Physical Sciences and Mathematics Commons^™

Efficient Integrity Verification Of Replicated Data In Cloud, Raghul Mukundan

Masters Theses

"The cloud computing is an emerging model in which computing infrastructure resources are provided as a service over the Internet. Data owners can outsource their data by remotely storing them in the cloud and enjoy on-demand high quality services from a shared pool of configurable computing resources. By using these data storage services, the data owners can relieve the burden of local data storage and maintenance. However, since data owners and the cloud servers are not in the same trusted domain, the outsourced data may be at risk as the cloud server may no longer be fully trusted. Therefore, data …

Intensity-Based Skeletonization Of Cryoem Gray-Scale Images Using A True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the …

Synthesis And Reactivity Of Pyridinediimine Iron Complexes: For The Breakdown Of Carbon Dioxide, Zachary Thammavongsy

WWU Graduate School Collection

The increase of greenhouse gases in our atmosphere, particularly carbon dioxide (CO2), has been recognized by the scientific, industrial, and political communities. The increase in CO2 concentration has been connected to negative effects on our environment (global warming). Despite the negative associations of CO2, chemists can synthesize useful organic products and fuel from it. Ideally, the two electron reduction of CO2 to CO can provide one of the two products of synthesis gas (CO and H2), which is used in the Fischer-Tropsch process to produce diesel fuel. This thesis aims to convert CO2 to CO, using a cheap and abundant …

Cougar Genetic Variation And Gene Flow In A Heterogeneous Landscape, Matthew J. (Matthew James) Warren

WWU Graduate School Collection

Management of game species requires an understanding not just of population abundance, but also the structure of and connections between populations. Like other large-bodied carnivores, the cougar (Puma concolor) exhibits density -dependent dispersal and is capable of long-distance movement; in the absence of barriers to movement, these traits should lead to high connectivity between individuals and a lack of genetic differentiation across areas of continuous habitat. Previous research has suggested that cougar movement may be influenced by landscape variables such as forest cover, elevation, human population density, and highways. I assessed the population structure of cougars (Puma concolor) in Washington …

Effects Of Ocean Acidification On Dispersal Behavior In The Larval Stage Of The Dungeness Crab And The Pacific Green Shore Crab, Anna-Mai F. (Anna-Mai Florentine) Christmas

WWU Graduate School Collection

The influence of acidification of the world's oceans on marine populations and communities is a subject of growing concern. In the case of crustaceans, issues such as calcium dynamics of the molting process and direct effects on survival and development rates of larvae have received, at most, limited attention. My thesis research looked at phenomena that are important in the success of larval crustacean stages, but have received no attention; namely, the effects of ocean acidification on the swimming speeds, feeding rate, and gross growth efficiency of stage one larvae of the Dungeness crab, Metacarcinus (Cancer) magister, and the Pacific …

Modeling Slope Failure In The Jones Creek Watershed, Acme, Washington, Brandon M. Brayfield

WWU Graduate School Collection

Mountain watersheds in the Pacific Northwest are particularly susceptible to shallow landslides and debris flows during periods of intense precipitation. The Jones Creek watershed near Acme, WA, is a 6.7 km2 basin that hosts several active landslides. Shallow mass wasting on the unvegetated landslide toes, and deep-seated rotational slide movement can lead to landslide dam outburst floods and debris flows. There are approximately 100 buildings constructed on a 0.75 km2 alluvial fan deposited by debris flows sourced in the watershed. Predicting the occurrence of mass wasting and deep-seated movement events as they relate to the duration and intensity of antecedent …

Relationship Between Lake Whatcom Algae Density, Water Quality And Filtration Rate At The Bellingham Water Treatment Plant, Wa, Bowei He

WWU Graduate School Collection

During the summer of 2009, the Bellingham drinking water treatment plant experienced severe reductions in filtration rates, resulting in mandatory water restrictions. Since then, summer water filtration rates continued to approach critical levels. In 2011, I conducted a study to investigate the phytoplankton and ambient water quality patterns in Lake Whatcom source water to see if any parameters could be used to predict low water filtration rates. In addition, I evaluated water quality and phytoplankton cell densities at different depths at the intake located in Lake Whatcom to see if drawing source water from different depths could help reduce water …

Sets Of Discontinuities Of Linearly Continuous Functions, Krzysztof Ciesielski

Faculty & Staff Scholarship

The class of linearly continuous functions f:Rⁿ-->R, that is, having continuous restrictions f|L to every straight line L, have been studied since the dawn of the twentieth century. In this paper we refine a description of the form that the sets D(f) of points of discontinuities of such functions can have. It has been proved by Slobodnik that D(f) must be a countable union of isometric copies of the graphs of Lipschitz functions h:K-->R, where K is a compact nowhere dense subset of R^n-1. Since the class Dⁿ of all …

Dynamic Two-Sided Pricing Under Sequential Innovation, Mei Lin, Xiajun Pan

Research Collection School Of Computing and Information Systems

Many two-sided platforms offer innovative hardware products that improve in quality and enter the market sequentially. We analyze the impact of the decrease in the production cost on a monopoly platform owner's dynamic two-sided pricing problem, in which buyers are strategic and exert a cross-side network effect to the seller side. Our findings show that a greater decrease in cost raises the optimal price of the low-quality product and allocates more buyer-side demand to the future market. Furthermore, such decrease in cost may also lead to a higher optimal price for the future higher-quality product, given a sufficiently significant quality …

Business Intelligence And Analytics: Research Directions, Ee Peng Lim, Hsinchun Chen, Guoqing Chen

Research Collection School Of Computing and Information Systems

Business intelligence and analytics (BIA) is about the development of technologies, systems, practices, and applications to analyze critical business data so as to gain new insights about business and markets. The new insights can be used for improving products and services, achieving better operational efficiency, and fostering customer relationships. In this article, we will categorize BIA research activities into three broad research directions: (a) big data analytics, (b) text analytics, and (c) network analytics. The article aims to review the state-of-the-art techniques and models and to summarize their use in BIA applications. For each research direction, we will also determine …

Special Type Of Subset Topological Spaces, Florentin Smarandache, W.B. Vasantha Kandasamy

Branch Mathematics and Statistics Faculty and Staff Publications

In this book we construct special subset topological spaces using subsets from semigroups or groups or rings or semirings. Such study is carried out for the first time and it is both interesting and innovative. Suppose P is a semigroup and S is the collection of all subsets of P together with the empty set, then S can be given three types of topologies and all the three related topological spaces are distinct and results in more types of topological spaces. When the semigroup is finite, S gives more types of finite topological spaces. The same is true in case …

Subset Non Associative Topological Spaces, Florentin Smarandache, W.B. Vasantha Kandasamy

Branch Mathematics and Statistics Faculty and Staff Publications

The concept of non associative topological space is new and innovative. In general topological spaces are defined as union and intersection of subsets of a set X. In this book authors for the first time define non associative topological spaces using subsets of groupoids or subsets of loops or subsets of groupoid rings or subsets of loop rings. This study leads to several interesting results in this direction.

Over hundred problems on non associative topological spaces using of subsets of loops or groupoids is suggested at the end of chapter two. Also conditions for these non associative subset topological spaces …

Subset Interval Groupoids, Florentin Smarandache, W.B. Vasantha Kandasamy

Branch Mathematics and Statistics Faculty and Staff Publications

The study of groupoids is meager and we have recently introduced the new notion of subset groupoids and have studied them. It is interesting to keep on record that interval groupoids have been studied by us in 2010. Further when the subsets of a loop are taken they also form only a subset groupoid and not a subset loop. Thus we do not have the concept of subset interval loop they only form a subset interval groupoid. Special elements like subset interval zero divisors, subset interval idempotents and subset interval units are studied. Concept of subset interval groupoid homomorphism is …

Stromatolites And Miss—Differences Between Relatives, N. Noffke, S. M. Awramik

OES Faculty Publications

Benthic microorganisms form highly organized communities called “biofilms.” A biofilm consists of the individual cells plus their extracellular polymeric substances (EPS). In marine and non-marine environments, benthic microbial communities interact with the physical sediment dynamics and other factors in the environment in order to survive. This interaction can produce distinctive sedimentary structures called microbialites. Binding, biostabilization, baffling, and trapping of sediment particles by microorganisms result in the formation of microbially induced sedimentary structures (MISS); however, if carbonate precipitation occurs in EPS, and these processes happen in a repetitive manner, a multilayered build-up can form—stromatolites. Stromatolites and MISS are first found …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Estimating Loop Length From Cryoem Images At Medium Resolutions, Andrew Mcknight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, Jing He

Computer Science Faculty Publications

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was …

Computational Genetic Neuroanatomy Of The Developing Mouse Brain: Dimensionality Reduction, Visualization, And Clustering, Shuiwang Ji

Computer Science Faculty Publications

Background: The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development.

Results: In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in …

Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features To Enhance Prediction Accuracy, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Disulfide bonds play an important role in protein folding and structure stability. Accurately predicting disulfide bonds from protein sequences is important for modeling the structural and functional characteristics of many proteins.

Methods: In this work, we introduce an approach of enhancing disulfide bonding prediction accuracy by taking advantage of context-based features. We firstly derive the first-order and second-order mean-force potentials according to the amino acid environment around the cysteine residues from large number of cysteine samples. The mean-force potentials are integrated as context-based scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Convergence Analysis Of Markov Chain Monte Carlo Linear Solvers Using Ulam--Von Neumann Algorithm, Hao Ji, Michael Mascagni, Yaohang Li

Computer Science Faculty Publications

The convergence of Markov chain--based Monte Carlo linear solvers using the Ulam--von Neumann algorithm for a linear system of the form x = Hx + b is investigated in this paper. We analyze the convergence of the Monte Carlo solver based on the original Ulam--von Neumann algorithm under the conditions that ||H|| < 1 as well as ρ(H) < 1, where ρ(H) is the spectral radius of H. We find that although the Monte Carlo solver is based on sampling the Neumann series, the convergence of Neumann series is not a sufficient condition for the convergence of the Monte Carlo solver. Actually, properties of H are not the only factors determining the convergence of the Monte Carlo solver; the underlying transition probability matrix plays an important role. An improper selection of the transition matrix may result in divergence even though the condition ||H|| <1 holds. However, if the condition ||H|| < 1 is satisfied, we show that there always exist certain transition matrices that guarantee convergence of the Monte Carlo solver. On the other hand, if ρ(H) <1 but ||H|| ≥ 1, the Monte Carlo linear solver may or may not converge. In particular, if the row sum ∑ n/j= 1|H_ij > 1 for every row in H or, more generally, ρ(H⁺) >1, where H⁺ is the nonnegative matrix where H+_ij = |H_ij|, we show that transition matrices leading to convergence of the Monte Carlo solver do not exist. Finally, given …

Conformational Sampling In Template Free Protein Loop Structure Modeling: An Overview, Yaohang Li

Computer Science Faculty Publications

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the …

Gpu-Optimized Code For Long-Term Simulations Of Beam-Beam Effects In Colliders, Y. Roblin, V. Morozov, B. Terzić, M. Aturban, D. Ranjan, M. Zubair

Computer Science Faculty Publications

We report on the development of the new code for long-term simulation of beam-beam effects in particle colliders. The underlying physical model relies on a matrix-based arbitrary-order symplectic particle tracking for beam transport and the Bassetti-Erskine approximation for beam-beam interaction. The computations are accelerated through a parallel implementation on a hybrid GPU/CPU platform. With the new code, a previously computationally prohibitive long-term simulations become tractable. We use the new code to model the proposed medium-energy electron-ion collider (MEIC) at Jefferson Lab.

Ensuring Application Specific Security, Privacy And Performance Goals In Rfid Systems, Farzana Rahman

Dissertations (1934 -)

Radio Frequency IDentification (RFID) is an automatic identification technology that uses radio frequency to identify objects. Securing RFID systems and providing privacy in RFID applications has been the focus of much academic work lately. To ensure universal acceptance of RFID technology, security and privacy issued must be addressed into the design of any RFID application. Due to the constraints on memory, power, storage capacity, and amount of logic on RFID devices, traditional public key based strong security mechanisms are unsuitable for them. Usually, low cost general authentication protocols are used to secure RFID systems. However, the generic authentication protocols provide …

Molecular Tweezers: Studies Directed Towards The Preparation Of Effective Charge Transport Materials, Khushabu Thakur

Dissertations (1934 -)

ABSTRACT

MOLECULAR TWEEZERS: STUDIES DIRECTED TOWARDS THE PREPARATION OF EFFECTIVE CHARGE TRANSPORT MATERIALS

Khushabu Thakur, B.Sc, M.Sc.

Marquette University, 2013

An important focus of the modern areas of photovoltaics and molecular electronics is to identify molecules or molecular assemblies that can promote effective charge/exciton transport over long distances. In order to be able to exert control and establish necessary structural parameters for reproducible production of self-assembled structures for long-distance charge transport, our laboratory has been actively engaged towards the preparation of a variety of well-defined, cofacially-arrayed polybenzenoid nanostructures in which aromatic donors are cofacially stacked.

Herein, we undertake the design …

Composition, Sources, And Age Of Dissolved And Particulate Organic Matter In The Delaware River And Estuary, Hadley Allaben Mcintosh

Dissertations, Theses, and Masters Projects

Estuaries are important sites of organic matter (OM) transformation, exchange, and burial but remain one of the least understood regions in the global carbon cycle. The carbon cycle within these regions is complex due to strong gradients in biological and physical processes, and increasing anthropogenic impacts. This is further complicated by the many sources of particulate and dissolved organic matter (OM) in estuaries, including materials derived from terrestrial and anthropogenic sources as well as aquatic and marine primary production. This study combined lipid biomarker analyses with stable and radiocarbon signatures of lipids and source-specific biomarkers to better understand the sources …

Gis Data: City Of Suffolk, Virginia Tidal Marsh Inventory, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Kory Angstadt, David Weiss, Carl H. Hershner

Data

The 2013 Tidal Marsh Inventory update for City of Suffolk, Virgnia was generated using on-screen digitizing techniques in the most recent version of ArcGIS® - ArcMap while viewing conditions observed in the most recent imagery from the Virginia Base Mapping Program (VBMP). Dominant plant community types were primarily determined during field surveys from shallow-draft boats moving along the shoreline. Land-based surveys were performed in some locations. One shapefile is developed that portrays tidal marsh areas represented as polygons. A metadata file accompanies the shapefile to define attribute accuracy, data development, and any use restrictions that pertain to the data.

Analysis Of Extreme Water Levels In The Lower Chesapeake Bay, Carissa N. Wilkerson

Dissertations, Theses, and Masters Projects

In order to better understand storm tides in the Lower Chesapeake Bay, water levels during eleven storms at eight stations were analyzed using several methods. Storm tide was separated into individual components: predicted tide, storm surge, and local anomaly. These components were quantified and then analyzed for spatial trends. Trends were verified using Principal Component Analysis (PCA). The predicted tide and the storm surge each exhibited spatial variability, while the anomaly was spatially uniform. Anomaly values varied from storm to storm, ranging from 0.01m to 0.3m.

Potential water levels were determined for each storm by applying a time-shift to match …

Post-Release Mortality Of School-Size Atlantic Bluefin Tuna (Thunnus Thynnus) In The U.S Recreational Troll Fishery, Benjamin Jon Marcek

Dissertations, Theses, and Masters Projects

Atlantic bluefin tuna Thunnus thynnus (ABFT) support commercial and recreational fisheries throughout the North Atlantic Ocean. Due to heavy fishing pressure over the course of several decades, the eastern and western stocks of ABFT were overfished and the current biomass of the western stock is estimated to be approximately 19% of the biomass necessary for maximum sustainable yield. Despite a variety of management measures, including the implementation of minimum sizes and reductions of the total allowable catch (TAC) and country-specific quotas, little change was observed in the status of the western stock. The U.S. commercial and recreational ABFT fisheries are …

Submarine Groundwater Discharge To The York River Estuary: Quantifying Groundwater Flux And Potential For Biogeochemical Cycling, Jenna Lynn Luek

Dissertations, Theses, and Masters Projects

No abstract provided.

Effects Of Episodic Turbulence On Diatoms: With Comments On The Use Of Evans Blue Stain For Live-Dead Determinations, Haley S. Garrison

Dissertations, Theses, and Masters Projects

Episodic turbulence is a short-lived, high-intensity phenomenon in marine environments produced by both anthropogenic and natural causes, such as boat propellers, strong winds, and breaking waves. Episodic turbulence has been shown to cause mortality in zooplankton, but its effects on marine phytoplankton have rarely been investigated. This study focused on two diatoms: Thalassiosira weissflogii and Skeletonema costatum. I found that exposure for 45 s to turbulence intensities above 2.5 cm2 s-3 caused 24-32% reduction in diatom abundance and increased the amount of intact dead cells to 22%. Turbulence also caused extracellular release of optically reactive DOM. At a turbulence level …