Numerical Analysis and Scientific Computing Commons^™

On The Design Of A Framework For Large-Scale Exploratory Graph Analytics, Oliver Andres Alvarado Rodriguez

Dissertations

Large-scale exploratory graph analytics merges data science with high-performance computing to extract critical insights from network-representable data. Data scientists routinely analyze data from the natural, social, and computing sciences by representing it as networks, or graphs, where objects become vertices and their relationships become edges. This representation allows data scientists to add graph analytics to their toolbox. However, designing tools for large-scale exploratory graph analytics is challenging due to the complexities of graph algorithms, such as high communication in distributed systems and large memory demands. These challenges can lead to overly complex software, which limits usability and development to a …

Certifying Stability In Runge-Kutta Schemes: Algebraic Conditions And Semidefinite Programming, Austin Juhl

Dissertations

Numerical stability is a critical property for a time-integration scheme. In the context of Runge-Kutta methods applied to stiff differential equations, A-stability is one of the most basic and practically important notions of stability. Dating back to the work of Dahlquist, it has been known that A-stability is equivalent to the Runge-Kutta stability function satisfying a particular convex feasibility problem. Specifically, up to a transformation, the stability function lies in the convex cone of positive functions. In recent years, sum-of-squares optimization and semidefinite programming have become valuable tools in developing rigorous certificates of stability in dynamical systems. Therefore, it is …

Numerical Techniques For Improving Simulations Of Tropical Cyclones, Yassine Tissaoui

Dissertations

The increasing frequency and intensity of tropical cyclones (TCs) due to climate change pose significant challenges for forecasting and mitigating their impacts. Despite advancements, accurately predicting TC rapid intensification (RI) remains a challenge. Large eddy simulation (LES) allows for explicitly resolving the large eddies involved in TC turbulence, thus providing an avenue for studying the mechanisms behind their intensification and RI. LES of a full tropical cyclone is very computationally expensive and its accuracy will depend on both explicit and implicit dissipation within an atmospheric model. This dissertation presents two novel numerical methodologies with the potential to improve the efficiency …

Finding Combinatorial Patterns In Real Valued Omics Data, Kenneth Smith

Dissertations

Precision medicine is a healthcare approach which tailors disease prevention and treatment to an individual, based on their genetics, environment, lifestyle, and physiological state. These factors interact to produce biological changes that can be measured to produce data called omics, and include genomics, lipidomics, and proteomics. Despite the abundance of omics data and analysis techniques, researchers still struggle to identify biological findings that replicate across data sets and translate into clinical applications. In this dissertation, we employ combinatorial optimization techniques to improve upon three steps in the precision medicine analysis pipeline: 1) data cleaning, 2) community detection, and 3) feature …

Bacterial Motion And Spread In Porous Environments, Yasser Almoteri

Dissertations

Micro-swimmers are ubiquitous in nature from soil and water to mammalian bodies and even many technological processes. Common known examples are microbes such as bacteria, micro-algae and micro-plankton, cells such as spermatozoa and organisms such as nematodes. These swimmers live and have evolved in multiplex environments and complex flows in the presence of other swimmers and types, inert particles and fibers, interfaces and non-trivial confinements and more. Understanding the locomotion and interactions of these individual micro-swimmers in such impure viscous fluids is crucial to understanding the emergent dynamics of such complex systems, and to further enabling us to control and …

Machine Learning And Network Embedding Methods For Gene Co-Expression Networks, Niloofar Aghaieabiane

Dissertations

High-throughput technologies such as DNA microarrays and RNA-seq are used to measure the expression levels of large numbers of genes simultaneously. To support the extraction of biological knowledge, individual gene expression levels are transformed into Gene Co-expression Networks (GCNs). GCNs are analyzed to discover gene modules. GCN construction and analysis is a well-studied topic, for nearly two decades. While new types of sequencing and the corresponding data are now available, the software package WGCNA and its most recent variants are still widely used, contributing to biological discovery.

The discovery of biologically significant modules of genes from raw expression data is …

Domain Decomposition Methods For Linear And Non-Linear Elliptic Problems, Tadanaga Takahashi

Dissertations

The primary purpose of this dissertation is to expand upon the circle of domain decomposition methods (DDM) which are algorithms that reformulate a boundary value problem in terms of multiple localized problems on subdomains. The first project involves expanding upon DDMs in a relatively mature field: the Helmholtz equation for wave scattering applications. The proposed method is an adaptation of a continuous cross-point Finite Element Non-overlapping DDM algorithm. The usual unbounded computational domain is truncated and then the near-field wave pattern is solved with a parallelized finite element method. Several improvements over the standard transmission operator are discussed in this …

A Practical Approach To Automated Software Correctness Enhancement, Aleksandr Zakharchenko

Dissertations

To repair an incorrect program does not mean to make it correct; it only means to make it more-correct, in some sense, than it is. In the absence of a concept of relative correctness, i.e. the property of a program to be more-correct than another with respect to a specification, the discipline of program repair has resorted to various approximations of absolute (traditional) correctness, with varying degrees of success. This shortcoming is concealed by the fact that most program repair tools are tested on basic cases, whence making them absolutely correct is not clearly distinguishable from making them relatively more-correct. …

Ensemble Data Fitting For Bathymetric Models Informed By Nominal Data, Samantha Zambo

Dissertations

Due to the difficulty and expense of collecting bathymetric data, modeling is the primary tool to produce detailed maps of the ocean floor. Current modeling practices typically utilize only one interpolator; the industry standard is splines-in-tension.

In this dissertation we introduce a new nominal-informed ensemble interpolator designed to improve modeling accuracy in regions of sparse data. The method is guided by a priori domain knowledge provided by artificially intelligent classifiers. We recast such geomorphological classifications, such as ‘seamount’ or ‘ridge’, as nominal data which we utilize as foundational shapes in an expanded ordinary least squares regression-based algorithm. To our knowledge …

Computational Studies Of Carbon Nanocluster Solidification, Chathuri C. Silva

Dissertations

A subset of micron-size meteoritic carbon particles formed in red giant atmospheres show a core-rim structure, likely condensed from a vapor phase into super-cooled carbon droplets that nucleated graphene sheets (~40Å) on randomly oriented 5-atom loops during solidification, followed by coating with a graphite rim. Similar particles form during slow cooling of carbon vapor in the lab.

Here we investigate the nucleation and growth of carbon rings and graphene sheets using density functional theory (DFT). Our objectives: (1). explore different computational techniques in DFT-VASP for various carbon structures and compare the results with literature, (2). investigate the nucleation and growth …

Developing A Computational Framework For A Construction Scheduling Decision Support Web Based Expert System, Feroz Ahmed

Dissertations

Decision-making is one of the basic cognitive processes of human behaviors by which a preferred option or a course of action is chosen from among a set of alternatives based on certain criteria. Decision-making is the thought process of selecting a logical choice from the available options. When trying to make a good decision, all the positives and negatives of each option should be evaluated. This decision-making process is particularly challenging during the preparation of a construction schedule, where it is difficult for a human to analyze all possible outcomes of each and every situation because, construction of a project …

Computational Modeling Of Radiation Interactions With Molecular Nitrogen, Tyler Reese

Dissertations

The ability to detect radiation through identifying secondary effects it has on its surrounding medium would extend the range at which detections could be made and would be a valuable asset to many industries. The development of such a detection instrument requires an accurate prediction of these secondary effects. This research aims to improve on existing modeling techniques and help provide a method for predicting results for an affected medium in the presence of radioactive materials. A review of radioactivity and the interactions mechanisms for emitted particles as well as a brief history of the Monte Carlo Method and its …

Evaluating Relevance And Reliability Of Twitter Data For Risk Communication, Xiaohui Liu

Dissertations

While Twitter has been touted to provide up-to-date information about hazard events, the relevance and reliability of tweets is yet to be tested. This research examined the relevance and reliability of risk information extracted from Twitter during the 2013 Colorado floods using five different approaches. The first approach examined the relationship between tweet volume and precipitation amount. The second approach explored the relationship between geo-tagged tweets and degree of damage. In the third approach, the spatiotemporal distribution of tweets was compared with flood extent. In the fourth approach, risk information from tweets were compared with survey responses obtained in a …

Selective Detection Of Volatile Organic Compounds Using Metal Oxide Sensor Arrays, Anton Dmitrievich Netchaev

Dissertations

Selective detection of organic contaminant using widely available and inexpensive metal oxide sensors has the potential to be used in various robotic platforms for navigation, harmful chemical leak detection, mobile environmental monitoring, etc. Selective gas detection in real world environments using easily available sensors has not been reported and can be used in many industries. A sensor system using only four commercially available sensors with accompanying signal conditioning and clustering algorithm capable of discriminatory detection of chemical marker is possible. Tests have shown that temperature, humidity and concentration fluctuations can be accounted for to produce systems for real world environments. …

Secure And Reliable Routing Protocol For Transmission Data In Wireless Sensor Mesh Networks, Nooh Adel Bany Muhammad

Dissertations

Abstract

Sensor nodes collect data from the physical world then exchange it until it reaches the intended destination. This information can be sensitive, such as battlefield surveillance. Therefore, providing secure and continuous data transmissions among sensor nodes in wireless network environments is crucial. Wireless sensor networks (WSN) have limited resources, limited computation capabilities, and the exchange of data through the air and deployment in accessible areas makes the energy, security, and routing major concerns in WSN. In this research we are looking at security issues for the above reasons. WSN is susceptible to malicious activities such as hacking and physical …