Transcription plays a pivotal role in the transfer of genetic information within living organisms. It serves as the initial step in gene expression, allowing cells to convert the instructions encoded in their DNA into functional molecules. Eukaryotic transcription initiation is a complex and dynamic process that requires joint efforts from...
Gastrointestinal (GI) colonization by Klebsiella pneumoniae is a risk factor for subsequent infection as well as transmission to other patients. Additionally, colonization is achieved by many strain types that exhibit high diversity in genetic content. However, how K. pneumoniae achieves colonization and whether the genetic factors it uses differ by...
Mission-critical systems are those imperative systems whose failures can result in catastrophic consequences. Traditional techniques, such as manual investigation and testing, cannot ensure the absence of errors and security vulnerabilities within these systems. This dissertation leverages formal methods to comprehensively examine several mission-critical systems and their essential components. For each...
The advent of advanced computing and AI has led to social technologies becoming agentic teammates in human-autonomy teams. Interpersonal trust, vital for team functioning, is crucial in determining these teams' success or failure. Trust, while essential, can be easily broken and requires maintenance and repair. This dissertation addresses two questions:...
Breast cancer patients have reported nonspecific neurologic symptoms such as fatigue, depression, and cognitive concerns while undergoing adjuvant therapy. Few neuroimaging studies have examined hormone therapy, an adjuvant therapy, and more research is needed to determine possible neurologic and cognitive effects. Previous estrogen research has found alterations in gray matter...
This dissertation uses the case of Colombia to examine the causes and reproductive mechanisms of civil wars that last more than fifty years, which I call perpetual civil wars. It draws on network analysis of violent events and political claims, content analysis of official archival documents and historical records of...
Swallowing impairment or dysphagia has many possible causes with severe sequelae. One major mediator of the relationship between causes and sequelae is the physiologic impairment of the swallowing mechanism. Assessing the physiology of swallowing impairment is of great importance so that treatment can target physiology to mitigate sequelae. The assessment...
The political history of late twentieth-century Southern Africa was dominated by violent liberation struggles against settler-colonial domination in Angola, Mozambique, Namibia, South Africa, and Zimbabwe. All five countries experienced prolonged settler colonialism, followed by conflicts in which revolutionary national liberation movements (NLMs) sought to both end settler-colonial domination and build...
Recent experiments in participatory democracy, such as Iceland’s 2013 Constitutional Reform process to Chicago’s annual participatory budgeting process, have empowered members of the public to directly make policy decisions. These new participatory democratic institutions depend on citizens having capacity to organize new institutions and the capacity to participate in them....
Derivative-free optimization (DFO) has received growing attention due to important problems arising in practice. Various research communities, ranging from machine learning to engineering design, have adopted distinct DFO methods. In this thesis, we present extensive studies as a meaningful step towards a comprehensive understanding of DFO methods. We study the...
In this work, I try to understand how the movements, attitudes, styles, and positions of the body in representational artworks can be understood as gestures—that is, as moments that interrupt the unfolding of narrative time and produce an interval. The interval is not merely a space that opens up between...
This dissertation theorizes the relation between blackface minstrelsy and contemporary Black performance. The project analyzes the use of nineteenth-century blackface minstrel conventions in Black theatrical performances during later eras where its usage seems counter-intuitive: during the Black freedom struggles of the 1960s; within Black feminist and queer performance of the...
In recent years, the understanding and identification of quantum materials supporting non-trivial band topology has progressed rapidly. This progress has been motivated in part by the potential application of topological quantum materials in quantum computers, sensors, and other next-generation devices. Despite this progress, the computation of bulk topological invariants in...
This dissertation focuses on quantifying protein folding stability determinants and presenting initial experiments that can guide the development of a novel assay that identifies cell-penetrating miniproteins. First, despite over a century of scholarship on protein folding stability, applying this knowledge to design proteins computationally remains limited. Usually, protein designers generate...
This project explores how the variation in language experiences and attitudes that Mexican American Spanish heritage speaker bilinguals in the United States have affects their speech perception in both their languages. Heritage language bilinguals speak as a first language a minority language that they have cultural ties to (e.g., Spanish...
This dissertation investigates how scope relations are constructed and evaluated during real-time human sentence processing. Theoretical approaches to processing scope relations exist in a multi-dimensional space where trade-offs are made around how quickly scope relations can be computed, how many mistakes are made in computing scope relations, and how many...
The field of distributed optimization algorithms is wide and growing, and new techniques for categorizing and analyzing existing algorithms are continually being developed. In this Thesis, we leverage control theoretic analysis and block diagram interpretations for existing algorithms to synthesize entirely new families of algorithms. These new algorithm families have...
Transitioning energy systems from a reliance on fossil fuels to low carbon energy sources is an essential solution for climate change mitigation. However, the industrial sector, which is directly responsible for more than a quarter of global carbon dioxide (CO2) emissions, continues to use fossil fuels for energy and feedstocks....
Necessity is the mother of innovation. In the wake of the pandemic, with no flow of samples and limited fabrication techniques available, necessity demanded a new material platform and adaptable methods to make complex oxide samples worth measuring. The material platform was KTaO3 , the younger successor to the mainstay...
This manuscript describes and contextualizes the research I performed as a PhD student in Northwestern University. The first three chapters, on Markov chains, stochastic thermodynamics, and large deviation theory, describe three interrelated topics that serve as the background for subsequent research detailed in the next three chapters, on understanding the...
This dissertation aims to develop innovative analytical methods that integrate engineering, marketing, and social science disciplines to incorporate heterogeneous consumer preferences into product design using network-based customer preference modeling. Both companies and designers frequently face difficulties in understanding and addressing customer preferences, which can result in product failure and loss...
Machine learning and deep learning have been proven successful across various scientific fields, such as computer vision, natural language processing, and recommendation systems. As models become more complex, with more parameters and intricate architectures, they can achieve higher prediction accuracy when trained on larger datasets. However, despite the great prediction...
The action of the automorphisms of a formal group on its deformation space is crucial to understanding periodic families in the homotopy groups of spheres and the unsolved Hecke orbit conjecture for unitary Shimura varieties. This action is called the Lubin-Tate action. We first show sufficient conditions for geometrically modelling...
Despite the increasing interest in biogenic secondary organic aerosols (SOAs), their role in the climate system remains the greatest source of uncertainty in global models. Cloud formation, critical for the net cooling effect provided by cloud cover, is dependent on the abundance of SOA particles and their ability to activate...
Although elevated stress and dietary change have each been associated with metabolic health decline for resettled populations in the Global North, considerably less attention is paid to the links between these two biosocial pathways. Addressing these linkages can elucidate interrelated diet and stress mechanisms that affect population health disparities over...
Submodularity is a well-known concept in integer programming and combinatorial optimization. Submodular set functions capture the diminishing returns phenomenon, which has wide-ranging applications in various domains. Typically, a submodular set function models the utility of homogenous items selected from a single ground set. Selecting an item or not is naturally...
Controlled delivery of foreign cargo into cells is a critical step in many biological studies and in cell engineering and analysis workflows. Recent advances in micro and nanotechnology, specifically in microfluidics and microfabrication have added significantly to the precision, accuracy, resolution and throughput of cell manipulation and analysis pipelines. These...
Metalloenzymes catalyze remarkable reactions in Nature using transition metal ions. Common earth-abundant metals like copper, iron, zinc, and magnesium catalyze reactions that are the basis of life. These metal sites lend their chemistries to facilitate these reactions, making studying the structure and properties important in understanding the enzymes' abilities and...
For many years silicon tethers have been used to increase yields and control the stereochemical and regiochemical outcomes of coupling reactions. Silicon tethers may be incorporated into a wide range of reaction types including alkene metathesis, cycloadditions, and glycosylations. This thesis focuses on the development of the use of silicon...
Drying oils have been used as a binding medium for oil paints since the 15th century. These oil paints transition from a liquid-like paste to a solid-like film as a result of crosslinks forming between the oil molecules. These reactions have been extensively studied chemically, but other material properties are...
Pollution-intensive industrial manufacturing processes threaten the health of ecosystems and societies through toxic waste streams and energy intensive processes that lead to greenhouse gas emissions. Biological systems present more sustainable routes to many useful industrial chemicals by using enzymes at low temperatures, but the time and effort required to optimized...
This dissertation focuses on quantifying protein folding stability determinants and presenting initial experiments that can guide the development of a novel assay that identifies cell-penetrating miniproteins. First, despite over a century of scholarship on protein folding stability, applying this knowledge to design proteins computationally remains limited. Usually, protein designers generate...
Temperature affects all biological processes, from the rate of cellular growth and metabolism to the stability of proteins that make up the machinery of life itself. Thus, all organisms must have the capacity to detect and respond to external temperature. Thermosensation endows animals with the ability to sense and respond...
This dissertation presents novel advancements in the field of continuous nonlinear optimization, focusing on the development of efficient second-order methods for second-order conic programs (SOCPs) and continuous nonlinear two-stage optimization problems. The primary focus is on the theory and computations of Sequential Quadratic Programming (SQP) methods, which are widely used...
Recent progress in semiconductor synthesis and photophysics has revealed a host of new materials with exciting properties for applications in optoelectronic devices such as sensors, photovoltaics, solid state lighting, and more. One of the most significant recent additions to the field is the class of hybrid and inorganic materials that...
Bacterial infections (BI) are a frequent, expensive, and life-threatening condition for critically ill patients. For patients with serious BI, minimizing the time between admission to the
intensive care unit (ICU) and administration of appropriate antibiotic therapy is crucial to
improve prognosis. However, the current gold-standard for identifying the appropriate
antimicrobials...
Herein, we present an overview of our studies of the morphology, dynamics, and formation of heterogeneous soft matter systems via the emerging technique of liquid phase transmission electron microscopy (LPTEM). This particular subset of materials, more commonly referred to as emulsions, is tremendously commercially and biologically relevant, encompassing applications in...
This dissertation explores the entanglements of performed refusals and witnessing practices in the face of gendered violences. I analyze how contemporary artists use staged performance to generate new modes for witnessing histories of gendered violence across temporal and national boundaries. In particular, I investigate four performances addressing local histories of...
Volunteers play an essential role in humanitarian and non-profit organizations that strive to improve society. 30% of the population in the United States volunteered in 2019, and this percentage has been stable for the past two decades. This dissertation is motivated by the scheduling decision process in nonprofit organizations. These...
The simplicity of morphogenesis, manifested as collective shape changes, emerges from complex biophysical regulations within a multicellular embryo. Constructing a spatio-temporal atlas of mechanical stresses is central for understanding the emergence of this simplicity. Developing a new mathematical theory for the static mechanics of three-dimensional multicellular aggregates involving pressures and...
Bacteria represent the most abundant form of life on Earth and have evolved to successfully colonize nearly every environmental niche. In doing so, bacteria predominately form multicellular communities known as biofilms, resulting in increased resilience, persistence, and emergent behaviors. Consequently, biofilms present an attractive target for engineering and synthetic biology,...
The literature on racial/ethnic diversity in schools largely shows evidence of positive academic outcomes for students in diverse schools relative to segregated schools. At the same time, there is ample research demonstrating the discrimination and marginalization that students of color experience in desegregated schools. In this dissertation, I seek to...
Visual information plays a critical role in controlling movement. People use visual information to plan future actions and correct current actions through feedforward and feedback processes, respectively. We can gain insights into these visually guided motor control processes by quantifying where people look during movement and measuring how much they...
Historians have long argued that humanitarianism—what Thomas Haskell once described as “alleviating the suffering of distant strangers”—first emerged in eighteenth-century Europe as part of a complex set of perceptual changes involving capitalist growth, Enlightenment ideas, and Christian values. Given these claims, it is no coincidence that humanitarianism has often been...
Topology optimization is a powerful tool for maximizing structural performance, enabling multifunctionality of the structure, and reducing the materials waste and cost for sustainable manufacturing. However, current topology optimization tools are limited to a few scales, and the potential of nested topology optimization in engineering design has yet to be...
Early transition metal organometallics chemisorbed on extremely Brønsted acidic sulfated metal oxides such as sulfated alumina (AlS) and sulfated zirconia (ZrS) produce highly active single-site catalysts for olefin polymerization, alkene and arene hydrogenation, and alkane hydrogenolysis, typically with a large percentage of catalytically significant sites. The low support conjugate basicity...
Photochemistry allows chemists to harness the energy in specific wavelengths of light and use it to achieve new chemical transformations. These chemical transformations are often impossible or energetically demanding under traditional thermal conditions. My dissertation focuses broadly on different strategies to apply visible-light photochemistry and photocatalysis to the development of...
Policies supporting families with young children provide an important context for human development. The two primary public policies available to caregivers around and after childbirth are parental leave and early care and education (ECE). A substantial body of research evaluates the effects of parental leave and ECE policies on various...
This dissertation observes interaction to explore the influence of group argument in decision-making in mock juries. The goals of this investigation were to observe two-sided deliberations of a task-oriented decision-making group, map the dichotomous arguments and provide insight into what influences were at play in the final decision. The study...
How molecular chirality manifests at the nano- to macroscale has been a scientific puzzle since Louis Pasteur discovered biochirality. In general, amphiphilic molecules can organize into a variety of assembly shapes including micelles, spherical vesicles, cylindrical micelles, and planar bilayers. However, when such amphiphilic molecules are chiral, helical ribbons, helicoidal...
Heart failure is a growing clinical problem, and inherited cardiomyopathies contribute significantly to heart failure. Among the many genes associated with inherited cardiomyopathies, mutations in FLNC, the gene encoding the cytoskeletal protein filamin C, associate with a range of cardiomyopathy and increased risk for arrhythmia and sudden cardiac death in...
In recent years, motivated by the approaching of quantum limit for classic information science, the development of quantum information science (QIS) has drawn considerable interest from chemists and physicians. Different from classical bits which can only be localized on two different states, quantum bit, which can be simplified as qubit,...
Nilotinib is a highly effective tyrosine kinase inhibitor used to treat Chronic Myeloid Leukemia (CML). While nilotinib successfully treats CML, a common and serious side effect is development of nilotinib-induced arterial disease (NAD) even in patients without pre-existing risk factors. This side effect is not seen with imatinib, a CML...
Mycobacterium tuberculosis (Mtb) infection elicits both protein and lipid antigen-specific T cell responses. However, the incorporation of lipid antigens into subunit vaccine strategies and formulations has been under-explored, and the properties of vaccine-induced Mtb lipid-specific memory T cells have remained elusive. Mycolic acid (MA), a major lipid component of the...
In the late 2000’s, scientific studies in cultural heritage saw a great advancement in macro X-ray fluorescence (XRF) imaging of paintings. These images are used to generate elemental distribution maps, which aid in identifying chemical elements and paint pig- ments as well as their locations throughout the layers of the...
Objective: To evaluate patient-reported experiences of telehealth and disparities in access, use, and satisfaction with telehealth visits during the COVID-19 pandemic (aim 1), to evaluate prevalence of portal use pre-, peri-, and post-pandemic, among the C3 cohort, and investigate any disparities in use by sociodemographic factors (aim 2), and to...
Heterogenous catalysis is the pillar of chemical production and a crucial aspect for optimization toward a sustainable future. To improve the current design of heterogeneous catalysts of maximal activity and product selectivity, gaining fundamental understanding of the catalytic active sites is crucial. The nature of active sites has been the...
In this thesis, I study the effects of spillovers in all-pay auctions and the effects ofregulating wages and hours on the labor market. In the first chapter, I study a model of
asymmetric all-pay auctions with spillovers. In this model, players compete for a prize, and
the sunk effort players...
Air pollution is a pervasive environmental issue that has significant impacts on human health. Urban areas are particularly susceptible to high levels of air pollution due to concentrated emissions and populations. Urban air pollution has been linked to a range of adverse health effects, including respiratory diseases, cardiovascular diseases,...
Biological systems that perform critical reactions like carbon dioxide reduction, water oxidation, or phosphonate ester hydrolysis consist of many separate components with many different degrees of
freedom. While the functionality of pieces of these systems can be replicated synthetically to some
degree, the integration of synthetic catalysts into an overall...
The main topic of this thesis is generation in derived categories of coherent sheaves on smooth projective varieties. We develop a new approach that allows us to give a new proof of a recent result by Olander that powers of an ample line bundle generate the bounded derived category of...
Equilibrium models of star formation successfully derive the globally-averaged Kennicutt-Schmidt (KS) relation, positing that star formation rates (SFRs) are self- regulated by the turbulence in the interstellar medium (ISM) generated by stellar feedback. However, these models make assumptions that may not be achieved in realistic galaxy systems. Cosmological zoom-in simulations,...
An important tenet in memory research is the dissociation between explicit and implicit memory systems in the brain. Whereas a robust literature exists on the consolidation of memories in the explicit domain, research on implicit memory consolidation is relatively understudied, particularly questions about what is being consolidated and the mechanisms...
On March 11, 1966, Indonesian President Soekarno suddenly transferred executive power to the Army, which has played a role in the Indonesian state and society since the late 1950s. This act replaced Soekarno’s own government with a military dictatorship dubbed the New Order, which lasted for nearly 32 years. Why...
As sound changes advance across large geographic areas, they progress unevenly across populations. The speakers who lead these changes often share macro-social identities, like place or social class affiliations (e.g. Nesbitt 2018; Wagner et al. 2016). But the features undergoing these macro-level sound changes also hold social meanings related to...
The negative early and late health consequences from exposure to artificial sources of radiation are particularly apparent in victims of radiological emergencies who were diagnosed with cancer, radiation pneumonitis, among other conditions. The renaissance of nuclear energy, increased use of ionizing radiation in the medical field, and nuclear threats from...
Polymers occupied nearly every facet of our daily lives, and enhancing their mechanical and fracture properties has long been an important topic in the field of polymer science. Based on the various need in applications, polymers are designed to have a range of characteristics such as tackiness, optical properties, mechanical...
Data for manuscript submission to PLoS ONE entitled:
Prior Uncertainty Impedes Discrete Locomotor Adaptation
Authors:
Jiang, Aojun
Grover, Francis M.
Bucklin, Mary
Deol, Jasjit
Shafer, Anna
Gordon, Keith E.
This data was used to compare the performance of a urine point-of-care assay and interviewer-administered timeline follow-back to the gold-standard for measuring recent and longer-term adherence of pre-exposure prophylaxis (PrEP) in dried blood spots (DBS). This data was used to produce the research findings presented in the peer-reviewed journal cited...
People sometimes gain a sudden idea through insight after being stuck on a problem. Researchers have been studying insight as a crucial component of creative problem-solving in the past decades. However, the role of insight in mathematical problem-solving remains unclear, while mathematics is essential in scientific development and ubiquitous in...