Physical Sciences and Mathematics Commons^™

The Fierce Green Fire: Vol. 1 Issue 2, Wofford College Environmental Studies Program

The Fierce Green Fire

No abstract provided.

Rapidly Reconfigurable Slow-Light System Based On Off-Resonant Raman Absorption, Praveen K. Vudyasetu, Ryan M. Camacho, John C. Howell

Mathematics, Physics, and Computer Science Faculty Articles and Research

We present a slow-light system based on dual Raman absorption resonances in warm rubidium vapor. Each Raman absorption resonance is produced by a control beam in an off-resonant Λ system. This system combines all optical control of the Raman absorption and the low-dispersion broadening properties of the double Lorentzian absorption slow light. The bandwidth, group delay, and central frequency of the slow-light system can all be tuned dynamically by changing the properties of the control beam. We demonstrate multiple pulse delays with low distortion and show that such a system has fast switching dynamics and thus fast reconfiguration rates.

Experimental Evaluation Of Transmission Link Characteristics In Body Area Networks, Apoorva Kiran Pandya

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Recent advances in digital electronics, embedded systems, and wireless communications have led the way to a new class of distributed Wireless Sensor Networks (WSNs). A Body Area Network (BAN) is a WSN consisting of miniaturized, low-power, autonomous, wireless biosensors, which are seamlessly placed or implanted in the human body to provide an adaptable and smart health care system. The possible applications of BAN are in health care services and medicine, assisting persons with disabilities, and entertainment and sports. The nodes in a BAN generally use IEEE 802.15.4 radios which have low- power consumption and are relatively immune to interference. In …

Linking Soil Loss To Sediment Delivery In Two Estuaries In Puerto Rico, Nekesha Bernadette Williams

USF Tampa Graduate Theses and Dissertations

Enhanced soil loss from the watershed is a major environmental issue. Increased soil loss from a watershed can potentially increase sediment delivery and loading to aquatic ecosystems such as rivers and estuaries. An increase in sediment delivery and loading to freshwater and transitional marine ecosystems can impact water quality and supply specifically by: (1) reducing water clarity, (2) transporting nutrient and pollutant laden sediments and (3) reducing the storage capacity of reservoirs. To address these broader environmental impacts of increased sediment delivery and loading to aquatic ecosystems it is imperative that potential source areas of sediments available for transport are …

Quasi-Decadal Spectral Peaks Of Tropical Western Pacific Ssts As A Precursor For Tropical Cyclone Threat, Shih-Yu (Simon) Wang, Adam J. Clark

Plants, Soils, and Climate Faculty Publications

A recent study identified significant spectral peaks in sea surface temperatures (SSTs) at quasi‐decadal frequency bands, which were unique to the tropical western Pacific (TWP). Using the multitaper method for spectral and coherence analysis, this study finds that the TWP SSTs at these quasi‐decadal time scales are coherent with western Pacific tropical cyclone threat [as measured by the power dissipation index (PDI)], but that the PDI lags TWP SSTs by about two years. Thus, the quasi‐decadal peaks in TWP SSTs may be a precursor for enhanced tropical cyclone threat two years later. Composite analyses are shown to illustrate how areal …

Improved In Situ Spring Constant Calibration For Colloidal Probe Atomic Force Microscopy, Sean P. Mcbride, Bruce M. Law

Physics Faculty Research

In colloidal probe atomic force microscopy (AFM) surface forces cannot be measured without an accurate determination of the cantilever spring constant. The effective spring constant k depends upon the cantilever geometry and therefore should be measured in situ; additionally, k may be coupled to other measurement parameters. For example, colloidal probe AFM is frequently used to measure the slip length b at solid/liquid boundaries by comparing the measured hydrodynamic force with Vinogradova slip theory (V-theory). However, in this measurement k and b are coupled, hence, b cannot be accurately determined without knowing k to high precision. In this paper, …

Dockomatic - Automated Ligand Creation And Docking, Casey W. Bullock, Reed B. Jacob, Owen M. Mcdougal, Greg Hampikian, Tim Andersen

Chemistry and Biochemistry Faculty Publications and Presentations

Background: The application of computational modeling to rationally design drugs and characterize macro biomolecular receptors has proven increasingly useful due to the accessibility of computing clusters and clouds. AutoDock is a well-known and powerful software program used to model ligand to receptor binding interactions. In its current version, AutoDock requires significant amounts of user time to setup and run jobs, and collect results. This paper presents DockoMatic, a user friendly Graphical User Interface (GUI) application that eases and automates the creation and management of AutoDock jobs for high throughput screening of ligand to receptor interactions.

Results: DockoMatic allows the user …

The Molecular Transport And Intercalation Of Guest Molecules Into Hydrogen–Bonded Metal-Organic Frameworks (Hmofs), Greg Anthony Hogan

Dissertations

The process of molecular transport and intercalation has been widely studied for many years, resulting in the discovery of molecular frameworks that are capable of hosting guest molecules or ions. Layered and porous metal-organic frameworks (MOFs) have been found to have applications in the field of catalysis, storage, separations, and ion-exchange. While MOFs are perhaps stronger materials, HMOFs have the advantage of being easily modifiable and more flexible. Because HMOFs have not been extensively studied for their ability to host molecules, and because their ability to withstand guest loss and guest exchange is essentially unknown, here we report the synthesis …

Saturated Hydraulic Conductivity Of Sulfuric Horizons In Coastal Floodplain Acid Sulfate Soils: Variability And Implications, Scott G. Johnston, Phillip Hirst, Peter Slavich, Richard T. Bush, Thor Aaso

Professor Scott G Johnston

The saturated hydraulic conductivity (Ks) of sulfuric horizons exerts a fundamental control on the connectivity between shallow groundwater and drains in coastal acid sulfate soils (CASS), strongly influencing rates of lateral seepage towards or from field drains. The Ks of sulfuric horizons was assessed on seven major coastal floodplains of eastern Australia using an in situ recovery technique conducted in ~ 0.4–0.65 m deep pits. Duplicate recovery tests were conducted in a total of 148 pits located in 32 separate geomorphic units across the seven coastal floodplains. Most pits were constructed in clay soils with acidic (pH < 4.0) shallow groundwater. The Ks spanned four orders of magnitude, ranging from < 0.5 m day− 1 to > 500 m day− …

Synthesis Of Mild–Hard Aao Templates For Studying Magnetic Interactions Between Metal Nanowires, Jin-Hee Lim, Aurelian Rotaru, Seong-Gi Min, Leszek Malkinski, John B. Wiley

Physics Faculty Publications

The sequential application of mild and hard anodization techniques in the fabrication of porous aluminamembranes allows one to decrease the number of continuous pores in anodized aluminium oxide (AAO) templates. Initially, standard mild anodization techniques were used to create porous templates with 100 nm interpore distances and 70 nm pore diameters. Hard anodization treatment on the same membrane then produced interpore distances of about 265 nm with diameters of 110 nm. At the interface between the two anodization steps, many of the mild-side pores were terminated to create a mild–hard membrane (Mi–Ha AAO) where the functional interpore distances were 200–300 …

Flexible Bootstrapping-Based Ontology Alignment, Prateek Jain, Pascal Hitzler, Amit P. Sheth

Kno.e.sis Publications

BLOOMS (Jain et al, ISWC2010) is an ontology alignment system which, in its core, utilizes the Wikipedia category hierarchy for establishing alignments. In this paper, we present a Plug-and-Play extension to BLOOMS, which allows to flexibly replace or complement the use of Wikipedia by other online or offline resources, including domain-specific ontologies or taxonomies. By making use of automated translation services and of Wikipedia in languages other than English, it makes it possible to apply BLOOMS to alignment tasks where the input ontologies are written in different languages.

Search For Gravitational Waves From Compact Binary Coalescence In Ligo And Virgo Data From S5 And Vsr1, J. Abadie, B. P. Abbott, R. Abbott, M. Abernathy, T. Accadia, F. Acernese, C. Adams, Shaon Ghosh, Rodica Martin

Department of Physics and Astronomy Faculty Scholarship and Creative Works

We report the results of the first search for gravitational waves from compact binary coalescence using data from the Laser Interferometer Gravitational-wave Observatory (LIGO) and Virgo detectors. Five months of data were collected during the concurrent S5 (LIGO) and VSR1 (Virgo) science runs. The search focused on signals from binary mergers with a total mass between 2 and 35 M. No gravitational waves are identified. The cumulative 90%-confidence upper limits on the rate of compact binary coalescence are calculated for nonspinning binary neutron stars, black hole-neutron star systems, and binary black holes to be 8.7×10−3 yr−1L−1 10 , 2.2×10−3 yr−1L−1 …

Agenda: 2010 World Energy Justice Conference: Emerging Solutions For The Energy Poor: Technological, Entrepreneurial And Institutional Challenges, University Of Colorado Boulder. Center For Energy & Environmental Security, Colorado Journal Of International Environmental Law And Policy

2010 World Energy Justice Conference (November 5)

This conference is a sequel to the 2009 World Energy Justice Conference (WEJC 2009) which began examining ways of mainstreaming safe, clean, and efficient energy for the world's Energy Poor (EP). The EP number two and a half billion people living on less than $1-2 a day who have no access to modern energy services. WEJC 2010 more fully develops these themes. WEJC 2010 will explore how the next round of global warming meetings in Cancun could design new flexibility mechanisms that give credits, for example, for the reduction of black carbon by the adoption of cookstoves, and embrace small …

Optical-Chemical-Microphysical Relationships And Closure Studies For Mixed Carbonaceous Aerosols Observed At Jeju Island; 3-Laser Photoacoustic Spectrometer, Particle Sizing, And Filter Analysis, B. A. Flowers, M. K. Dubey, C. Mazzoleni, E. A. Stone, J. J. Schauer, S. W. Kim, S. C. Yoon

Michigan Tech Publications

Transport of aerosols in pollution plumes from the mainland Asian continent was observed in situ at Jeju, South Korea during the Cheju Asian Brown Cloud Plume-Asian Monsoon Experiment (CAPMEX) field campaign throughout August and September 2008 using a 3-laser photoacoustic spectrometer (PASS-3), chemical filter analysis, and size distributions. The PASS-3 directly measures the effects of morphology (e.g. coatings) on light absorption that traditional filter-based instruments are unable to address. Transport of mixed sulfate, carbonaceous, and nitrate aerosols from various Asian pollution plumes to Jeju accounted for 74% of the deployment days, showing large variations in their measured chemical and optical …

Power And Sample Size For Three-Level Cluster Designs, Tina Cunningham

Theses and Dissertations

Over the past few decades, Cluster Randomized Trials (CRT) have become a design of choice in many research areas. One of the most critical issues in planning a CRT is to ensure that the study design is sensitive enough to capture the intervention effect. The assessment of power and sample size in such studies is often faced with many challenges due to several methodological difficulties. While studies on power and sample size for cluster designs with one and two levels are abundant, the evaluation of required sample size for three-level designs has been generally overlooked. First, the nesting effect introduces …

Exploring Evaluation In School Districts: School District Evaluators And Their Practice, Susan Hibbard

USF Tampa Graduate Theses and Dissertations

This study explored the evaluation practices of internal evaluators in public school districts in a large southern state. The individuals who conduct evaluations in school districts as internal evaluators were identified and background information was collected. The education and training in evaluation was investigated and the types of evaluations typically conducted by those individuals. Respondents (n = 134) revealed conducting evaluations was a secondary role and part of their main job responsibilities. The types of evaluations carried out and the way in which evaluation was practices were revealed. A descriptive framework of the individuals who conduct evaluations in school districts …

Importance Of Electronic Relaxation For Inter-Coulombic Decay In Aqueous Systems, Craig P. Schwartz, Shervin Fatehi, Richard J. Saykally, David Prendergast

Chemistry Faculty Publications and Presentations

Inspired by recent photoelectron spectroscopy experiments on hydroxide solutions, we have examined the conditions necessary for enhanced (and, in the case of solutions, detectable) inter-Coulombic decay (ICD)—Auger emission from an atomic site other than that originally excited. We present general guidelines, based on energetic and spatial overlap of molecular orbitals, for this enhancement of inter-Coulombic decay-based energy transfer in solutions. These guidelines indicate that this decay process should be exhibited by broad classes of biomolecules and suggest a design criterion for targeted radiooncology protocols. Our findings show that photoelectron spectroscopy cannot resolve the current hydroxide coordination controversy.

Search For Gravitational Waves From Compact Binary Coalescence In Ligo And Virgo Data From S5 And Vsr1, J. Abadie, B. P. Abbott, R. Abbott, M. Abernathy, T. Accadia, F. Acernese, C. Adams, R. Adhikari, P. Ajith, B. Allen, G. Allen, E. Amador Ceron, R. S. Amin, S. B. Anderson, W. G. Anderson, F. Antonucci, M. A. Arain, M. Araya, M. Aronsson, K. G. Arun, Y. Aso, S. Aston, P. Astone, D. E. Atkinson, P. Aufmuth, C. Aulbert, S. Babak, P. Baker, G. Ballardin, T. Ballinger, S. Ballmer, Tiffany Z. Summerscales

Faculty Publications

We report the results of the first search for gravitational waves from compact binary coalescence using data from the Laser Interferometer Gravitational-Wave Observatory and Virgo detectors. Five months of data were collected during the Laser Interferometer Gravitational-Wave Observatory's S5 and Virgo's VSR1 science runs. The search focused on signals from binary mergers with a total mass between 2 and 35M□. No gravitational waves are identified. The cumulative 90%-confidence upper limits on the rate of compact binary coalescence are calculated for nonspinning binary neutron stars, black hole-neutron star systems, and binary black holes to be 8.7×10⊃- 3yr⊃-1L10-1, 2.2×10⊃-3yr⊃-1L10-1, and 4.4×10⊃- 4yr⊃-1L10-1, …

Semi-Supervised Data Organization For Interactive Anomaly Analysis, Javed A. Aslam, Sergey Bratus, Virgil Pavlu

Javed A. Aslam

We consider the problem of interactive iterative analysis of datasets that consist of a large number of records represented as feature vectors. The record set is known to contain a number of anomalous records that the analyst desires to locate and describe in a short and comprehensive manner. The nature of the anomaly is not known in advance (in particular, it is not known, which features or feature values identify the anomalous records, and which are irrelevant to the search), and becomes clear only in the process of analysis, as the description of the target subset is gradually refined. This …

The Kerf Toolkit For Intrusion Analysis, Javed A. Aslam, Sergey Bratus, David Kotz, Ron Peterson, Brett Tofel, Daniela Rus

Javed A. Aslam

To aid system administrators with post-attack intrusion analysis, the Kerf toolkit provides an integrated front end and powerful correlation and data-representation tools, all in one package.

General Bounds On Statistical Query Learning And Pac Learning With Noise Via Hypothesis Boosting, Javed A. Aslam, Scott E. Decatur

Javed A. Aslam

We derive general bounds on the complexity of learning in the Statistical Query model and in the PAC model with classification noise. We do so by considering the problem of boosting the accuracy of weak learning algorithms which fall within the Statistical Query model. This new model was introduced by Kearns to provide a general framework for efficient PAC learning in the presence of classification noise. We first show a general scheme for boosting the accuracy of weak SQ learning algorithms, proving that weak SQ learning is equivalent to strong SQ learning. The boosting is efficient and is used to …

Distributed Energy-Conserving Routing Protocols, Qun Li, Javed A. Aslam, Daniela Rus

Javed A. Aslam

This paper discusses several distributed power-aware routing protocols in wireless ad-hoc networks (especially sensor networks). We seek to optimize the lifetime of the network. We have developed three distributed power-aware algorithms and analyzed their efficiency in terms of the number of message broadcasts and the overall network lifetime modeled as the time to the first message that can not be sent. These are: (1) a distributed min Power algorithm (modeled on a distributed version of Dijkstra's algorithm), (2) a distributed max-min algorithm, and (3) the distributed version of our the centralized online max-min zPmin algorithm presented in [12]. The first …

The Mycobacterium Tuberculosis Drugome And Its Polypharmacological Implications, Sarah L. Kinnings, Li Xie, Kingston H. Fung, Richard M. Jackson, Lei Xie, Phillip E. Bourne

Publications and Research

We report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. The approach has been applied to the genome of Mycobacterium tuberculosis (M.tb), the causative agent of one of today’s most widely spread infectious diseases. The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’. The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be chemically druggable …

Roadmap For Selected Key Measurements Of Lhcb, Raymond Mountain, Marina Artuso, S. Blusk, Alessandra Borgia

Physics - All Scholarship

Six of the key physics measurements that will be made by the LHCb experiment, concerning CP asymmetries and rare B decays, are discussed in detail. The "road map" towards the precision measurements is presented, including the use of control channels and other techniques to understand the performance of the detector with the first data from the LHC.

Computational Biology, Harvey Greenberg, Allen Holder

Mathematical Sciences Technical Reports (MSTR)

Computational biology is an interdisciplinary field that applies the techniques of computer science, applied mathematics, and statistics to address biological questions. OR is also interdisciplinary and applies the same mathematical and computational sciences, but to decision-making problems. Both focus on developing mathematical models and designing algorithms to solve them. Models in computational biology vary in their biological domain and can range from the interactions of genes and proteins to the relationships among organisms and species.

Distribution Of Zooplankton Densities Associated With The Florida Current And Subsurface, Amy Hirons, Jonathan Shenker, Alexander Soloviev

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

The Fierce Green Fire: Vol. 1 Issue 1, Wofford College Environmental Studies Program

The Fierce Green Fire

No abstract provided.

Dnmt1 Stability Is Regulated By Proteins Coordinating Deubiquitination And Acetylation-Driven Ubiquitination, Zhanwen Du, Jing Song, Yong Wang, Yiqing Zhao, Kishore Guda, Shuming Yang, Hung Ying Kao, Yan Xu, Joseph Willis, Sanford D. Markowitz, David Sedwick, Robert M. Ewing, Zhenghe Wang

Chemistry Faculty Publications

DNA methyltransferase 1 (DNMT1) is the primary enzyme that maintains DNA methylation. We describe a previously unknown mode of regulation of DNMT1 protein stability through the coordinated action of an array of DNMT1-associated proteins. DNMT1 was destabilized by acetylation by the acetyltransferase Tip60, which triggered ubiquitination by the E3 ligase UHRF1, thereby targeting DNMT1 for proteasomal degradation. In contrast, DNMT1 was stabilized by histone deacetylase 1 (HDAC1) and the deubiquitinase HAUSP (herpes virus–associated ubiquitin-specific protease). Analysis of the abundance of DNMT1 and Tip60, as well as the association between HAUSP and DNMT1, suggested that during the cell cycle the initiation …

Endogenous Sirnas And Noncoding Rna-Derived Small Rnas Are Expressed In Adult Mouse Hippocampus And Are Up-Regulated In Olfactory Discrimination Training., Neil Smalheiser, G Lugli, Jyothi Thimmapuram, E.H. Cook, J Larson

Cyber Center Publications

We previously proposed that endogenous siRNAs may regulate synaptic plasticity and long-term gene expression in the mammalian brain. Here, a hippocampal-dependent task was employed in which adult mice were trained to execute a nose-poke in a port containing one of two simultaneously present odors in order to obtain a reward. Mice demonstrating olfactory discrimination training were compared to pseudo-training and nose-poke control groups; size-selected hippocampal RNA was subjected to Illumina deep sequencing. Sequences that aligned uniquely and exactly to the genome without uncertain nucleotide assignments, within exons or introns of MGI annotated genes, were examined further. The data confirm that …

Breathing Fresh Air Into The Philosophy Of Mathematics, Marco Panza

MPP Published Research

A review of Paolo Mancosu (ed.): The Philosophy of Mathematical Practice.