Physical Sciences and Mathematics Commons^™

The Root Cause Of Failure In Complex It Projects: Complexity Itself, Kaitlynn M. Whitney, Charles B. Daniels

Engineering Management & Systems Engineering Faculty Publications

Increased demand for better technology and perpetual global expansion continue to provide developers with many project opportunities for success, as well as failure. While no industry is immune from project failure, the Information Technology (IT) industry is shown to be more susceptible to risk and failure than those of other industries. Agile project management, which facilitates adaptation to changing circumstances and alleviates rigid formal controls, has become more popular in the software development industry though is not entirely compatible with traditional project management approaches.In this paper we will examine the primary causes of IT project management failure stated in modern …

Employing Learning To Improve The Performance Of Meta-Raps, Fatemah Al-Duoli, Ghaith Rabadi

Engineering Management & Systems Engineering Faculty Publications

In their search for satisfactory solutions to complex combinatorial problems, metaheuristics methods are expected to intelligently explore the solution space. Various forms of memory have been used to achieve this goal and improve the performance of metaheuristics, which warranted the development of the Adaptive Memory Programming (AMP) framework [1]. This paper follows this framework by integrating Machine Learning (ML) concepts into metaheuristics as a way to guide metaheuristics while searching for solutions. The target metaheuristic method is Meta-heuristic for Randomized Priority Search (Meta-RaPS). Similar to most metaheuristics, Meta-RaPS consists of construction and improvement phases. Randomness coupled with a greedy heuristic …

Warcreate And Wail: Warc, Wayback, And Heritrix Made Easy, Mat Kelly, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

[First slide]

The Problem

Institutional Tools, Personal Archivists

• ON YOUR MACHINE

-Complex to Operate

-Require Infrastructure

• DELEGATED TO INSTITUTIONS

-$$$

-Lose original perspective

• Locale content tailoring (DC vs. San Francisco)
• Observation Medium (PC web browser vs. Crawler)

Bacterial Colonization And Extinction On Marine Aggregates: Stochastic Model Of Species Presence And Abundance, Andrew M. Kramer, M. Maille Lyons, Fred C. Dobbs, John M. Drake

OES Faculty Publications

Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while …

Intercalibraton In Chemical Oceanography-- Getting The Right Number, Gregory A. Cutter

OES Faculty Publications

Intercalibration has a strict metrological definition, but in brief, it's an open sharing of methods and results between laboratories to achieve the most accurate data with the fewest random and systematic errors. In the field of chemical oceanography where concentrations of many constituents can be in the nano- to picomolar range, the salt water matrix can be difficult to analyze, and knowing the exact concentrations, or even chemical forms, of biologically required elements is essential, intercalibration is a very relevant and needed tool. Implementing it is not simple because errors can occur at any step in the process of taking …

Using Ammonium Pore Water Profiles To Assess Stoichiometry Of Deep Remineralization Processes In Methanogenic Continental Margin Sediments, David J. Burdige, Tomoko Komada

OES Faculty Publications

In many continental margin Sediments, a deep reaction zone exists which is separated from remineralization processes near the sediment surface. Here, methane diffuses upward to a depth where it is oxidized by downwardly diffusing sulfate. However, the methane sources that drive this anaerobic oxidation of methane (AOM) in the sulfate-methane transition zone (SMT) may vary among sites. In particular, these sources can be thought of as either (i) "internal" sources from in situ methanogenesis (regardless of where it occurs in the sediment column) that are ultimately coupled to organic matter deposition and burial, or (ii) "external" sources such as hydrocarbon …

Surface Production Fuels Deep Heterotrophic Respiration In Northern Peatlands, J. Elizabeth Corbett, David J. Burdige, Malak M. Tfaily, Angela R. Dial, William T. Cooper, Paul H. Glaser, Jeffrey P. Chanton

OES Faculty Publications

Multiple analyses of dissolved organic carbon (DOC) from pore waters were conducted to define the processes that govern carbon balance in peatlands: (1) source, reactivity, and transport of DOC with respect to vegetation, peat, and age of carbon substrate, (2) reactivity of DOC with respect to molecular size, and (3) lability to photoxidation of surficial DOC. We found that surface organic production fuels heterotrophic respiration at depth in advection-dominated peatlands, especially in fens. Fen DOC was Δ¹⁴Cenriched relative to the surrounding fen peat, and fen respiration products were similar to this enriched DOC indicating that DOC was the …

Development And Deployment Of A Point-Source Digital Inline Holographic Microscope For The Study Of Plankton And Particles To A Depth Of 6000 M, Alexander B. Bochdansky, Manfred H. Jericho, Gerhard J. Herndl

OES Faculty Publications

Bochdansky, A. B., Jericho, M. H., & Herndl, G. J. (2013). Development and deployment of a point-source digital inline holographic microscope for the study of plankton and particles to a depth of 6000 m. Limnology and Oceanography: Methods, 11, 28-40. doi: 10.4319/lom.2013.11.28

Microbially Induced Sedimentary Structures Recording An Ancient Ecosystem In The Ca. 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia, Nora Noffke, Daniel Christian, David Wacey, Robert M. Hazen

OES Faculty Publications

Microbially induced sedimentary structures (MISS) result from the response of microbial mats to physical sediment dynamics. MISS are cosmopolitan and found in many modern environments, including shelves, tidal flats, lagoons, riverine shores, lakes, interdune areas, and sabkhas. The structures record highly diverse communities of microbial mats and have been reported from numerous intervals in the geological record up to 3.2 billion years (Ga) old. This contribution describes a suite of MISS from some of the oldest well-preserved sedimentary rocks in the geological record, the early Archean (ca. 3.48 Ga) Dresser Formation, Western Australia. Outcrop mapping at the meter to …

A Technical Framework For Resource Synchronization, Martin Klein, Robert Sanderson, Herbert Van De Sompel, Simeon Warner, Bernhard Haslhofer, Carl Lagoze, Michael L. Nelson

Computer Science Faculty Publications

This is the second paper in D-Lib Magazine about the ResourceSync effort conducted by the National Information Standards Organization (NISO) and the Open Archives Initiative (OAI). The first part provided a perspective on the resource synchronization problem and introduced a template that organized possible components of a resource synchronization framework in a modular manner. This paper details a technical framework devised using that template.

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 …

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.

Turbulent Collision-Coalescence In Maritime Shallow Convection, A. A. Wyszogrodzki, W.W. Grabowski, L. P. Wang, Orlando Ayala

Engineering Technology Faculty Publications

This paper discusses cloud simulations aiming at quantitative assessment of the effects of cloud turbulence on rain development in shallow ice-free convective clouds. Cloud fields from large-eddy simulations (LES) applying bin microphysics with the collection kernel enhanced by cloud turbulence are compared to those with the standard gravitational collection kernel. Simulations for a range of cloud condensation nuclei (CCN) concentrations are contrasted. Details on how the parameterized turbulent collection kernel is used in LES simulations are presented. Because of the disparity in spatial scales between the bottom-up numerical studies guiding the turbulent kernel development and the top-down LES simulations of …

Duality Of The Weak Parallelogram Laws On Banach Spaces, Raymond Cheng, Charles B. Harris

Mathematics & Statistics Faculty Publications

This paper explores a family of weak parallelogram laws for Banach spaces. Some basic properties of such spaces are obtained. The main result is that a Banach space satisfies a lower weak parallelogram law if and only if its dual satisfies an upper weak parallelogram law, and vice versa. Connections are established between the weak parallelogram laws and the following: subspaces, quotient spaces, Cartesian products, and the Rademacher type and co-type properties.

Hyperspectral Image Classification Using A Spectral-Spatial Sparse Coding Model, Ender Oguslu, Guoqing Zhou, Jiang Li, Lorenzo Bruzzone (Ed.)

Electrical & Computer Engineering Faculty Publications

We present a sparse coding based spectral-spatial classification model for hyperspectral image (HSI) datasets. The proposed method consists of an efficient sparse coding method in which the l₁/l_q regularized multi-class logistic regression technique was utilized to achieve a compact representation of hyperspectral image pixels for land cover classification. We applied the proposed algorithm to a HSI dataset collected at the Kennedy Space Center and compared our algorithm to a recently proposed method, Gaussian process maximum likelihood (GP-ML) classifier. Experimental results show that the proposed method can achieve significantly better performances than the GP-ML classifier when training data …

Brust-Schiffrin Synthesis Of Catalytic Bipodal Pdpt Nanoparticles With Some Mechanistic Insights, Sangbum Han, Vara P. Sheela, Wei Cao, Balasubramanian Ramjee

Applied Research Center Publications

Brust–Schiffrin reduction of Pd and Pt precursors in the presence of resorcinarene amine surfactant led to the formation of substantially Pt rich, PdPt bimetallic nanoparticles of a V-shape or variants on the V-shape. New insights into this reaction are provided on the basis of reversed Brust–Schiffrin syntheses, DLS, UV-vis, and NMR analysis. Based on our experiments we conclude that the resorcinarene amine surfactant is part of the inverse micelle formed from TOABr and it also selectively complexes with the Pd salts prior to their reduction. Remarkably, the composition of the bipodal nanoparticles could be varied substantially by varying the reaction …

Integration Of Multispectral Face Recognition And Multi-Ptz Camera Automated Surveillance For Security Applications, Chung-Hao Chen, Yi Yao, Hong Chang, Andreas Koschan, Mongi Abidi

Electrical & Computer Engineering Faculty Publications

Due to increasing security concerns, a complete security system should consist of two major components, a computer-based face-recognition system and a real-time automated video surveillance system. A computer-based face-recognition system can be used in gate access control for identity authentication. In recent studies, multispectral imaging and fusion of multispectral narrow-band images in the visible spectrum have been employed and proven to enhance the recognition performance over conventional broad-band images, especially when the illumination changes. Thus, we present an automated method that specifies the optimal spectral ranges under the given illumination. Experimental results verify the consistent performance of our algorithm via …

Investigation Of Nbnx Thin Films And Nanoparticles Grown By Pulsed Laser Deposition And Thermal Diffusion, Ashraf Hassan Farha

Electrical & Computer Engineering Theses & Dissertations

Niobium nitride films (NbNx) were grown on Nb and Si (100) substrates using pulsed laser deposition (PLD), laser heating, and thermal diffusion methods. Niobium nitride films were deposited on Nb substrates using PLD with a Q-switched Nd: YAG laser (λ = 1064 nm, 40 ns pulse width, and 10 Hz repetition rate) at different laser fluences, different nitrogen background pressures and deposition temperatures. The effect of changing PLD parameters for films done by PLD was studied. The seen observations establish guidelines for adjusting the laser parameters to achieve the desired morphology and phase of the grown NbNx films.

When the …

Visualizing And Understanding Tectonism And Volcanism On Earth And Other Terrestrial Bodies, Mladen M. Dordevic

Physics Theses & Dissertations

This dissertation presents new methods of visualizing, teaching, assessing, modeling, and understanding tectonics on Earth and other celestial bodies. Tectonics is the study of planetary lithospheres and includes impact, plate, plume, cryo- and gravitational mechanisms. This dissertation is concerned with plate tectonics and plate/mantle plume interactions. Plate tectonics describes the mainly horizontal motion of lithospheric plates over the asthenosphere. Lithosphere is created at ridges and consumed at subduction zones. In addition to the plate tectonic system, mantle plumes also contribute to mass motions in the subsurface Earth. Both plate tectonics and plume upwelling processes help shape the present form of …

Next-Peak: A Normal-Exponential Two-Peak Model For Peak-Calling In Chip-Seq Data, Nak-Kyeong Kim, Rasika V. Jayatillake, John L. Spouge

Mathematics & Statistics Faculty Publications

Background: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.

Results: We propose a rigorous statistical model, the normal-exponential two-peak (NEXT-peak) model, which parallels the physical processes generating the empirical data, and which can naturally incorporate mappability information. The model therefore estimates total strength of binding (even if some binding locations do not map uniquely into a reference genome, effectively censoring them); it also assigns an error to an estimated binding location. The comparison study …

Mesoscopic Methods In Engineering And Science, Jos Derksen, Dmitry Eskin, Li-Shi Luo, Manfred Krafczyk

Mathematics & Statistics Faculty Publications

(First paragraph) Matter, conceptually classified into fluids and solids, can be completely described by the microscopic physics of its constituent atoms or molecules. However, for most engineering applications a macroscopic or continuum description has usually been sufficient, because of the large disparity between the spatial and temporal scales relevant to these applications and the scales of the underlying molecular dynamics. In this case, the microscopic physics merely determines material properties such as the viscosity of a fluid or the elastic constants of a solid. These material properties cannot be derived within the macroscopic framework, but the qualitative nature of the …

John H. Steele, 1926–2013, Elizabeth Turner, Eileen E. Hofmann, Dian J. Gifford, Dale B. Haidvogel

CCPO Publications

No abstract provided.