Physical Sciences and Mathematics Commons^™

Effect Of Side Chains On Organic Donor (D) And Acceptor (A) Complexes And Photophysical Properties Of D-A Dyads, Amarnath Bheemaraju

Open Access Dissertations

This dissertation aims to understand the effect of incompatible side chains on the complexes of pi-conjugated electron-rich donors and electron-deficient acceptors in solution. The role of incompatible side chains were studied in simple mixtures of organic donor and acceptor molecules that form donor-acceptor complexes. The incompatible branched and linear alkane side chains on the acceptor and donor respectively prevented complex formation between naphthalene diimide acceptor and naphthalene ether donor. However, the incompatible hydrocarbon-fluorocarbon and polar-non polar side chain pairs did not affect complex formation between the donor and acceptor. In quaterthiophene-naphthalene diimide dyads, the incompatibility of the side chain on …

Query-Dependent Selection Of Retrieval Alternatives, Niranjan Balasubramanian

Open Access Dissertations

The main goal of this thesis is to investigate query-dependent selection of retrieval alternatives for Information Retrieval (IR) systems. Retrieval alternatives include choices in representing queries (query representations), and choices in methods used for scoring documents. For example, an IR system can represent a user query without any modification, automatically expand it to include more terms, or reduce it by dropping some terms. The main motivation for this work is that no single query representation or retrieval model performs the best for all queries. This suggests that selecting the best representation or retrieval model for each query can yield improved …

Computational Affect Detection For Education And Health, David G. Cooper

Open Access Dissertations

Emotional intelligence has a prominent role in education, health care, and day to day interaction. With the increasing use of computer technology, computers are interacting with more and more individuals. This interaction provides an opportunity to increase knowledge about human emotion for human consumption, well-being, and improved computer adaptation. This thesis explores the efficacy of using up to four different sensors in three domains for computational affect detection. We first consider computer-based education, where a collection of four sensors is used to detect student emotions relevant to learning, such as frustration, confidence, excitement and interest while students use a computer …

Subjects Of Scale / Spaces Of Possibility: Producing Co-Operative Space In Theory And Enterprise, Janelle Terese Cornwell

Open Access Dissertations

This dissertation addresses key questions raised in Human Geography and Economic Geography concerning scale and the production of space, alternative economic geographies and co-operative economic development. It is the product of a five year ethnographic investigation with co-operative enterprises in Western Massachusetts and the broader Connecticut River Valley of Western New England. It explores neglected questions about how subjects are producing co-operative economic identities, enterprises and development strategies amid capitalist cultural dominance; and how structural, financial and governmental aspects of their enterprises participate in cultivating the desire and capacity to expand co-operative space. In line with poststructuralist feminist perspectives within …

Generalized Expectation Criteria For Lightly Supervised Learning, Gregory Druck

Open Access Dissertations

Machine learning has facilitated many recent advances in natural language processing and information extraction. Unfortunately, most machine learning methods rely on costly labeled data, which impedes their application to new problems. Even in the absence of labeled data we often have a wealth of prior knowledge about these problems. For example, we may know which labels particular words are likely to indicate for a sequence labeling task, or we may have linguistic knowledge suggesting probable dependencies for syntactic analysis. This thesis focuses on incorporating such prior knowledge into learning, with the goal of reducing annotation effort for information extraction and …

Tree-Based Methods And A Mixed Ridge Estimator For Analyzing Longitudinal Data With Correlated Predictors, Melissa Nicole Eliot

Open Access Dissertations

Due to recent advances in technology that facilitate acquisition of multi-parameter defined phenotypes, new opportunities have arisen for predicting patient outcomes based on individual specific cell subset changes. The data resulting from these trials can be a challenge to analyze, as predictors may be highly correlated with each other or related to outcome within levels of other predictor variables. As a result, applying traditional methods like simple linear models and univariate approaches such as odds ratios may be insufficient. In this dissertation, we describe potential solutions including tree-based methods, ridge regression, mixed modeling, and a new estimator called a mixed …

Measurements Of Gravity Driven Granular Channel Flows, Kevin Facto

Open Access Dissertations

This dissertation presents experiments that studied two gravity driven granular channel flows. The first experiment used magnetic resonance imaging to measure the density and displacement distributions of poppy seeds flowing in a rough walled channel. Time-averaged measurements of normalized velocity and density showed little flow speed dependence. Instantaneous measurements, however, showed marked velocity dependence in the displacement distributions. There was evidence of aperiodic starting and stopping at lower flow speeds and the onset of density waves on a continuous flow at higher speeds. The second experiment measured forces in all three spatial directions at the boundary of a flow of …

Spatial Evolutionary Game Theory: Deterministic Approximations, Decompositions, And Hierarchical Multi-Scale Models, Sung-Ha Hwang

Open Access Dissertations

Evolutionary game theory has recently emerged as a key paradigm in various behavioral science disciplines. In particular it provides powerful tools and a conceptual framework for the analysis of the time evolution of strategic interdependence among players and its consequences, especially when the players are spatially distributed and linked in a complex social network. We develop various evolutionary game models, analyze these models using appropriate techniques, and study their applications to complex phenomena. In the second chapter, we derive integro-differential equations as deterministic approximations of the microscopic updating stochastic processes. These generalize the known mean-field ordinary differential equations and provide …

Selective Inhibition And Mechanistic Studies Of The Human O2 Sensor, Prolyl Hydroxylase Domain 2 (Phd2), Shannon Coates Flagg

Open Access Dissertations

Prolyl Hydroxylase Domain 2 (PHD2) has been identified as a key oxygen sensor in humans along with Factor Inhibiting Hypoxia Inducible Factor (FIH). As such PHD2 and FIH play critical roles in myriad pathways of medical relevance by hydroxylation of their target substrate hypoxia inducible factor (HIF), a transcription factor responsible for the regulation of over 100+ genes. With such critical roles in human physiology the ability to selectively regulate these two enzymes could potentially lead the way for novel therapeutic treatments of a vast array of disease states from cancer to myocardial infarction. We report on three classes of …

A Mathematical Growth Model Of The Viral Population In Early Hiv-1 Infections, Elena Edi Giorgi

Open Access Dissertations

In this thesis we develop a mathematical model to describe HIV-1 evolution during the first stages of infection (approximately within 40-60 days since onset), when one can assume exponential growth and random accumulation of mutations under a neutral drift. We analyze the Hamming distance (HD) distribution under different models (synchronous and asynchronous) in the absence of selection and recombination. In the second part of the thesis, we introduce recombination and develop a combinatorial approach to estimate the new HD distribution. We conclude describing a T statistic to test significance differences between the HD of two genetic samples, which we derive …

Finding Blame For Environmental Outcomes: A Cognitive Style Approach To Understanding Stakeholder Attributions, Attitudes, And Values, Christopher Thomas Hawkins

Open Access Dissertations

This study sought to connect two bodies of knowledge--integrative complexity and attribution theory. Integrative complexity is a term that indicates the simplicity vs. complexity of a person's mental frame and perceptual skill. A person who perceives nuance and subtle differences typically scores higher on an integrative complexity measure. Attribution theories are concerned with how individuals perceive causation for various events. The limited research into the linkages between perceived causation for an event and how complexly a person thinks about the domain of that event, coupled with the dearth of attribution research in the natural resource management literature, inspired this research. …

Knot Contact Homology And Open Strings, Jason Frederick Mcgibbon

Open Access Dissertations

In this thesis, we give a topological interpretation of knot contact homology, by considering intersections of a particular class of chains of open strings with the knot itself. In doing so, we provide evidence toward a differential graded algebra structure on the algebra generated by chains of open strings.

Infrared And X-Ray Studies Of The Galactic Center, Hui Dong

Open Access Dissertations

The purpose of this dissertation is to locate evolved massive stars within the central 50 pc of the Galactic Center. These stars are considered to be the descendants of O stars and should be less than 10 Myr old. They trace young star clusters within the Galactic Center. Through these stars and young star clusters, we hope to understand the star formation mode and history within the Galactic Center, as well as the properties of evolved massive stars in the high metallicity environment. We first study the Chandra X-ray deep survey of the Arches and Quintuplet clusters, two of the …

Exploiting Structure In Coordinating Multiple Decision Makers, Hala Mostafa

Open Access Dissertations

This thesis is concerned with sequential decision making by multiple agents, whether they are acting cooperatively to maximize team reward or selfishly trying to maximize their individual rewards. The practical intractability of this general problem led to efforts in identifying special cases that admit efficient computation, yet still represent a wide enough range of problems. In our work, we identify the class of problems with structured interactions, where actions of one agent can have non-local effects on the transitions and/or rewards of another agent. We addressed the following research questions: 1) How can we compactly represent this class of problems? …

Variations On Stigmergic Communication To Improve Artificial Intelligence And Biological Modeling, Megan Marie Olsen

Open Access Dissertations

Stigmergy refers to indirect communication that was originally found in biological systems. It is used for self-organization by ants, bees, and flocks of birds, by allowing individuals to focus on local information. Through local communication among individuals, larger patterns are formed without centralized communication. This self-organization is just one type of system studied within complex systems. Systems of ants, bees, and flocks of birds are considered complex because they exhibit emergent behavior: the outcome is more than the sum of the individual parts. Emergent behavior can be found in many other systems as well. One example is the Internet, which …

Controlled Oxygen Activation In Human Oxygen Sensor Fih, Evren Saban

Open Access Dissertations

One of the primary oxygen sensors in human cells, which controls gene expression by hydroxylating the hypoxia inducible transcription factor (HIFα) is the factor inhibiting HIF (FIH). As FIH is an alpha-ketoglutarate dependent non-heme iron dioxygenase, oxygen activation is thought to precede substrate hydroxylation. The coupling between oxygen activation and substrate hydroxylation was hypothesized to be very tight, in order for FIH to fulfill its function as a regulatory enzyme. Coupling was investigated by looking for reactive oxygen species production during turnover. Alkylsulfatase (AtsK), a metabolic bacterial enzyme with a related mechanism and similar turnover frequency, was used for comparison, …

Statistical Methods For Nonlinear Dynamic Models With Measurement Error Using The Ricker Model, David Joseph Resendes

Open Access Dissertations

In ecological population management, years of animal counts are fit to nonlinear, dynamic models (e.g. the Ricker model) because the values of the parameters are of interest. The yearly counts are subject to measurement error, which inevitably leads to biased estimates and adversely affects inference if ignored. In the literature, often convenient distribution assumptions are imposed, readily available estimated measurement error variances are not utilized, or the measurement error is ignored entirely. In this thesis, ways to estimate the parameters of the Ricker model and perform inference while accounting for measurement error are investigated where distribution assumptions are minimized and …

Interactive Perception Of Articulated Objects For Autonomous Manipulation, Dov Katz

Open Access Dissertations

This thesis develops robotic skills for manipulating novel articulated objects. The degrees of freedom of an articulated object describe the relationship among its rigid bodies, and are often relevant to the object's intended function. Examples of everyday articulated objects include scissors, pliers, doors, door handles, books, and drawers. Autonomous manipulation of articulated objects is therefore a prerequisite for many robotic applications in our everyday environments. Already today, robots perform complex manipulation tasks, with impressive accuracy and speed, in controlled environments such as factory floors. An important characteristic of these environments is that they can be engineered to reduce or even …

Search Using Social Media Structures, Jangwon Seo

Open Access Dissertations

Social applications on the Web have appeared as communication spaces for sharing knowledge and information. In particular, social applications can be considered valuable information sources because information in the applications is not only easily accessible but also revealing in that the information accrues via interactions between people. In this work, we address methods for finding relevant information in social media applications that use unique properties of these applications. In particular, we focus on three unique structures in social media: hierarchical structure, conversational structure, and social structure. Hierarchical structures are used to organize information according to certain rules. Conversational structures are …

Discovering And Using Implicit Data For Information Retrieval, Xing Yi

Open Access Dissertations

In real-world information retrieval (IR) tasks, the searched items and/or the users' queries often have implicit information associated with them -- information that describes unspecified aspects of the items or queries. For example, in web search tasks, web pages are often pointed to by hyperlinks (known as anchors) from other pages, and thus have human-generated succinct descriptions of their content (anchor text) associated with them. This indirectly available information has been shown to improve search effectiveness for different retrieval tasks. However, in many real-world IR challenges this information is sparse in the data; i.e., it is incomplete or missing in …

Improving Data Center Resource Management, Deployment, And Availability With Virtualization, Timothy Wood

Open Access Dissertations

The increasing demand for storage and computation has driven the growth of large data centers--the massive server farms that run many of today's Internet and business applications. A data center can comprise many thousands of servers and can use as much energy as a small city. The massive amounts of computation power contained in these systems results in many interesting distributed systems and resource management problems. In this thesis we investigate challenges related to data centers, with a particular emphasis on how new virtualization technologies can be used to simplify deployment, improve resource efficiency, and reduce the cost of reliability, …

Capillary Interactions Among Microparticles And Nanoparticles At Fluid Interfaces, Chuan Zeng

Open Access Dissertations

Particles can be adsorbed to liquid-fluid interface to minimize interfacial energy. The adsorbed particles interact in many ways. There has been a lot of theoretical predictions as well as experimental measurements of the interaction potential between particles confined at interfaces. Experimentally, we track multiple particles using optical microscope image processing of isolated pairs of particles and of more concentrated systems. Statistical methods were implemented to compute microparticle interaction forces from tracking data. The accuracy of different methods were tested with Monte Carlo simulation, which showed that care is needed to avoid artifacts. Our measurements confirmed the absence of significant pair-interactions …

Search For Contact Interactions With Dimuons At The Atlas Detector, Emily Thompson

Open Access Dissertations

The Standard Model has been very successful over the last few decades in its agreement with experimental evidence; however there are some remaining puzzles in our understanding of the Universe which have yet to be solved. Even if the Higgs boson and Super Symmetry are discovered, questions still arise, such as why Nature is primarily made of matter when antimatter should have been produced in equal amounts at the beginning of the Universe, why the fundamental particles have the mass hierarchy that they do, what the nature of dark matter is, or whether or not quarks and leptons are themselves …

Scaling Multi-Agent Learning In Complex Environments, Chongjie Zhang

Open Access Dissertations

Cooperative multi-agent systems (MAS) are finding applications in a wide variety of domains, including sensor networks, robotics, distributed control, collaborative decision support systems, and data mining. A cooperative MAS consists of a group of autonomous agents that interact with one another in order to optimize a global performance measure. A central challenge in cooperative MAS research is to design distributed coordination policies. Designing optimal distributed coordination policies offline is usually not feasible for large-scale complex multi-agent systems, where 10s to 1000s of agents are involved, there is limited communication bandwidth and communication delay between agents, agents have only limited partial …

Design And Synthesis Of A New Class Of Self-Cross-Linked Polymer Nanogels, Siriporn Jiwpanich

Open Access Dissertations

The design and engineering of nanoscopic drug delivery vehicles that stably encapsulate lipophilic drug molecules, transport their loaded cargo to specific target sites, and release their payload in a controlled manner are of great interest in therapeutic applications, especially for cancer chemotherapy. This dissertation focuses on chemically cross-linked, water-soluble polymer nanoparticles, termed nanogels, which constitute a promising scaffold and offer the potential to circumvent encapsulation stability issues. A facile synthetic method for a new class of self-cross-linked polymer nanogels, synthesized by an intra/intermolecular disulfide cross-linking reaction in aqueous media, is described here. This simple emulsion-free method affords noncovalent lipophilic guest …

Mutational Analysis Of Geopilin Function In Geobacter Sulfurreducens, Lubna V. Richter

Open Access Dissertations

Geobacter sulfurreducens possesses type IV pili that are considered to be conductive nanowires and a crucial structural element in biofilm formation, enabling electron transfer to insoluble metal oxides in anaerobic sediments and to graphite anodes in microbial fuel cells. The molecular mechanism by which electrons are transferred through the nanowires to the electron acceptor is not fully understood. Prior to the work described in this thesis, the gene (pilA) encoding the structural pilus subunit had been identified, but little was known about the functional translation start codon, the length of the mature secreted protein, or what renders the pili conductive. …

Autonomous Robot Skill Acquisition, George D. Konidaris

Open Access Dissertations

Among the most impressive of aspects of human intelligence is skill acquisition—the ability to identify important behavioral components, retain them as skills, refine them through practice, and apply them in new task contexts. Skill acquisition underlies both our ability to choose to spend time and effort to specialize at particular tasks, and our ability to collect and exploit previous experience to become able to solve harder and harder problems over time with less and less cognitive effort.

Hierarchical reinforcement learning provides a theoretical basis for skill acquisition, including principled methods for learning new skills and deploying them during problem solving. …

Molecular Designs For Organic Semiconductors: Design, Synthesis And Charge Transport Properties, Tejaswini Sharad Kale

Open Access Dissertations

Understanding structure-property relationship of molecules is imperative for designing efficient materials for organic semiconductors. Organic semiconductors are based on π-conjugated molecules, either small molecules or macromolecules such as dendrimers or polymers. Charge transport through organic materials is one of the most important processes that drive organic electronic devices. We have investigated the charge transport properties in various molecular designs based on dendrons, dendron-rod-coil molecular triads, and conjugated oligomers. The charge transport properties were studied using bottom contact field effect transistors, in which the material was deposited by spin coating.

In case of dendrons, their generation and density of charge transporting …

Enabling Peer-To-Peer Swarming For Multi-Commodity Dissemination, Daniel Sadoc Menasche

Open Access Dissertations

Peer-to-peer swarming, as used by BitTorrent, is one of the de facto solutions for content dissemination in today’s Internet. By leveraging resources provided by users, peer-to-peer swarming is a simple, scalable and efficient mechanism for content distribution. Although peer-to-peer swarming has been widely studied for a decade, prior work has focused on the dissemination of one commodity (a single file). This thesis focuses on the multi-commodity case.

We have discovered through measurements that a vast number of publishers currently disseminate multiple files in a single swarm (bundle). The first contribution of this thesis is a model for content availability. We …

Colloidal Microcapsules: Surface Engineering Of Nanoparticles For Interfacial Assembly, Debabrata Patra

Open Access Dissertations

Colloidal Microcapsules (MCs), i.e. capsules stabilized by nano-/microparticle shells are highly modular inherently multi-scale constructs with applications in many areas of material and biological sciences e.g. drug delivery, encapsulation and microreactors. These MCs are fabricated by stabilizing emulsions via self-assembly of colloidal micro/nanoparticles at liquid-liquid interface. In these systems, colloidal particles serve as modular building blocks, allowing incorporation of the particle properties into the functional capabilities of the MCs. As an example, nanoparticles (NPs) can serve as appropriate antennae to induce response by external triggers (e.g. magnetic fields or laser) for controlled release of encapsulated materials. Additionally, the dynamic nature …