VictorJuiz/thesis huggingface dataset:
Predicting Phonon Transport in Two-dimensional Materials

Over the last decade, substantial attention has been paid to novel nanostructures based on two-dimensional (2D) materials. Among the hundreds of 2D materials that have been successfully synthesized in recent years, graphene, boron nitride, and molybdenum disulfide are the ones that have been intensively studied. It has been demonstrated that these materials exhibit thermal conductivities significantly higher than those of bulk samples of the same material. However, little is known about the physics of phonons in these materials, especially when tensile strain is applied. Properties of these materials are still not well understood, and modelling approaches are still needed to support engineering design of these novel nanostructures. In this thesis, I use state-of-the-art atomistic simulation techniques in combination with statistical thermodynamics formulations to obtain the phonon properties (lifetime, group velocity, and heat capacity) and thermal conductivities of unstrained and strained samples of graphene, boron nitride, molybdenum disulfide, and also superlattices of graphene and boron nitride. Special emphasis is given to the role of the acoustic phonon modes and the thermal response of these materials to the application of tensile strain. I apply spectral analysis to a set of molecular dynamics trajectories to estimate phonon lifetimes, harmonic lattice dynamics to estimate phonon group velocities, and Bose-Einstein statistics to estimate phonon heat capacities. These phonon properties are used to predict the thermal conductivity by means of a mode-dependent equation from kinetic theory. In the superlattices, I study the variation of the frequency dependence of the phonon properties with the periodicity and interface configuration (zigzag and armchair) for superlattices with period lengths within the coherent regime. The results showed that the thermal conductivity decreases significantly from the shortest period length to the second period length, 13% across the interfaces and 16% along the interfaces. For greater periods, the conductivity across the interfaces continues decreasing at a smaller rate of 11 W/mK per period length increase, driven by changes in the phonon group velocities (coherent effects). In contrast, the conductivity along the interfaces slightly recovers at a rate of 2 W/mK per period, driven by changes in the phonon relaxation times (diffusive effects).

Keywords: 2D materials
Phonon transport
Simulations
Superlattices
Tensile strain
Advisor: Amon, Cristina H
The Development and Decline of Malediction in the Charters of Anglo-Saxon England

This thesis focuses on the use of maledictory sanction clauses to protect charters, whether written grants of land or privileges, in Anglo-Saxon England. Based on a specially designed and created database of all Anglo-Latin sanction clauses from authentic and substantially authentic single sheets from the ninth to the eleventh century (approximately 171 documents), it traces the formulation of the clause through the pre-Conquest period, revealing lexical, structural, and thematic patterns. Because they were subject to scribal creativity, sanction clauses reflect themes of importance to their draftsmen and run parallel to punitive and infernal concepts emphasized in contemporary works. The thesis begins with a historical overview of medieval cursing and examines each of the elements potentially included in a sanction clause. It then presents data that was collected in a century-by-century arrangement in order to reveal potential patterns. Finally, it looks at the Anglo-Norman Cartulary of Christ Church, Canterbury, extant in three medieval copies. The cartulary’s compiler recasts his source materials, altering them to fit a common mold. This recasting included the addition, deletion, and modification of the sources’ sanction clauses. Such interpretive acts tell us much about the intent of the early English cartularists, the archival environment that produced such a compiler, and the perceived function of malediction in the post-Conquest period. This dissertation suggests that sanction clauses dropped from contemporary diplomatic use, not because of a newfound perception of their inefficiency—they were, arguably, fairly inefficient modes of preservation all along—but because of the gradual secularization of the previously highly religious genre. The detail with which formulation of the Anglo-Latin sanction clause is laid out herein sheds further light on its intricacies and provides material for further study of its significance in the broader Anglo-Saxon social context.

Keywords: Anglo-Saxon
Charters
Curses
Diplomatics
Malediction
Medieval
Advisor: Orchard, Andy
Computational Methods for Predicting and Validating the Causes of Mendelian Disease

We still do not know the genetic basis of roughly half of the estimated 7,000 Mendelian diseases. For some diseases, the responsible variants will not be discovered with standard genetic sequencing. If the variant falls outside of the exome, occurs in a repetitive region, or is a larger structural change, it is unlikely to be found by whole exome sequencing. For other diseases, the variant might be found, but the association with the disease has not yet been discovered. In these cases, making such a discovery requires several steps. Computational approaches are necessary to accurately prioritize harmful variants based on available knowledge. Then, additional information is needed to substantiate the association, such as functional tests, animal models, or identifying unrelated families with the same variant. This thesis presents several contributions to help researchers determine the genetic basis of unsolved Mendelian diseases: First, a method was developed that improves variant prioritization for a class of variants that are usually ignored by analysis pipelines: synonymous variants. After curating known examples from the literature, machine learning methods were trained to prioritize these variants based on a set of designed features. Second, finding additional families is a substantial hurdle in rare disease research. By collecting detailed phenotype information, computational methods can be used to find patients with a similar presentation. This leads to improved variant prioritization by combining sequencing data from several similar patients, without ever needing to explicitly define cohorts. The power of matchmaking methods grows exponentially with the size of the database, but simulations suggest that several hundred thousand cases are needed to identify the genetic basis of most Mendelian diseases. Finally, these matchmaking algorithms are implemented in a web portal, PhenomeCentral, which is used by several consortia and hundreds of clinicians and researchers. While this platform is a repository of several thousand undiagnosed cases, matchmaking between platforms is critical to achieve the numbers of cases predicted to be necessary. Towards this end, the Matchmaker Exchange (MME) was established and an API developed. Case profiles are exchanged within a secure federated network to reduce the time for researchers to validate genetic hypotheses.

Keywords: deep phenotyping
genomics
high throughput sequencing
machine learning
patient matchmaking
rare diseases
Advisor: Brudno, Michael
From Software Threads to Parallel Hardware with LegUp High-level Synthesis

High-level synthesis (HLS) can automatically synthesize software to hardware. With the design specification in software, HLS can reduce the lengthy design cycles of hardware, and make the performance and energy-efficiency benefits of hardware accessible to those without hardware skills. Since the introduction of the first C-based HLS tools more than a decade ago, however, the adaption of the technology has been slow by both software and hardware engineers. We attribute this to two key factors: 1) For hardware engineers, there is still a gap between HLS-generated hardware and human-designed hardware, partly due to the inability of HLS tools to fully exploit hardware parallelism, and 2) for software engineers, HLS remains to be a difficult endeavour, as many parts of the design, such as system integration, largely remain a manual process. This dissertation provides an HLS framework, LegUp, which seeks to address both issues. LegUp can compile an entire software program to hardware to produce a hardware-only system, or it can also automatically partition the program to generate a processor-accelerator hybrid system, wherein the compute-intensive program segments are accelerated by hardware, with the remaining segments executed in software on a processor. In both cases, a complete system is generated, including necessary memories and interconnect. To allow one to easily exploit hardware parallelism, we provide HLS support for synthesizing parallel software to parallel hardware. In particular, we support automatically compiling a multi-threaded program with Pthreads and OpenMP to parallel hardware accelerators that operate concurrently within a hardware-only or a processor-accelerator hybrid system. In the context of parallel hardware, we investigate architectural and memory optimizations that help to improve circuit performance and area, and discuss a method of using the producer-consumer pattern in software to infer a streaming circuit in hardware. With these techniques, we show that LegUp can produce high-performance hardware that can be competitive to circuits that are generated by commercial HLS tools, and demonstrate that LegUp-generated circuits can also outperform software executing on x86 processors.

Keywords: Field-programmable gate array
Hardware/Software co-design
High-level synthesis
LegUp High-Level Synthesis Framework
Parallel hardware
System-on-Chip
Advisor: Anderson, Jason H
Brown, Stephen D
CHIME and Probing the Origin of Fast Radio Bursts

The time-variable long-wavelength sky harbours a number of known but unsolved astrophysical problems, and surely many more undiscovered phenomena. With modern tools such problems will become tractable, and new classes of astronomical objects will be revealed. These tools include digital telescopes made from powerful computing clusters, and improved theoretical methods. In this thesis we employ such devices to understand better several puzzles in the time-domain radio sky. Our primary focus is on the origin of fast radio bursts (FRBs), a new class of transients of which there seem to be thousands per sky per day. We offer a model in which FRBs are extragalactic but non-cosmological pulsars in young supernova remnants. Since this theoretical work was done, observations have corroborated the picture of FRBs as young rotating neutron stars, including the non-Poissonian repetition of FRB 121102. We also present statistical arguments regarding the nature and location of FRBs. These include reinstituting the classic V/Vmax-test to measure the brightness distribution of FRBs, i.e., constraining ∂log N/∂log S. We find consistency with a Euclidean distribution. This means current observations cannot distinguish between a cosmological population and a more local uniform population, unless added assumptions are made. We also showed that the rate of FRBs at low frequencies is consistent with the rate at 1.4\,GHz, which is promising for upcoming high-impact experiments. One of these is the Canadian Hydrogen Intensity Mapping Experiment (CHIME). We outline this instrument and its three back-ends: a cosmology experiment whose goal is to measure dark energy through 21 cm intensity mapping, a pulsar back-end, and an FRB project that is expected to be by far the fastest survey in the foreseeable future. We describe the creation of a digital beamforming back-end on the CHIME Pathfinder, which acts as a test-bed for the three final experiments just described. We also discuss the commissioning of a 24/7 real-time VLBI FRB search between the Pathfinder's synthetic beam and the Algonquin Radio Observatory (ARO) 46 m telescope, including early results. Finally, we present a study of the microstructure in B0329+54's individual pulses in full-polarization and present results on its quasi-periodic structure.

Keywords: CHIME
fast radio bursts
pulsars
radio astronomy
transient astrophysics
Advisor: Pen, Ue-Li
Vanderlinde, Keith
Health System Stewardship in Arctic Regions

This thesis responds to health system challenges in Arctic regions where there are complex and interrelated challenges related to climate change and environmental effects impacts, geographic remoteness, indigenous health needs and values, and health equity. Specifically, the United States (US), Canada, Norway and Finland are studied. The need to further understand the health system context has been emphasized in many international and Arctic forums. How health systems situate or optimize performance in the Arctic context has not been studied previously. This thesis explores how health systems respond with a stewardship framework that aspires to adopt ethical and multi-sector approaches to health. To broaden our lens, we developed new methods that recognize both indigenous knowledge and western science. We captured indigenous and national perspectives, and we enveloped notions of common values (humanity, cultural responsiveness, teaching, nourishment, community voice, kinship, respect, holism and empowerment) that provide a basis for health system comparisons in Arctic nations. Policies and strategies within circumpolar nations that respond to shared context and challenges were identified. In particular, we used a case study approach to highlight how circumpolar health systems organize and respond through health system stewardship functions to the shared circumpolar challenges. Overall, Canada and the United States demonstrated higher levels of self-determination, and Norway and Finland exhibited strengths in strategies and policies influencing work across sectors. While the emphasis on stewardship functions differed, government statements that promoted work across sectors were present in all nations, as were dialogues on the self-determination of indigenous peoples. The findings provide some ssurance that there are common values and goals in Arctic regions, and that the concept of stewardship is an effective response within this context. The findings provide a collection of policy resources and a direction for value-based stewardship of health systems in Arctic regions at the regional, national, self-governing and international level of governments. The development of a performance framework and scorecard for this context will enhance the ability to learn from different approaches to stewardship, and guide trusting relationships and health equity in circumpolar nations.

Keywords: Circumpolar
Climate change
Governance
Health equity
Health systems
Indigenous
Advisor: Brown, Adalsteinn
Dissolution of the Sentence: Reading the Theological, Philosophical, and Literary Dimensions of the Propositional Form with G.W.F. Hegel and Gertrude Stein

This thesis is concerned with the problem of sentences, and the latent capacities of the propositional form, as brought to the fore in the works of G. W. F. Hegel and Gertrude Stein. The analysis proceeds in a comparative manner, asking after the joint contributions that both of these authors make to adequate and novel theorizations of syntax as a way of expressing philosophical, theological, and literary truth. One principal argument is that both authors work out such contributions under a presupposed theological pressure in their thought and writing. We inquire into the effect that such an epistemological predicament has on the formation and theorization of syntactic functions. Both Hegel and Stein offer challenging critiques of our notions of the “theological,” and their works exhibit what will be approached as “dispersed” and “implicit” theological modalities, which affect these authors’ sentences in manifold ways. The basic form of the proposition – “S is P” – is questioned throughout, with specific reference to Hegel’s “speculative sentence” and Stein’s “completed sentence” as the vital linguistic offerings both of these authors make, offerings that in turn affect both the production and the theorization of sentences in works like Hegel’s Phenomenology of Spirit and Science of Logic and Stein’s Lectures in America, Making of Americans, and Tender Buttons. Such theorizations are here gathered from disparate traditions, but always with an eye to their original historical emergence. This analysis should help to highlight the challenges both authors issue against more current models of propositional functioning such as performativity, description, participation, enactment, subsumption, predication, and copulation. The final aim is a thorough presentation of the contributions these authors make to an understanding of the capacities of the proposition, the value of syntactic experimentation, and the gathering of novel linguistic practices forged in the fire of a competing set of theological, epistemological, and literary ambitions.

Keywords: Hegel
language
proposition
sentences
Stein
syntax
Advisor: Comay, Rebecca
Self-Assembly and Surface-Patterning of Polymer-Functionalized Nanoparticles

This thesis explores the preparation of polymer-functionalized nanoparticles, the surface-segregation of their polymer ligands to generate patchy nanocolloids, and the use of patchy and non-patchy polymer-functionalized nanoparticles as building blocks for self-assembly. In Chapter 3, the self-assembly of nanospheres uniformly functionalized with polymer was explored. Both chain-like and globular structures were generated from the same spherical nanoparticle building blocks by tuning the interplay of nanoscale forces. The molecular weight of polymer ligands and the polarity and ionic strength of the self-assembly medium were changed to adjust the interparticle hydrophobic attraction and electrostatic repulsion in order to obtain the desired self-assembled structure. The experimental results were in agreement with theoretical predictions for the most thermodynamically favourable self-assemblies. Hierarchical structures made from assembled globules of nanospheres were also generated and the reversibility of the self-assemblies was demonstrated. In Chapter 4, the segregation of polymer ligands into pinned micelles on the surface of nanospheres was explored. Single and multi-patch nanospheres were generated by studying the interplay of nanosphere curvature and polymer molecular weight. The statistics of patchy nanosphere species was quantified and compared to theoretical predictions. Permanent crosslinking of polymer patches was achieved in addition to tomography of the generated colloids to further characterize the morphology. In Chapter 5, the surface segregation of polymer ligands on nanoparticles with different shapes and composition such as spherocylindrical nanorods, nanorods with a dumbbell shape, and nanocubes was demonstrated. The surface segregation of different polymers (including pH-responsive and conductive polymers) on nanospheres was also achieved demonstrating the versatility of the polymer segregation approach for nanopatterning. In addition, the self-assembly of patchy nanospheres and nanocubes was explored yielding new self-assembled structures such as an open checkerboard formed from patchy nanocubes. The use of one-patch nanospheres as colloidal surfactants stabilizing a solvent-polymer interface was also achieved.

Keywords: colloid
microphase separation
nanoparticle
patchy particles
polymer
self-assembly
Advisor: Kumacheva, Eugenia
Axion Theas: Wonder, Space, and Place in Pausanias' Periegesis Hellados

The Periegesis Hellados presents a description of the sites and sights of Roman Greece in ten carefully constructed books. These books present the fruits of author’s extensive travels and careful textual research over the course of several decades (between the 130’s and ca. AD 175-80) and compiled into a unified composite itinerary. There is no doubt that Pausanias travels through an “already written landscape,” and his travel experience is necessarily informed by and sometimes clearly motivated by his literary encounters. This project investigates Pausanias’ engagement with literary antecedents, with a particular focus on the antiquarian impulse to excerpt and compile anecdotes in thematic catalogues, which broadly resemble wonder-texts (paradoxographies). The organizing principle of these thematic catalogues contrasts with the topographical (spatial) structure of the frame narrative of the Periegesis. In part, this study aims to resolve the perceived tension between the travel account and the antiquarian mode in Pausanias’ project in order to show that they serve complementary rather than competing ends. Resolution of these competing paradigms allows in turn for a more coherent understanding of the Periegesis as unified subject. This study argues that wonder (thauma) is a unifying theme of Periegesis Hellados. Through epiphanies and descriptions of marvels, whether in catalogues or tied to particular features on his route, Pausanias negotiates the unbridgeable ontological distance between human and divine agents through a discourse of the marvelous that is firmly rooted geographic specificity. This study suggests the Periegesis Hellados can be broadly understood as an attempted re-enchantment of Hellas in the imperial age.

Keywords: Catalog literature
Paradoxography
Thauma
Travel Writing
Wonder
Advisor: Burgess, Jonathan S
Art's Challenge: An Analysis of the Role of Aesthetics in the Work of Hugo von Hofmannsthal

Art poses itself to us as a challenge: when we confront a work of art, we are in turn confronted with the question of how to be after the encounter. My research pursues Hofmannsthal’s treatment of this challenge by examining his depiction of the aesthetic encounter in literary form. I argue that Hofmannsthal’s evolving understanding of the aesthetic begins to incorporate the ethical by way of a dialogical structure that emerges out of the encounter with art, things, and people. This kind of encounter is characterised simultaneously by the viewer’s creative boldness and reverential humility. To illustrate this, I analyse a selection of Hofmannsthal’s works treating the aesthetic and its role in the encounter. In Chapter 1, I consider the meaning of beauty in Das Märchen der 672. Nacht, a tale which depicts uncanny encounters with beautiful objects. For Chapter 2, I offer a reading of Die Briefe des Zurückgekehrten, a series of fictional letters which culminate in an encounter with Van Gogh’s paintings. Augenblicke in Griechenland, the focus of Chapter 3, explores what I interpret to be the dialogical nature of the encounter with art of the past. In Chapter 4, the final chapter, I analyse the tale Die Frau ohne Schatten (which forms a pendant to Das Märchen der 672. Nacht) with a view to the parallel stories of the two-fold rebirth of art and ethical human relations. Hofmannsthal’s work almost never ends in resolution, except in such fairy-tale stories as Die Frau ohne Schatten. But even the resolution of this story is, from a certain perspective, a false one. An analysis of the marriage of ethics and aesthetics leads us to an inescapable aporia. Hofmannsthal’s way to the aporia, however, is one that raises fundamental questions about our understanding of art, what it does, and how we respond.

Keywords: Aesthetic encounter
Dialogical philosophy
Ekphrasis
Hofmannsthal
Modernism
Philosophy and Literature
Advisor: Zilcosky, John