Physical Sciences and Mathematics Commons^™

Improving Predicted Protein Loop Structure Ranking Using A Pareto-Optimality Consensus Method, Yaohang Li, Ionel Rata, See-Wing Chiu, Erik Jakobsson

Computer Science Faculty Publications

Background

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction.

Results

We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy …

Fully Generalized Two-Dimensional Constrained Delaunay Mesh Refinement, Panagiotis A. Foteinos, Andrey N. Chernikov, Nikos P. Chrisochoides

Computer Science Faculty Publications

Traditional refinement algorithms insert a Steiner point from a few possible choices at each step. Our algorithm, on the contrary, defines regions from where a Steiner point can be selected and thus inserts a Steiner point among an infinite number of choices. Our algorithm significantly extends existing generalized algorithms by increasing the number and the size of these regions. The lower bound for newly created angles can be arbitrarily close to $30^{\circ}$. Both termination and good grading are guaranteed. It is the first Delaunay refinement algorithm with a $30^{\circ}$ angle bound and with grading guarantees. Experimental evaluation of our algorithm …

Structure Prediction For The Helical Skeletons Detected From The Low Resolution Protein Density Map, Kamal Al Nasr, Weitao Sun, Jing He

Computer Science Faculty Publications

Background: The current advances in electron cryo-microscopy technique have made it possible to obtain protein density maps at about 6-10 Å resolution. Although it is hard to derive the protein chain directly from such a low resolution map, the location of the secondary structures such as helices and strands can be computationally detected. It has been demonstrated that such low-resolution map can be used during the protein structure prediction process to enhance the structure prediction.

Results: We have developed an approach to predict the 3-dimensional structure for the helical skeletons that can be detected from the low resolution protein density …

The Joint Distribution Of Bivariate Exponential Under Linearly Related Model, Norou Diawara, Kumer Pial Das

Mathematics & Statistics Faculty Publications

In this paper, fundamental results of the joint distribution of the bivariate exponential distributions are established. The positive support multivariate distribution theory is important in reliability and survival analysis, and we applied it to the case where more than one failure or survival is observed in a given study. Usually, the multivariate distribution is restricted to those with marginal distributions of a specified and familiar lifetime family. The family of exponential distribution contains the absolutely continuous and discrete case models with a nonzero probability on a set of measure zero. Examples are given, and estimators are developed and applied to …

Prediction Of Brain Tumor Progression Using A Machine Learning Technique, Yuzhong Shen, Debrup Banerjee, Jiang Li, Adam Chandler, Yufei Shen, Frederic D. Mckenzie, Jihong Wang, Nico Karssemeijer (Ed.), Ronald M. Summers (Ed.)

Electrical & Computer Engineering Faculty Publications

A machine learning technique is presented for assessing brain tumor progression by exploring six patients' complete MRI records scanned during their visits in the past two years. There are ten MRI series, including diffusion tensor image (DTI), for each visit. After registering all series to the corresponding DTI scan at the first visit, annotated normal and tumor regions were overlaid. Intensity value of each pixel inside the annotated regions were then extracted across all of the ten MRI series to compose a 10 dimensional vector. Each feature vector falls into one of three categories:normal, tumor, and normal but progressed to …

Breathing Like A Fish, Petros J. Katsioloudis

STEMPS Faculty Publications

The article offers information on industrial oxygen rebreathers, an underwater breathing equipment used by divers. It states that rebreather is an electromechanical device that supply breathing gas through infusion of oxygen and reprocessing of carbon dioxide by using a chemical scrubber. It mentions that most rebreathers comprise of breathing loop, breathing lungs, and a canister where the scrubber is placed with the partial pressure (pO₂) sensors and interface devices like heads-up display (HUD) to show pO₂ levels. It also discusses types of rebreathers such as the oxygen rebreather, the oldest rebreather mainly used by navy diver, and …

Finite Element Analysis Of Ring-Shaped Emission Profile In Plasma Bullet, Yukinori Sakiyama, David B. Graves, Julien Jarrige, Mounir Laroussi

Electrical & Computer Engineering Faculty Publications

Using a one-way coupled model of neutral gas flow and plasma dynamics we report a mechanism to explain the ring-shaped emission pattern that has been observed experimentally in plasma bullets at atmospheric pressure. We solve a fluid model with the local field approximation in one-dimensional cylindrical coordinates, corresponding to a cross-section of a plasma bullet. Pulselike uniform electric field is assumed to be applied perpendicular to the simulation domain. Time and spatially resolved spectroscopic measurements support the simulation results.

Destruction Of Α -Synuclein Based Amyloid Fibrils By A Low Temperature Plasma Jet, Erdinc Karakas, Agatha Munyanyi, Lesley Greene, Mounir Laroussi

Electrical & Computer Engineering Faculty Publications

Amyloid fibrils are ordered beta-sheet aggregates that are associated with a number of neurodegenerative diseases such as Alzheimer and Parkinson. At present, there is no cure for these progressive and debilitating diseases. Here we report initial studies that indicate that low temperature atmospheric pressure plasma can break amyloid fibrils into smaller units in vitro. The plasma was generated by the plasma pencil, a device capable of emitting a long, low temperature plasma plume/jet. This avenue of research may facilitate the development of a plasma-based medical treatment.

Experimental Studies On The Plasma Bullet Propagation And Its Inhibition, Erdinc Karakas, Mounir Laroussi

Electrical & Computer Engineering Faculty Publications

Plasma bullets generated by atmospheric pressure low temperature plasma jets have recently been an active research topic due to their unique properties and their enhanced plasma chemistry. In this paper, experimental insights into the plasma bullet lifetime and its velocity are reported. Data obtained from intensified charge-coupled device camera and time-resolved optical emission spectroscopy (OES) elucidated the existence of a weakly ionized channel between the plasma bullet and its source (such as the plasma pencil). Factors responsible for the inhibition of the propagation of the bullet, such as low helium mole fraction, the magnitude of the applied voltage, and the …

Transmitter Optimization In Multiuser Wireless Systems With Quality Of Service Constraints, Danda B. Rawat

Electrical & Computer Engineering Theses & Dissertations

In this dissertation, transmitter adaptation for optimal resource allocation in wireless communication systems are investigated. First, a multiple access channel model is considered where many transmitters communicate with a single receiver. This scenario is a basic component of a. wireless network in which multiple users simultaneously access the resources of a wireless service provider. Adaptive algorithms for transmitter optimization to meet Quality-of-Service (QoS) requirements in a distributed manner are studied. Second, an interference channel model is considered where multiple interfering transmitter-receiver pairs co-exist such that a given transmitter communicates with its intended receiver in the presence of interference from other …

Effects Of Multitemperature Nonequilibrium On Compressible Homogeneous Turbulence, Wei Liao, Yan Peng, Li-Shi Luo

Mathematics & Statistics Faculty Publications

We study the effects of the rotational-translational energy exchange on the compressible decaying homogeneous isotropic turbulence (DHIT) in three dimensions through direct numerical simulations. We use the gas-kinetic scheme coupled with multitemperature nonequilibrium based on the Jeans-Landau-Teller model. We investigate the effects of the relaxation time of rotational temperature, Z_R, and the initial ratio of the rotational and translational temperatures, T_R0 / T_L0, on the dynamics of various turbulence statistics including the kinetic energy K (t), the dissipation rate ε (t), the energy spectrum E (k,t), the root mean square of the velocity divergence θ′ …

Probability Models For Blackjack Poker, Charlie H. Cooke

Mathematics & Statistics Faculty Publications

For simplicity in calculation, previous analyses of blackjack poker have employed models which employ sampling with replacement. in order to assess what degree of error this may induce, the purpose here is to calculate results for a typical hand where sampling without replacement is employed. It is seen that significant error can result when long runs are required to complete the hand. The hand examined is itself of particular interest, as regards both its outstanding expectations of high yield and certain implications for pair splitting of two nines against the dealer's seven. Theoretical and experimental methods are used in order …

Linear Dependency For The Difference In Exponential Regression, Indika Sathish, Norou Diawara

Mathematics & Statistics Faculty Publications

In the field of reliability, a lot has been written on the analysis of phenomena that are related. Estimation of the difference of two population means have been mostly formulated under the no-correlation assumption. However, in many situations, there is a correlation involved. This paper addresses this issue. A sequential estimation method for linearly related lifetime distributions is presented. Estimations for the scale parameters of the exponential distribution are given under square error loss using a sequential prediction method. Optimal stopping rules are discussed using concepts of mean criteria, and numerical results are presented.

Exchange Across The Shelf Break At High Southern Latitudes, J. M. Klinck, M. S. Dinniman

CCPO Publications

Exchange of water across the Antarctic shelf break has considerable scientific and societal importance due to its effects on circulation and biology of the region, conversion of water masses as part of the global overturning circulation and basal melt of glacial ice and the consequent effect on sea level rise. The focus in this paper is the onshore transport of warm, oceanic Circumpolar Deep Water (CDW); export of dense water from these shelves is equally important, but has been the focus of other recent papers and will not be considered here. A variety of physical mechanisms are described which could …

On The Nature Of Winter Cooling And The Recent Temperature Shift On The Northern Gulf Of Alaska Shelf, Markus A. Janout, Thomas J. Weingartner, Thomas C. Royer, Seth L. Danielson

CCPO Publications

[1] In spring 2006 and 2007, northern Gulf of Alaska (GOA) shelf waters were ∼1.5°C below average throughout the similar to ∼250 m deep shelf and the salinity-dependent winter stratification was anomalously weak due to above (below) average surface (bottom) salinities. Spring 2007 and 2008 temperatures were also similar to ∼-1.5°C below average, but the anomalies were confined to the upper 100 m due to moderate salt stratification. Shelf temperatures in these 2 years were among the lowest observed since the early 1970s, thus interrupting an approximately 30-year warming trend. We examined winter cooling processes using historical conductivity-temperature-depth (CTD) profiles …

Nutrient Cycles And Marine Microbes In A Co2-Enriched Ocean, David A. Hutchins, Margaret R. Mulholland, Feixue Fu

OES Faculty Publications

The ocean carbon cycle is tightly linked with the cycles of the major nutrient elements nitrogen, phosphorus, and silicon. It is therefore likely that enrichment of the ocean with anthropogenic CO2 and attendant acidification will have large consequences for marine nutrient biogeochemistry, and for the microbes that mediate many key nutrient transformations. The best available evidence suggests that the nitrogen cycle may respond strongly to higher CO2 through increases in global N2 fixation and possibly denitrification, as well as potential decreases in nitrification. These trends could cause nitrification to become a nitrogen cycle "bottleneck," by increasing the flux of N2 …

Coupled Ray-Tracing And Fokker-Planck Ebw Modeling For Spherical Tokamaks, Jakub Urban, Joan Decker, Y. Peysson, Josef Preinhaelter, Gary Taylor, Linda L. Vahala, George Vahala

Electrical & Computer Engineering Faculty Publications

The AMR (Antenna—Mode-conversion—Ray-tracing) code [1, 2] has been recently coupled with the LUKE [3] Fokker-Planck code. This modeling suite is capable of complex simulations of electron Bernstein wave (EBW) emission, heating and current drive. We employ these codes to study EBW heating and current drive performance under spherical tokamak (ST) configurations—typical NSTX discharges are employed. EBW parameters, such as frequency, antenna position and direction, are varied and optimized for particular configurations and objectives. In this way, we show the versatility of EBWs.

(Re-) Discovering Lost Web Pages, Martin Klein, Michael L. Nelson

Computer Science Presentations

PDF of a powerpoint presentation from a Mathematics & Computer Science Seminar at Emory University, Atlanta, Georgia, October 2, 2009. Also available on Slideshare.

Circulation, Vol. 16, No. 1, Center For Coastal Physical Oceanography, Old Dominion University, Tom Gatski

CCPO Circulation

Fall 2009 issue of CCPO Circulation featuring article "Simulation and Modeling of Turbulence" by Dr. Tom Gatski

Monte Carlo Model Of Light Propagation In Tissues And The Effects Of Phase Changes On The Light Intensity, Rakesh Choula

Electrical & Computer Engineering Theses & Dissertations

Lasers, due to their unique properties, have a wide range of applications in the medical field. For accurate laser treatments that focus on bio-tissues, prior knowledge of the amount of laser power, spot size and its irradiation time are necessary. In order to predict the effects of lasers on tissues and their bio-effects, a first necessary step is the creation of a model that can predict the temperature distributions within the tissue following laser excitation. This involves modeling light propagation through the tissue with inclusion of internal scattering, and assessment of the energy deposited by the incoming photons. The next …

Fault-Tolerance And Recovery In Wireless Sensor Networks, Kevin M. Somervill

Electrical & Computer Engineering Theses & Dissertations

The topic of Wireless Sensor Networks (WSNs) has gained considerable attention in the research community due to the variety of applications and interesting challenges in developing and deploying such networks. The typical WSN is significantly energy constrained and often deployed in harsh or even hostile environments, resulting in sensor nodes that are prone to failure. Failing nodes alter the topology of the network resulting in segmented routing paths and lost messages, ultimately reducing network efficiency. These issues spur the desire to develop energy-efficient, Fault-Tolerant (FT) algorithms that enable the network to persist in spite of the failed nodes. This work …

Image Registration Using Conformal Log Polar Mapping, Bala Krishna Vadapally

Electrical & Computer Engineering Theses & Dissertations

Image Registration is the process of aligning, or overlaying two images of the same scene that were taken at different times and/or from different viewing angles and/or by sensors with different modalities or resolutions. The variations in the imaging environment induce the difference between the images of the same scene. In our situation, we have two images of the same scene taken with two sensors, one in the visible and the other in the infrared (IR) domain. The cameras are placed adjacent to each other on a stable platform, and the images are captured almost simultaneously. This means that the …

Solvent Dependent Morphologies In Thiol-Ene Photopolymerization: A Facile Route To Synthesis Of Resorcinarene Nanocapsules, Zaharoula Marie Kalaitzis

Chemistry & Biochemistry Theses & Dissertations

Synthesis of morphologically distinct polymeric nanostructures is vital for their wide ranging applications from nanomedicine to material science. Among various polymeric nanostructures, nanocapsules in particular have attracted a lot of attention as nanoreactors and drug delivery vehicles in nanomedicine. Often, synthesis of nanocapsules is achieved by template-based approaches. A direct, template-free method for the fabrication of nanocapsules and a variety of other morphologically distinct polymeric architectures was developed. The photopolymerization of a resorcinarene thiol-ene surfactant in various solvents lead to the formation of nanocapsules, nanoparticles, fibers, distorted honeycomb-like lattices, and sheets. The progress of the polymerization reaction and the morphology …

First Records Of Hypleurochilus Geminatus And Centropristis Philadelphica From Chesapeake Bay, Aimee D. Halvorson

Virginia Journal of Science

During the fall of 2007, Centropris philadelphica (rock seabass) and Hypleurochilus geminatus (Crested blenny) were collected from Chesapeake Bay. These captures are significant as they represent the first substantiated record of C. philadelphica from Chesapeake Bay and only the second and third validated records of H. geminatus. Additionally, the first record of H. geminatus from Chesapeake Bay was only recently recognized since the specimen had been previously misidentified as Parablennius marmoreus (seaweed blenny). The collection of seven individuals of H. geminatus in 2007, from two locations, indicates that the species may be resident within the Chesapeake Bay estuary.

Phytoplankton Blooms: Their Occurrence And Composition Within Virginia's Tidal Tributaries, Harold G. Marshall, Todd A. Egerton

Virginia Journal of Science

Sporadic algal bloom development within a 10 year monitoring program in Virginia tidal tributaries of Chesapeake Bay is reviewed. These blooms were common events, characteristically producing a color signature to the surface water, typically short lived, occurring mainly from spring into autumn throughout different salinity regions of these rivers, and were produced primarily by dinoflagellates. The abundance threshold levels that would identify bloom status from a non-bloom presence were species specific, varied with the taxon's cell size, and ranged from ca. 10 to 10⁴ cells mL^-1. Among the most consistent sporadic bloom producers were the dinoflagellates Akashiwo …

A Smart-Phone Application For Improving Communication Skills In Children With Autism, Lakshmi Padmaja Battagiri

Electrical & Computer Engineering Theses & Dissertations

The prevalence of autism, a complex neurobiological disorder, has grown at a staggering rate in the recent past. Today, one out of 150 American children is diagnosed with autism. Generally, the disorder appears during an individual's first three years of life of and persists through his/her entire life span. The individual faces various social interaction, communication and behavioral problems. Developmental disabilities, extreme withdrawal, lack of social behaviour, severe language and attention deficits, repetitive behaviours and limited interests are the characteristics of this disorder. There is no verified cure yet, but several therapies and intervention systems especially focused on the early …

Rapid Prototyping Augmented Skin Pathology For Medical Simulation And Training, Annette Castelino

Electrical & Computer Engineering Theses & Dissertations

The goal of this research is to study how augmented reality technology could be applied in training medical students for better clinical practice and diagnosis in the treatment of skin conditions using skin pathology prototypes. Described within this thesis is an innovative method of producing skin abscess prototypes that augment the Standardized Patient (SP) for simulation purposes.

The method adopted is a combination of the cost-effective technique of rapid prototyping (RP) — 3D inkjet printing and 3D graphics modeling. The visual and haptic realism of these developed prototypes along with the use of moulage enable the SP to exhibit realistic …

A Robust Method To Detect Concealed Weapons, Anand Gone

Electrical & Computer Engineering Theses & Dissertations

Concealed weapons detection is a large problem that is faced by the Police Department nowadays. There are many disasters caused by poor detection of the weapons. Since public safety is at risk there is a need to design an efficient detector that can detect the weapons hidden under the clothing. This thesis presents a novel method for detecting concealed weapons under clothing using image processing techniques. In this thesis IR imagery is used to capture an image which works on the principle of law of black body radiation. Image thresholding is performed on the captured data using Sauvola's adaptive thresholding …

Development Of Chemometric Models And Calibration Transfer For Rapid Diesel And Jet Fuel Analysis Using Near Infrared Spectroscopy, Christopher Matthew Larkin

Chemistry & Biochemistry Theses & Dissertations

Fuel quality assurance and analysis, as it pertains to the United States armed forces, is crucial for maintaining operability and upholding safety regulations with respect to fuel class. Currently a great amount of effort, money and manpower are dedicated to this task as fuel analysis takes place in off-site laboratories where quality assessment and property determination is performed manually by highly qualified lab technicians. This presents the military with a logistics problem with respect to refueling, transport, and fuel storage as the typical tum-around time is 1-2 weeks. In this thesis it has been demonstrated that near-infrared spectroscopy, in conjunction …

Behavioral Enhancement Of Onshore Transport By Postlarval Caribbean Spiny Lobster (Panulirus Argus), Jason S. Goldstein, Mark J. Butler Iv

Biological Sciences Faculty Publications

We conducted a series of laboratory experiments to examine the orientation, settlement, and metamorphosis of Caribbean spiny lobster (Panulirus argus) pueruli (postlarvae) in response to cues characteristic of their nursery in back-reef tropical lagoons. Our results suggest that pueruli were attracted to coastal water sources and the metabolites of red macroalgae (Laurencia spp.) when compared with oceanic water and artificial seawater treatments. Pueruli were not attracted to waterborne cues from sea grass, were repelled by hypersaline or hyposaline water, and discerned coastal cues from water collected as far as 30 km offshore from the reef. We also conducted experiments to …