nature" by applying many of the same tools and ideas used to characterize glasses to study dynamical features of protein side-chains. We demonstrate the presence of supercooled liquid-like dynamics in a biomolecular system.

Advisor: Chandler, David
Imaging thoughts - an investigation of neural circuits encoding changes in behavior in zebrafish

Experience influences how we perceive the world, how we interact with our environment, and how we develop. In fact, almost all animals can modify their behavior as a result of experience. Psychologists have long distinguished between different forms of learning and memory, and later determined that they are encoded in distinct brain areas. Neuroscientists dating back to Santiago Ramón y Cajal suggested that learning and memory might be encoded as changes in synaptic connections between neurons, but it wasn’t until the second half of the 20th century that experimental evidence corroborated this idea. Specific firing patterns of neurons during learning results in strengthening or weakening of synapses, and morphological modifications that can lead to long lasting changes in neural circuits. The molecular mechanisms that drive these changes are remarkably conserved across vertebrates. However, understanding how synaptic plasticity is integrated at a network level remains a big challenge in neuroscience. Relatively few studies have focused on how neural circuits encode changes in behavior in a natural context./nIn this dissertation I present two such examples using calcium imaging and optogenetic techniques in larval zebrafish. First, in collaboration with others, I studied neural activity that drives the onset of the very first behavior of the fish, tail coiling. We characterized the transition of spontaneous activity in the spinal cord from a sporadic, uncorrelated state, to a regular and synchronized state. We determined that this transition occurred through coalescence of local microcircuits, and that inhibiting the early sporadic activity impaired normal development of the central pattern generator network. Second, I studied how experience of prey affects hunting behavior and underlying neural activity. I developed a paradigm to assess the effect of prior hunting on prey capture behavior and showed that experienced fish initiate more captures than their naïve counterparts. I next established that experience does not affect the ability of the fish to see prey. Rather, experience increases the probability that activity in visual areas will evoke a capture initiation. This is accomplished by increasing the impact of information transfer from visual to motor areas, possibly due to increased activity in forebrain areas for experienced fish.

Advisor: Isacoff, Ehud Y
Targeted learning of individual effects and individualized treatments using an instrumental variable

We consider estimation of causal effects when treatment assignment is potentially subject to unmeasured confounding, but a valid instrumental variable is available. Moreover, our models capture treatment effect heterogeneity, and we allow conditioning on an arbitrary subset of baseline covariates in estimating causal effects. We develop detailed methodology to estimate several types of quantities of interest: 1) the dose-response curve, where our parameter of interest is the projection unto a finite-dimensional working model; 2) the mean outcome under an optimal treatment regime, subject to a cost constraint; and 3) the mean outcome under an optimal intent-to-treat regime, subject to a cost constraint, in which an optimal intervention is done on the instrumental variable. These quantities have a central role for calculating and evaluating individualized treatment regimes. We use semiparametric modeling throughout and make minimal assumptions. Our estimate of the dose-response curve allows treatment to be continuous and makes slightly weaker assumptions than previous research. This work is the first to estimate the effect of an optimal treatment regime in the instrumental variables setting. For each of our parameters of interest, we establish identifiability, derive the efficient influence curve, and develop a new targeted minimum loss-based estimator (TMLE). In accordance with the TMLE methodology, these substitution estimators are asymptotically efficient and double robust. Detailed simulations confirm these desirable properties, and that our estimators can greatly outperform standard approaches. We also apply our estimator to a real dataset to estimate the effect of parents' education on their infant's health.

Advisor: van der Laan, Mark
An investigation of the relationship of student performance to their opportunity-to-learn in PISA 2012 mathematics: The case of Indonesia

Consisting of three chapters, this dissertation investigates the possibilities for using data from a large-scale international test (specifically the PISA 2012 test in mathematics) for designing effective policies in education, specifically for developing countries, like Indonesia. The first chapter investigated the internal structure of the PISA 2012 math test and examined how the outcomes were related to the high-stakes 9th grade national examination in mathematics by using common persons linking. In addition, the associations of selected student- and school-level background variables were examined to better explain the variability of student mathematics performance across four content areas included in the test. Next, the second chapter proposed a new model for measuring the students’ opportunity-to-learn (OTL) based on provided indicators of the mathematics classroom learning experience. The best-fit model was then chosen due to its strength in explaining the variability of student performance. Finally, the last chapter investigated selected student and school background information to provide insights on how they were associated with aspects of the proposed OTL measures before and after a school clustering effect was added. The data analyses were performed using a multidimensional partial credit model with latent regression based on the Indonesian data. The findings revealed that both the mathematics test and the OTL measures were multidimensional. No correlation was found between the 9th graders’ performance in PISA and in the national examination in mathematics. Amongst the selected background variables, SES and grade levels showed stronger associations with the student performance and the OTL level across their sub-domains or aspects, respectively. Students with higher SES were found to attend public schools that offered better OTL. Incorporating the school clustering effect, it was shown that the students’ OTL varied relatively more between schools, rather than within schools. In conclusion, this dissertation provides useful information on how the Indonesian students performed in the assessment framework laid out by PISA mathematics and how they perceived their classroom learning experience as indicators of their OTL. This information can be used to leverage and target evidence-based policy decisions to improve the quality of the national education system.

Advisor: Wilson, Mark
Fuller, Bruce
Complex Boundary Integral Equation Formulation and Stability Analysis of a Maxwell Model and of an Elastic Model of Solid-Solid Phase Transformations

We study a viscoelastic model of the solid-solid phase change of/nolivine to its denser $\beta$-spinel state at high pressures and/ntemperatures reachable in laboratory experiments matching conditions/ntypical of Earth's mantle. Using a previously unknown technique, the/nequations are transformed to the problem of finding two complex/nanalytic functions in the sample satisfying certain conditions on the/nouter boundary. The Sherman-Lauricella boundary integral equation is/nused in a numerical algorithm that eliminates the bottleneck of having/nto solve a large matrix equation at every timestep. The method is/nimplemented and used to compute the solution of a number of/nnon-axisymmetric test problems, some static and some dynamic in time./nNext we develop an alternative formulation in which the Lam\'e/nequations of linearized elasticity are used to model the deformation/nof the two phases, and we allow for compressibility. The formulation/nis novel in that separate reference configurations are maintained for/nthe core and shell regions of the sample that grow or shrink in time/nby accretion or removal at the boundary, one at the expense of the/nother. We then compare the behavior of the evolution of this system/nto the incompressible viscoelastic case and to an alternative elastic/nmodel. Finally, we study the stability of circular interfaces with/naxisymmetric initial data under the evolution equations. For various/nparameter values of the circular interface evolution, we find families/nof small perturbations of the circular interface and radial interface/nvelocity jump that either grow or decay exponentially in time. In/nunstable cases, the growth rate increases without bound as the wave/nnumber of the perturbation increases. In stable cases, the evolution/nequations are well-posed until the interface leaves the stability/nregime, at which point the numerical solutions blow up in an/noscillatory manner. Examples of stable and unstable behavior are/npresented.

Advisor: Wilkening, Jon
Bones of Contention: Forensic Science and Human Rights Violations from the Katyn Forest to The Hague

This dissertation is a history of the use of mass grave exhumations in investigating human rights violations, war crimes, and acts of atrocity in the second half of the twentieth century. This history follows forensic scientists and non-governmental organizations to conflict zones around the world, from Germany in World War II to Latin America, Iraqi Kurdistan, and the former Yugoslavia. As it does so, it tells a history of the increasingly international and scientific nature of human rights investigations, in which forensic scientists and the bones they dig up came to play an important role in the historical and legal reconstructions of genocides and other human rights violations./nIn 1930s and 1940s Germany, as elsewhere on the European continent, forensic evidence and forensic experts were common features of criminal investigations and prosecutions. It was in the unlikely context of Nazi Germany, though, that forensic science merged with humanitarian and human rights sensibilities and brought about the first international, scientist-led, forensic investigation of a mass grave containing victims of large-scale violence. In 1943, some of Europe’s most respected forensic scientists gathered at a pit in the Katyn Forest, in the western Soviet Union, containing the bodies of some five thousand Polish officers in uniform. The team was tasked with determining which of Europe’s totalitarian regimes was responsible for their deaths. This grand forensic experiment and its aftermath anticipated both the value and the challenges of introducing human bodies into legal and historical reconstructions of past events./nAfter Katyn, large-scale, human rights-driven forensic exhumations did not reemerge for another four decades. When they did, they met an entirely different geopolitical landscape, one in which such investigations found increased resonance with governments, as well as with victims’ families and survivors of genocide and other atrocities. This traction helped sustain and proliferate their use around the globe. The thawing of the Cold War allowed space for grassroots calls for transitional justice, efforts to end ongoing human rights abuses and genocides, and to investigate ones that had already occurred. This culminated after the Srebrenica genocide, where forensic evidence was used on an unprecedented scale. In telling a history of how and why international scientists, NGOs, national governments, and international criminal tribunals came to view forensic evidence as valuable in the global post-Cold War project of documenting and prosecuting international crimes, this dissertation is distinguished from recent historiography by its focus on the motivations and actions of the individual practitioners who undertook this human rights project.

Advisor: Hoffmann, Stefan-Ludwig
Amazonia: A Laboratory for Fiction

Amazonia: A Laboratory for Fiction, analyzes the process and the forms through which Amazonia became a literary topic in the twentieth century. This dissertation proposes that the emergence of modern literature about the region articulates a distrust of the discourses and practices of imperial and neo-colonial territorial apprehension. It proposes the study of a regional tradition, looking at Hispanic and Brazilian texts in dialogue, and it focuses on the self-referential practices of this tradition. By doing so, this dissertation claims that Amazonia has served as a laboratory of representation and fiction that has contributed to the transformation and evolution of the Latin American novel. Ultimately, what is at stake in this research is the emergence of modern literature as a means to destabilize the imageries and practices that have forced Amazonia’s integration into processes of modernization. To this extent, this dissertation is an inquiry into the relationship between aesthetics, science, and politics, and constitutes a critique of History. It intervenes in debates on theory of the novel, postcolonial studies, and eco-criticism. The first chapter shows how Euclides da Cunha’s À margem da história (1909) forges a new national language informed by science and poetics that ultimately creates a new imagery of the region as an inapprehensible space. Da Cunha’s essays inaugurate a literary tradition that the “novelas de la selva” further develop by continuing to challenge the modes through which it has been portrayed. To this extent, the second chapter focuses on how José Eustasio Rivera’s La vorágine (1924) questions the domestication of nature rendered by the aesthetic of modernismo and stages a crisis of representation from which Amazonia surfaces as a disorienting and unconquerable site. The creation of the novel La vorágine itself is the outcome. Rivera’s novel consolidates the modern literature of the region as a self-referencing tradition that underscores its own aesthetic practices, becoming a site that debates and questions the discursive constructs through which the Amazon has been imagined. Following this, the third chapter studies how Alejo Carpentier’s Los pasos perdidos (1953) constructs the “selva” as an artifice through a mechanism of quotation of previous texts like La vorágine, thus generating a critical gap between the text and the “real” geographical referent. The fourth chapter analyzes Milton Hatoum’s Órfãos do Eldorado (2008) as a critique of the inscription of Amazonia into western “civilizing” discourses of History through the idea of memory as a means to reconstruct the ruins of the present left by modernization.

Advisor: Brizuela, Natalia
Tyrosinase inhibitors identified from phytochemicals and their mechanism of control

The enzyme tyrosinase is responsible for catalyzing the first steps of the melanin formation pathway. Essential oil of the fresh leaves of Polygonumodoratum (Polygonaceae), commonly known as Vietnam coriander, was found to inhibit the oxidation catalyzed by tyrosinase (EC 1.14.18.1). Twenty five scent compounds were characterized in the essential oil by GC-MS analysis. Aldehyde compounds are noted to be the most abundant, followed by alcoholic compounds but to a much lesser extent. Alkanals; dodecanal (55.49%), and decanal (11.57%); were the two most abundant in the essential oil, followed by anisaldehyde (6.35%). Dodecanal and decanal inhibited the oxidation of both L-tyrosine and L-3,4-dihydroxyphenylalanine (L-DOPA) catalyzed by mushroom tyrosinase./nIn our search for plant derived tyrosinase inhibitors, benzaldehydes were explored. A series of benzaldehyde structural analogues inhibited the tyrosinase-catalyzed oxidation of L-3,4-dihydroxyphenylalanine (L-DOPA) and a handful suppressed melanogenesis activity. The mechanism behind tyrosinase suppression has not been well understood. In cell free experiments, it is likely that the aldehyde group forms a Schiff base with the primary amino acid group on the enzyme. The hydroxyl and methoxy groups then contribute by stabilizing a newly formed complex that suppresses the enzyme./nThe final class of phytochemicals explored for their enzyme inhibition mechanisms were tannins. The hydrolysable tannin gallic acid has been reported as a tyrosinase inhibitor but the mechanism has not been clearly understood. Enzymatic assays found that gallic acid inhibited the oxidation of L-3,4-dihydroxyphenylalanine (L-DOPA) catalyzed by mushroom tyrosinase but the tannin was not oxidized when mixed with the enzyme. The available oxygen in the reaction mixture was used for the oxidation of gallic acid and L-DOPA. The enzymatically generated intermediates produced complex mixtures, and thus gallic acid suppressed the initial rate of pigmented product formation.

Advisor: Kubo, Isao