Physical Sciences and Mathematics Commons^™

Development Of Novel Protein Digestion And Quantitation Methods For Mass Spectrometic Analysis, Yongling Ai

Dissertations

Proteins are the workhorses of biology, playing multifaceted roles in maintaining cellular function, signaling, and response to environmental cues. Understanding their abundance and dynamics is pivotal for unraveling the complexities of biological processes, which underpins the foundations of molecular and cellular biology. Accurate measurement of protein quantities provides insights into cellular homeostasis, facilitates the discovery of biomarkers, and sheds light on the molecular mechanisms of diseases, bridging the gap between the molecular intricacies of proteins and their functional consequences in health and disease. The evolution of protein quantitation methodologies, from classical colorimetric assays to sophisticated mass spectrometry-based approaches, has expanded …

Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin

Dissertations

Clustering analysis has been conducted extensively in single-cell RNA sequencing (scRNA-seq) studies. scRNA-seq can profile tens of thousands of genes' activities within a single cell. Thousands or tens of thousands of cells can be captured simultaneously in a typical scRNA-seq experiment. Biologists would like to cluster these cells for exploring and elucidating cell types or subtypes. Numerous methods have been designed for clustering scRNA-seq data. Yet, single-cell technologies develop so fast in the past few years that those existing methods do not catch up with these rapid changes and fail to fully fulfil their potential. For instance, besides profiling transcription …

Molecular Mechanisms Of Amyloid-Like Fibril Formation, Sharareh Jalali

Dissertations

Proteins play a critical role in living systems by performing most of the functions inside cells. The latter is determined by the protein's three-dimensional structure when it is folded in its native state. However, under pathological conditions, proteins can misfold and aggregate, accounting for the formation of highly ordered insoluble assemblies known as amyloid fibrils. These assemblies are associated with diseases like Parkinson's and Alzheimer's. Strong evidence suggests that three mechanisms are critical for forming amyloid fibrils. These mechanisms are the nucleation of amyloid fibrils in solution (primary nucleation) as well as on the surface of existing fibrils (secondary nucleation) …

Exploring Topological Phonons In Different Length Scales: Microtubules And Acoustic Metamaterials, Ssu-Ying Chen

Dissertations

The topological concepts of electronic states have been extended to phononic systems, leading to the prediction of topological phonons in a variety of materials. These phonons play a crucial role in determining material properties such as thermal conductivity, thermoelectricity, superconductivity, and specific heat. The objective of this dissertation is to investigate the role of topological phonons at different length scales.

Firstly, the acoustic resonator properties of tubulin proteins, which form microtubules, will be explored The microtubule has been proposed as an analog of a topological phononic insulator due to its unique properties. One key characteristic of topological materials is the …

Models And Algorithms For Promoting Diverse And Fair Query Results, Md Mouinul Islam

Dissertations

Ensuring fairness and diversity in search results are two key concerns in compelling search and recommendation applications. This work explicitly studies these two aspects given multiple users' preferences as inputs, in an effort to create a single ranking or top-k result set that satisfies different fairness and diversity criteria. From group fairness standpoint, it adapts demographic parity like group fairness criteria and proposes new models that are suitable for ranking or producing top-k set of results. This dissertation also studies equitable exposure of individual search results in long tail data, a concept related to individual fairness. First, the dissertation focuses …

Quantifying Balance: Computational And Learning Frameworks For The Characterization Of Balance In Bipedal Systems, Kubra Akbas

Dissertations

In clinical practice and general healthcare settings, the lack of reliable and objective balance and stability assessment metrics hinders the tracking of patient performance progression during rehabilitation; the assessment of bipedal balance plays a crucial role in understanding stability and falls in humans and other bipeds, while providing clinicians important information regarding rehabilitation outcomes. Bipedal balance has often been examined through kinematic or kinetic quantities, such as the Zero Moment Point and Center of Pressure; however, analyzing balance specifically through the body's Center of Mass (COM) state offers a holistic and easily comprehensible view of balance and stability.

Building upon …

Learning Representations For Effective And Explainable Software Bug Detection And Fixing, Yi Li

Dissertations

Software has an integral role in modern life; hence software bugs, which undermine software quality and reliability, have substantial societal and economic implications. The advent of machine learning and deep learning in software engineering has led to major advances in bug detection and fixing approaches, yet they fall short of desired precision and recall. This shortfall arises from the absence of a 'bridge,' known as learning code representations, that can transform information from source code into a suitable representation for effective processing via machine and deep learning.

This dissertation builds such a bridge. Specifically, it presents solutions for effectively learning …

Fortifying Robustness: Unveiling The Intricacies Of Training And Inference Vulnerabilities In Centralized And Federated Neural Networks, Guanxiong Liu

Dissertations

Neural network (NN) classifiers have gained significant traction in diverse domains such as natural language processing, computer vision, and cybersecurity, owing to their remarkable ability to approximate complex latent distributions from data. Nevertheless, the conventional assumption of an attack-free operating environment has been challenged by the emergence of adversarial examples. These perturbed samples, which are typically imperceptible to human observers, can lead to misclassifications by the NN classifiers. Moreover, recent studies have uncovered the ability of poisoned training data to generate Trojan backdoored classifiers that exhibit misclassification behavior triggered by predefined patterns.

In recent years, significant research efforts have been …

Bacterial Motion And Spread In Porous Environments, Yasser Almoteri

Dissertations

Micro-swimmers are ubiquitous in nature from soil and water to mammalian bodies and even many technological processes. Common known examples are microbes such as bacteria, micro-algae and micro-plankton, cells such as spermatozoa and organisms such as nematodes. These swimmers live and have evolved in multiplex environments and complex flows in the presence of other swimmers and types, inert particles and fibers, interfaces and non-trivial confinements and more. Understanding the locomotion and interactions of these individual micro-swimmers in such impure viscous fluids is crucial to understanding the emergent dynamics of such complex systems, and to further enabling us to control and …

Diversification And Fairness In Top-K Ranking Algorithms, Mahsa Asadi

Dissertations

Given a user query, the typical user interfaces, such as search engines and recommender systems, only allow a small number of results to be returned to the user. Hence, figuring out what would be the top-k results is an important task in information retrieval, as it helps to ensure that the most relevant results are presented to the user. There exists an extensive body of research that studies how to score the records and return top-k to the user. Moreover, there exists an extensive set of criteria that researchers identify to present the user with top-k results, and result diversification …

Human-Ai Complex Task Planning, Sepideh Nikookar

Dissertations

The process of complex task planning is ubiquitous and arises in a variety of compelling applications. A few leading examples include designing a personalized course plan or trip plan, designing music playlists/work sessions in web applications, or even planning routes of naval assets to collaboratively discover an unknown destination. For all of these aforementioned applications, creating a plan requires satisfying a basic construct, i.e., composing a sequence of sub-tasks (or items) that optimizes several criteria and satisfies constraints. For instance, in course planning, sub-tasks or items are core and elective courses, and degree requirements capture their complex dependencies as constraints. …

Program Analysis For Android Security And Reliability, Sydur Rahaman

Dissertations

The recent, widespread growth and adoption of mobile devices have revolutionized the way users interact with technology. As mobile apps have become increasingly prevalent, concerns regarding their security and reliability have gained significant attention. The ever-expanding mobile app ecosystem presents unique challenges in ensuring the protection of user data and maintaining app robustness. This dissertation expands the field of program analysis with techniques and abstractions tailored explicitly to enhancing Android security and reliability. This research introduces approaches for addressing critical issues related to sensitive information leakage, device and user fingerprinting, mobile medical score calculators, as well as termination-induced data loss. …

Fluid Dynamics Of Interacting Particles: Bouncing Droplets And Colloid-Polymer Mixtures, Lauren Barnes

Dissertations

Interacting particles are a common theme across various physical systems, particularly on the atomic and sub-atomic scales. While these particles cannot be seen with the human eye, insight into such systems can be gained by observing macroscopic systems whose physical behavior is similar. This dissertation consists of three different chapters, each presenting a different problem related to interacting particles, as follows:

Chapter 1 explores chaotic trajectories of a droplet bouncing on the surface of a vertically vibrating fluid bath, with a simple harmonic force acting on the droplet. The bouncing droplet system has attracted recent interest because it exhibits behaviors …

Boundary Integral Equation Methods For Superhydrophobic Flow And Integrated Photonics, Kosuke Sugita

Dissertations

This dissertation presents fast integral equation methods (FIEMs) for solving two important problems encountered in practical engineering applications.

The first problem involves the mixed boundary value problem in two-dimensional Stokes flow, which appears commonly in computational fluid mechanics. This problem is particularly relevant to the design of microfluidic devices, especially those involving superhydrophobic (SH) flows over surfaces made of composite solid materials with alternating solid portions, grooves, or air pockets, leading to enhanced slip.

The second problem addresses waveguide devices in two dimensions, governed by the Helmholtz equation with Dirichlet conditions imposed on the boundary. This problem serves as a …

Toward Smart And Efficient Scientific Data Management, Jinzhen Wang

Dissertations

Scientific research generates vast amounts of data, and the scale of data has significantly increased with advancements in scientific applications. To manage this data effectively, lossy data compression techniques are necessary to reduce storage and transmission costs. Nevertheless, the use of lossy compression introduces uncertainties related to its performance. This dissertation aims to answer key questions surrounding lossy data compression, such as how the performance changes, how much reduction can be achieved, and how to optimize these techniques for modern scientific data management workflows.

One of the major challenges in adopting lossy compression techniques is the trade-off between data accuracy …

Data-Driven 2d Materials Discovery For Next-Generation Electronics, Zeyu Zhang

Dissertations

The development of material discovery and design has lasted centuries in human history. After the concept of modern chemistry and material science was established, the strategy of material discovery relies on the experiments. Such a strategy becomes expensive and time-consuming with the increasing number of materials nowadays. Therefore, a novel strategy that is faster and more comprehensive is urgently needed. In this dissertation, an experiment-guided material discovery strategy is developed and explained using metal-organic frameworks (MOFs) as instances. The advent of 7r-stacked layered MOFs, which offer electrical conductivity on top of permanent porosity and high surface area, opened up new …

Variable Resolution Smoothed Particle Hydrodynamics Schemes For 2-D And 3-D Viscous Flows, Francesco Ricci

Dissertations

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian particle-based method for the numerical solution of the partial differential equations that govern the motion of fluids. The main aim of this thesis work is to better enable the applicability of SPH to problems involving multi-scale fluid dynamics. In the first part of the thesis, the capability of the SPH method to simulate three-dimensional isotropic turbulence is investigated with a detailed comparison of Lagrangian and Eulerian SPH formulations. The main reason for this first investigation is to provide an assessment of the error introduced by the particle disorder on the SPH discrete operators …

Computational And Experimental Investigation Of Elemental Sulfur And Polysulfide, Jyoti Sharma

Dissertations

Petroleum processing results in the generation of significant quantities of elemental sulfur (S₈), leading to a surplus of sulfur worldwide. Despite its abundance and low cost, the use of sulfur in value-added organic compound synthesis is limited due to its unpredictable and misunderstood reactivity. This dissertation aims to address this issue by tackling it from two angles. Firstly, by utilizing Density Functional Theory (DFT) calculations, the reactivity of sulfur in the presence of nucleophiles is studied. This facilitates the identification of organic polysulfide intermediates that can be generated under different conditions, as well as the corresponding reactivity for …

Machine Learning And Network Embedding Methods For Gene Co-Expression Networks, Niloofar Aghaieabiane

Dissertations

High-throughput technologies such as DNA microarrays and RNA-seq are used to measure the expression levels of large numbers of genes simultaneously. To support the extraction of biological knowledge, individual gene expression levels are transformed into Gene Co-expression Networks (GCNs). GCNs are analyzed to discover gene modules. GCN construction and analysis is a well-studied topic, for nearly two decades. While new types of sequencing and the corresponding data are now available, the software package WGCNA and its most recent variants are still widely used, contributing to biological discovery.

The discovery of biologically significant modules of genes from raw expression data is …

Trustworthy Machine Learning Through The Lens Of Privacy And Security, Thi Kim Phung Lai

Dissertations

Nowadays, machine learning (ML) becomes ubiquitous and it is transforming society. However, there are still many incidents caused by ML-based systems when ML is deployed in real-world scenarios. Therefore, to allow wide adoption of ML in the real world, especially in critical applications such as healthcare, finance, etc., it is crucial to develop ML models that are not only accurate but also trustworthy (e.g., explainable, privacy-preserving, secure, and robust). Achieving trustworthy ML with different machine learning paradigms (e.g., deep learning, centralized learning, federated learning, etc.), and application domains (e.g., computer vision, natural language, human study, malware systems, etc.) is challenging, …

Ai Approaches To Understand Human Deceptions, Perceptions, And Perspectives In Social Media, Chih-Yuan Li

Dissertations

Social media platforms have created virtual space for sharing user generated information, connecting, and interacting among users. However, there are research and societal challenges: 1) The users are generating and sharing the disinformation 2) It is difficult to understand citizens' perceptions or opinions expressed on wide variety of topics; and 3) There are overloaded information and echo chamber problems without overall understanding of the different perspectives taken by different people or groups.

This dissertation addresses these three research challenges with advanced AI and Machine Learning approaches. To address the fake news, as deceptions on the facts, this dissertation presents Machine …

Mapping Programs To Equations, Hessamaldin Mohammadi

Dissertations

Extracting the function of a program from a static analysis of its source code is a valuable capability in software engineering; at a time when there is increasing talk of using AI (Artificial Intelligence) to generate software from natural language specifications, it becomes increasingly important to determine the exact function of software as written, to figure out what AI has understood the natural language specification to mean. For all its criticality, the ability to derive the domain-to-range function of a program has proved to be an elusive goal, due primarily to the difficulty of deriving the function of iterative statements. …

Importance Of Vegetation In Tsunami Mitigation: Evidence From Large Eddy Simulations With Fluid-Structure Interactions, Abhishek Mukherjee

Dissertations

Communities worldwide are increasingly interested in nature-based solutions like coastal forests for the mitigation of coastal risks. Still, it remains unclear how much protective benefit vegetation provides, particularly in the limit of highly energetic flows after tsunami impact. The present thesis, using a three-dimensional incompressible computational fluid dynamics model with a fluid-structure interaction approach, aims to quantify how energy reflection and dissipation vary with different degrees of rigidity and vegetation density of a coastal forest.

In this study, tree trunks are represented as cylinders, and the elastic modulus of hardwood trees such as pine or oak is used to characterize …

Continuum Modeling Of Active Nematics Via Data-Driven Equation Discovery, Connor Robertson

Dissertations

Data-driven modeling seeks to extract a parsimonious model for a physical system directly from measurement data. One of the most interpretable of these methods is Sparse Identification of Nonlinear Dynamics (SINDy), which selects a relatively sparse linear combination of model terms from a large set of (possibly nonlinear) candidates via optimization. This technique has shown promise for synthetic data generated by numerical simulations but the application of the techniques to real data is less developed. This dissertation applies SINDy to video data from a bio-inspired system of mictrotubule-motor protein assemblies, an example of nonequilibrium dynamics that has posed a significant …

V-Shaped Temperature Dependences And Pressure Dependence Of Elementary Reactions Of Hydroxyl Radicals With Several Organophosphorus Compounds, Xiaokai Zhang

Dissertations

Organophosphorus compounds have brought increasing attention since they are widely used as flame-retardants, which can take effect in combustion via reactions with reactive radicals. These reactions are influenced by variables such as temperature and pressure, resulting in a temperature and pressure dependent rate constant. Studying this reaction kinetics has great importance in both combustion reaction and atmospheric environment.

This study is focused on kinetics of several elementary reactions of combustion importance. The kinetics of hydroxyl radicals were studied using pulsed laser photolysis coupled to transient UV-vis absorption spectroscopy over the 295 - 837 K temperature range and the 1 - …

Coronal Magnetometry And Energy Release In Solar Flares, Yuqian Wei

Dissertations

As the most energetic explosive events in the solar system and a major driver for space weather, solar flares need to be thoroughly understood. However, where and how the free magnetic energy stored in the corona is released to power the solar flares remains not well understood. This lack of understanding is, in part, due to the paucity of coronal magnetic field measurements and the lack of comprehensive understanding of nonthermal particles produced by solar flares. This dissertation focuses on studies that utilize microwave imaging spectroscopy observations made by the Expanded Owens Valley Solar Array (EOVSA) to diagnose the nonthermal …

Deep Hybrid Modeling Of Neuronal Dynamics Using Generative Adversarial Networks, Soheil Saghafi

Dissertations

Mechanistic modeling and machine learning methods are powerful techniques for approximating biological systems and making accurate predictions from data. However, when used in isolation these approaches suffer from distinct shortcomings: model and parameter uncertainty limit mechanistic modeling, whereas machine learning methods disregard the underlying biophysical mechanisms. This dissertation constructs Deep Hybrid Models that address these shortcomings by combining deep learning with mechanistic modeling. In particular, this dissertation uses Generative Adversarial Networks (GANs) to provide an inverse mapping of data to mechanistic models and identifies the distributions of mechanistic model parameters coherent to the data.

Chapter 1 provides background information on …

A Survey On Online Matching And Ad Allocation, Ryan Lee

Theses

One of the classical problems in graph theory is matching. Given an undirected graph, find a matching which is a set of edges without common vertices. In 1990s, Richard Karp, Umesh Vazirani, and Vijay Vazirani would be the first computer scientists to use matchings for online algorithms [8]. In our domain, an online algorithm operates in the online setting where a bipartite graph is given. On one side of the graph there is a set of advertisers and on the other side we have a set of impressions. During the online phase, multiple impressions will arrive and the objective of …

Bright Light Therapy And Depression: Assessing Suitability Using Entrainment Maps, Charles A. Mainwaring

Theses

Bright Light Therapy has been shown to be efficacious to mood disorders including Major Depression. Researchers use the Jewett-Forger-Kronauer model of the circadian rhythm with the Unified Model of melatonin including a mathematical term implementing feedback from the melatonin system into the circadian system to quantify the effects of bright light. Early investigations into intrinsic period, light sensitivity, and the circadian pacemaker's sensitivity to blood melatonin concentration may be indicators of subsets of patients with long intrinsic periods exhibiting symptoms of depression.

Using Materialized Views For Answering Graph Pattern Queries, Michael Lan

Dissertations

Discovering patterns in graphs by evaluating graph pattern queries involving direct (edge-to-edge mapping) and reachability (edge-to-path mapping) relationships under homomorphisms on data graphs has been extensively studied. Previous studies have aimed to reduce the evaluation time of graph pattern queries due to the potentially numerous matches on large data graphs.

In this work, the concept of the summary graph is developed to improve the evaluation of tree pattern queries and graph pattern queries. The summary graph first filters out candidate matches which violate certain reachability constraints, and then finds local matches of query edges. This reduces redundancy in the representation …