Physical Sciences and Mathematics Commons^™

Deconstructing Cation-Pi Interactions: Understanding The Binding Energies Involved With Metal And Aromatic Amino Acid Residues, Jen E. Werner, Lyudmila V. Slipchenko, Yen Bui

The Summer Undergraduate Research Fellowship (SURF) Symposium

The Effective Fragment Potential (EFP) method is a computationally efficient technique for describing non-covalent interactions, such as hydrogen bonding and van der Waals forces. Cation-pi interactions are a type of non-covalent interactions and are thought to be important in biological processes, such as permittivity of ion channels. The goal of our work is to establish that the EFP method reliably describes the strength, directionality, and composition of cation-pi interactions. Optimal geometries were found for a series of biologically relevant cations (K⁺, Li⁺, Na⁺, Ca²⁺, and Mg²⁺) and aryl moieties appearing …

Experimental Design And Construction For Critical Velocity Measurement In Spin-Orbit Coupled Bose-Einstein Condensates, Ting-Wei Hsu, Yong P. Chen

The Summer Undergraduate Research Fellowship (SURF) Symposium

Quantum simulation using ultra-cold atoms, such as Bose-Einstein Condensates (BECs), offers a very flexible and well controlled environment to simulate physics in different systems. For example, to simulate the effects of spin orbit coupling (SOC) on electrons in solid state systems, we can make a SOC BEC which mimics the behavior of SOC electrons. The goal of this project is to see how the superfluid property of BECs change in the presence of SOC. In particular, we plan to measure the critical velocity of an 87Rb BEC with and without SOC by stirring it with a laser. This laser needs …

Quantifying Groundwater/Surface-Water Interactions In Tributaries To The Wabash River Using Radon‐222 And Other Environmental Isotopes, Philine Bogeholz, Marty Frisbee

The Summer Undergraduate Research Fellowship (SURF) Symposium

Groundwater/surface-water interactions have not been extensively studied in tile-drained watersheds where natural recharge processes are “short circuited” by routing water out of the soil-zone and into nearby drainage ditches. This practice likely impacts baseflow generation in the Wabash River of Indiana. If true, then how is baseflow affected in small tributaries to the Wabash? To answer this question, we investigated groundwater/surface-water interactions in four small tributary drainages to the Wabash River and Sugar Creek. These drainages share common geologic characteristics and are deeply incised providing a window into groundwater flow processes. We sampled these drainages for general geochemistry, radon-222 ( …

Model Selection For Gaussian Mixture Models For Uncertainty Qualification, Yiyi Chen, Guang Lin, Xuan Liu

The Summer Undergraduate Research Fellowship (SURF) Symposium

Clustering is task of assigning the objects into different groups so that the objects are more similar to each other than in other groups. Gaussian Mixture model with Expectation Maximization method is the one of the most general ways to do clustering on large data set. However, this method needs the number of Gaussian mode as input(a cluster) so it could approximate the original data set. Developing a method to automatically determine the number of single distribution model will help to apply this method to more larger context. In the original algorithm, there is a variable represent the weight of …

Hyperscaling Violation And Electroweak Symmetry Breaking, Daniel Elander, Robert Lawrence, Maurizio Piai

Department of Physics and Astronomy Faculty Publications

We consider a class of simplifed models of dynamical electroweak symmetry breaking built in terms of their fve-dimensional weakly-coupled gravity duals, in the spirit of bottom-up holography. The sigma-model consists of two abelian gauge bosons and one real, non-charged scalar feld coupled to gravity in fve dimensions. The scalar potential is a simple exponential function of the scalar feld. The background metric resulting from solving the classical equations of motion exhibits hyperscaling violation, at least at asymptotically large values of the radial direction. We study the spectrum of scalar composite states of the putative dual feld theory by fuctuating the …

Image Segmentation Using Fuzzy-Spatial Taxon Cut, Lauren Barghout

MODVIS Workshop

Images convey multiple meanings that depend on the context in which the viewer perceptually organizes the scene. This presents a problem for automated image segmentation, because it adds uncertainty to the process of selecting which objects to include or not include within a segment. I’ll discuss the implementation of a fuzzy-logic-natural-vision-processing engine that solves this problem by assuming the scene architecture prior to processing. The scene architecture, a standardized natural-scene-perception-taxonomy comprised of a hierarchy of nested spatial-taxons. Spatial-taxons are regions (pixel-sets) that are figure-like, in that they are perceived as having a contour, are either `thing-like', or a `group of …

Video Event Understanding With Pattern Theory, Fillipe Souza, Sudeep Sarkar, Anuj Srivastava, Jingyong Su

MODVIS Workshop

We propose a combinatorial approach built on Grenander’s pattern theory to generate semantic interpretations of video events of human activities. The basic units of representations, termed generators, are linked with each other using pairwise connections, termed bonds, that satisfy predefined relations. Different generators are specified for different levels, from (image) features at the bottom level to (human) actions at the highest, providing a rich representation of items in a scene. The resulting configurations of connected generators provide scene interpretations; the inference goal is to parse given video data and generate high-probability configurations. The probabilistic structures are imposed using energies that …

Metacognition: Using Confidence Ratings For Type 2 And Type 1 Roc Curves, S A. Klein

MODVIS Workshop

In the past five years there has been a surge of renewed interest in metacognition ("thinking about thinking"). The typical experiment involves a binary judgment followed by a multilevel confidence rating. It is a confusing topic because the rating could be made either on one's confidence in the binary response (standard rating Type 1 ROC) or on one's confidence sorted by whether the response was correct (Type 2 ROC). Both are metacognition. After a few remarks on challenging aspects of the Type 2 approach, I will present some interesting results for Type 1 ROC for both memory and vision research. …

Two Correspondence Problems Easier Than One, Aaron Michaux, Zygmunt Pizlo

MODVIS Workshop

Computer vision research rarely makes use of symmetry in stereo reconstruction despite its established importance in perceptual psychology. Such stereo reconstructions produce visually satisfying figures with precisely located points and lines, even when input images have low or moderate resolution. However, because few invariants exist, there are no known general approaches to solving symmetry correspondence on real images. The problem is significantly easier when combined with the binocular correspondence problem, because each correspondence problem provides strong non-overlapping constraints on the solution space. We demonstrate a system that leverages these constraints to produce accurate stereo models from pairs of binocular images …

Binocular 3d Motion Perception As Bayesian Inference, Martin Lages, Suzanne Heron

MODVIS Workshop

The human visual system encodes monocular motion and binocular disparity input before it is integrated into a single 3D percept. Here we propose a geometric-statistical model of human 3D motion perception that solves the aperture problem in 3D by assuming that (i) velocity constraints arise from inverse projection of local 2D velocity constraints in a binocular viewing geometry, (ii) noise from monocular motion and binocular disparity processing is independent, and (iii) slower motions are more likely to occur than faster ones. In two experiments we found that instantiation of this Bayesian model can explain perceived 3D line motion direction under …

Formal Aspects Of Non-Rigid-Shape-From-Motion Perception, Vicky Froyen, Qasim Zaidi

MODVIS Workshop

Our world is full of objects that deform over time, for example animals, trees and clouds. Yet, the human visual system seems to readily disentangle object motions from non-rigid deformations, in order to categorize objects, recognize the nature of actions such as running or jumping, and even to infer intentions. A large body of experimental work has been devoted to extracting rigid structure from motion, but there is little experimental work on the perception of non-rigid 3-D shapes from motion (e.g. Jain, 2011). Similarly, until recently, almost all formal work had concentrated on the rigid case. In the last fifteen …

Object Recognition And Visual Search With A Physiologically Grounded Model Of Visual Attention, Frederik Beuth, Fred H. Hamker

MODVIS Workshop

Visual attention models can explain a rich set of physiological data (Reynolds & Heeger, 2009, Neuron), but can rarely link these findings to real-world tasks. Here, we would like to narrow this gap with a novel, physiologically grounded model of visual attention by demonstrating its objects recognition abilities in noisy scenes.

To base the model on physiological data, we used a recently developed microcircuit model of visual attention (Beuth & Hamker, in revision, Vision Res) which explains a large set of attention experiments, e.g. biased competition, modulation of contrast response functions, tuning curves, and surround suppression. Objects are represented by …

Modeling Visual Features To Recognize Biological Motion: A Developmental Approach, Giulio Sandini, Nicoletta Noceti, Alessia Vignolo, Alessandra Sciutti, Francesco Rea, Alessandro Verri, Francesca Odone

MODVIS Workshop

In this work we deal with the problem of designing and developing computational vision models – comparable to the early stages of the human development – using coarse low-level information.

More specifically, we consider a binary classification setting to characterize biological movements with respect to non-biological dynamic events. To this purpose, our model builds on top of the optical flow estimation, and abstract the representation to simulate the limited amount of visual information available at birth. We take inspiration from known biological motion regularities explained by the Two-Thirds Power Law, and design a motion representation that includes different low-level features, …

Simulations Of Nanoscale Ni/Al Multilayer Foils With Intermediate Ni2al3 Growth, I. E. Gunduz, S. Onel, C. C. Doumanidis, C. Rebholz, Steven F. Son

Purdue Energetics Research Center Articles

Nanoscale multilayers of binary metallic systems, such as nickel/aluminum, exhibit self-propagating exothermic reactions due to the high formation enthalpy of the intermetallic compounds. Most of the previous modelingapproaches on the reactions of this system rely on the use of mass diffusionwith a phenomenological derived diffusion coefficient representing single-phase (NiAl) growth, coupled with heat transport. We show that the reaction kinetics, temperatures, and thermal front width can be reproduced more satisfactorily with the sequential growth of Ni2Al3 followed by NiAl, utilizing independently obtained interdiffusivities. The computational domain was meshed with a dynamically generated bi-modal grid consisting of fine and coarse zones …

Optimal "Big Data" Aggregation Systems - From Theory To Practical Application, William J. Culhane Iv

Open Access Dissertations

The integration of computers into many facets of our lives has made the collection and storage of staggering amounts of data feasible. However, the data on its own is not so useful to us as the analysis and manipulation which allows manageable descriptive information to be extracted. New tools to extract this information from ever growing repositories of data are required.

Some of these analyses can take the form of a two phase problem which is easily distributed to take advantage of available computing power. The first phase involves computing some descriptive partial result from some subset of the original …

Partition Density Functional Theory, Jonathan R. Nafziger

Open Access Dissertations

Partition density functional theory (PDFT) is a method for dividing a molecular electronic structure calculation into fragment calculations. The molecular density and energy corresponding to Kohn Sham density-functional theory (KS-DFT) may be exactly recovered from these fragments. Each fragment acts as an isolated system except for the influence of a global one-body 'partition' potential which deforms the fragment densities. In this work, the developments of PDFT are put into the context of other fragment-based density functional methods. We developed three numerical implementations of PDFT: One within the NWChem computational chemistry package using basis sets, and the other two developed from …

The Effect Of Macromolecular Crowding On The Structure Of The Protein Complex Superoxide Dismutase, Ajith Rathnaweera Rajapaksha Mudalige

Open Access Dissertations

Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied.^ We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using …

Overcoming Uncertainty For Within-Network Relational Machine Learning, Joseph J. Pfeiffer

Open Access Dissertations

People increasingly communicate through email and social networks to maintain friendships and conduct business, as well as share online content such as pictures, videos and products. Relational machine learning (RML) utilizes a set of observed attributes and network structure to predict corresponding labels for items; for example, to predict individuals engaged in securities fraud, we can utilize phone calls and workplace information to make joint predictions over the individuals. However, in large scale and partially observed network domains, missing labels and edges can significantly impact standard relational machine learning methods by introducing bias into the learning and inference processes. In …

Ergodic Properties Of Countable Extensions, Samuel Joshua Roth

Open Access Dissertations

First, we study countably piecewise continuous, piecewise monotone interval maps. We establish a necessary and sufficient criterion for the existence of a non-decreasing semiconjugacy to an interval map of constant slope in terms of the existence of an eigenvector of an operator acting on a space of measures. Then we give examples, both Markov and non-Markov, for which the criterion is violated. ^ Next, we establish a criterion for the existence of a constant slope map on the extended real line conjugate to a given countably piecewise monotone interval map. We require the given interval map to be continuous, Markov, …

Architectural Techniques To Extend Multi-Core Performance Scaling, Hamza Bin Sohail

Open Access Dissertations

Multi-cores have successfully delivered performance improvements over the past decade; however, they now face problems on two fronts: power and off-chip memory bandwidth. Dennard's scaling is effectively coming to an end which has lead to a gradual increase in chip power dissipation. In addition, sustaining off-chip memory bandwidth has become harder due to the limited space for pins on the die and greater current needed to drive the increasing load . My thesis focuses on techniques to address the power and off-chip memory bandwidth challenges in order to avoid the premature end of the multi-core era. ^ In the first …

Stability Of Machine Learning Algorithms, Wei Sun

Open Access Dissertations

In the literature, the predictive accuracy is often the primary criterion for evaluating a learning algorithm. In this thesis, I will introduce novel concepts of stability into the machine learning community. A learning algorithm is said to be stable if it produces consistent predictions with respect to small perturbation of training samples. Stability is an important aspect of a learning procedure because unstable predictions can potentially reduce users' trust in the system and also harm the reproducibility of scientific conclusions. As a prototypical example, stability of the classification procedure will be discussed extensively. In particular, I will present two new …

Privacy-Preserving Social Network Analysis, Christine Marie Task

Open Access Dissertations

Data privacy in social networks is a growing concern that threatens to limit access to important information contained in these data structures. Analysis of the graph structure of social networks can provide valuable information for revenue generation and social science research, but unfortunately, ensuring this analysis does not violate individual privacy is difficult. Simply removing obvious identifiers from graphs or even releasing only aggregate results of analysis may not provide sufficient protection. Differential privacy is an alternative privacy model, popular in data-mining over tabular data, that uses noise to obscure individuals' contributions to aggregate results and offers a strong mathematical …

Mass Spectrometric Characterization Of Peptide Radical Ions And Implication For Radical Chemistry, Lei Tan

Open Access Dissertations

Gas-phase radical ion chemistry has attracted increasing research interest from the mass spectrometry (MS) society because it provides new capabilities in bio-analysis which often complements traditional MS methods developed from even-electron ions. Fundamental studies of biomolecule related radical species are essential to broadening the scope of radical chemistry and pushing the frontiers of its analytical applications. This dissertation mainly discusses the gas-phase chemistry of peptide sulfinyl radicals (-SO·), which has been rarely studied before. In order to establish an effective research approach, a method that can generate site-specific peptide sulfinyl radical ion has been developed. This method is based on …

Heat Trace And Heat Content Asymptotics For Schrodinger Operators Of Stable Processes/Fractional Laplacians, Luis Guillermo Acuna Valverde

Open Access Dissertations

Let V be a bounded and integrable potential over R^d and 0 < α ≤ 2. We show the existence of an asymptotic expansion by means of Fourier Transform techniques and probabilistic methods for the following quantities [special characters omitted] and [special characters omitted] as t ↓ 0. These quantities are called the heat trace and heat content in R^d with respect to V, respectively. Here, p((α)/ t)(x, y) and p( ^H_V/t)(x, y) denote, respectively, the heat kernels of the heat semigroups with infinitesimal generators given by (-Δ)(α/2) and H_V = (-Δ)(α/2) + V. The former operator is known as the fractional Laplacian whereas the latter one is known as the fractional Schrödinger Operator. ^ The study …

Learning Compact Hashing Codes With Complex Objectives From Multiple Sources For Large Scale Similarity Search, Qifan Wang

Open Access Dissertations

Similarity search is a key problem in many real world applications including image and text retrieval, content reuse detection and collaborative filtering. The purpose of similarity search is to identify similar data examples given a query example. Due to the explosive growth of the Internet, a huge amount of data such as texts, images and videos has been generated, which indicates that efficient large scale similarity search becomes more important.^ Hashing methods have become popular for large scale similarity search due to their computational and memory efficiency. These hashing methods design compact binary codes to represent data examples so that …

Orderability And Rigidity In Contact Geometry, Peter Weigel

Open Access Dissertations

We study the existence of positive loops of contactomorphisms on a Liouville-fillable contact manifold (&Sgr;, ξ = ker(α)). Previous results (see [1]) show that a large class of Liouville-fillable contact manifolds admit contractible positive loops. In contrast, we show that for any Liouville-fillable (&Sgr;, α) with dim(&Sgr;) ≥ 7, there exists a Liouville-fillable contact structure ξ' on &Sgr; which admits no positive loop at all. Further, ξ' can be chosen to agree with ξ' on the complement of a Darboux ball. We then define a relative version of orderability for a Legendrian submanifold, and discuss the relationship between the two …

Effect Of Maleic Acid On The Selectivity Of Glucose And Fructose Dehydration And Degradation, Ximing Zhang

Open Access Dissertations

5-Hydroxymethyfurfural (HMF), a platform chemical can upgrade to a variety of fuels and polymers, can be manufactured from lignocellulose. This study focuses on the Lewis and Brønsted acid effect on hexose dehydration for HMF production. We report the positive effect of maleic acid, a dicarboxylic acid used as Brønsted acid, on the selectivity of hexose dehydration to 5-hydroxymethyfurfural (HMF), and subsequent hydrolysis to levulinic and formic acids. We also describe the kinetic analysis of a Lewis acid (AlCl ₃) alone and in combination with HCl or maleic acid to catalyze the isomerization of glucose to fructose, dehydration of fructose …

Permutohedra, Configuration Spaces And Spineless Cacti, Yongheng Zhang

Open Access Dissertations

It has been known that the configuration space F(R², n) of n distinct ordered points in R² deformation retracts to a regular CW complex with n!permutohedra P_n as the top dimensional cells. In this paper, we show that there exists a similar but different permutohedral structure of the spaceCact(n) of spineless cacti with n lobes. Based on these structures, direct homotopy equivalences between F (R², n) and Cact(n) are then given. It is well known that the little 2-discs space D₂(n) is homotopy equivalent toF(R², n). …

Modular Approach To Spintronics, Kerem Yunus Camsari

Open Access Dissertations

There has been enormous progress in the last two decades, effectively combining spintronics and magnetics into a powerful force that is shaping the field of memory devices. New materials and phenomena continue to be discovered at an impressive rate, providing an ever-increasing set of building blocks that could be exploited in designing transistor-like functional devices of the future. The objective of this thesis is to provide a quantitative foundation for this building block approach, so that new discoveries can be integrated into functional device concepts, quickly analyzed and critically evaluated. Through careful benchmarking against available theory and experiments we establish …

Consequences Of Short-Term Water Temperature Variability To Fish: Current And Future Climate Change Impacts, David P. Coulter

Open Access Dissertations

Water temperature has a profound influence on aquatic ectotherms by affecting all aspects of biological organization; from chemical and molecular functioning to whole-organism and population-level impacts. Natural processes and anthropogenic activities can create conditions where temperatures vary greatly through space and time. While exposure to temperature changes lasting ≥ 24 hours have been examined in some species, it is unclear how more rapid (< 24 hours; sub-daily) thermal fluctuations affect aquatic ectotherms. I used a combination of field observations, laboratory experiments, and modeling simulations to understand: 1) how habitat quality of aquatic ectotherms is affected in thermally dynamic environments; 2) the role of sub-daily temperature fluctuations on growth, survival, and stress responses in juvenile and adult fish; 3) how fish early life stages are affected by sub-daily temperature fluctuations; and 4) what impact thermally dynamic environments have on a model species at a population-level. A model quantifying habitat quality around power plant thermal discharges indicated that elevated and variable discharge temperatures affected habitat quality over a relatively small spatial area for aquatic ectotherms. Models examining elevated temperatures representing climate warming showed that the effects of industrial discharges and climate warming could have an interactive effect on habitat quality by increasing the spatial area and duration over which industrial thermal effluents impact aquatic ectotherms. Laboratory experiments indicated that closely related fishes can respond differently to the same sub-daily temperature fluctuations. Yellow perch (Perca flavescens) had higher consumption and growth under sub-daily temperature fluctuations but developed skin lesions; an indication of thermal stress. In contrast, these same fluctuations reduced growth in physiologically similar walleye (Sander vitreus) …