Computer Sciences Commons^™

Proton Computed Tomography: Matrix Data Generation Through General Purpose Graphics Processing Unit Reconstruction, Micah Witt

Electronic Theses, Projects, and Dissertations

Proton computed tomography (pCT) is an image modality that will improve treatment planning for patients receiving proton radiation therapy compared with the current techniques, which are based on X-ray CT. Images are reconstructed in pCT by solving a large and sparse system of linear equations. The size of the system necessitates matrix-partitioning and parallel reconstruction algorithms to be implemented across some sort of cluster computing architecture. The prototypical algorithm to solve the pCT system is the algebraic reconstruction technique (ART) that has been modified into parallel versions called block-iterative-projection (BIP) methods and string-averaging-projection (SAP) methods. General purpose graphics processing units …

Social Correlation In Latent Spaces For Complex Networks, Freddy Chong Tat Chua

Dissertations and Theses Collection (Open Access)

This dissertation addresses the subject of measuring social correlation among users within a complex social network. Social correlation is closely related to the measurement of social influence in social sciences. While social influence focuses on the existence of causal influence among users, we take a computational approach to measure correlation strength among users based on their shared interactions. We call this social correlation. To formally model social correlation, we propose a framework which contains two major parts. The first part is that of representing users behavior in a computationally efficient and accurate manner. For example, social media users perform many …

Criticality And Quenched Disorder: Harris Criterion Versus Rare Regions, Thomas Vojta, José A. Hoyos

Physics Faculty Research & Creative Works

We employ scaling arguments and optimal fluctuation theory to establish a general relation between quantum Griffiths singularities and the Harris criterion for quantum phase transitions in disordered systems. If a clean critical point violates the Harris criterion, it is destabilized by weak disorder. At the same time, the Griffiths dynamical exponent z' diverges upon approaching the transition, suggesting unconventional critical behavior. In contrast, if the Harris criterion is fulfilled, power-law Griffiths singularities can coexist with clean critical behavior, but z' saturates at a finite value. We present applications of our theory to a variety of systems including quantum spin chains, …

Role Of Electron Saddle Swaps In The Photon Spectra Following Li³⁺ Charge-Exchange Collisions With H*(N = 2), Na(3s), Na*(3p), And Li(2s) Targets, Sebastian Otranto, R. Hoekstra, Ronald E. Olson

Physics Faculty Research & Creative Works

The role of electron saddle swaps in collisions of bare Li with metastable hydrogen and alkali-metal atoms is investigated by means of the classical trajectory Monte Carlo method. In particular, we show that oscillations as a function of collision energy in the photon spectra resulting from charge exchange are directly related to the number of potential-saddle crossings that a receding electron can achieve during a given reaction. The range of impact energies spanned is 0.01-50 keV/amu, an area of interest for diagnostic purposes in tokamak nuclear fusion power reactors.

Predicting Response In Mobile Advertising With Hierarchical Importance-Aware Factorization Machine, Richard Jayadi Oentaryo, Ee Peng Lim, Jia Wei Low, David Lo, Michael Finegold

Research Collection School Of Computing and Information Systems

Mobile advertising has recently seen dramatic growth, fueled by the global proliferation of mobile phones and devices. The task of predicting ad response is thus crucial for maximizing business revenue. However, ad response data change dynamically over time, and are subject to cold-start situations in which limited history hinders reliable prediction. There is also a need for a robust regression estimation for high prediction accuracy, and good ranking to distinguish the impacts of different ads. To this end, we develop a Hierarchical Importance-aware Factorization Machine (HIFM), which provides an effective generic latent factor framework that incorporates importance weights and hierarchical …

A Fast Algorithm For The Inversion Of Quasiseparable Vandermonde-Like Matrices, Sirani M. Perera, Grigory Bonik, Vadim Olshevsky

Publications

The results on Vandermonde-like matrices were introduced as a generalization of polynomial Vandermonde matrices, and the displacement structure of these matrices was used to derive an inversion formula. In this paper we first present a fast Gaussian elimination algorithm for the polynomial Vandermonde-like matrices. Later we use the said algorithm to derive fast inversion algorithms for quasiseparable, semiseparable and well-free Vandermonde-like matrices having O(n2) complexity. To do so we identify structures of displacement operators in terms of generators and the recurrence relations(2-term and 3-term) between the columns of the basis transformation matrices for quasiseparable, semiseparable and well-free polynomials. Finally we …

Designs Of Fullerene-Based Frameworks For Hydrogen Storage, Yi Gao, Xiaojun Wu, Xiao Cheng Zeng

Holland Computing Center: Faculty Publications

No abstract provided.

Designs Of Fullerene-Based Frameworks For Hydrogen Storage, Yi Gao, Xiaojun Wu, Xiao Cheng Zeng

Holland Computing Center: Faculty Publications

No abstract provided.

Functional Evolution Of Plp-Dependent Enzymes Based On Active-Site Structural Similarities, Jonathan Catazaro, Adam Caprez, Ashu Guru, David Swanson, Robert Powers

Holland Computing Center: Faculty Publications

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can …

A Comparative Study Of Reservoir Computing For Temporal Signal Processing, Alireza Goudarzi, Peter Banda, Matthew R. Lakin, Christof Teuscher, Darko Stefanovic

Computer Science Faculty Publications and Presentations

Reservoir computing (RC) is a novel approach to time series prediction using recurrent neural networks. In RC, an input signal perturbs the intrinsic dynamics of a medium called a reservoir. A readout layer is then trained to reconstruct a target output from the reservoir's state. The multitude of RC architectures and evaluation metrics poses a challenge to both practitioners and theorists who study the task-solving performance and computational power of RC. In addition, in contrast to traditional computation models, the reservoir is a dynamical system in which computation and memory are inseparable, and therefore hard to analyze. Here, we compare …

Hidden Markov Model With Information Criteria Clustering And Extreme Learning Machine Regression For Wind Forecasting, Dao Lam, Shuhui Li, Donald C. Wunsch

Electrical and Computer Engineering Faculty Research & Creative Works

This paper proposes a procedural pipeline for wind forecasting based on clustering and regression. First, the data are clustered into groups sharing similar dynamic properties. Then, data in the same cluster are used to train the neural network that predicts wind speed. For clustering, a hidden Markov model (HMM) and the modified Bayesian information criteria (BIC) are incorporated in a new method of clustering time series data. to forecast wind, a new method for wind time series data forecasting is developed based on the extreme learning machine (ELM). the clustering results improve the accuracy of the proposed method of wind …

Epistasis In Predator-Prey Relationships, Iuliia Inozemtseva

College of Graduate Studies: Theses & Dissertations

Epistasis is the interaction between two or more genes to control a single phenotype. We model epistasis of the prey in a two-locus two-allele problem in a basic predator- prey relationship. The resulting model allows us to examine both population sizes as well as genotypic and phenotypic frequencies. In the context of several numerical examples, we show that if epistasis results in an undesirable or desirable phenotype in the prey by making the particular genotype more or less susceptible to the predator or dangerous to the predator, elimination of undesirable phenotypes and then genotypes occurs.

Nonlinear Development And Secondary Instability Of Traveling Crossflow Vortices, Fei Li, Meelan M. Choudhari, Lian Duan, Chau-Lyan Chang

Mechanical and Aerospace Engineering Faculty Research & Creative Works

Building upon the prior research targeting the laminar breakdown mechanisms associated with stationary crossflow instability over a swept-wing configuration, this paper investigates the secondary instability of traveling crossflow modes as an alternate scenario for transition. For the parameter range investigated herein, this alternate scenario is shown to be viable unless the initial amplitudes of the traveling crossflow instability are lower than those of the stationary modes by considerably more than one order of magnitude. The linear growth predictions based on the secondary instability theory are found to agree well with both parabolized stability equations and direct numerical simulation, and the …

Crystallization In Nano-Confinement Seeded By A Nanocrystal -- A Molecular Dynamics Study, Heng Pan, Costas Grigoropoulos

Mechanical and Aerospace Engineering Faculty Research & Creative Works

Seeded crystallization and solidification in nanoscale confinement volumes have become an important and complex topic. Due to the complexity and limitations in observing nanoscale crystallization, computer simulation can provide valuable details for supporting and interpreting experimental observations. In this article, seeded crystallization from nano-confined liquid, as represented by the crystallization of a suspended gold nano-droplet seeded by a pre-existing gold nanocrystal seed, was investigated using molecular dynamics simulations in canonical (NVT) ensemble. We found that the crystallization temperature depends on nano-confinement volume, crystal orientation, and seed size as explained by classical two-sphere model and Gibbs-Thomson effect.

Contact Process On Generalized Fibonacci Chains: Infinite-Modulation Criticality And Double-Log Periodic Oscillations, Hatem Barghathi, David Nozadze, Thomas Vojta

Physics Faculty Research & Creative Works

We study the nonequilibrium phase transition of the contact process with aperiodic transition rates using a real-space renormalization group as well as Monte Carlo simulations. The transition rates are modulated according to the generalized Fibonacci sequences defined by the inflation rules A → AB^k and B → A. For k=1 and 2, the aperiodic fluctuations are irrelevant, and the nonequilibrium transition is in the clean directed percolation universality class. For k ≥ 3, the aperiodic fluctuations are relevant. We develop a complete theory of the resulting unconventional "infinite-modulation" critical point, which is characterized by activated dynamical scaling. Moreover, observables …

Dynamical (E,2e) Studies Of Tetrahydropyran And 1,4-Dioxane, J. D. Builth-Williams, G. Da Silva, L. Chiari, D. B. Jones, Hari Chaluvadi, Don H. Madison, M. J. Brunger

Physics Faculty Research & Creative Works

We present experimental and theoretical results for the electron-impact ionization of the highest occupied molecular orbitals of tetrahydropyran and 1,4-dioxane. Using an (e,2e) technique in asymmetric coplanar kinematics, angular distributions of the slow ejected electron, with an energy of 20 eV, are measured when incident electrons at 250 eV ionize the target and scatter through an angle of either -10° or -15°. The data are compared with calculations performed at the molecular 3-body distorted wave level. Fair agreement between the theoretical model and the experimental measurements was observed. The similar structures for these targets provide key insights for assessing the …

Kapitza Resistance Of Si/Sio₂ Interface, Bowen Deng, Aleksandr V. Chernatynskiy, Marat Khafizov, David H. Hurley, Simon R. Phillpot

Physics Faculty Research & Creative Works

A phonon wave packet dynamics method is used to characterize the Kapitza resistance of a Si/SiO₂ interface in a Si/SiO₂/Si heterostructure. By varying the thickness of SiO₂ layer sandwiched between two Si layers, we determine the Kapitza resistance for the Si/SiO ₂ interface from both wave packet dynamics and a direct, non-equilibrium molecular dynamics approach. The good agreement between the two methods indicates that they have each captured the anharmonic phonon scatterings at the interface. Moreover, detailed analysis provides insights as to how individual phonon mode scatters at the interface and their contribution to the Kapitza …

Phonon Thermal Transport Through Tilt Grain Boundaries In Strontium Titanate, Zexi Zheng, Xiang Chen, Bowen Deng, Aleksandr V. Chernatynskiy, Shengfeng Yang, Jinjun Xiong, Youping Chen

Physics Faculty Research & Creative Works

In this work, we perform nonequilibrium molecular dynamics simulations to study phonon scattering at two tilt grain boundaries (GBs) in SrTiO₃. Mode-wise energy transmission coefficients are obtained based on phonon wave-packet dynamics simulations. The Kapitza conductance is then quantified using a lattice dynamics approach. The obtained results of the Kapitza conductance of both GBs compare well with those obtained by the direct method, except for the temperature dependence. Contrary to common belief, the results of this work show that the optical modes in SrTiO₃ contribute significantly to phonon thermal transport, accounting for over 50% of the Kapitza …

Strong-Randomness Infinite-Coupling Phase In A Random Quantum Spin Chain, Fawaz Hrahsheh, José A. Hoyos, Rajesh Narayanan, Thomas Vojta

Physics Faculty Research & Creative Works

We study the ground-state phase diagram of the Ashkin-Teller random quantum spin chain by means of a generalization of the strong-disorder renormalization group. In addition to the conventional paramagnetic and ferromagnetic (Baxter) phases, we find a partially ordered phase characterized by strong randomness and infinite coupling between the colors. This unusual phase acts, at the same time, as a Griffiths phase for two distinct quantum phase transitions, both of which are of infinite-randomness type. We also investigate the quantum multicritical point that separates the two-phase and three-phase regions, and we discuss generalizations of our results to higher dimensions and other …

Introduction To Parallel Computation, Clinton Mckay

Graduate Student Theses, Dissertations, & Professional Papers

Introduction to Parallel Computing is a course designed to educate students on how to use the parallel libraries and tools provided by modern operating systems and massively parallel computer graphics hardware.

Using a series of lectures and hands-on exercises. Students will learn about parallel algorithms and concepts that will aid them in analyzing a problem and constructing a parallel solution, if possible, using the tools available to their disposal.

The course consists of lectures, projects, quizzes, and homework. The combination of these components will deliver the necessary domain knowledge to students, test them, and in the process train them to …

Mobile Indoor Positioning For Augmented Reality Systems, Robert B. Glass

Theses and Dissertations

This thesis explores the creation and setup of a prototype that allows users of the device to interact within an indoor real world environment and a virtual environment simultaneously using high-tech common technology. The prototype is comprised of a small mobile device such as a cellular mobile phone, Raspberry Pi computer, a battery powered handheld Pico projector, and software developed for the Android OS. The software can easily be ported to other mobile and non-mobile operating systems. The mobile device must contain accelerometer, magnetometer, and gyroscope embedded sensors as well as 802.11 wireless network chip. The prototype software implements an …

Triply Differential (E,2e) Studies Of Phenol, Silva G. Da, R. F. Neves, L. Chiari, D. B. Jones, E. Ali, Don H. Madison, C. G. Ning, K. L. Nixon, M. C. Lopes, M. J. Brunger

Physics Faculty Research & Creative Works

We have measured (e,2e) triple differential cross sections (TDCS) for the electron-impact ionisation of phenol with coplanar asymmetrical kinematics for an incident electron energy of 250 eV. Experimental measurements of the angular distribution of the slow outgoing electrons at 20 eV are obtained when the incident electron scatters through angles of -5°, -10°, and -15°, respectively. The TDCS data are compared with calculations performed within the molecular 3-body distorted wave model. In this case, a mixed level of agreement, that was dependent on the kinematical condition being probed, was observed between the theoretical and experimental results in the binary peak …

Cms Use Of A Data Federation, Kenneth A. Bloom, C.

Kenneth Bloom Publications

CMS is in the process of deploying an Xrootd based infrastructure to facilitate a global data federation. The services of the federation are available to export data from half the physical capacity and the majority of sites are configured to read data over the federation as a back-up. CMS began with a relatively modest set of use-cases for recovery of failed local file opens, debugging and visualization. CMS is finding that the data federation can be used to support small scale analysis and load balancing. Looking forward we see potential in using the federation to provide more flexibility in the …

Identifying Aging-Related Genes In Mouse Hippocampus Using Gateway Nodes, Kathryn Dempsey Cooper, Hesham Ali

Interdisciplinary Informatics Faculty Publications

Background: High-throughput studies continue to produce volumes of metadata representing valuable sources of information to better guide biological research. With a stronger focus on data generation, analysis models that can readily identify actual signals have not received the same level of attention. This is due in part to high levels of noise and data heterogeneity, along with a lack of sophisticated algorithms for mining useful information. Networks have emerged as a powerful tool for modeling high-throughput data because they are capable of representing not only individual biological elements but also different types of relationships en masse. Moreover, well-established graph …

Richardson Extrapolation-Based High Accuracy High Efficiency Computation For Partial Differential Equations, Ruxin Dai

Theses and Dissertations--Computer Science

In this dissertation, Richardson extrapolation and other computational techniques are used to develop a series of high accuracy high efficiency solution techniques for solving partial differential equations (PDEs).

A Richardson extrapolation-based sixth-order method with multiple coarse grid (MCG) updating strategy is developed for 2D and 3D steady-state equations on uniform grids. Richardson extrapolation is applied to explicitly obtain a sixth-order solution on the coarse grid from two fourth-order solutions with different related scale grids. The MCG updating strategy directly computes a sixth-order solution on the fine grid by using various combinations of multiple coarse grids. A multiscale multigrid (MSMG) method …

Computing Mountain Passes, Garret Bolton

All Master's Theses

There are many equations in the applied sciences whose solutions correspond to critical points of a function describing specific phenomenon. For example, molecules have a unique potential energy, and one stable conformation of a molecule can be thought of as a low point on a potential energy surface. Finding the mountain pass point between two confirmations of a molecule is analogous to finding the energy of a biological structure that is an intermediate conformation between two stable states. Mathematicians have developed theorems and abstract techniques to find these mountain pass points. However, using such approaches is often difficult, especially because …

Scale-Up And On-Line Monitoring Of Gas-Solid Systems Using Advanced And Non-Invasive Measurement Techniques, Muthanna H. Al-Dahhan, Shreekanta Aradhya, Faraj Zaid, Neven Ali, Thaar Aljuwaya

Chemical and Biochemical Engineering Faculty Research & Creative Works

Industry relies on gas-solid systems for numerous processes. Flow dynamics play an important role in achieving the desired results. The present study proposes, validates and demonstrates a novel mechanistic scale-up approach based on maintaining similar radial profile or cross sectional distribution of gas holdup in two different gas-solid systems in order to achieve hydrodynamics similarity using advanced measurement techniques. This new methodology for scale-up and design has been implemented on gas-solid spouted bed which has been used for drying, granulation and coating. The development can be extrapolated to other gas-solid systems encountered in phosphate processes.

Adaptive Resonance Theory And Diffusion Maps For Clustering Applications In Pattern Analysis, Donald C. Wunsch, David J. Morris, Rui Xu

Electrical and Computer Engineering Faculty Research & Creative Works

Adaptive Resonance is primarily a theory that learning is regulated by resonance phenomena in neural circuits. Diffusion maps are a class of kernel methods on edge-weighted graphs. While either of these approaches have demonstrated success in image analysis, their combination is particularly effective. These techniques are reviewed and some example applications are given.

Selection Of Step Size For Total Variation Minimization In Ct, Anna N. Yeboah

College of Graduate Studies: Theses & Dissertations

Medical image reconstruction by total variation minimization is a newly developed area in computed tomography (CT). In compressed sensing literature, it hasbeen shown that signals with sparse representations in an orthonormal basis may be reconstructed via l1-minimization. Furthermore, if an image can be approximately modeled to be piecewise constant, then its gradient is sparse. The application of l1-minimization to a sparse gradient, known as total variation minimization, may then be used to recover the image. In this paper, the steepest descent method is employed to update the approximation of the image. We propose a way to estimate an optimal step …

Reading In Binary Data And Creating An R User Interface, Malika J. Onstad, Brett Amidan, Kimberly Freeman

STAR Program Research Presentations

The Bonneville Power Administration (BPA) employs Phasor Measurement Units (PMUs) to measure variables such as Voltage, Frequency, and Phasor Angles every sixtieth of a second. These measurements result in terabytes of data which are analyzed to detect abnormalities in the power grid. Recently BPA has switched the data file format from DST to PDAT. A function does not currently exist to read in PDAT files in order to prepare the data for analysis. In order to do this the raw PMU data must be sorted and extracted to ensure its accuracy prior to analysis. This research worked to produce a …