Physical Sciences and Mathematics Commons^™

Fast Algorithms For Brownian Dynamics Simulation With Hydrodynamic Interactions, Zhi Liang

Dissertations

In the Brownian dynamics simulation with hydrodynamic interactions, one needs to generate the total displacement vectors of Brownian particles consisting of two parts: a deterministic part which is proportional to the product of the Rotne-Prager-Yamakawa (RPY) tensor D [1, 2] and the given external forces F; and a hydrodynamically correlated random part whose covariance is proportional to the RPY tensor. To be more precise, one needs to calculate Du for a given vector u and compute √Dv for a normally distributed random vector v. For an arbitrary N-particle configuration, D is a 3N x 3N matrix and u, v are …

Analytical And Computational Methods For The Study Of Rare Event Probabilities In Dispersive And Dissipative Waves, Daniel S. Cargill

Dissertations

The main focus of this dissertation is the application of importance sampling (IS) to calculate the probabilities associated with rare events in nonlinear, large-dimensional lightwave systems that are driven by noise, including models for fiber-based optical communication system and mode-locked lasers. Throughout the last decade, IS has emerged as a valuable tool for improving the efficiency of simulating rare events in such systems. In particular, it has shown great success in simulating various sources of transmission impairments found in optical communication systems, with examples ranging from large polarization fluctuations resulting from randomly varying fiber birefringence to large pulse-width fluctuations resulting …

Utilization Of A Tropospheric-Stratospheric Lidar System To Study Mountain Induced Gravity Waves Over Jenny Jump State Forest, Anthony Teti

Theses

Gravity waves are a dominant driver of the middle and lower atmospheric circulation. Yet such waves have been difficult to study due to their inherent small spatial and temporal scales and synoptic occurrence, and thus require advanced experimental systems. In this thesis first results are presented from a newly constructed tropospheric-stratospheric lidar operating at the New Jersey Institute of Technology-United Astronomy Clubs of New Jersey site in Jenny Jump State Forest in northwest New Jersey. The system utilizes a 4-W 532-nm Nd:YAG laser transmitter and a 4-inch telescope receiver to collect backscattered photons from the lower atmosphere in order to …

Energy Methods For Reaction-Diffusion Problems, Xing Zhong

Dissertations

Nonlinear reaction-diffusion equations arise in many areas of applied sciences such as combustion modeling, population dynamics, chemical kinetics, etc. A fundamental problem in the studies of these equations is to understand the long time behavior of solutions of the associated Cauchy problem. These kinds of questions were originally studied in the context of combustion modeling.

For suitable nonlinearity and a monotone increasing one-parameter family of initial data starting with zero data, small values of the parameter lead to extinction, whereas large values of the parameter may lead to spreading, i.e., the solution converging locally uniformly to a positive spatially independent …

Structural Analysis And Auditing Of Snomed Hierarchies Using Abstraction Networks, Yue Wang

Dissertations

SNOMED is one of the leading healthcare terminologies being used worldwide. Due to its sheer volume and continuing expansion, it is inevitable that errors will make their way into SNOMED. Thus, quality assurance is an important part of its maintenance cycle.

A structural approach is presented in this dissertation, aiming at developing automated techniques that can aid auditors in the discovery of terminology errors more effectively and efficiently. Large SNOMED hierarchies are partitioned, based primarily on their relationships patterns, into concept groups of more manageable sizes. Three related abstraction networks with respect to a SNOMED hierarchy, namely the area taxonomy …

Instabilities In Newtonian Films And Nematic Liquid Crystal Droplets, Te-Sheng Lin

Dissertations

The instabilities of Newtonian films and nematic liquid crystal droplets within the framework of the long wave (lubrication) approximation are studied. For Newtonian films, it is found that, under destabilizing gravitational force, a contact line, modeled by a commonly used precursor film model, leads to free surface instabilities without any additional natural or imposed perturbations. In addition, there is a coupling between the surface instabilities and the transverse (fingering) instabilities which leads to complex behavior. All the observed phenomena are characterized by a single parameter D = (3Ca)^1/3 cot α where Ca is the capillary number and …

Effects Of Information Importance And Distribution On Information Exchange In Team Decision Making, Babajide James Osatuyi

Dissertations

Teams in organizations are strategically built with members from domains and experiences so that a wider range of information and options can be pooled. This strategic team structure is based on the assumption that when team members share the information they have, the team as a whole can access a larger pool of information than any one member acting alone, potentially enabling them to make better decisions. However, studies have shown that teams, unlike individuals, sometimes do not effectively share and use the unique information available to them, leading to poorer decisions. Research on information sharing in team decision making …

Evolution Of 3-D Magnetic Topology In Flare-Productive Active Regions, Yixuan Li

Dissertations

Solar eruptive phenomena, such as flares and coronal mass ejections (CMEs), derive their energy from complex magnetic fields and are the principal source of disturbances that affect space weather. Although physical mechanism and dynamic morphology of flares have been a subject of intense research, many aspects of the flaring process still remain unclear. The objective of this dissertation is to advance the understanding of the physics behind solar flares based on observations, simulations and nonlinear force-free (NLFF) field modeling of magnetic fields.

The data used in this study are obtained from several ground-based or space-borne instruments, including BBSO/DVMG, Hinode/SOT/SP, SDO/HMI …

Registration And Categorization Of Camera Captured Documents, Venkata Gopal Edupuganti

Dissertations

Camera captured document image analysis concerns with processing of documents captured with hand-held sensors, smart phones, or other capturing devices using advanced image processing, computer vision, pattern recognition, and machine learning techniques. As there is no constrained capturing in the real world, the captured documents suffer from illumination variation, viewpoint variation, highly variable scale/resolution, background clutter, occlusion, and non-rigid deformations e.g., folds and crumples. Document registration is a problem where the image of a template document whose layout is known is registered with a test document image. Literature in camera captured document mosaicing addressed the registration of captured documents with …

Transport Of Terrigenous Sediment And Horseshoe Crab Eggs In The Swash Zone Of An Estuarine Foreshore In Delaware Bay, New Jersey, Usa, Sherestha Saini

Dissertations

Identification of processes responsible for egg exhumation and transport in the swash zone is paramount to conservation of species that use the intertidal foreshore. One example where the understanding of these processes is critical to egg exhumation, transport and deposition is in Delaware Bay, USA. Beaches in Delaware Bay provide foraging grounds to many shorebird species that migrate thousands of miles from Central and South America to feed on nutrient rich horseshoe crab eggs during their peak spawning season. Eggs laid at depth by horseshoe crabs are exhumed and transported by bioturbation, wave and swash processes and made available to …

Example Based Texture Synthesis And Quantification Of Texture Quality, Chandralekha De

Dissertations

Textures have been used effectively to create realistic environments for virtual worlds by reproducing the surface appearances. One of the widely-used methods for creating textures is the example based texture synthesis method. In this method of generating a texture of arbitrary size, an input image from the real world is provided. This input image is used for the basis of generating large textures. Various methods based on the underlying pattern of the image have been used to create these textures; however, the problem of finding an algorithm which provides a good output is still an open research issue. Moreover, the …

Dispersibility Of And Adsorption On Functionalized Carbon Nanotubes, Susana Addo Ntim

Dissertations

As the applications of carbon nanotubes (CNTs) proliferate, mass production and widespread use of these nanocarbons will continue to rise. While raw, unrefined, and hydrophobic carbon nanotubes tend to settle out of aqueous media/environments, water dispersible, functionalized CNTs (F-CNTs) will contaminate water resources and will also be highly bioavailable on exposure. Therefore, there is a need to develop an understanding of the fate of F-CNTs in aqueous media.

The colloidal behavior of aqueous dispersions of F-CNTs formed via carboxylation and polymer wrapping with polyvinyl pyrrolidone (PVP) is investigated. The presence of polymer on the nanotube surface provides steric stabilization, and …

Mathematical Models Of Combustion At High Pressure, Daniel Fong

Dissertations

In this dissertation, we develop new mathematical theories of flame propagation that are valid at elevated, or extreme, pressures. Of particular interest is the regime of burning in which the pressure exceeds the critical pressure of the species undergoing chemical reaction. Fluids and flames are known to behave differently under these extreme conditions as opposed to atmospheric pressure. The focus of this dissertation is to investigate these differences by deriving reduced models that contain the unique features.

In the first part of this dissertation, we analyze the structure of laminar diffusion flames at high pressure in the limit of large …

Design And Synthesis Studies Of New S-Adenosyl-L-Methionine Analogues, Shanshan Wu

Theses

S-Adenosyl-L-Methionine (SAM), which is involved in methyl group transfers, is the second most abundant coenzyme in the human body. It is made from adenosinetriphosphate (ATP) and methionine catalyzed by adenosyltransferase. Methyltransferases (MTs) transfer the activated methyl group from the sulfur center to a specific position in a variety of substrates, e.g., DNA, RNA, proteins, and secondary metabolites. Methyltransferases have been linked to various diseases, including cancer.

In recent years, more and more SAM analogues have been reported. These analogues show activities in biological target labeling. The purpose of this thesis is to design and synthesize new SAM analogues to inhibit …

A Comparative Analysis Of Machine Learning Algorithms For Genome Wide Association Studies, Neha Singh

Theses

Variations present in human genome play a vital role in the emergence of genetic disorders and abnormal traits. Single Nucleotide Polymorphism (SNP) is considered as the most common source of genetic variations. Genome Wide Association Studies (GWAS) probe these variations present in human population and find their association with complex genetic disorders. Now these days, recent advances in technology and drastic reduction in costs of Genome Wide Association Studies provide the opportunity to have a plethora of genomic data that delivers huge information of these variations to analyze. In fact, there is significant difference in pace of data generation and …

Heterogeneity-Aware And Energy-Aware Scheduling And Routing In Wireless Sensor Networks, Mahesh Kumar Vasanthu Somashekar

Theses

A Wireless Sensor Network (WSN) is a group of specialized transducers, called sensor nodes, with a communication infrastructure intended to monitor and record conditions at diverse locations. Since WSN applications are usually deployed in an open environment, the network is exposed to rough weather conditions, such as rain and snow. Another problem that WSN applications need to deal with is the energy constraints of sensor nodes. Both problems adversely affect the lifetime of WSN applications. A lot of research has been conducted to prolong the lifetime of WSN applications considering energy constraints of sensor nodes, but not much research has …

Reducing The Risk Of Software Cost Estimation, Shixian Yang

Theses

Inaccurate cost estimation is a well-known problem in software development. The common cost estimation models are point estimates that are unable to quantify uncertainties. Furthermore, it is difficult to calibrate the uncertainties in cost estimation due to the lack of information. The purpose of this thesis is to prove that probability techniques could be synthesized into COCOMO (Constructive Cost Model) to quantify uncertainties. Another aim is to find out how to get more insight on reducing the risk of cost estimation. In this thesis, some historical data is presented to show the variance in factors of COCOMO. Monte Carlo simulation …

Phenotype Prediction And Feature Selection In Genome-Wide Association Studies, Andrew Roberts

Theses

Genome wide association studies (GWAS) search for correlations between single nucleotide polymorphisms (SNPs) in a subject genome and an observed phenotype. GWAS can be used to generate models for predicting phenotype based on genotype, as well as aiding in identification of specific genes affecting the biological mechanism underlying the phenotype.

In this investigation, phenotype prediction models are constructed from GWAS training data and are evaluated for performance on test data. Three methods are used to rank SNPs by their correlation with the phenotype: the univariate Wald test, a multivariate, support vector machine (SVM) based technique, and a hybrid method where …

Data Mining Of Tetraloop-Tetraloop Receptors In Rna Xml Files, Sinan Ramazanoglu

Theses

RNA (Ribonucleic acid) Motifs are tertiary structures that play an important role in the folding mechanism of the RNA molecule. The overall function of a RNA Motif depends on its specific bp (base pairs) sequence that constitutes the secondary structure. Data mining is a novel method in both discovering potential tertiary structures within DNA (Deoxyribonucleic acid), RNA, and protein molecules and storing the information in databases. The RNA Motif of interest is the tetraloop-tetraloop receptor, which is composed of a highly conserved 11 nt (nucleotide) sequence and a tetraloop with the generic form of GNRA (where N = any base …

Using An Ontology To Improve The Web Search Experience, Tian Tian

Dissertations

The search terms that a user passes to a search engine are often ambiguous, referring to homonyms. The results in these cases are a mixture of links to documents that contain different meanings of the search terms. Current search engines provide suggested query completions in a dropdown list. However, such lists are not well organized, mixing completions for different meanings. In addition, the suggested search phrases are not discriminating enough. Moreover, current search engines often return an unexpected number of results. Zero hits are naturally undesirable, while too many hits are likely to be overwhelming and of low precision.

This …

Terahertz Wireless Communication, Ke Su

Dissertations

The goal of this thesis is to explore Terahertz (THz) wireless communication technology. More specifically the objective is to develop and characterize several THz communication systems and study the effect of atmosphere propagation through fog droplets and dust particles on THz communications.

For demonstration, a THz continuous wave (CW) photomixing system is designed. Terahertz signals are phase encoded with both analog ramp signals and pseudorandom binary data, transmitted over a short distance, and detected. The limitation of transmission bandwidth, low single to noise ratio, vibration effects are also analyzed. In order to study and compare propagation features of THz links …

Design And Implementation Of A Cyberinfrastructure For Rna Motif Search, Prediction And Analysis, Dongrong Wen

Dissertations

RNA secondary and tertiary structure motifs play important roles in cells. However, very few web servers are available for RNA motif search and prediction. In this dissertation, a cyberinfrastructure, named RNAcyber, capable of performing RNA motif search and prediction, is proposed, designed and implemented.

The first component of RNAcyber is a web-based search engine, named RmotifDB. This web-based tool integrates an RNA secondary structure comparison algorithm with the secondary structure motifs stored in the Rfam database. With a user-friendly interface, RmotifDB provides the ability to search for ncRNA structure motifs in both structural and sequential ways. The second component of …

Approximate String Matching Methods For Duplicate Detection And Clustering Tasks, Oleksandr Rudniy

Dissertations

Approximate string matching methods are utilized by a vast number of duplicate detection and clustering applications in various knowledge domains. The application area is expected to grow due to the recent significant increase in the amount of digital data and knowledge sources. Despite the large number of existing string similarity metrics, there is a need for more precise approximate string matching methods to improve the efficiency of computer-driven data processing, thus decreasing labor-intensive human involvement.

This work introduces a family of novel string similarity methods, which outperform a number of effective well-known and widely used string similarity functions. The new …

Non-Destructive Evaluation Of Agglomerated Cork Products Using Thz Spectroscopy And Imaging, Han Zhang

Theses

Terahertz spectroscopy from 0.15 to 0.3 THz is used to classify agglomerated cork products. Position dependent scattering of radiation allows one to image the internal structure of cork products. Previous studies have focused on natural (solid) cork stoppers. In this study, the feasibility of classifying agglomerated cork structures using THz imaging and spectroscopy is investigated. Both THz images and spectra are used to classify the agglomerated cork samples. Classification of the samples used three methods: visible examination of the THz images, statistical analysis of the pixel intensities, and a polynomial regression of the THz spectral data averaged over all pixels. …

An Examination Of Coordination Among Friends And Strangers From A Coordination Theory Perspective, Christopher D. Wamble

Theses

Within mobile social coordination, there is a field of study known as outeraction, the communicative processes used by people to manage future interactions. It is an important area of research because it identifies how informal interactions support complex collaboration between individuals and groups. Outeraction is primarily conducted through the interpersonal communication channels of texting, instant messaging (IM), face-to-face, and mobile phone or Skype conversations. Currently this area of research in mobile outeraction support systems is weak. It lacks a firm foundation in system building, has very few if any conceptual frameworks, and little empirical knowledge of user requirements and attitudes …