VictorJuiz/thesis huggingface dataset:
Development of Metallic Magnetic Calorimeters for Nuclear Safeguards Applications

Many nuclear safeguards applications could benefit from high-resolution gamma-ray spectroscopy achievable with metallic magnetic calorimeters. This dissertation covers the development of a system for these applications based on gamma-ray detectors developed at the University of Heidelberg. It demonstrates new calorimeters of this type, which achieved an energy resolution of 45.5 eV full-width at half-maximum at 59.54 keV, roughly ten times better than current state of the art high purity germanium detectors. This is the best energy resolution achieved with a gamma-ray metallic magnetic calorimeter at this energy to date. In addition to demonstrating a new benchmark in energy resolution, an experimental system for measuring samples with metallic magnetic calorimeters was constructed at Lawrence Livermore National Laboratory. This system achieved an energy resolution of 91.3 eV full-width at half-maximum at 59.54 keV under optimal conditions. Using this system it was possible to characterize the linearity of the response, the count-rate limitations, and the energy resolution as a function of temperature of the new calorimeter. With this characterization it was determined that it would be feasible to measure Pu-242 in a mixed isotope plutonium sample. A measurement of a mixed isotope plutonium sample was performed over the course of 12 days with a single two-pixel metallic magnetic calorimeter. The relative concentration of Pu-242 in comparison to other plutonium isotopes was determined by direct measurement to less than half a percent accuracy. This is comparable with the accuracy of the best-case scenario using traditional indirect methods. The ability to directly measure the relative concentration of Pu-242 in a sample could enable more accurate accounting and detection of indications of undeclared activities in nuclear safeguards, a better constraint on source material in forensic samples containing plutonium, and improvements in verification in a future plutonium disposition treaty.

Advisor: Vetter, Kai
An Adapted Shared Storybook Reading Program Implemented in Inclusive Preschool Classrooms: An Investigation of its Use and Effectiveness

The Pathways to Literacy reading program (Lee, Mims, & Browder, 2011) has been demonstrated to be effective at increasing both engagement and comprehension during shared storybook reading for students with exceptional needs. To date, research on Pathways to Literacy has been limited to students in early elementary school rather than preschool, which is when shared reading is usually emphasized as part of the general education curriculum. In these investigations, the reading program has been administered in one-on-one instructional settings, often in special education classrooms. No existing research has examined the ability of participating students to generalize newly learned skills to novel adapted books. The current study seeks to add to the literature by investigating the use of the Pathways to Literacy reading program in inclusive preschool settings. Three questions were addressed. First, using a multiple baseline design across three students, the question of whether or not the reading program remained effective for the target student when introduced in this new setting was asked. Second, whether or not the target students were able to generalize their skills in the areas of engagement, listening comprehension, and communication was addressed via the introduction of novel adapted books. Finally, teachers' perceptions of the reading program were explored. Of particular interest were questions related to what changes they would recommend so that the reading program can be used in this new setting. Results suggest that the Pathways to Literacy reading program was effective in increasing both engagement and listening comprehension and communication for the targeted preschool students and these skills generalized to novel adapted books. Pre- and post-intervention interviews suggest that the teachers found the goals, procedures, and outcomes of the Pathways to Literacy reading program were generally appropriate for preschool students.

Advisor: Cunningham, Anne E
Robust Scheduling for Queueing Networks

Queueing networks are used to model complicated processing environments such as data centers, call centers, transportation networks, health systems, etc. A queueing network consists of multiple interconnected queues with some routing structure, and a set of servers that have different and possibly overlapping capabilities in processing tasks (jobs) of different queues. One of the most important challenges in designing processing systems is to come up with a low-complexity and efficient scheduling policy./nIn this thesis, we consider the problem of robust scheduling for various types of processing networks. We call a policy robust if it does not depend on system parameters such as arrival and service rates. A major challenge in designing efficient scheduling policies for new large-scale processing networks is the lack of reliable estimates of system parameters; thus, designing a robust scheduling policy is of great practical interest. We develop a novel methodology for designing robust scheduling policies for queueing networks. The key idea of our design is to use the queue-length changes information to learn the right allocation of service resources to different tasks by stochastic gradient projection method. Our scheduling policy is oblivious to the knowledge of arrival rates and service rates of tasks in the network. Further, we propose a new fork-join processing network for scheduling jobs that are represented as directed acyclic graphs. We apply our robust scheduling policy to this fork-join network, and prove rate stability of the network under some mild assumptions./nNext, we consider the stability of open multiclass queueing networks under longest-queue (LQ) scheduling. LQ scheduling is of great practical interest since (a) it requires only local decisions per group of queues; (b) the policy is robust to knowledge of arrival rates, service rates and routing probabilities of the network. Throughput-optimality of LQ scheduling policy for open multiclass queueing network is still an open problem. We resolve the open problem for a special case of multiclass queueing networks with two servers that can each process two queues, and show that LQ is indeed throughput-optimal./nFinally, we consider transportation networks that can be well modeled by queueing networks. We abstractly model a network of signalized intersections regulated by fixed-time controls as a deterministic queueing network with periodic arrival and service rates. This system is characterized by a delay-differential equation. We show that there exists a unique periodic trajectory of queue-lengths, and every trajectory or solution of the system converges to this periodic trajectory, independent of the initial conditions.

Advisor: Walrand, Jean C
Characterization of the Transcription Activator-Like Effectors of Xanthomonas axonopodis pv. manihotis and identification of susceptibility targets in the host cassava

This work provides a comprehensive study of the molecular events mediated by the transcription activator-like (TAL) effectors of Xanthomonas axonopodis pv. manihotis (Xam) during infection of its host plant cassava (Manihot esculenta). TAL effectors are secreted via the bacterial type III secretion system into plant cells where they localize to the nucleus, bind specific sequences of nucleotides in plant promoters, and activate the expression of downstream genes. The DNA binding activity of Xam TAL effectors is carried out by a central domain containing a variable number of 34 amino acid repeats, where the 12th and 13th amino acid residues, the repeat variable diresidues (RVDs), of each repeat dictate which nucleotide will be bound at that site. Genetic analysis of the TAL effectors of highly virulent Xam strain Xam668 showed a virulence role for TAL20Xam668, which contributes to in planta bacterial growth and watersoaking symptom development, and TAL14Xam668, which contributes to in planta bacterial growth. RNA-Sequencing (RNA-Seq) revealed a single host gene target of TAL20Xam668, MeSWEET10a, which is a member of the SWEET family of sugar transporters. Designer TAL effectors that activate MeSWEET10a complemented the Xam668∆TAL20 mutant phenotype, revealing the role of MeSWEET10a in cassava’s susceptibility to Xam. SWEETs are known X. oryzae pv. oryzae TAL effector-targeted susceptibility genes in rice and thus this result establishes the activation of SWEET sugar transporters as a common mechanism of disease promotion for diverse species of Xanthomonas. In contrast to TAL20Xam668 which has a single target gene, RNA-Seq showed that TAL14Xam668 activates over 50 genes during the infection process. A subset of the TAL14Xam668-targeted genes were tested for activation by TAL14CIO151 from Xam strain CIO151 and, although TAL14CIO151 and TAL14Xam668 differ by only a single RVD, they display differential activation of host gene targets. TAL14CIO151 complements the TAL14Xam668 mutant defect, implying that shared target genes are important for TAL14Xam668-mediated disease susceptibility. This type of complementation with closely related TAL effectors is a novel approach to narrowing down biologically relevant susceptibility genes of TAL effectors with multiple targets. The comparison of the activities of TAL14Xam668 and TAL14CIO151 provides an example of how TAL effector target activation by two strains within a single species of Xanthomonas can be dramatically affected by a small change in RVD-nucleotide affinity at a single site and reflects the parameters of RVD-nucleotide interaction determined using artificial TAL effectors in transient systems. Finally, we present proof-of-concept experiments showing TAL effector-induced resistance to Xam in cassava.

Advisor: Staskawicz, Brian
Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21(DE3) Biosafety Strain

Synthetic auxotrophs are organisms engineered to require the presence of a particular molecule for viability. We show that these organisms can be generated by engineering ligand-dependence into essential genes. We demonstrate a method for generating a Synthetic auxotroph based on a Ligand-Dependent Essential gene (SLiDE), using six essential genes as test cases: pheS, dnaN, tyrS, metG, orn, and adk. We show that a single SLiDE strain can have a 1 x 108-fold increase in viability when chemically complemented with the ligand benzothiazole. The optimized SLiDE engineering protocol required less than one week and $100 USD. We combined multiple SLiDE strain alleles into the industrial E. coli strain BL21(DE3), yielding an organism that exceeds the biosafety criteria with an escape frequency below the limit of detection of 3 x 10-11.

Advisor: Anderson, John C
Quantum Feedback and Traveling-wave Parametric Amplification in Superconducting Circuits

Feedback control in classical systems is an indispensable, ubiquitous tool. The theoretical basis for achieving optimal classical control is well understood, and crucially relies on a very classical assumption: that measurements of the state of a system under control need not perturb that state. In a quantum context this assumption is fundamentally invalid. Although many aspects of the theory of quantum feedback control are relatively well developed, the technological basis for feedback control of a single quantum system has only very recently matured. We demonstrate the experimental realization of a quantum feedback control protocol, perpetually stabilizing the coherent Rabi oscillations of a superconducting qubit. This is the first utilization of quantum feedback control for stabilizing a dynamical process, and the first application of quantum feedback in a solid-state system of any kind. This demonstration comprises the first half of this thesis. The feedback protocol is predicated on the ability to make high-fidelity quantum measurements, which are enabled by quantum-limited Josephson parametric amplifiers (JPAs). The design and realization of the novel Josephson traveling-wave parametric amplifier (JTWPA) comprises the second half of this thesis. The JTWPA achieves order-of-magnitude improvements over state of the art JPAs in bandwidth and signal power handling while providing quantum-limited noise performance, potentially enabling the simultaneous readout of dozens of superconducting qubits and the generation of broadband multi-mode squeezing in the microwave domain.

Advisor: Siddiqi, Irfan
Coflow: A Networking Abstraction for Distributed Data-Parallel Applications

Over the past decade, the confluence of an unprecedented growth in data volumes and the rapid rise of cloud computing has fundamentally transformed systems software and corresponding infrastructure. To deal with massive datasets, more and more applications today are scaling out to large datacenters. These distributed data-parallel applications run on tens to thousands of machines in parallel to exploit I/O parallelism, and they enable a wide variety of use cases, including interactive analysis, SQL queries, machine learning, and graph processing./nCommunication between the distributed computation tasks of these applications often result in massive data transfers over the network. Consequently, concentrated efforts in both industry and academia have gone into building high-capacity, low-latency datacenter networks at scale. At the same time, researchers and practitioners have proposed a wide variety of solutions to minimize flow completion times or to ensure per-flow fairness based on the point-to-point flow abstraction that forms the basis of the TCP/IP stack./nWe observe that despite rapid innovations in both applications and infrastructure, application- and network-level goals are moving further apart. Data-parallel applications care about all their flows, but today’s networks treat each point-to-point flow independently. This fundamental mismatch has resulted in complex point solutions for application developers, a myriad of configuration options for end users, and an overall loss of performance./nThe key contribution of this dissertation is bridging this gap between application-level performance and network-level optimizations through the coflow abstraction. Each multipoint-to-multipoint coflow represents a collection of flows with a common application-level performance objective, enabling application-aware decision making in the network. We describe complete solutions including architectures, algorithms, and implementations that apply coflows to multiple scenarios using central coordination, and we demonstrate through large-scale cloud deployments and trace-driven simulations that simply knowing how flows relate to each other is enough for better network scheduling, meeting more deadlines, and providing higher performance isolation than what is otherwise possible using today’s application-agnostic solutions./nIn addition to performance improvements, coflows allow us to consolidate communication optimizations across multiple applications, simplifying software development and relieving end users from parameter tuning. On the theoretical front, we discover and characterize for the first time the concurrent open shop scheduling with coupled resources family of problems. Because any flow is also a coflow with just one flow, coflows and coflow-based solutions presented in this dissertation generalize a large body of work in both networking and scheduling literatures.

Advisor: Stoica, Ion
Operator algebras in Solovay's model

We develop the theory of operator algebras in the Solovay model obtained by applying Solovay's construction to a countable transitive model of the axiom of constructibility. We exposit an approach to verifying familiar theorems in the Solovay model by appealing to its absoluteness properties. In this way, we verify a substantial portion of the elementary theory of operator algebras. In this Solovay model, we define a continuum analog of the ultraweak topology, which we call the continuum-weak topology. We define a V*-algebra to be a concrete algebra of operators that is closed in the continuum-weak topology. We show that every separable C*-algebra has an enveloping V*-algebra. If the separable C*-algebra is commutative, then its enveloping V*-algebra is isomorphic to the V*-algebra of bounded complex-valued functions on its spectrum. More generally, if the separable C*-algebra is type I, then its enveloping V*-algebra is isomorphic to a direct sum of type I factors, one for each irreducible representation.

Advisor: Rieffel, Marc A
An I/O-Complexity Lower Bound for All Recursive Matrix Multiplication Algorithms by Path-Routing

Via novel path-routing techniques we prove a lower bound on the I/O-complexity of all recursive matrix multiplication algorithms computed in serial or in parallel and show that it is tight for all square and near-square matrix multiplication algorithms. Previously, tight lower bounds were known only for the classical $\Theta\left(n^3\right)$ matrix multiplication algorithm and those similar to Strassen's algorithm that lack multiple vertex copying. We first prove tight lower bounds on the I/O-complexity of Strassen-like algorithms, under weaker assumptions, by constructing a routing of paths between the inputs and outputs of sufficiently small subcomputations in the algorithm's CDAG. We then further extend this result to all recursive divide-and-conquer matrix multiplication algorithms, and show that our lower bound is optimal for algorithms formed from square and nearly square recursive steps. This requires combining our new path-routing approach with a secondary routing based on the Loomis-Whitney Inequality technique used to prove the optimal I/O-complexity lower bound for classical matrix multiplication.

Advisor: Holtz, Olga V
A Cross-Linguistic Study of Locomotor Experience and Psychological Development: Walking Onset Is Linked to Advanced Receptive and Productive Vocabularies in Berkeley and Shanghai

Whether motoric activities hold psychological effect has been a controversial. Recently, Campos and his colleagues (Campos et al, 2000) have shown the acquisition of prone locomotion not only precedes but also causes various changes in psychological abilities, including perception, cognition, and socio-emotional development. This dissertation work deals with another major motoric achievement during infancy, upright locomotion, and whether it brings about psychological changes. It focuses on an original phenomenon that walking brings about increased receptive and productive vocabularies (Walle & Campos, 2014). If this relation reflects the consequence of an epigenetic event, then it should be present regardless of when the infant typically begins to walk, the infant’s culture, and the infant’s native language. This study sought to replicate the previously reported link between walking and language development in American infants and investigate whether this relation exists cross-nationally in typically developing Chinese infants exposed to Mandarin. Urban Chinese infants not only provide a distinct linguistic and cultural population in which to study this relation but also typically begin walking approximately 6 weeks later than American infants. Our results demonstrated that (1) walking infants in both the American and Chinese samples had greater receptive and productive vocabularies than same-aged crawling infants, (2) differences between crawling and walking infants were proportionally similar in each sample, and (3) the walking-language relation was present for both noun and non-noun vocabularies. These findings provide further support of a relation between infant walking onset and language development, independent of age. Avenues for future research of the processes involved in this relation, as well as additional populations of interest to investigate, are discussed.

Advisor: Campos, Joseph J.
The LITSE Algorithm: Theory and Application

In this dissertation, we present a novel method -- the Learning with Iteration and Tree-based Search Estimation algorithm -- for the estimation of the malarial haplotype composition in one or more individuals and the corresponding haplotype population frequencies, focusing in particular on the case where individuals have been infected by more than one strain. This estimation must take place in the presence of pooled readings of the genetic composition of the parasites present./nThe approach consists of the combination of a parameterized tree-based combinatorial search and a refinement phase incorporating the Expectation Maximization algorithm. The EM algorithm is particularly attractive as it is structured to be applied to situations involving both observed and unobserved information./nA test of an implementation of the algorithm on simulated data demonstrates its effectiveness in accurately estimating the haplotype compositions, both prior to and following the refinement. Its effectiveness established, the algorithm is then applied to a set of laboratory-produced malarial strain data./nIn addition, the algorithm has also been made available to other researchers through a dedicated website allowing submissions and the downloading of results./nWhile the current research focused on the application of the method to malarial parasites, the method is general enough to be applied to cases of infection by other organisms./nFinally, the dissertation presents several suggestions for future work in enhancing the algorithm both computationally and statistically and extending its scope to related research topics.

Advisor: Hubbard, Alan
Material and Optical Design Rules for High Performance Luminescent Solar Concentrators

This dissertation will highlight a path to achieve high photovoltaic conversion efficiency in luminescent solar concentrators, devices which absorb sunlight with a luminescent dye and then re-emit it into a waveguide where it is ultimately collected by a photovoltaic cell. Luminescent concentrators have been studied for more than three decades as potential low-cost but not high efficiency photovoltaics. Astute application of the blackbody radiation law indicates that photonic design is necessary to achieve high efficiency: a reflective filter must be used to trap luminescence at all angles while allowing higher energy photons to pass through. In addition, recent advances in the synthesis of colloidal nanomaterials have created the possibility for lumophores with broad absorption spectra, narrow-bandwidth emission, high luminescence quantum yield, tunable Stokes shifts and tunable Stokes ratios. Together, these factors allow luminescent solar concentrators to achieve the optical characteristics necessary for high efficiency./nWe have fabricated and tested the first generation of these devices. Our experiments demonstrate that the application of carefully matched photonic mirrors and luminescent quantum dots can allow luminescent concentration factors to reach record values while maintaining high photon collection efficiency. Finally, the photonic mirror dramatically mitigates the negative impact of scattering in the waveguide, allowing efficient photon collection over distances much longer than the scattering length of the waveguide./nAfter demonstrating the possibility for high performance, we theoretically explore the efficacy of luminescent concentrators with dielectric reflectors as the high-bandgap top-junctions in two-junction devices. Simple thermodynamic calculations indicate that this approach can be nearly as good as a traditional vertically stacked tandem. The major barriers to such a device are the optical design of narrow-bandwidth, angle-insensitive reflectors with near-unity reflectivity in the reflection band and near unity transmissivity in the pass-band. Additionally, lumophores with narrow emission line widths and carefully controlled Stokes shifts are required. If new lumophores and optical designs can be created that meet the demanding needs of this application, high performance two-junction photovoltaics that collect both the direct and diffuse light could be achieved.

Advisor: Alivisatos, A. Paul