Physical Sciences and Mathematics Commons^™

Bayesian Structural Causal Inference With Probabilistic Programming, Sam A. Witty

Doctoral Dissertations

Reasoning about causal relationships is central to the human experience. This evokes a natural question in our pursuit of human-like artificial intelligence: how might we imbue intelligent systems with similar causal reasoning capabilities? Better yet, how might we imbue intelligent systems with the ability to learn cause and effect relationships from observation and experimentation? Unfortunately, reasoning about cause and effect requires more than just data: it also requires partial knowledge about data generating mechanisms. Given this need, our task then as computational scientists is to design data structures for representing partial causal knowledge, and algorithms for updating that knowledge in …

Machine Learning Modeling Of Polymer Coating Formulations: Benchmark Of Feature Representation Schemes, Nelson I. Evbarunegbe

Masters Theses

Polymer coatings offer a wide range of benefits across various industries, playing a crucial role in product protection and extension of shelf life. However, formulating them can be a non-trivial task given the multitude of variables and factors involved in the production process, rendering it a complex, high-dimensional problem. To tackle this problem, machine learning (ML) has emerged as a promising tool, showing considerable potential in enhancing various polymer and chemistry-based applications, particularly those dealing with high dimensional complexities.

Our research aims to develop a physics-guided ML approach to facilitate the formulations of polymer coatings. As the first step, this …

Applying Density Functional Theory Simulations To Study The Charge Balancing And Structure Directing Roles Of Fluoride In Zeolite Synthesis, Tongkun Wang

Doctoral Dissertations

Zeolites represent a major cornerstone of today’s energy industry as the most-used petrochemical catalyst by weight in the world. Constituted by tetrahedra of T-atoms including Si, Al, Ge and Ti, zeolites form a huge family of nano-porous crystalline materials which also provide reliable candidates for novel, energy related applications such as efficient separations, hydrogen-purifying/storing and conversions from biomass to biofuel. However, the formation mechanism of zeolite is still not clear, as synthesis processes are complicated by requirements including structure directing agents (SDAs), hydroxide or fluoride medium, and experimental conditions like temperature. Attempts for designing new zeolite structures still fall in …

Effective And Efficient Transfer Learning In The Era Of Large Language Models, Tu Vu

Doctoral Dissertations

Substantial progress has been made in the field of natural language processing (NLP) due to the advent of large language models (LLMs)—deep neural networks with millions or billions of parameters pre-trained on large amounts of unlabeled data. However, these models have common weaknesses, including degenerate performance in data-scarce scenarios, and substantial computational resource requirements. This thesis aims to develop methods to address these limitations for improved applicability and performance of LLMs in resource-constrained settings with limited data and/or computational resources. To address the need for labeled data in data-scarce scenarios, I present two methods, in Chapter 2 and Chapter 3, …

Tev-Scale Lepton Number Violation: 0Νββ Decay, The Origin Of Matter, And Energy Frontier Probes, Sebastian Urrutia Quiroga

Doctoral Dissertations

Lepton number violation (LNV) offers promising theoretical pathways to several unresolved problems in particle and nuclear physics and unveils a diverse range of phenomenology across different energy scales. TeV-scale LNV is especially relevant for both its experimental accessibility and its broad-ranging impact, making it a key area of interest for both theoretical and experimental physicists. In this thesis, we explore three distinct scenarios within the LNV research landscape. Our first analysis concerns the implications of TeV-scale LNV effects in thermal leptogenesis and its complementary sensitivity in neutrinoless double beta (0νββ) decay and collider experiments. We employed a simplified model to …

Heat Flow In The Southern Margin Of Salar De Atacama: Deep Groundwater Temperature Distributions And The Implications For Subsurface Flow And Land Surface Energy Budgets, Graham Thomas

Masters Theses

Salar de Atacama (SdA) located in Northern Chile is home to one of the planet’s largest salar systems and lithium resources. Managing groundwater resources in salars is not obvious due to the lack of scientific understanding on the connectivity between the freshwater and brine systems. Using heat as a tracer in SdA provides a cost-effective method to further investigate groundwater flow in salars. This study employs 372 temperature-depth profiles from 90 boreholes between 2013-18 to understand the distinct thermal zones and flow between them in SdA. Three thermal zones exist within the southern margin of SdA’s thermal regime, at higher …

Microplastics In Local Communities’ Tap Water, Zachary T. Rattell

Masters Theses

Microplastics are an emerging environmental contaminant. One of the ways microplastics can get into the environment is by the breakdown of larger plastics. These plastics can come from industrial practices, discarded fabrics, agriculture, and general plastic waste. As these plastics are broken down microplastics leach into the environment. The widespread use of plastics has resulted in the spread of microplastic contaminants all over the world. Microplastics have been reported to be in drinking water, so this paper is looking at the presence of microplastics in local communities of different demographics and socioeconomic statuses. In other studies of different drinking water …

Thermal Conductivity And Mechanical Properties Of Interlayer-Bonded Graphene Bilayers, Afnan Mostafa

Masters Theses

Graphene, an allotrope of carbon, has demonstrated exceptional mechanical, thermal, electronic, and optical properties. Complementary to such innate properties, structural modification through chemical functionalization or defect engineering can significantly enhance the properties and functionality of graphene and its derivatives. Hence, understanding structure-property relationships in graphene-based metamaterials has garnered much attention in recent years. In this thesis, we present molecular dynamics studies aimed at elucidating structure-property relationships that govern the thermomechanical response of interlayer-bonded graphene bilayers.

First, we present a systematic and thorough analysis of thermal transport in interlayer-bonded twisted bilayer graphene (IB-TBG). We find that the introduction of interlayer C-C …

The Fate Of The Crossbridge After Phosphate Rebinding: Implications For Fatigue, Christopher P. Marang

Doctoral Dissertations

In response to repeated intense contractile activity, a muscle’s ability to generate force decreases due to the created state of muscular fatigue. This compromised force production state is dependent on changes within the microenvironment of muscle thought to alter the function of the force generating, contractile protein myosin. For example, phosphate (P_i), elevated during fatigue, has been suggested to alter how myosin generates force. However, the effects of P_i are not straightforward, as muscle fiber data suggest that P_i's interaction with myosin may be force-dependent. In particular, P_i has no effect on maximal shortening …

Semi-Infinite Flags And Zastava Spaces, Andreas Hayash

Doctoral Dissertations

ABSTRACT SEMI-INFINITE FLAGS AND ZASTAVA SPACES SEPTEMBER 2023 ANDREAS HAYASH, B.A., HAMPSHIRE COLLEGE M.S., UNIVERSITY OF MASSACHUSETTS AMHERST Ph.D, UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Ivan Mirković We give an interpretation of Dennis Gaitsgory’s semi-infinite intersection cohomol- ogy sheaf associated to a semisimple simply-connected algebraic group in terms of finite-dimensional geometry. Specifically, we construct machinery to build factoriza- tion spaces over the Ran space from factorization spaces over the configuration space, and show that under this procedure the compactified Zastava space is sent to the support of the semi-infinite intersection cohomology sheaf in the Beilinson-Drinfeld Grassmannian. We also construct …

Atomistic Simulations Of Intrinsically Disordered Protein Folding And Dynamics, Xiping Gong

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) are crucial in biology and human diseases, necessitating a comprehensive understanding of their structure, dynamics, and interactions. Atomistic simulations have emerged as a key tool for unraveling the molecular intricacies and establishing mechanistic insights into how these proteins facilitate diverse biological functions. However, achieving accurate simulations requires both an appropriate protein force field capable of describing the energy landscape of functionally relevant IDP conformations and sufficient conformational sampling to capture the free energy landscape of IDP dynamics. These factors are fundamental in comprehending potential IDP structures, dynamics, and interactions. I first conducted explicit solvent simulations to …

Facets Of The Union-Closed Polytope, Daniel Gallagher

Doctoral Dissertations

In the haze of the 1970s, a conjecture was born to unknown parentage...the union-closed sets conjecture. Given a family of sets $\FF$, we say that $\FF$ is union-closed if for every two sets $S, T \in \FF$, we have $S \cup T \in \FF$. The union-closed sets conjecture states that there is an element in at least half of the sets of any (non-empty) union-closed family. In 2016, Pulaj, Raymond, and Theis reinterpreted the conjecture as an optimization problem that could be formulated as an integer program. This thesis is concerned with the study of the polytope formed by taking …

Design And Fabrication Of A Trapped Ion Quantum Computing Testbed, Christopher A. Caron

Masters Theses

Here we present the design, assembly and successful ion trapping of a room-temperature ion trap system with a custom designed and fabricated surface electrode ion trap, which allows for rapid prototyping of novel trap designs such that new chips can be installed and reach UHV in under 2 days. The system has demonstrated success at trapping and maintaining both single ions and cold crystals of ions. We achieve this by fabricating our own custom surface Paul traps in the UMass Amherst cleanroom facilities, which are then argon ion milled, diced, mounted and wire bonded to an interposer which is placed …

Architecture Of Extraction: Imagining New Modes Of Inhabitation And Reclamation In The Mining Lifecyle, Erica Dewitt

Masters Theses

Mining is the primary method through which modern society obtains the minerals needed to fuel the global economy, provide for modern energy requirements, and support the built environment. Presently, mining accounts for nearly 1% of the global ice-free land surface, with a dramatic increase anticipated in the coming decades. Mining permanently changes and often destroys the pre-existing topography, hydrology, and ecology of the ground, and efforts to reclaim mining landscapes—with the aim of encouraging reforestation and soil replenishment—are often unsuccessful, rendering the land of abandoned mines both unusable and uninhabitable.

This thesis addresses the current state of mining in the …

Genetic Associations Of Alzheimer’S Disease And Mild Cognitive Impairment, Scott Hebert

Masters Theses

Over 6 million people are estimated to have been living with Alzheimer’s Disease (AD) in 2020, with another 12 million living with Mild Cognitive Impairment (MCI). Research has been conducted to evaluate genetic links to AD, but more research is needed on the subject. The Alzheimer’s Disease Neuroimaging Initiative (ADNI) has been conducting a longitudinal study of AD and MCI since 2004 and offering their data to research teams around the world. Diagnostic and demographic data was collected from participants, as well as data regarding single nucleotide polymorphisms (SNPs). SNP data was transformed to a binary format regarding whether the …

Forecasting Covid-19 With Temporal Hierarchies And Ensemble Methods, Li Shandross

Masters Theses

Infectious disease forecasting efforts underwent rapid growth during the COVID-19 pandemic, providing guidance for pandemic response and about potential future trends. Yet despite their importance, short-term forecasting models often struggled to produce accurate real-time predictions of this complex and rapidly changing system. This gap in accuracy persisted into the pandemic and warrants the exploration and testing of new methods to glean fresh insights.

In this work, we examined the application of the temporal hierarchical forecasting (THieF) methodology to probabilistic forecasts of COVID-19 incident hospital admissions in the United States. THieF is an innovative forecasting technique that aggregates time-series data into …

Graph Representation Learning With Box Embeddings, Dongxu Zhang

Doctoral Dissertations

Graphs are ubiquitous data structures, present in many machine-learning tasks, such as link prediction of products and node classification of scientific papers. As gradient descent drives the training of most modern machine learning architectures, the ability to encode graph-structured data using a differentiable representation is essential to make use of this data. Most approaches encode graph structure in Euclidean space, however, it is non-trivial to model directed edges. The naive solution is to represent each node using a separate "source" and "target" vector, however, this can decouple the representation, making it harder for the model to capture information within longer …

Deformations Of Geometrically Frustrated Elastic Sheets, Meng Xin

Doctoral Dissertations

The wrinkling and buckling of thin solids are common phenomena in our daily life and can be observed in many situations, such as crumpled papers, stretched plastics, compressed metals, clothes on our bodies and even furrowed human skin. Understanding of these phenomena has therefore long drawn interest of scholars. In this thesis, we discuss two buckling problems numerically and analytically. First, we study the wrinkling mechanism of stretched sheets with clamped edges. A central puzzle underlying this canonical example of “tensional wrinkling” has been the origin of compressive stress, which eventually leads to buckling instability. We elucidate the source of …

Evidence Assisted Learning For Clinical Decision Support Systems, Bhanu Pratap Singh Rawat

Doctoral Dissertations

Clinical decision support systems (CDSS) provide intelligently filtered knowledge and patient-specific and population information to the clinicians, nursing staff and healthcare professionals. CDSS can significantly improve the quality, safety, efficiency and effectiveness of health care. Over the last decade, American hospitals have adopted electronic health records (EHRs) widely resulting in a massive collection of clinical notes such as admission notes, physician notes, nursing notes and discharge summaries. For the past couple of decades, most of the work in CDSS has been focused on developing knowledge-based systems using structured data such as medications and ICD codes. In contrast, the EHR notes …

Conservation Value Of Suburban Woodlands For A Declining Songbird, Melanie L. Klein

Doctoral Dissertations

Urbanization and suburbanization (hereafter, used interchangeably) can create some of the most drastically altered habitats of all anthropogenic land uses. Despite this, many wildlife species, including roughly 20% of the world’s birds, can be found in cities. Furthermore, research has shown that suburban forest patches can have important conservation value for birds. As urbanized areas rapidly grow, in terms of both geographical extent and human population, and as numerous bird species experience population declines, understanding how avian species fare in these areas has never been more vital. Not only is this knowledge timely for avian conservation, but for the human …

Analysis Of Nonequilibrium Langevin Dynamics For Steady Homogeneous Flows, Abdel Kader A. Geraldo

Doctoral Dissertations

First, we propose using rotating periodic boundary conditions (PBCs) [13] to simulate nonequilibrium molecular dynamics (NEMD) in uniaxial or biaxial stretching flow. These specialized PBCs are required because the simulation box deforms with the flow. The method extends previous models with one or two lattice remappings and is simpler to implement than PBCs proposed by Dobson [10] and Hunt [24]. Then, using automorphism remapping PBC techniques such as Lees-Edwards for shear flow and Kraynik-Reinelt for planar elongational flow, we demonstrate expo-nential convergence to a steady-state limit cycle of incompressible two-dimensional
NELD. To demonstrate convergence [12], we use a technique similar …

Improving User Experience By Optimizing Cloud Services, Ishita Dasgupta

Doctoral Dissertations

Today, cloud services offer myriads of applications, tailor made for different users in the field of weather, health, finance, entertainment, etc. These services fulfill varying genres of user demands over the Internet. For example, these services can be live (live weather radar, ESPN Live) or on-demand services (weather forecasting, Netflix). While these applications cater to different customer requirements, it is necessary for these services to be efficient with respect to latency, scalability, robustness and quality of experience. These systems need to constantly evolve to provide the best user experience and meet the most current demands of the customer. For instance, …

Benthic Foraminifera As Tools Of Paleoceanography: Three Case Studies From The Late Cretaceous Of The North Pacific Ocean And Western Interior Seaway, And The Miocene-Pleistocene Of The Ross Sea, Antarctica, Serena N. Dameron

Doctoral Dissertations

This dissertation is a widespread compilation of research covering vastly different times and locations. Despite these differences, the use of foraminifera helps to unravel their geologic history, revealing the paleoenvironmental, paleoclimatic, and paleoceanographic conditions of each location. What unites each study is how water mass, food supply and oxygen concentration play a critical role on the microfossil assemblage. This dissertation is broken up into three unique chapters. Chapter 1 reexamines some old ideas of how benthic foraminifera can be used as water mass indicators. A 13-myr record from Shatsky Rise in the paleo-central Pacific Ocean contains several instances water mass …

An Introspective Approach For Competence-Aware Autonomy, Connor Basich

Doctoral Dissertations

Building and deploying autonomous systems in the open world has long been a goal of both the artificial intelligence (AI) and robotics communities. From autonomous driving, to health care, to office assistance, these systems have the potential to transform society and alter our everyday lives. The open world, however, presents numerous challenges that question the typical assumptions made by the models and frameworks often used in contemporary AI and robotics. Systems in the open world are faced with an unconstrained and non-stationary environment with a range of heterogeneous actors that is too complex to be modeled in its entirety. Moreover, …

Data-Driven Computational Methods For Quasi-Stationary Distribution And Sensitivity Analysis, Yaping Yuan

Doctoral Dissertations

The goal of the dissertation is to develop the computational methods for quasi-stationary- distributions(QSDs) and the sensitivity analysis of a QSD against the modification of the boundary conditions and against the diffusion approximation.
Many models in various applications are described by Markov chains with absorbing states. For example, any models with mass-action kinetics, such as ecological models, epidemic models, and chemical reaction models, are subject to the population-level randomness called the demographic stochasticity, which may lead to extinction in finite time. There are also many dynamical systems that have interesting short term dynamics but trivial long term dynamics, such as …

Development Of Biomolecule Nanoparticle Conjugate For Targeted Delivery Of Therapeutics, Peidong Wu

Doctoral Dissertations

Delivery of therapeutics specifically to the disease site is the final goal for the field of drug discovery. Considerable efforts in understanding disease biology have contributed to identifying novel therapeutics such as small molecules, proteolysis targeting chimeras (PROTACs), peptides, proteins, and nucleic acids. However, improving their efficacy as well as minimizing their off-target toxicity remains challenging. Developing vectors that could not only efficiently encapsulate these therapeutics but also direct these therapeutics to the target site is a potential solution to address these challenges. In this dissertation, a block-copolymer-based nanoparticle platform has been developed optimized, and decorated with various kinds of …

Data-Driven Modeling And Analytics For Greening The Energy Ecosystem, John Wamburu

Doctoral Dissertations

The energy ecosystem is undergoing a major transition from primarily using carbon-intensive energy sources to greener and renewable sources of energy. For instance, electric vehicles (EVs) are rapidly increasing in popularity thereby eliminating gas-based carbon emissions. Similarly, the increased adoption of solar is injecting greener energy into the grid, thus reducing the grid’s overall carbon footprint. At the same time, the proliferation of networked devices and sensors in the grid is enabling energy usage analysis at fine granularity. In this thesis, I argue that data-driven modeling and analytics applied to energy usage data can facilitate optimal carbon reduction in the …

Fourth Order Dispersion In Nonlinear Media, Georgios Tsolias

Doctoral Dissertations

In recent years, there has been an explosion of interest in media bearing quartic
dispersion. After the experimental realization of so-called pure-quartic solitons, a
significant number of studies followed both for bright and for dark solitonic struc-
tures exploring the properties of not only quartic, but also setic, octic, decic etc.
dispersion, but also examining the competition between, e.g., quadratic and quartic
dispersion among others.
In the first chapter of this Thesis, we consider the interaction of solitary waves in
a model involving the well-known φ⁴ Klein-Gordon theory, bearing both Laplacian and biharmonic terms with different prefactors. As a …

The Coeval Mass Assembly Of The Universe Via Supermassive Black Hole Accretion And Star Formation In Galaxies, Alyssa Sokol

Doctoral Dissertations

The possible co-evolution between galaxies and their central supermassive black holes is supported by the similarity in shape between the Star Formation Rate Density (SFRD) and Black Hole Accretion Rate Density (BHARD) out to z$\sim$ 3. This apparent connection between BH growth and star formation is only established globally; while both trends peak at z$\sim$ 2, the amount of stellar and black hole mass assembly occurring within the same galaxies is unknown. Computing these trends for the same galaxies will mitigate the present sample mismatch and can be accomplished with an IR-selected sample; however, the approach relies on a robust …

The Use Of Biological Soil Health Indicators To Quantify The Benefits Of Cover Crops, Alexander Wu

Masters Theses

Soils provide many essential functions that support the world. With a decline in soil health, these functions also decrease in efficiency, and can threaten the health of billions of people around the world. Typically, soil health tests do not use biological indicators, however microbes drive and perform vital functions to increase soil health. One way to increase soil health is through the use of cover crops to reduce soil erosion during fallow periods, increasing soil organic matter, as well as collecting nutrients from soil into their biomass. These cover crops are then terminated through various methods such as herbicides, disk …