Physical Sciences and Mathematics Commons^™

Hamiltonian Bifurcations In Schrodinger Trimers, Casayndra H. Basarab

Dissertations

The phase space of the three-mode discrete NLS in the nonlinear regime with periodic boundary conditions is investigated by reducing the degree of freedom from three down to two. The families of standing waves are enumerated and normal forms are used to describe several families of relative periodic orbits whose topologies change due to Hamiltonian Hopf bifurcations and transcritical bifurcations. The Hamiltonian Hopf bifurcation occurs when eigenvalues on the imaginary axis collide and split and has two types: elliptic and hyperbolic. These two types arise in the DNLS problem, and the families of periodic orbits are discussed as a conserved …

Structural Exploration And Inference Of The Network, Ruihua Cheng

Dissertations

This dissertation consists of two parts. In the first part, a learning-based method for classification of online reviews that achieves better classification accuracy is extended. Automatic sentiment classification is becoming a popular and effective way to help online users or companies to process and make sense of customer reviews. The method combines two recent developments. First, valence shifters and individual opinion words are combined as bigrams to use in an ordinal margin classifier. Second, relational information between unigrams expressed in the form of a graph is used to constrain the parameters of the classifier. By combining these two components, it …

Efficient High-Order Integral Equation Methods For The Heat Equation, Shaobo Wang

Dissertations

Efficient high-order integral equation methods have been developed for solving the boundary value problems of the heat equation with complex geometries in two and three dimensions. First of all, the classical heat potential theory is applied to convert such problems to Volterra integral equations of the second kind via the heat layer potentials. Some advantages of the integral formulation as compared with standard finite difference and finite element methods include reduction of the dimension of the problem by one, high order accuracy, unconditional stability, insensitivity to different geometries, and elimination of truncating the computational domain and the need of artificial …

Algorithms For Pre-Microrna Classification And A Gpu Program For Whole Genome Comparison, Ling Zhong

Dissertations

MicroRNAs (miRNAs) are non-coding RNAs with approximately 22 nucleotides that are derived from precursor molecules. These precursor molecules or pre-miRNAs often fold into stem-loop hairpin structures. However, a large number of sequences with pre-miRNA-like hairpin can be found in genomes. It is a challenge to distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (referred to as pseudo pre-miRNAs). The first part of this dissertation presents a new method, called MirID, for identifying and classifying microRNA precursors. MirID is comprised of three steps. Initially, a combinatorial feature mining algorithm is developed to identify suitable feature sets. Then, the …

Numerical Simulations Of Dense Granular Systems With And Without Cohesive Effects, Lenka Kovalcinova

Dissertations

Granular materials are collections of objects ranging from sand grains that form sand piles or even sand castles to collections of large objects such as a group of meteors in outer space. The considered range of sizes of granular particles is such that the effect of thermal fluctuations is not relevant. However, the interaction between the particles may be very complex, involving inelasticity and friction, in addition to repulsive and possibly attractive interaction forces. These interactions that may be history dependent, make the systems that consist of a large number of particles complex to analyze and difficult to understand using …

An Integrated Transport Solution To Big Data Movement In High-Performance Networks, Daqing Yun

Dissertations

Extreme-scale e-Science applications in various domains such as earth science and high energy physics among multiple national institutions within the U.S. are generating colossal amounts of data, now frequently termed as “big data”. The big data must be stored, managed and moved to different geographical locations for distributed data processing and analysis. Such big data transfers require stable and high-speed network connections, which are not readily available in traditional shared IP networks such as the Internet. High-performance networking technologies and services featuring high bandwidth and advance reservation are being rapidly developed and deployed across the nation and around the globe …

Accelerating Data-Intensive Scientific Visualization And Computing Through Parallelization, Dongliang Chu

Dissertations

Many extreme-scale scientific applications generate colossal amounts of data that require an increasing number of processors for parallel processing. The research in this dissertation is focused on optimizing the performance of data-intensive parallel scientific visualization and computing.

In parallel scientific visualization, there exist three well-known parallel architectures, i.e., sort-first/middle/last. The research in this dissertation studies the composition stage of the sort-last architecture for scientific visualization and proposes a generalized method, namely, Grouping More and Pairing Less (GMPL), for order-independent image composition workflow scheduling in sort-last parallel rendering. The technical merits of GMPL are two-fold: i) it takes a prime factorization-based …

Context-Aware Collaborative Storage And Programming For Mobile Users, Mohammad A. Khan

Dissertations

Since people generate and access most digital content from mobile devices, novel innovative mobile apps and services are possible. Most people are interested in sharing this content with communities defined by friendship, similar interests, or geography in exchange for valuable services from these innovative apps. At the same time, they want to own and control their content. Collaborative mobile computing is an ideal choice for this situation. However, due to the distributed nature of this computing environment and the limited resources on mobile devices, maintaining content availability and storage fairness as well as providing efficient programming frameworks are challenging.

This …

Termination, Correctness And Relative Correctness, Nafi Diallo

Dissertations

Over the last decade, research in verification and formal methods has been the subject of increased interest with the need of more secure and dependable software. At the heart of software dependability is the concept of software fault, defined in the literature as the adjudged or hypothesized cause of an error. This definition, which lacks precision, presents at least two challenges with regard to using formal methods: (1) Adjudging and hypothesizing are highly subjective human endeavors; (2) The concept of error is itself insufficiently defined, since it depends on a detailed characterization of correct system states at each stage of …

Magnetic Reconnection In Small And Large Scales On The Sun, Xin Chen

Dissertations

Almost all solar activities observed are related to the solar magnetic field, especially the topological restructuring of magnetic fields, the so-called magnetic reconnection in solar physics. They are occurring at different scales related to various phenomena, during minimum or maximum of the solar cycle, from the photosphere to the solar corona.

For small-scale activities, type II spicules which display high velocity upflows observed at the limb, have the most possible underlying driving mechanism of magnetic reconnection. A set of tools is developed for detecting small-scale solar magnetic cancellations and the disk counterpart of type II spicules (the so-called Rapid Blueshifted …

A Data Science Approach To Pattern Discovery In Complex Structures With Applications In Bioinformatics, Lei Hua

Dissertations

Pattern discovery aims to find interesting, non-trivial, implicit, previously unknown and potentially useful patterns in data. This dissertation presents a data science approach for discovering patterns or motifs from complex structures, particularly complex RNA structures. RNA secondary and tertiary structure motifs are very important in biological molecules, which play multiple vital roles in cells. A lot of work has been done on RNA motif annotation. However, pattern discovery in RNA structure is less studied. In the first part of this dissertation, an ab initio algorithm, named DiscoverR, is introduced for pattern discovery in RNA secondary structures. This algorithm works by …

Schema-Aware Keyword Search On Linked Data, Ananya Dass

Dissertations

Keyword search is a popular technique for querying the ever growing repositories of RDF graph data on the Web. This is due to the fact that the users do not need to master complex query languages (e.g., SQL, SPARQL) and they do not need to know the underlying structure of the data on the Web to compose their queries. Keyword search is simple and flexible. However, it is at the same time ambiguous since a keyword query can be interpreted in different ways. This feature of keyword search poses at least two challenges: (a) identifying relevant results among a multitude …

Collaborative Development Of A Small Business Emergency Planning Model, Arthur Henry Hendela

Dissertations

Small businesses, which are defined by the US Small Business Administration as entities with less than 500 employees, suffer interruptions from diverse risks such as financial events, legal situations, or severe storms exemplified by Hurricane Sandy. Proper preparations can help lessen the length of the interruption and put employees and owners back to work. Large corporations generally have large budgets available for planning, business continuity, and disaster recovery. Small businesses must decide which risks are the most important and how best to mitigate those risks using minimal resources.

This research uses a series of surveys followed by mathematical modeling to …

New Facet Of Solar Activities Revealed By High-Resolution Imaging At He I 10830 Å, Zhicheng Zeng

Dissertations

Major solar activities such as major flares and associated coronal mass ejections (CMEs), have a great impact on space weather, which requires us to develop the ability to predict them. Despite the extensive studies already made, however, many basic processes, such as energy accumulation processes in solar active regions and the triggering mechanism of solar activities, are still not well understood.

One reason why the basic processes are hard to be understood is that the large-scale activities are complicated, involving many small-scale energy releases, making it hard to understand the basic picture of the events. Small-scale solar activities, such as …

Thermochemical Properties Of Fluorinated Hydrocarbons, Hydroperoxides, And Fluorinated Hydroperoxides; Thermochemistry And Kinetics On Dissociation And Association Reactions Of Oxiranyl Radical, Heng Wang

Dissertations

Thermochemical properties on fluorinated hydrocarbons, alcohol, hydroperoxides, and alkyl hydroperoxides are determined. Reaction kinetics and modeling on the three member ring cyclic ether radical, oxiranyl radical, are studied under atmospheric and combustion environments.

Molecular geometries, vibration frequencies, internal rotor potentials, and thermo-chemical properties (ΔfHº298, S°(T) and C°p(T)) for fluorinated-hydrocarbons, thermochemical properties and bond energies, for alkyl and fluoro hydroperoxides and fluoro alcohols are determined with comparison of data from a number of different ab initio, density functional theory (DFT) and composite calculation methods, and basis sets.

Kinetic parameters for unimolecular decomposition and isomerization reactions of the oxiranyl radical are determined …

Studies On Purification And Functionalization Of Carbon Nanotubes And Their Aqueous Phase Behavior, Zheqiong Wu

Dissertations

Carbon nanotubes (CNTs) are known to have unique mechanical, thermal and electrical properties which make them attractive for a wide range of applications ranging from batteries to sensors. CNTs are rolled up graphene sheets where the single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) are classified according to the number of concentric rings. In this dissertation, the focus is on several different aspects of MWCNTs. These include purification, functionalization and colloidal behavior.

MWCNTs are insoluble in solvents and therefore some degree of functionalization is required prior to their real-world applications. Oxidation debris is generated during carboxylation which is usually the first …

Mediating Chance Encounters Through Opportunistic Social Matching, Julia M. Mayer

Dissertations

Chance encounters, the unintended meeting between people unfamiliar with each other, serve as an important social lubricant helping people to create new social ties, such as making new friends or finding an activity, study or collaboration partner. Unfortunately, social barriers often prevent chance encounters in environments where people do not know each other and people have to rely on serendipity to meet or be introduced to interesting people around them. Little is known about the underlying dynamics of chance encounters and how systems could utilize contextual data to mediate chance encounters. This dissertation addresses this gap in research literature by …

Data Analytics With Mapreduce In Apache Spark And Hadoop Systems, Zongxuan Du

Theses

MapReduce comes from a traditional problem solving method: separating a big problem and solving each small parts. With the target of computing larger dataset in more efficient and cheaper way, this is implement into a programming mode to deal with massive quantity of data. The users get a map function and use it to abstract dataset into key / value logical pair and then use a reduce function to group all value with the same key. With this mode, task can be automatic spread the job into clusters grouped by lots of normal computers. MapReduce program can be easily implemented …

Uusing The Kdj As A Trading Strategy On Biotech Companies, Shijie Zha

Theses

Mean Reversion is the most commonly used model in quantitative trading. This model is associated with several factors, like ma5 and ma10 line. These factors are the most significant in stock markets. However, the disadvantages of this model are lag and inaccuracy.

In this research, we get the historical and current stock data by web crawler, analyze the quantitative data and build a new model involved with the KDJ. Taking biotech companies marketed in the United States and B-share marketed in China as the research subjects, the result shows increased profits compared with the Mean Reversion model. It also shows …

Radiative Properties Of Silicon Related Materials, Scott Sanowitz

Theses

The objective of this thesis is to study the optical properties of silicon, as a function of temperature, in the infrared range of wavelengths. The wavelength range, considered in this study, is between 1 micron and 20 microns. The temperature range observed is from 50 degrees Celsius to 1000 degrees Celsius. Varying wafer thickness and doping are taken into account. The thickness of the native oxide, silicon dioxide, must be taken into account as well as its orientation (front side versus back side). The effect of layering wafers one onto another is investigated. It is shown that all these parameters …

Semi Supervised Weighted Maximum Variance Dimensionality Reduction, Pranitha Surya Andalam

Theses

In the recent years, we have huge amounts of data which we want to classify with minimal human intervention. Only few features from the data that is available might be useful in some scenarios. In those scenarios, the dimensionality reduction methods play a major role for extracting useful features. The two parameter weighted maximum variance (2P-WMV) is a generalized dimensionality reduction method of which principal component analysis (PCA) and maximum margin criterion (MMC) are special cases.. In this paper, we have extended the 2P-WMV approach from our previous work to a semi-supervised version. The objective of this work is specially …

Gene Network Understanding And Analysis, Maria E. Somoza

Theses

Gene regulatory network (GRN) is a collection of regulators that interact with each other in the cell to govern the gene expression levels of mRNA and proteins. These regulators can either be DNA, RNA, protein and their complex. Transcriptional gene regulation is an important mechanisms in which an in-depth study can lead to various practical applications, and a greater understanding of how organisms control their cellular behavior. One of the most widely studied organisms in gene regulatory networks are the Mycobacterium tuberculosis and Corynebacterium glutamicum ATCC 13032.

Gene co-expression networks are of biological interests due to co-expressed genes which are …

Semantics And Result Disambiguation For Keyword Search On Tree Data, Cem Aksoy

Dissertations

Keyword search is a popular technique for searching tree-structured data (e.g., XML, JSON) on the web because it frees the user from learning a complex query language and the structure of the data sources. However, the convenience of keyword search comes with drawbacks. The imprecision of the keyword queries usually results in a very large number of results of which only very few are relevant to the query. Multiple previous approaches have tried to address this problem. Some of them exploit structural and semantic properties of the tree data in order to filter out irrelevant results while others use a …

Terahertz Wireless Communication Through Atmospheric Atmospheric Turbulence And Rain, Jianjun Ma

Dissertations

This dissertation focusses on terahertz (THz) wireless communication technology in different weather conditions. The performance of the communication links is mainly studied under propagation through atmospheric turbulence and rain. However, as real outdoor weather conditions are temporally and spatially varying, it is difficult to obtain reproducible atmospheric conditions to verify results of independent measurements making it a challenge to measure and analyze the impact of outdoor atmospheric weather on communication links. Consequently, dedicated indoor weather chambers are designed to produce controllable weather conditions to emulate the real outdoor weather as closely as possible. To emulate turbulent air conditions, an enclosed …

Task-Based User Profiling For Query Refinement (Toque), Chao Xu

Dissertations

The information needs of search engine users vary in complexity. Some simple needs can be satisfied by using a single query, while complicated ones require a series of queries spanning a period of time. A search task, consisting of a sequence of search queries serving the same information need, can be treated as an atomic unit for modeling user’s search preferences and has been applied in improving the accuracy of search results. However, existing studies on user search tasks mainly focus on applying user’s interests in re-ranking search results. Only few studies have examined the effects of utilizing search tasks …

Opto-Mechanical Design Of Synchrotron Radiation-Based Far-Infrared Spectroscopic Ellipsometer With Strong Magnetic-Field, Ahmad Abbas Chaudhry

Theses

The objective of this dissertation is to present opto-mechanical design of a synchrotron radiation based far-infrared spectroscopic ellipsometer with a strong external magnetic-field capability. Since high magnetic field has enabled major breakthrough in science such instrument will be highly important to the field of condensed matter physics and characterization of advanced electronic materials. This instrument will be installed at the multi-User facility with the most advanced synchrotron light source: Natonal Synchrotron Source (NSLS-II) at Brookhaven National Laboratory (BNL).The proposed here instrument is capable to measure full Mueller matrix spectroscopic ellipsometry spectra in high magnetic fields of up to 9 Tesla. …

Effects Of Human Development On Aeolian Sediment Transport Rates Within An Adjacent Undeveloped Backshore Enclave, Kayla L. Kaplan

Theses

Sandy backshore enclaves are created where shorefront buildings are lost during high magnitude storms. Subsequent foredune growth in these enclaves is critical to providing protection to landward development. Conditions for foredune growth and sediment flux within an enclave can be influenced by the presence of adjacent buildings. The objectives of this research are to assess the following questions: what is the nature of sediment flux on a beach within an enclave, what are the potential constraints to transport on a beach within an enclave and, are natural processes alone able to sustain a foredune in an enclave. A field investigation …

Triplex Dna Receptor-Gold Nanoparticle Conjugates For Detection Of Oxidized Dna Base, Qingyu Xing

Theses

Oxidations of DNA nucleobases are believed to be one of the sources of aging and some age-dependent disease, such as cancer. Human body have various mechanisms to repair damaged DNA and base-excision-repair is one mechanism for removing those oxidized nucleobases. This mechanism processes in the cells by cutting the oxidized nucleobases from deoxyribose and letting them excrete though urine. Detection of those abnormal nucleobases in urine has been suggested as a convenient way of early cancer diagnosis. 5-OHU (5-hydroxyuracil), the oxidation product of cytosine, is one of those abnormal nucleobases and it potentially forms base pairs with all four DNA …