Physical Sciences and Mathematics Commons^™

Modeling Of Flexible Drug-Like Molecules : Qsar Of Gbr 12909 Analog Dat/Sert Selectivity, Kathleen Mary Gilbert

Dissertations

The dopamine reuptake inhibitor GBR 12909 and related dialkyl piperazine and piperidine analogs have been studied as agonist substitution therapies acting on the dopamine transporter (DAT) to treat cocaine addiction. Undesirable binding to the serotonin transporter (SERT) can vary greatly depending on the specific substituents on the molecule. This study uses Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices (CoMSIA) techniques to determine a stable and predictive model for DAT/SERT selectivity for a set of flexible GBR 12909 analogs.

Families of analogs were constructed from six pairs of naphthyl-substituted piperazine and piperidine templates identified by hierarchical clustering as …

Influences Of Surfactant On The Breakup Of A Fluid Jet In Viscous Surrounding, Muhammad Irfan Hameed

Dissertations

The effect of insoluble surfactant on the breakup of a fluid jet surrounded by another viscous fluid at low Reynolds number is studied both theoretically and experimentally. Equations governing the evolution of the interface and surfactant concentration are derived using a long wavelength approximation for the case of an inviscid jet and a slightly viscous jet surrounded by a more viscous fluid. These one dimensional partial differential equations governing the evolution of the slender jet are solved numerically for given initial interfacial perturbations and surfactant concentration. It is found that the presence of insoluble surfactant at the interface retards the …

Dynamics Of Filaments, Flares And Coronal Mass Ejections (Cmes), Ju Jing

Dissertations

The objective of this dissertation is to investigate the connection between the dynamics of solar surface phenomena such as filament eruptions, flares, the coronal mass ejections (CMEs), the core of so-called solar activity, and the properties of the associated magnetic field for the development of forecasts of solar activity and space weather. Both statistical and case studies have been carried out.

The topics covered in this dissertation are: the statistical relationship among phenomena of solar activity, in particular, filament eruptions, flares and coronal mass ejections (CMEs); the correlation between magnetic reconnection rate and flux rope acceleration of two-ribbon flares; the …

The Effects Of Digital Audio On Social Presence, Motivation And Perceived Learning In Asynchronous Learning Networks, Eunhee Kim

Dissertations

This study explores the possibilities of applying digital audio to the ALN environment, so that students can speak and listen rather than type and read. Two sets of 1x2 field experiments (text vs. digital audio) were conducted with two formats of digital audio -recorded voice messages and narrated Microsoft PowerPoint presentation - used in several NJIT courses conducted via ALN. The perceptions of communication media were measured from two different user perspectives: active use when the subjects created their assignments using prescribed communication media (audio or text) and passive use when the subjects viewed/listened to other students' work.

The perceptions …

Some Topics On Deterministic Scheduling Problems, Yumei Huo

Dissertations

Sequencing and scheduling problems are motivated by allocation of limited resources over time. The goal is to find an optimal allocation where optimality is defined by some problem specific objectives.

This dissertation considers the scheduling of a set of ri tasks, with precedence constraints, on m >= 1 identical and parallel processors so as to minimize the makespan. Specifically, it considers the situation where tasks, along with their precedence constraints, are released at different times, and the scheduler has to make scheduling decisions without knowledge of future releases. Both preemptive and nonpreemptive schedules are considered. This dissertation shows that optimal …

Evaluating Rhizodegradation Of Petroleum Hydrocarbons And Polycyclic Aromatic Hydrocarbons In Wetland Sediments Containing Spartina Patens, Robert J. Lippencott

Dissertations

Biodegradation of petroleum hydrocarbons (PHC) and 16 polycyclic aromatic hydrocarbon (PAH) compounds was evaluated in sediments from a stormwater basin that was a former salt marsh at an active oil refinery. Spartina patens were grown in basin sediments during a field study and a greenhouse study over three consecutive growing seasons. Ninety percent (90%) survival was observed in field study plots containing sediments with <12% PHC. In the greenhouse study, planted and bulk sediments were monitored for PHC, PAH, microbial density, nutrients, pH, redox and root biomass at 2.5 and 7.5 cm in sediments with <12% PHC. The sediments contained on average 6.5% to 9.5% PHC and 56 to 124 parts per million (ppm) total PAH. The plants exhibited a 95% survival rate and added from 1% to 2% root biomass to the sediment. Microbial densities in planted sediments were significantly higher than in bulk sediments (p<0.05). Oxidizing conditions were prevalent in all treatments at both depths; however, reducing conditions developed in the planted sediments at 7.5 cm. PHC was 35% to 37% lower in the planted sediments vs. bulk sediment at the end of the study. Planted sediment PAH concentrations were generally lower than in bulk sediments. Low MW PAHs (2 and 3-Rings) were either absent or at relatively low concentrations in all treatments. Phenanthrene concentrations in bulk sediments did not change, but were reduced by 95% in planted sediments (p<0.01), with half-life estimates of 141 to 165 days at 2.5 cm. Temporal changes in high MW PAHs ( 4-Rings) were not observed over the greenhouse study period. Differences in PAH concentrations between planted and bulk sediments exhibited a decreasing trend with PAH molecular weight. Evaluation of differences in planted and bulk sediment PAH concentrations suggests that lower MW PAHs degrade better under oxidizing conditions, and higher MW PAHs under reducing conditions in the planted sediments. Comparison of planted and bulk sediment PAH concentrations links depth and redox conditions to decreases in PAH as a function of PAH MW. Therefore, it was concluded that spatio-temporal variations and cycling of redox conditions should be considered to properly evaluate biodegradation of PAH.

Theory And Algorithms For Swept Manifold Intersections, Yuriy Mileyko

Dissertations

Recent developments in such fields as computer aided geometric design, geometric modeling, and computational topology have generated a spate of interest towards geometric objects called swept volumes. Besides their great applicability in various practical areas, the mere geometry and topology of these entities make them a perfect testbed for novel approaches aimed at analyzing and representing geometric objects. The structure of swept volumes reveals that it is also important to focus on a little simpler, although a very similar type of objects - swept manifolds. In particular, effective computability of swept manifold intersections is of major concern.

The main goal …

Scheduling Policies For Disks And Disk Arrays, Chang Liu

Dissertations

Recent rapid advances of magnetic recording technology have enabled substantial increases in disk capacity. There has been less than 10% improvement annually in the random access time to small data blocks on the disk. Such accesses are very common in OLTP applications, which tend to have stringent response time requirements. Scheduling of disk requests is intended to improve their response time, reduce disk service time, and increase disk access bandwidth with respect to the default FCFS scheduling policy.

Shortest Access Time First policy has been shown to outperform other classical disk scheduling policies in numerous studies. Before verifying this conclusion, …

Image Watermarking, Steganography, And Morphological Processing, Yi-Ta Wu

Dissertations

With the fast development of computer technology, research in the fields of multimedia security, image processing, and robot vision have recently become popular. Image watermarking, steganogrphic system, morphological processing and shortest path planning are important subjects among them. In this dissertation, the fundamental techniques are reviewed first followed by the presentation of novel algorithms and theorems for these three subjects.

The research on multimedia security consists of two parts, image watermarking and steganographic system. In image watermarking, several algorithms are developed to achieve different goals as shown below. In order to embed more watermarks and to minimize distortion of watermarked …

Collaborative Examinations In Asyncronous Learning Networks : Field Experiments On Collaborative Learning Through Online Assessments, Jia Shen

Dissertations

With the proliferation of computer networks and the emergence of virtual teams, learning and knowledge sharing in the online environment has become an increasingly important topic. Applying constructivism and collaborative learning theories to assessment, the collaborative online exam is designed featuring students' active participation in various phases of the exam process through small group activities online. A participatory online exam process is designed featuring similar procedures except that students' involvement in each phase of the exam is individual. The collaborative online exam and the participatory online exam are investigated regarding student exam study strategies, group process, exam outcomes, faculty satisfaction, …

Electromagnetic And Acoustic Propagation In Strip Lines And Porous Media, Lin Zhou

Dissertations

Wave propagation in two physical structures is described and analyzed in this dissertation. In the first problem, the propagation of a normally incident plane acoustic wave through a three dimensional rigid slab with periodically placed holes is modeled and analyzed. The spacing of the holes A and B, the wavelength λ and the thickness of the slab L are order one parameters compared to the characteristic size D of the holes, which is a small quantity. Scattering matrix techniques are used to derive expressions for the transmission and reflection coefficients of the lowest mode. These expressions depend only on the …

Algorithms And Complexity Analyses For Some Combinational Optimization Problems, Hairong Zhao

Dissertations

The main focus of this dissertation is on classical combinatorial optimization problems in two important areas: scheduling and network design.

In the area of scheduling, the main interest is in problems in the master-slave model. In this model, each machine is either a master machine or a slave machine. Each job is associated with a preprocessing task, a slave task and a postprocessing task that must be executed in this order. Each slave task has a dedicated slave machine. All the preprocessing and postprocessing tasks share a single master machine or the same set of master machines. A job may …

Just-In-Time Hypermedia, Li Zhang

Dissertations

Many analytical applications, especially legacy systems, create documents and display screens in response to user queries "dynamically" or in real time . These documents and displays do not exist in advance, and thus hypermedia must be generated 'just in time" -automatically and dynamically.

This dissertation details the idea of 'just-in-time" hypermedia and discusses challenges encountered in this research area. A fully detailed literature review about the research issues and related research work is given. A framework for the 'just-in-time" hypermedia compares virtual documents with static documents, as well as dynamic with static hypermedia functionality. Conceptual 'just-in-time" hypermedia architecture is proposed …

High-Dimensional Indexing Methods Utilizing Clustering And Dimensionality Reduction, Lijuan Zhang

Dissertations

The emergence of novel database applications has resulted in the prevalence of a new paradigm for similarity search. These applications include multimedia databases, medical imaging databases, time series databases, DNA and protein sequence databases, and many others. Features of data objects are extracted and transformed into high-dimensional data points. Searching for objects becomes a search on points in the high-dimensional feature space. The dissimilarity between two objects is determined by the distance between two feature vectors. Similarity search is usually implemented as nearest neighbor search in feature vector spaces. The cost of processing k-nearest neighbor (k-NN) queries via a sequential …

Improving Document Representation By Accumulating Relevance Feedback : The Relevance Feedback Accumulation (Rfa) Algorithm, Razvan Stefan Bot

Dissertations

Document representation (indexing) techniques are dominated by variants of the term-frequency analysis approach, based on the assumption that the more occurrences a term has throughout a document the more important the term is in that document. Inherent drawbacks associated with this approach include: poor index quality, high document representation size and the word mismatch problem. To tackle these drawbacks, a document representation improvement method called the Relevance Feedback Accumulation (RFA) algorithm is presented. The algorithm provides a mechanism to continuously accumulate relevance assessments over time and across users. It also provides a document representation modification function, or document representation learning …

The Control Of Frequency Of A Conditional Oscillator Simultaneously Subjected To Multiple Oscillatory Inputs, Christina L. Ambrosio

Dissertations

A conditional oscillator is one that requires input to oscillate. An example of such is the gastric mill network of the stomatogastric ganglion of the crab Cancer borealis which requires modulatory input from outside the stomatogastric ganglion and fast input from the pyloric network of the animal in order to become active. This dissertation studies how the frequency of the gastric mill network is determined when it is simultaneously subjected to two different rhythmic inputs whose timing may be mismatched. We derive a mathematical model of the gastric mill network and deduce that the difference in timing between the pyloric …

Order Scheduling In Dedicated And Flexible Machine Environments, Haibing Li

Dissertations

Order scheduling models are relatively new in the field of scheduling. Consider a facility with m parallel machines that can process k different products (job types). Each machine can process a given subset of different product types. There are n orders from n different clients. Each order requests specific quantities of the various different products that can be produced concurrently on their given subsets of machines; it may have a release date, a weight and a due date. Preemptions may be allowed. An order can not be shipped until the processing of all the products for the order has been …

Development Of An Underwater Infrared Camera To Detect Manatees, Edward O. Keith

Marine & Environmental Sciences Faculty Reports

In calendar year 2004, watercraft related mortality was the second leading cause of death of the Florida manatee (Trichechus manatus latirostris) accounting for 25% of total known manatee deaths. In an attempt to reduce this significant cause of manatee mortality, the Florida Fish and Wildlife Research Institute has instituted two rounds of Manatee Avoidance Technology grants. Herein I report the results of an evaluation of the ability of underwater infrared video cameras to detect captive manatees and other non-living targets. If such cameras could detect manatees at sufficient distances, they could be mounted in the bows of watercraft …

A Linear Regression Framework For Receiver Operating Characteristic(Roc) Curve Analysis, Zheng Zhang, Margaret S. Pepe

UW Biostatistics Working Paper Series

In the field of medical diagnostic testing, the receiver operating characteristics(ROC) curve has long been used as a standard statistical tool to assess the accuracy of tests that yield continuous results. Although previous research in this area focused mostly on estimating the ROC curve, recently it has been recognized that the accuracy of a given test may fluctuate depending on certain factors, which motivates modelling covariate effects on the ROC curve. Comparing the corresponding ROC curves between two or more tests is a special case of covariate effect modelling. In this manuscript, we introduce a linear regression framework to model …

Attributable Risk Function In The Proportional Hazards Model, Ying Qing Chen, Chengcheng Hu, Yan Wang

UW Biostatistics Working Paper Series

As an epidemiological parameter, the population attributable fraction is an important measure to quantify the public health attributable risk of an exposure to morbidity and mortality. In this article, we extend this parameter to the attributable fraction function in survival analysis of time-to-event outcomes, and further establish its estimation and inference procedures based on the widely used proportional hazards models. Numerical examples and simulations studies are presented to validate and demonstrate the proposed methods.

Exact Dynamics Of A Reaction-Diffusion Model With Spatially Alternating Rates, M. Mobilia, Beate Schmittmann, R. K. P. Zia

Beate Schmittmann

We present the exact solution for the full dynamics of a nonequilibrium spin chain and its dual reaction-diffusion model, for arbitrary initial conditions. The spin chain is driven out of equilibrium by coupling alternating spins to two thermal baths at different temperatures. In the reaction-diffusion model, this translates into spatially alternating rates for particle creation and annihilation, and even negative “temperatures” have a perfectly natural interpretation. Observables of interest include the magnetization, the particle density, and all correlation functions for both models. Two generic types of time dependence are found: if both temperatures are positive, the magnetization, density, and correlation …

Energy Balanced Broadcasting Through Delayed Intelligence, Michael R. Gosnell, Ryan Arbarelli, Maggie Xiaoyan Cheng, Bruce M. Mcmillin

Computer Science Faculty Research & Creative Works

Ad hoc wireless networks are growing in popularity and usefulness, however they rely on broadcasting as a fundamental process for routing. Improvements to broadcasting have made ad hoc networks more feasible, but sometimes benefit only specific situations. Delayed intelligence (DI) is proposed as a new load balancing approach where small delays are introduced to allow distributed responsibility delegation. Preliminary results show delayed intelligence, when applied in existing broadcasting methods such as passive clustering, can be used to improve the energy disparity and therefore extend ad hoc network lifetime.

Top Quark And Charged Higgs Production At Hadron Colliders, Nikolaos Kidonakis

Faculty Articles

I present a brief theoretical update on top quark pair production at the Tevatron and give values of the NNLO-NNNLL cross section for both m_t=175 and 178 GeV. I then present a calculation of the cross section for charged Higgs production in association with a top quark at the LHC, including NNLO soft-gluon corrections.

A Toy Rock Climbing Robot, Matthew P. Bell

Dartmouth College Undergraduate Theses

The goal of this thesis was to build a simple toy rock climbing robot, and to explore problems related to grasping, path planning, and robot control. The robot is capable of climbing a wall of pegs either under manual control through a host system and an infrared interface, or on the basis of a set of pre-recorded keyframes. In addition, the robot can climb certain peg configurations using a cyclic gait. The robot climbs in an open-loop mode without sensor feedback. All communications are sent through the IR connection, and the tether to the robot consists only of two power …

Sharing The Big Apple : A Survey Study Of People, Place And Locatability, Samer Nadim Karam

Theses

Over the past half century social trends and new technologies have weakened local social ties and thus, the fabric of civil society itself. Mobile location-aware community systems offer one path to redress these problems by enhancing community cohesion and the formation of social capital by helping people to meet each other and coordinate their actions. However, little is known about the general population's desire and attitude towards these systems.

The design space described by the People-to-People-to-Geographical-Places Framework (P3-Framework), was used to guide a survey study of the impact of 'place' on people's social information needs and their willingness to share …

Short-Term Effects Of Bulkheads On The Bayshore Of Fire Island, New York, Dipanjali Chavan

Theses

Construction of bulkheads as a method of shore protection is common on the bay shoreline of Fire Island, New York but there are few studies that assess the effects of these structures on beach change in estuarine and lagoon environments. A short-term field study was conducted at Cherry Grove on Fire Island to assess the effect of a bulkhead on the fronting profile and to the adjacent beaches on the east side of the bulkhead. Data on winds, waves, and currents were gathered daily at high water. Data on profile change and depth of sediment activation were gathered at low …

Structure And Dynamics Of Soluble Guanylyl Cyclase, Kentaro Sugino

Theses

Soluble guanylyl cyclase (sGC) is one of the key enzymes involved in many fundamental biological processes including vasodilatation. It can be allosterically activated by synthetic compound such as YC-l. Recently, the 3D structure of adenylyl cyclase (AC), which is a homologue of sGC, was determined. Using AC as template and homology modeling, the 3D structure of sGC is predicted. Prior experimental work has suggested two binding modes of YC- 1. In the current investigation, molecular dynamics simulations (MD) were conducted to seek more detail of molecular mechanism of sGC activation.

From these MD simulations, a tentative mechanism of sGC activation …

Approximation Algorithms For Variants Of The Traveling Salesman Problem, Ankur Gupta

Theses

The traveling salesman problem, hereafter abbreviated and referred to as TSP, is a very well known NP-optimization problem and is one of the most widely researched problems in computer science. Classical TSP is one of the original NP - hard problems [1]. It is also known to be NP - hard to approximate within any factor and thus there is no approximation algorithm for TSP for general graphs, unless P = NP. However, given the added constraint that edges of the graph observe triangle inequality, it has been shown that it is possible achieve a good approximation to the optimal …

Rebuild Performance Enhancement Using Onboard Caching And Delayed Vacation Termination In Clustered Raid 5, Akheel Ahmed

Theses

The Clustered Raid 5 (CRAID5) architecture with a parity group size(G) smaller than the number of disks(N) increases the load by the declustering ratio denoted by α = (G -1)/(N -1), which can be lesser than that in Raid 5 while switching to, and subsequently operating in rebuild mode. The Nearly Random Permutation (NRP) layout provides the flexibility to vary the declustering ratio (α) for a given N, and the Vacationing Server Model (VSM) of processing the rebuild requests provides acceptable rebuild and user response times.

The rebuild performance and the user response time can be improved by introducing an …

Ferromagnetism In Nanocrystalline Epitaxial Co:Tio2 Thin Films, Aswini K. Pradhan, D. Hunter, J.B. Dadson, T.M. Williams, Kai Zhang, K. Lord, B. Lasley, Rakhim R. Rakhimov, Jun Zhang, David J. Sellmyer, U.N. Roy, Y. Cui, A. Burger, C. Hopkins, N. Pearson, A.L. Wilkerson

David Sellmyer Publications

We report on the observation of remarkable room-temperature ferromagnetism in nanocrystalline epitaxial Co:TiO₂ films grown on sapphire (0001) substrates by a pulsed-laser deposition technique using high-density targets. The films were characterized by x-ray measurements, atomic force microscopy, micro-Raman, electron-paramagnetic resonance, and magnetization studies. The films exhibit three-dimensional islandlike growth that contains nanocrystalline particles. Our experimental results suggest that the remarkable ferromagnetism in Co:TiO₂ films is controlled either by the interstitial Co²⁺ ions or small clusters, which are mainly present at the interface and on the surface of the films. Our work clearly indicates that Co interstitials and …