Theses and Dissertations from UMD
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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM
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Item Patterns and Complexity in Biological Systems: A Study of Sequence Structure and Ontology-based Networks(2010) Glass, Kimberly; Girvan, Michelle; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Biological information can be explored at many different levels, with the most basic information encoded in patterns within the DNA sequence. Through molecular level processes, these patterns are capable of controlling the states of genes, resulting in a complex network of interactions between genes. Key features of biological systems can be determined by evaluating properties of this gene regulatory network. More specifically, a network-based approach helps us to understand how the collective behavior of genes corresponds to patterns in genetic function. We combine Chromatin-Immunoprecipitation microarray (ChIP-chip) data with genomic sequence data to determine how DNA sequence works to recruit various proteins. We quantify this information using a value termed "nmer-association.'' "Nmer-association'' measures how strongly individual DNA sequences are associated with a protein in a given ChIP-chip experiment. We also develop the "split-motif'' algorithm to study the underlying structural properties of DNA sequence independent of wet-lab data. The "split-motif'' algorithm finds pairs of DNA motifs which preferentially localize relative to one another. These pairs are primarily composed of known transcription factor binding sites and their co-occurrence is indicative of higher-order structure. This kind of structure has largely been missed in standard motif-finding algorithms despite emerging evidence of the importance of complex regulation. In both simple and complex regulation, two genes that are connected in a regulatory fashion are likely to have shared functions. The Gene Ontology (GO) provides biologists with a controlled terminology with which to describe how genes are associated with function and how those functional terms are related to each other. We introduce a method for processing functional information in GO to produce a gene network. We find that the edges in this network are correlated with known regulatory interactions and that the strength of the functional relationship between two genes can be used as an indicator of how informationally important that link is in the regulatory network. We also investigate the network structure of gene-term annotations found in GO and use these associations to establish an alternate natural way to group the functional terms. These groups of terms are drastically different from the hierarchical structure established by the Gene Ontology and provide an alternative framework with which to describe and predict the functions of experimentally identified groups of genes.Item Cryogenic test of gravitational inverse square law below 100-micrometer length scales(2010) Yethadka Venkateswara, Krishna Raj; Paik, Ho Jung; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The inverse-square law is a hallmark of theories of gravity, impressively demonstrated from astronomical scales to sub-millimeter scales, yet we do not have a complete quantized theory of gravity applicable at the shortest distance scale. Problems within modern physics such as the hierarchy problem, the cosmological constant problem, and the strong CP problem in the Standard Model motivate a search for new physics. Theories such as large extra dimensions, ‘fat gravitons,’ and the axion, proposed to solve these problems, can result in a deviation from the gravitational inverse-square law below 100 μm and are thus testable in the laboratory. We have conducted a sub-millimeter test of the inverse-square law at 4.2 K. To minimize Newtonian errors, the experiment employed a near-null source, a disk of large diameter-to-thickness ratio. Two test masses, also disk-shaped, were positioned on the two sides of the source mass at a nominal distance of 280 μm. As the source was driven sinusoidally, the response of the test masses was sensed through a superconducting differential accelerometer. Any deviations from the inverse-square law would appear as a violation signal at the second harmonic of the source frequency, due to symmetry. We improved the design of the experiment significantly over an earlier version, by separating the source mass suspension from the detector housing and making the detector a true differential accelerometer. We identified the residual gas pressure as an error source, and developed ways to overcome the problem. During the experiment we further identified the two dominant sources of error - magnetic cross-talk and electrostatic coupling. Using cross-talk cancellation and residual balance, these were reduced to the level of the limiting random noise. No deviations from the inverse-square law were found within the experimental error (2σ) down to a length scale λ = 100 μm at the level of coupling constant |α|≤2. Extra dimensions were searched down to a length scale of 78 μm (|α|≤4). We have also proposed modifications to the current experimental design in the form of new tantalum source mass and installing additional accelerometers, to achieve an amplifier noise limited sensitivity.Item Investigating and accounting for physics graduate students' tutorial classroom practice(2010) Goertzen, Renee Michelle; Scherr, Rachel E; Redish, Edward F; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Physics Education researchers have been working to understanding how students learn physics, which has led to the creation of a body of research-based curricula. It is equally important to study novice instructors, graduate teaching assistants (TAs), who often teach these students. The study of TAs has similarities to how students have been studied: it is important to identify what preconceptions they often enter the classroom with, what resources they may have that they could apply to their physics teaching, and how both the classroom environment and past experiences affect what they are doing in the classroom. Although TAs are responsible for a significant portion of students' instruction at many universities, science TAs and their teaching have not been the focus of any significant amount of study. This dissertation begins to fill this gap by examining physics graduate students who teach discussion sections for introductory courses using tutorials, which are guided worksheets completed by groups of students. While assisting students with their conceptual understanding of physics, TAs are also expected to convey classroom norms of constructing arguments and listening and responding to the reasoning of others. Physics graduate students enter into the role of tutorial TA having relative content expertise but minimal or no pedagogical expertise. This analysis contends that considering the broader influences on TAs can account for TA behavior. Observations from two institutions (University of Colorado, Boulder and University of Maryland, College Park) show that TAs have different valuations (or buy-in) of the tutorials they teach, which have specific, identifiable consequences in the classroom. These differences can be explained by differences in the TAs' different teaching environments. Next, I examine cases of a behavior shared by three TAs, in which they focus on relatively superficial indicators of knowledge. Because the beliefs that underlie their teaching decisions vary, I argue that understanding and addressing the TAs individual beliefs will lead to more effective professional development. Lastly, this analysis advocates a new perspective on TA professional development: one in which TAs' ideas about teaching are taken to be interesting, plausible, and potentially productive.Item Controlling Molecular-Scale Motion: Exact Predictions for Driven Stochastic Systems(2010) Horowitz, Jordan Michael; Jarzynski, Christopher; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Despite inherent randomness and thermal fluctuations, controllable molecular devices or molecular machines are currently being synthesized around the world. Many of these molecular complexes are non-autonomous in that they are manipulated by external stimuli. As these devices become more sophisticated, the need for a theoretical framework to describe them becomes more important. Many non-autonomous molecular machines are modeled as stochastic pumps: stochastic systems that are driven by time-dependent perturbations. A number of exact theoretical predictions have been made recently describing how stochastic pumps respond to arbitrary driving. This work investigates one such prediction, the current decomposition formula, and its consequences. The current decomposition formula is a theoretical formula that describes how stochastic systems respond to non-adiabatic time-dependent perturbations. This formula is derived for discrete stochastic pumps modeled as continuous-time Markov chains, as well as continuous stochastic pumps described as one-dimensional diffusions. In addition, a number of interesting consequences following from the current decomposition formula are reported. For stochastic pumps driven adiabatically (slowly), their response can be given a purely geometric interpretation. The geometric nature of adiabatic pumping is then exploited to develop a method for controlling non-autonomous molecular machines. As a second consequence of the current decomposition formula, a no-pumping theorem is proved which provides conditions for which stochastic pumps with detailed balance exhibit no net directed motion in response to non-adiabatic cyclic driving. This no-pumping theorem provides an explanation of experimental observations made on 2- and 3-catenanes.Item Experimental Characterization of Turbulent Superfluid Helium(2010) Paoletti, Matthew S.; Lathrop, Daniel P; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Fundamental processes in turbulent superfluid 4He are experimentally characterized by refining a visualization technique recently introduced by Bewley et al. A mixture of hydrogen and helium gas is injected into the bulk fluid, which produces a distribution of micron-sized hydrogen tracer particles that are visualized and individually tracked allowing for local velocity measurements. Tracer trajectories are complex since some become trapped on the quantized vortices while others flow with the normal fluid. This technique is first applied to study the dynamics of a thermal counterflow. The resulting observations constitute the first direct confirmation of two-fluid motions in He II and provide a quantitative test of the expression for the dependence of the normal fluid velocity, vn, on the applied heat flux, q, derived by L. D. Landau in 1941. Nearly 20,000 individual reconnection events are identified for the first time and used to characterize the dynamics by the minimum separation distance, $delta(t)$, between two reconnecting vortices. Dimensional arguments predict that this separation behaves asymptotically as $delta(t) approx A left ( kappa vert t-t_0 vert right ) ^{1/2}$, where $kappa=h/m$ is the quantum of circulation. The major finding of the experiments is strong support for this asymptotic form with $kappa$ as the dominant controlling quantity. Nevertheless there are significant event-to-event fluctuations that are equally well fit by two modified expressions: (a) an arbitrary power-law expression $delta(t)=B vert t-t_0 vert ^{alpha}$ and (b) a correction-factor expression $delta(t)=Aleft (kappa vert t-t_0 vert right ) ^{1/2}(1+c vert t-t_0 vert )$. In light of various physical interpretations we regard the correction-factor expression (b), which attributes the observed deviations from the predicted asymptotic form to fluctuations in the local environment and boundary conditions, as best describing the experimental data. The observed dynamics appear statistically time-reversible, suggesting that an effective equilibrium has been established in quantum turbulence on the time scales investigated. The hydrogen tracers allow for the first measurements of the local velocity statistics of a turbulent quantum fluid. The distributions of velocity in the decaying turbulence are strongly non-Gaussian with 1/v3 power-law tails in contrast to the near-Gaussian statistics of homogenous and isotropic turbulence of classical fluids. The dynamics of many vortex reconnection events are examined and simple scaling arguments show that they yield the observed power-law tails.Item A Continuum Model for Flocking: Obstacle Avoidance, Equilibrium, and Stability(2010) Mecholsky, Nicholas Alexander; Ott, Edward; Antonsen, Jr., Thomas M; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The modeling and investigation of the dynamics and configurations of animal groups is a subject of growing attention. In this dissertation, we present a partial-differential-equation based continuum model of flocking and use it to investigate several properties of group dynamics and equilibrium. We analyze the reaction of a flock to an obstacle or an attacking predator. We show that the flock response is in the form of density disturbances that resemble Mach cones whose configuration is determined by the anisotropic propagation of waves through the flock. We investigate the effect of a flock `pressure' and pairwise repulsion on an equilibrium density distribution. We investigate both linear and nonlinear pressures, look at the convergence to a ‘cold’ (T → 0) equilibrium solution, and find regions of parameter space where different models produce the same equilibrium. Finally, we analyze the stability of an equilibrium density distribution to long-wavelength perturbations. Analytic results for the stability of a constant density solution as well as stability regimes for constant density solutions to the equilibrium equations are presented.Item COMPARING AND CONTRASTING DIFFERENT METHODS FOR PROBING STUDENT EPISTEMOLOGY AND EPISTEMOLOGICAL DEVELOPMENT IN INTRODUCTORY PHYSICS(2009) McCaskey, Timothy Lee; Redish, Edward F; Elby, Andrew R; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this dissertation, I perform and compare three different studies of introductory physics students' epistemological views - their views about the nature of knowledge and how it is learned. Physics education research (PER) shows that epistemological views affect how students learn, so they are important to understand and diagnose. The first study uses a Likert-scale instrument, adapted from the Maryland Physics Expectation Survey, designed to assess to what extent students see physics knowledge as coherent (rather than piecemeal), conceptual (rather than just formulas), and constructed (rather than absorbed). Using this survey, I documented several results, including that (i) a large lecture class can produce favorable changes in students' epistemological views, at least in the context of the class, and (ii) teaching a rushed modern physics unit at the end of an introductory sequence can lead to negative epistemological effects. The second study uses the Force Concept Inventory with modified instructions: students indicated both the answer they think a scientist would give and the answer that makes the most sense to them personally. A "split" between these two answers shows that the student does not think she has reconciled her common sense with the formal physics concepts. This study showed that attention to reconciliation in a course allows students to see initially-counterintuitive ideas as making sense. Finally, I did a detailed study of one student by (i) watching video of her in tutorial, where she and three other students answered a structured series of conceptual and quantitative physics questions, (ii) formulating interviews based largely on what I observed in the video, and (iii) interviewing her while the tutorial was still fresh in her head. I repeated this cycle every week for a semester. I found that her tendency to focus on the multiple and ambiguous meanings of words like "force" hampered her ability to reconcile physics concepts with common sense. This last method is time-consuming, but it produces rich data and allows for a fine-grained analysis of individual students. The first two survey methods are best suited for measuring the effect of epistemologically-centered course reforms on large groups of students.Item The Dynamics of Variability in Introductory Physics Students' Thinking: Examples from Kinematics(2009) Frank, Brian Wallace; Scherr, Rachel E; Hammer, David; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Physics education research has long emphasized the need for physics instruction to address students' existing intuitions about the physical world as an integral part of learning physics. Researchers, however, have not reached a consensus-view concerning the nature of this intuitive knowledge or the specific role that it does (or might) play in physics learning. While many early characterizations of student misconceptions cast students' intuitive thinking as largely static, unitary in structure, and counter-productive for the purpose of learning correct physics, much of contemporary research supports a conceptualization of intuitive thought as dynamic, manifold in structure, and generative in the development of expertise. This dissertation contributes to ongoing inquiry into the nature of students' intuitive thought and its role in learning physics through the pursuit of dynamic systems characterizations of student reasoning, with a particular focus on how students settle into and shift among multiple patterns of reasoning about motion. In one thread of this research, simple experimental designs are used to demonstrate how individual students can be predictably biased toward and away from different ways of thinking about the same physical situation when specific parameters of questions posed to students are varied. I qualitatively model students' thinking in terms of the activations and interactions among fine-grained intuitive knowledge and static features of the context. In a second thread of this research, case studies of more dynamic shifts in students' conceptual reasoning are developed from videos of student discussions during collaborative classroom activities. These show multiple local stabilities of students' thinking as well, with evidence of group-level dynamics shifting on the time scale of minutes. This work contributes to existing research paradigms that aim to characterize student thinking in physics education in two important ways: (1) through the use of methods that allow for forms of empirical accountability that connect descriptive models of student thinking to experimental data, and (2) through the theoretical development of explanatory mechanisms that account for patterns in students' reasoning at multiple levels of analysis.Item Nonlinear Dyanmics in Biological Systems: Actin Networks and Gene Networks(2009) Pomerance, Andrew; Losert, Wolfgang; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Two problems in biological systems are studied: (i) experiments in microscale deformations of actin networks and (ii) a theoretical treatment of the stability of discrete state network models of genetic control. In the experiments on actin networks, we use laser tweezers to locally deform actin networks at the micron scale as a model of the action of molecular motors and other cellular components, and we image the network during deformation using confocal microscopy. Using these tools, we observe two nonlinear effects. The first observation is that there are two time scales of relaxation in the network: the stress induced by deformation relaxes rather quickly, however, the strain relaxes at a different rate. Additionally, upon removing the deforming force, the initial rate at which the strain relaxes seems to be independent of the amount of stress still in the network. The second observation is that large deformations are irreversible, and imaging the network implies that a large-scale snapping event seems to accompany this irreversibility. In the theoretical treatment of gene networks, we focus on the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed uncorrelated random network structure. Real gene networks typically have nontrivial topology significantly different from the random network paradigm. In order to address such situations, we present a general method for determining the stability of large Boolean networks of any specified network topology and predicting their steady-state behavior in response to small perturbations. Additionally, we generalize to the case where individual genes have a distribution of `expression biases,' and we consider non-synchronous update, as well as extension of our method to non-Boolean models in which there are more than two possible gene states. We find that stability is governed by the maximum eigenvalue of a modified adjacency matrix (&lambdaQ<\sub>), and we test this result by comparison with numerical simulations. We also discuss the possible application of our work to experimentally inferred gene networks and present approximations to &lambdaQ<\sub> in several cases.Item A Search for Muon Neutrinos from Gamma-Ray Bursts wih the IceCube 22-String Detector(2009) Roth, A Philip; Hoffman, Kara; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Two searches are conducted for muon neutrinos from Gamma-Ray Bursts (GRBs) using the IceCube detector. Gamma-Ray Bursts are brief and transient emissions of keV/MeV radiation occuring with a rate of a few per day uniformly in the sky. Swift and other satellites of the Third Interplanetary Network (IPN3) detect these GRBs and send notices out via the GRB Coordinate Network (GCN). The fireball model describing the physics of GRBs predicts the emission of muon neutrinos from these bursts. IceCube is a cubic kilometer neutrino detector buried in the deep antarctic ice at the South Pole that can be used to find these prediceted but still unobserved neutrinos. It is sensitive to them by detecting Cherenkov light from secondary muons produced when the neutrinos interact in or near the instrumented volume. The construction of IceCube has been underway since the austral summer of 2004-2005 and will continue until 2011. The growing IceCube detector will soon be sensitivite to the high energy neutrino emission from GRBs that is predicted by the fireball model. A blind and triggered search of the 22-string IceCube data for this neutrino emission was conducted. The principal background to the observation of neutrinos in IceCube is muons generated in cosmic-ray air-showers in the atmosphere above the detector. Atmospheric neutrinos make up a separate irreducible background to the detection of extraterrestrial neutrinos. A binned stacked search of 41 bursts occuring in the northern hemisphere greatly reduces the muon background by looking for tracks moving up through the detector. The atmospheric neutrino background is greatly reduced by the temporal constraints of the search, making it effectively background free. 40 individual unbinned searches of bursts occuring in the southern hemisphere extend IceCube's sensitivity to the higher background regions above the horizon. No significant excesses over background expectations are found in either search. A 90% confidence upper limit on the neutrino fluence from northern hemisphere bursts is set at 6.52 x 10-3 erg cm-2 with 90% of the expected signal between 87.9 TeV and 10.4 PeV.