Physical Sciences and Mathematics Commons^™

Lack Of Equivalence In The Elemental And Stable Isotope Chemistry Within The Sagittal Otolith Pair Of The Summer Flounder, Paralichthys Dentatus, Antranik Kajajian, Jason J. Schaffler, Cynthia M. Jones

OES Faculty Publications

In fish that are not bilaterally symmetrical, the left and right sagittae are often not symmetrical, exhibiting divergent growth patterns and mass, and may have differences in chemical composition. We investigated this in the asymmetrical summer flounder Paralichthys dentatus, collected from different nursery habitats along the US east coast. Significant differences were detected in otolith mass, δ¹³C, δ¹⁸O, Li:Ca, Mg:Ca, and Sr:Ca, and overall chemical signatures. These results refute the hypothesis of left-right equivalence that is prevalent for bilaterally symmetrical fishes. We tested whether a specific side was better suited for classification. The best models …

Automated Identification Of Cell Type Specific Genes In The Mouse Brain By Image Computing Of Expression Patterns, Rongjian Li, Wenlu Zhang, Shuiwang Ji

Computer Science Faculty Publications

Background: Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are expressed only in specific cell-types. Analysis of cell-type-specific gene expression patterns can provide insights into the relationship between genes, connectivity, brain regions, and cell-types. However, automated methods for identifying cell-type-specific genes are lacking to date.

Results: Here, we describe a set of computational methods for identifying cell-type-specific genes in the mouse brain by automated image computing of in situ hybridization (ISH) expression patterns. We applied invariant image feature …

Moved But Not Gone: An Evaluation Of Real-Time Methods For Discovering Replacement Web Pages, Martin Klein, Michael L. Nelson

Computer Science Faculty Publications

Inaccessible Web pages and 404 “Page Not Found” responses are a common Web phenomenon and a detriment to the user’s browsing experience. The rediscovery of missing Web pages is, therefore, a relevant research topic in the digital preservation as well as in the Information Retrieval realm. In this article, we bring these two areas together by analyzing four content- and link-based methods to rediscover missing Web pages. We investigate the retrieval performance of the methods individually as well as their combinations and give an insight into how effective these methods are over time. As the main result of this work, …

Toward A Real Time Multi-Tissue Adaptive Physics Based Non-Rigid Registration Framework For Brain Tumor Resection, Fotis Drakopoulos, Panagiotis Foteinos, Yixun Liu, Nikos Chrisochoides

Computer Science Faculty Publications

This paper presents an adaptive non-rigid registration method for aligning pre-operative MRI with intra-operative MRI (iMRI) to compensate for brain deformation during brain tumor resection. This method extends a successful existing Physics-Based Non-Rigid Registration (PBNRR) technique implemented in ITKv4.5. The new method relies on a parallel adaptive heterogeneous biomechanical Finite Element (FE) model for tissue/tumor removal depicted in the iMRI. In contrast the existing PBNRR in ITK relies on homogeneous static FE model designed for brain shift only (i.e., it is not designed to handle brain tumor resection). As a result, the new method (1) accurately captures the intra-operative deformations …

Automatic Curvilinear Quality Mesh Generation Driven By Smooth Boundary And Guaranteed Fidelity, Jing Xu, Andrey N. Chernikov

Computer Science Faculty Publications

The development of robust high-order finite element methods requires the construction of valid high-order meshes for complex geometries without user intervention. This paper presents a novel approach for automatically generating a high-order mesh with two main features: first, the boundary of the mesh is globally smooth; second, the mesh boundary satisfies a required fidelity tolerance. Invalid elements are eliminated. Example meshes demonstrate the features of the algorithm.

Gpu Accelerated Long-Term Simulations Of Beam-Beam Effects In Colliders, B. Terzić, V. Morozov, Y. Roblin, F. Lin, H. Zhang, M. Aturban, D. Ranjan, M. Zubair

Computer Science Faculty Publications

We present an update 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 particle tracking (including a symplectic option) for beam transport and the generalized 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, previously computationally prohibitive long-term simulations become tractable. The new code will be used to model the proposed Medium-energy Electron-Ion Collider (MEIC) at Jefferson Lab.

Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He

Computer Science Faculty Publications

Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM …

A Nonrigid Registration Method For Correcting Brain Deformation Induced By Tumor Resection, Yixun Liu, Chengjun Yao, Fotis Drakopoulos, Jinsong Wu, Liangfu Zhou, Nikos Chrisochoides

Computer Science Faculty Publications

Purpose: This paper presents a nonrigid registration method to align preoperative MRI with intraoperative MRI to compensate for brain deformation during tumor resection. This method extends traditional point-based nonrigid registration in two aspects: (1) allow the input data to be incomplete and (2) simulate the underlying deformation with a heterogeneous biomechanical model.

Methods: The method formulates the registration as a three-variable (point correspondence, deformation field, and resection region) functional minimization problem, in which point correspondence is represented by a fuzzy assign matrix; Deformation field is represented by a piecewise linear function regularized by the strain energy of a heterogeneous biomechanical …

Advances In The Analysis And Prediction Of Turbulent Viscoelastic Flows, T. B. Gatski, L. Thais, G. Mompean

CCPO Publications

It has been well-known for over six decades that the addition of minute amounts of long polymer chains to organic solvents, or water, can lead to significant turbulent drag reduction. This discovery has had many practical applications such as in pipeline fluid transport, oil well operations, vehicle design and submersible vehicle projectiles, and more recently arteriosclerosis treatment. However, it has only been the last twenty-five years that the full utilization of direct numerical simulation of such turbulent viscoelastic flows has been achieved. The unique characteristics of viscoelastic fluid flow are dictated by the nonlinear differential relationship between the flow strain …

Accelerated Flooding Along The U.S. East Coast: On The Impact Of Sea-Level Rise, Tides, Storms, The Gulf Stream, And The North Atlantic Oscillations, Tal Ezer, Larry P. Atkinson

CCPO Publications

Recent studies identified the U.S. East Coast north of Cape Hatteras as a 'hotspot' for accelerated sea-level rise ( SLR), and the analysis presented here shows that the area is also a 'hotspot for accelerated flooding.' The duration of minor tidal flooding [defined as 0.3 m above MHHW (mean higher high water)] has accelerated in recent years for most coastal locations from the Gulf of Maine to Florida. The average increase in annual minor flooding duration was ∼20 h from the period before 1970 to 1971-1990, and ∼50 h from 1971-1990 to 1991-2013; spatial variations in acceleration of flooding resemble …

Relative Permeability Of Homogenous-Wet And Mixed-Wet Porous Media As Determined By Pore-Scale Lattice Boltzmann Modeling, C. J. Landry, Z. T. Karpyn, O. Ayala

Engineering Technology Faculty Publications

We present a pore-scale study of two-phase relative permeability in homogenous-wet porous media, and porous media altered to a mixed-wet state. A Shan-Chen type multicomponent lattice Boltzmann (LB) model is employed to determine pore-scale fluid distributions and relative permeability. Mixed-wet states are created by altering the wettability of solid surfaces in contact with the nonwetting phase at the end of steady state simulation of initially homogenous-wet porous media. To ensure accurate representation of fluid-solid interfacial areas, we compare LB simulation results to experimental measurements of interfacial fluid-fluid and fluid-solid areas determined by X-ray computed microtomography imaging of water and oil …

Length Effects Of A Built-In Flapping Flat Plate On The Flow Over A Traveling Wavy Foil, Nansheng Liu, Yan Peng, Xiyun Lu

Mathematics & Statistics Faculty Publications

Flow over the traveling wavy foil with a built-in rigid flapping plate at its trailing edge has been numerically studied using the multi-relaxation-time Lattice Boltzmann method and immersed boundary method. The effect of the plate length on the propulsive performance such as the thrust force, energy consumption, and propeller efficiency has been investigated. Three modes (body force dominated, body and tail force competing and tail force dominated modes) have been identified that are associated with different hydrodynamics and flow structures. It is revealed that there exists a better performance plate length region and, within this region, a high propeller efficiency …

Modelling Cholera In Periodic Environments, Drew Posny, Jin Wang

Mathematics & Statistics Faculty Publications

We propose a deterministic compartmental model for cholera dynamics in periodic environments. The model incorporates seasonal variation into a general formulation for the incidence (or, force of infection) and the pathogen concentration. The basic reproduction number of the periodic model is derived, based on which a careful analysis is conducted on the epidemic and endemic dynamics of cholera. Several specific examples are presented to demonstrate this general model, and numerical simulation results are used to validate the analytical prediction.

Physical Analysis Of Vo2 Films Grown By Atomic Layer Deposition And Rf Magnetron Sputtering, Madhavi Tangirala, Kai Zhang, David Nminibapiel, Venkateswara Pallem, Christian Dussarrat, Wei Cao, Thomas N. Adam, Corbet S. Johnson, Hani E. Elsayed-Ali, Helmut Baumgart

Electrical & Computer Engineering Faculty Publications

Among the many vanadium suboxides and different stoichiometries, VO₂ has received considerable attention due to its remarkable metal-insulator transition (MIT) behavior, which causes a significant reversible change in its electrical and optical properties occurring across the phase transition at 67°C. The initially amorphous VO₂ thin films were fabricated by the emerging, Atomic Layer Deposition (ALD) technique with (tetrakis[ethylmethylamino]vanadium) {V(NEtMe)₄} as precursor and H₂O vapor as oxidation agent. For benchmarking we have also used the RF Magnetron Sputtering technique to deposit metallic vanadium thin films, which were later oxidized during furnace annealing. Post annealing of …

Nursing Pain Assessment & Management: A 3d Interactive Simulation, Enilda Romero-Hall, Ginger S. Watson, Yiannis Papelis, Hector Garcia

STEMPS Faculty Publications

In this design case, a team developed a 3D interactive simulation for nursing students and professional nurses to train and practice pain assessment and management procedures. In the simulation environment, the trainees interact with three emotionally expressive animated patients. The three patients vary in their ethnicity, age, and emotion intensity. Successful completion of the scenario requires that the trainee perform of a series of pain assessment and management tasks. The trainee is evaluated on the efficiency and appropriate sequencing of the tasks.

The purpose of this paper is to describe the decisions made regarding the type of virtual patients used, …

Sensor Selection And Integration To Improve Video Segmentation In Complex Environments, Adam R. Reckley, Wei-Wen Hsu, Chung-Hao Chen, Gangfeng Ma, E-Wen Huang

Electrical & Computer Engineering Faculty Publications

Background subtraction is often considered to be a required stage of any video surveillance system being used to detect objects in a single frame and/or track objects across multiple frames in a video sequence. Most current state-of-the-art techniques for object detection and tracking utilize some form of background subtraction that involves developing a model of the background at a pixel, region, or frame level and designating any elements that deviate from the background model as foreground. However, most existing approaches are capable of segmenting a number of distinct components but unable to distinguish between the desired object of interest and …

Plasma Processes And Polymers Special Issue On: Plasma And Cancer, Mounir Laroussi, Michael Keidar

Electrical & Computer Engineering Faculty Publications

During the last two decades, research efforts on the application of low temperature plasmas in biology and medicine have positioned nonequilibrium lowtemperature plasmas as a technology that has the potential of revolutionizing healthcare.[1,2] Low temperature plasmas can be applied in direct contact with living tissues to inactivate bacteria,[3] to disinfect wounds and accelerate wound healing,[4] and to induce damage in some cancer cells.[5–11]

Robust Calibration Of Cameras With Telephoto Lens Using Regularized Least Squares, Mingpei Liang, Xinyu Huang, Chung-Hao Chen, Gaolin Zheng, Alade Tokuta

Electrical & Computer Engineering Faculty Publications

Cameras with telephoto lens are usually used to recover details of an object that is either small or located far away from the cameras. However, the calibration of this kind of cameras is not as accurate as the one of cameras with short focal lengths that are commonly used in many vision applications. This paper has two contributions. First, we present a first-order error analysis that shows the relation between focal length and estimation uncertainties of camera parameters. To our knowledge, this error analysis with respect to focal length has not been studied in the area of camera calibration. Second, …

An Itk Implementation Of A Physics-Based Non-Rigid Registration Method For Brain Deformation In Image Guided Neurosurgery, Yixun Liu, Andriy Kot, Fotis Drakopoulos, Chengjun Yao, Andriy Fedorov, Andinet Enquobahrie, Oliver Clatz, Nikos P. Chrisochoides

Electrical & Computer Engineering Faculty Publications

As part of the ITK v4 project efforts, we have developed ITK filters for physics-based non-rigid registration (PBNRR), which satisfies the following requirements: account for tissue properties in the registration, improve accuracy compared to rigid registration, and reduce execution time using GPU and multi-core accelerators. The implementation has three main components: (1) Feature Point Selection, (2) Block Matching (mapped to both multi-core and GPU processors), and (3) a Robust Finite Element Solver. The use of multi-core and GPU accelerators in ITK v4 provides substantial performance improvements. For example, for the non-rigid registration of brain MRIs, the performance of the block …

Stability Of High Band Gap P3ht: Pcbm Organic Solar Cells Using Tiox Interfacial Layer, Kurniawan Foe, Gon Namkoong, Matthew Samson, Enas M. Younes, Ilho Nam, Tarek M. Abdel-Fattah

Electrical & Computer Engineering Faculty Publications

We fabricated a poly [3-hexylthiophene] (P3HT) and [6,6] -phenyl-C61-butyric acid methyl ester (PC₆₁BM with the TiO_x layer. We found that a solution based TiO_x coated at a spin speed of 3000 rpm improved the photon absorption of the active layer. An optimized TiO_x layer was also used as the interfacial layer to investigate the stability of P3HT: PC₆₁BM OPC. After 70 days of storage, we observed that the short-circuit current density (J_SC) dropped by 16.2%, fill factor (FF) dropped by 10.6%, and power conversion efficiency (PCE) dropped approximately by 25%, while …

Industrial Wireless Sensor Networks, Shancang Li, Hongjian Sun, Arumugam Nallanathan, Li Xu, Shanshan Zhao, Qindong Sun

Information Technology & Decision Sciences Faculty Publications

(First Paragraph) Industrial wireless sensor networks (IWSNs) incorporate wireless sensor networks with intelligent industrial systems providing many advantages over existing industrial applications, such as wireless communication, low cost, rapid deployment, self-organization, intelligent controlling, and processing capability. With the proliferation of wireless sensor networks in industrial applications, IWSNs technologies promise to play a significant role in developing more reliable, efficient, stable, flexible, and application-centric industrial systems.

A Distributed Consensus Algorithm For Decision Making In Service-Oriented Internet Of Things, Shancang Li, George Oikonomou, Theo Tryfonas, Thomas M. Chen, Li Da Xu

Information Technology & Decision Sciences Faculty Publications

In a service-oriented Internet of things (IoT) deployment, it is difficult to make consensus decisions for services at different IoT edge nodes where available information might be insufficient or overloaded. Existing statistical methods attempt to resolve the inconsistency, which requires adequate information to make decisions. Distributed consensus decision making (CDM) methods can provide an efficient and reliable means of synthesizing information by using a wider range of information than existing statistical methods. In this paper, we first discuss service composition for the IoT by minimizing the multi-parameter dependent matching value. Subsequently, a cluster-based distributed algorithm is proposed, whereby consensuses are …

Ionizing Radiation Detection Using Microstructured Optical Fiber, Stanton Dehaven

Electrical & Computer Engineering Theses & Dissertations

Ionizing radiation detecting microstructured optical fibers are fabricated, modeled and experimentally measured for X-ray detection in the 10-40 keV energy range. These fibers operate by containing a scintillator material which emits visible light when exposed to ionizing radiation. An X-ray source characterized with a CdTe spectrometer is used to quantify the X-ray detection efficiency of the fibers. The solid state CdTe detector is considered 100% efficient in this energy range. A liquid filled microstructured optical fiber (MOF) is presented where numerical analysis and experimental observation leads to a geometric theory of photon transmission using total internal reflection. The model relates …

Lattice-Boltzmann Simulations Of The Thermally Driven 2d Square Cavity At High Rayleigh Numbers, Dario Contrino, Pierre Lallemand, Pietro Asinari, Li-Shi Luo

Mathematics & Statistics Faculty Publications

The thermal lattice Boltzmann equation (TLBE) with multiple-relaxation-times (MRT) collision model is used to simulate the steady thermal convective flows in the two-dimensional square cavity with differentially heated vertical walls at high Rayleigh numbers. The MRT-TLBE consists of two sets of distribution functions, i.e., a D2Q9 model for the mass-momentum equations and a D2Q5 model for the temperature equation. The dimensionless flow parameters are the following: the Prandtl number Pr = 0.71 and the Rayleigh number Ra = 10⁶, 10⁷, and 10⁸. The D2Q9 + D2Q5 MRT-TLBE is shown to be second-order accurate and …

Rheological Signatures In Limit Cycle Behaviour Of Dilute, Active, Polar Liquid Crystalline Polymers In Steady Shear, M. Gregory Forest, Panon Phuworawong, Qi Wang, Ruhai Zhou

Mathematics & Statistics Faculty Publications

We consider the dilute regime of active suspensions of liquid crystalline polymers (LCPs), addressing issues motivated by our kinetic model and simulations in Forest et al. (Forest et al. 2013 Soft Matter 9, 5207-5222 (doi:10.1039/c3sm27736d)). In particular, we report unsteady two-dimensional heterogeneous flow-orientation attractors for pusher nanorod swimmers at dilute concentrations where passive LCP equilibria are isotropic. These numerical limit cycles are analogous to longwave (homogeneous) tumbling and kayaking limit cycles and two-dimensional heterogeneous unsteady attractors of passive LCPs in weak imposed shear, yet these states arise exclusively at semi-dilute concentrations where stable equilibria are nematic. The results in Forest …

Scalar Wave Scattering By Two-Layer Radial Inhomogeneities, Umaporn Nuntaplook, John Adam

Mathematics & Statistics Faculty Publications

It is shown that the iteration technique gives a better approximation for the problem with long wavelengths.

Estimating Sustainable Harvests Of Eastern Oysters, Crassostrea Virginica, Thomas M. Soniat, Nathan Cooper, Eric N. Powell, John M. Klinck, Mahdi Abdelguerfi, Shengru Tu, Roger Mann, Patrick D. Banks

CCPO Publications

Sustainability of a fishery is traditionally and typically considered achieved if the exploited population does not decline in numbers or biomass over time as a result of fishing relative to biological reference point goals. Oysters, however, exhibit atypical population dynamics compared with many other commercial species. The population dynamics often display extreme natural interannual variation in numbers and biomass, and oysters create their own habitat--the reef itself. With the worldwide decline of oyster reef habitat and the oyster fisheries dependent thereon, the maintenance of shell has received renewed attention as essential to population sustainability. We apply a shell budget model …

Cyclostationary Empirical Orthogonal Function Sea-Level Reconstruction, B. D. Hamlington, R. R. Leben, M. W. Strassburg, K.-Y. Kim

CCPO Publications

Since 1993, satellite altimetry has provided accurate measurements of sea surface height with near-global coverage. These measurements led to the first definitive estimates of global mean sea-level (GMSL) rise and have improved understanding of how sea levels are changing regionally at decadal time scales. These relatively short records, however, provide no information about the state of the ocean prior to 1993, and with the modern altimetry record spanning only 20 years, the lower frequency signals that are known to be present in the ocean are difficult or impossible to resolve. Tide gauges, on the other hand, have measured sea level …

Repeated Load Relaxation Testing Of Pure Polycrystalline Nickel At Room Temperature Using Nanoindentation, D. E. Stegall, M. A. Mamun, B. Crawford, A, A. Elmustafa

Mechanical & Aerospace Engineering Faculty Publications

We present the results of repeated relaxation tests using nanoindentation to derive the activation volume of the dislocation velocity and the ratios of the dislocation density and dislocation velocity. An experimental technique, based on classical uniaxial relaxation experiments, was developed to establish a constant strain during repeated load relaxation transients and then to calculate the stiffness of unloading, and therefore the hardness, across the transients with acceptable results. We found that the activation volume of the dislocation velocity from our nanoindentation methodology was in good agreement when compared to the same reported for uniaxial experiments. © 2014 AIP Publishing LLC.

Microfluidic Electrical Sorting Of Particles Based On Shape In A Spiral Microchannel, John Dubose, Xinyu Lu, Saurin Patel, Shizhi Qian, Sang Woo Joo

Mechanical & Aerospace Engineering Faculty Publications

Shape is an intrinsic marker of cell cycle, an important factor for identifying a bioparticle, and also a useful indicator of cell state for disease diagnostics. Therefore, shape can be a specific marker in label-free particle and cell separation for various chemical and biological applications. We demonstrate in this work a continuous-flow electrical sorting of spherical and peanut-shaped particles of similar volumes in an asymmetric double-spiral microchannel. It exploits curvature-induced dielectrophoresis to focus particles to a tight stream in the first spiral without any sheath flow and subsequently displace them to shape-dependent flow paths in the second spiral without any …