Physical Sciences and Mathematics Commons^™

From Artifacts To Aggregations: Modeling Scientific Life Cycles On The Semantic Web, Alberto Pepe, Matthew Mayernik, Christine Borgman, Herbert Van De Sompel

Alberto Pepe

In the process of scientific research, many information objects are generated, all of which may remain valuable indefinitely. However, artifacts such as instrument data and associated calibration information may have little value in isolation; their meaning is derived from their relationships to each other. Individual artifacts are best represented as components of a life cycle that is specific to a scientific research domain or project. Current cataloging practices do not describe objects at a sufficient level of granularity nor do they offer the globally persistent identifiers necessary to discover and manage scholarly products with World Wide Web standards. The Open …

Ligand-Dependent Effects On The Conformational Equilibrium Of The Na+,K+-Atpase As Monitored By Voltage Clamp Fluorometry, Robert Dempski, Stefan Geys, Ernst Bamberg

Robert E. Dempski

Voltage clamp fluorometry was used to monitor conformational changes associated with electrogenic partial reactions of the Na(+),K(+)-ATPase after changes in the concentration of internal sodium (Na(+)(i)) or external potassium (K(+)(o)). To probe the effects of the Na(+)(i) concentration on the Na(+) branch of the Na(+),K(+)-ATPase, oocytes were depleted of Na(+)(i) and then loaded with external sodium (Na(+)(o)) using the amiloride-sensitive epithelial sodium channel. The K(+) branch of the Na(+),K(+)-ATPase was studied by exposing the oocytes to different K(+)(o) concentrations in the presence and absence of Na(+)(o) to obtain additional information on the apparent affinity for K(+)(o). Our results demonstrate that …

The Study Of The 1s4–2pj Optogalvanic Transients In A Neon Discharge Plasma, Naveed Piracha, R. Feaver, T. Gilani, Rizwan Ahmed, R. Ali, M. Baig

Naveed K. Piracha

Time dependent optogalvanic signals induced by the 1s4→2pj laser excitations have been studied in neon DC plasma. The decay rates related to all the four 1si levels have been derived by fitting the waveforms with a mathematical rate equation model. The temporal signatures of three transitions namely 638.3, 650.7 and 724.5nm related to the 2p7, 2p8 and 2p10 upper levels, respectively, have been found to be different from the rest of the transitions. We relate these effects to the population redistribution of decaying channels and to the processes responsible for the optogalvanic effect.

Numerical Studies Of A Nonlinear Heat Equation With Square Root Reaction Term, Ron Buckmire, Karl Mcmurtry, Ronald Mickens

Ron Buckmire

Interest in calculating numerical solutions of a highly nonlinear parabolic partial differential equation with fractional power diffusion and dissipative terms motivated our investigation of a heat equation having a square root nonlinear reaction term. The original equation occurs in the study of plasma behavior in fusion physics. We begin by examining the numerical behavior of the ordinary differential equation obtained by dropping the diffusion term. The results from this simpler case are then used to construct nonstandard finite difference schemes for the partial differential equation. A variety of numerical results are obtained and analyzed, along with a comparison to the …

Simulation Of Ultrashort Laser Pulse Propagation And Plasma Generation In Nonlinear Media. Dissertation, Jeremy Gulley

Jeremy R. Gulley

In this dissertation, a modified nonlinear Schrödinger equation is derived, which describes the propagation of ultrashort laser pulses through nonlinear materials in which plasma generation and laser-induced damage can occur. Differences between this model and models currently used in the literature are investigated and analyzed by numerical simulations. Ultrafast laser-induced material modification is investigated using this method by simulating the propagation of fully 3+1D (3 spatial plus 1 time dimension) laser pulses, which are numerically constructed from experimentally measured beam profiles and pulse shape data. The latest of these investigations reveals that standard rate-equation models for the free-electron plasma generation …

Mountain Building Across A Lithospheric Boundary During Arc Construction: The Cretaceous Peninsular Ranges Batholith In The Sierra San Pedro Martir Of Baja California, Mexico, K Schmidt, S Paterson, Ann Blythe, C Kopf

Ann Blythe

The Jura-Cretaceous Peninsular Ranges batholith (PRB) of Southern and Baja California contains a remarkable example of variation in crustal composition and structure across a batholith-parallel lithospheric-scale discontinuity. This lithospheric boundary between western oceanic-floored and eastern continental-floored crust influenced contractional deformation, arc magmatism, and differential exhumation of western and eastern zones in the batholith during its evolution. In the Sierra San Pedro Martir of Baja California, Mexico, a ca. 20 km wide, doubly vergent fan structure occurs across the PRB basement transition that consists of inward-dipping mylonite thrust sheets on the sides of the fan that gradually transition to a steeply-dipping …

Homologation Of Α-Amino Acids To Β-Amino Acids Via A Modified Arndt-Eistert Synthesis, Brian Brennan, James Carolan, '10

Brian B. Brennan

No abstract provided.

Utilizing Phage Display To Identify Novel Peptides That Bind To Sickle Cell Hemoglobin, Brian Brennan, Chris Betzle, '10

Brian B. Brennan

No abstract provided.

The Development Of A Novel Therapeutic For The Treatment Of Sickle Cell Disease, Brian Brennan, Steven Sturlis, '10

Brian B. Brennan

No abstract provided.

Novel Therapeutics In The Treatment Of Sickle Cell Disease: Expression And Purification Of Hemoglobin And Sickle Cell Hemoglobin, Brian Brennan, Susan Zhong, '11

Brian B. Brennan

No abstract provided.

Utilizing Phage Display To Identify Novel Peptides That Bind To Sickle Cell Hemoglobin, Brian Brennan, Chris Betzle, '10

Brian B. Brennan

No abstract provided.

The Synthesis And Characterization Of A Peptide Hemoglobin Ligand, Brian Brennan, Chris Brackett, '11

Brian B. Brennan

No abstract provided.

The Synthesis Of A Peptoid For Use As A Novel Therapeutic In The Treatment Of Sickle-Cell Disease, Brian Brennan, Michael Chiodo, '11

Brian B. Brennan

No abstract provided.

Electrostatic Deposition Of Polycations And Polyanions Onto Cysteine Monolayers, Mark Anderson

Mark R. Anderson

Electrochemical impedance spectroscopy and the quartz crystal microbalance are used to monitor the deposition of polyelectrolytes onto an interface modified with a monolayerofcysteine. When using an anionic redox probe, Fe(CN)−46, the impedance of the cysteine modified electrode is a function of the solution pH; the charge-transfer resistance being higher at basic pH, and smaller under acidic conditions relative to the value found when the solution is buffered near the pI for cysteine. This behavior is consistent with the electrostatic interaction between the anionic redox probe and the net charge of the interface. After exposure of the cysteine-modified interface to 0.10 …

Topology Explains Why Automobile Shades Fold Oddly, Ramin Naimi, Curtis Feist

Ramin Naimi

We use braids and linking number to explain why automobile shades fold into an odd number of loops.

Book Review: The Great Warming: Climate Change And The Rise And Fall Of Civilizations, James Fleming

James R. Fleming

No abstract provided.

Overview Of The Lambda-* Performance Reasoning Frameworks, Gabriel A. Moreno, Jeffery Hansen

Gabriel A. Moreno

Differentiating Web Service Offerings, Halina Kaminski, Khalid Sherdil, Hanan Lutfiyya, Nazim Madhavji, Mark Perry

Mark Perry

The advent of Service Oriented Architecture (SOA) paradigm and increasing use of Web Services (WS) implies that the future will see a large number of services transferred between providers and consumers, using many applications or agents working on behalf of humans. Discovering and using the services is the easy part. Negotiating and selecting the best services from amongst the plethora of similar ones, depending on their cost and quality, is the challenging issue. However, existing WS-I standards neither cater to provision of Service Level Agreements (SLAs), nor their exchange between parties. These standards are confined merely to WS description (WSDL). …

Who Counts Your Votes?, Halina Kaminski, Lila Kari, Mark Perry

Mark Perry

Open and fair elections are paramount to modern democracy. Although some people claim that the penciland- paper systems used in countries such as Canada and UK are still the best method of avoiding vote rigging, recent election problems have sparked great interest in managing the election process through the use of electronic voting systems. It is a goal of this paper to describe a voting system that is secret and secure as well as verifiable and useable over an existing computer network. We have designed and implemented an electronic voting system – Verifiable E-Voting (VEV) – with an underlying protocol …

Local Spectral Analysis Via A Bayesian Mixture Of Smoothing Splines” Journal Of The American Statistical Association, Sally Wood, Ori Rosen, David Stoffer

Sally Wood

No abstract provided.

Balancing The R With The E In Reu Programs, Sarah Spence Adams, Rick Gillman, Darren Narayan

Sarah Spence Adams

Externally or internally funded Research Experience for Undergraduates (REU) programs offer students the opportunity to work with faculty on unsolved problems and can serve as a highlight of their undergraduate career. The overall goal of these formative programs is that students and faculty have an enjoyable experience as they investigate the horizon of knowledge. However, there is a question on how much a program should focus on research and how much emphasis should be placed on the experience. In the end, both aspects should be given considerable weight.

Amphipathic Small Molecules Mimic The Binding Mode And Function Of Endogenous Transcription Factors, Brian Brennan, Sara Buhrlage, Caleb Bates, Steven Rowe, Aaron Minter, Chinmay Majmudar, David Wemmer, Hashim Al-Hashimi, Anna Map

Brian B. Brennan

Small molecules that reconstitute the binding mode(s) of a protein and in doing so elicit a programmed functional response offer considerable advantages in the control of complex biological processes. The development challenges of such molecules are significant, however. Many protein–protein interactions require multiple points of contact over relatively large surface areas. More significantly, several binding modes can be superimposed upon a single sequence within a protein, and a true small molecule replacement must be preprogrammed for such multimodal binding. This is the case for the transcriptional activation domain or TAD of transcriptional activators as these motifs utilize a poorly characterized …

Identification Of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests, Yuanyuan Xiao, Mark Segal

Mark R Segal

The recent availability of whole-genome scale data sets that investigate complementary and diverse aspects of transcriptional regulation has spawned an increased need for new and effective computational approaches to analyze and integrate these large scale assays. Here, we propose a novel algorithm, based on random forest methodology, to relate gene expression (as derived from expression microarrays) to sequence features residing in gene promoters (as derived from DNA motif data) and transcription factor binding to gene promoters (as derived from tiling microarrays). We extend the random forest approach to model a multivariate response as represented, for example, by time-course gene expression …

Ethically Notable Videogames: Moral Dilemmas And Gameplay, Jose Zagal

Jose P Zagal

In what ways can we use games to make moral demands of players and encouraging them to reflect on ethical issues? In this article we propose an ethically notable game as one that provides opportunities for encouraging ethical reasoning and reflection. Our analysis of the videogames Ultima IV, Manhunt, and Fire Emblem: Radiant Dawn highlights the central role that moral dilemmas can play towards creating ethically notable games. We discuss the different ways that these are implemented, such as placing players in situations in which their understanding of an ethical system is challenged, or by creating moral tension between the …

Visualdsolve: Visualizing Differential Equations With Mathematica, Second Edition, Stan Wagon, Antonin Slavik, Dan Schwalbe

Stan Wagon, Retired

No abstract provided.

Detecting Denial Of Service Attacks In Tor, Norman Danner, Danny Krizanc, Marc Liberatore

Norman Danner

Tor is currently one of the more popular systems for anonymizing near real-time communications on the Internet. Recently, Borisov et al. proposed a denial of service based attack on Tor (and related systems) that significantly increases the probability of compromising the anonymity provided. In this paper, we propose an algorithm for detecting such attacks and examine the effectiveness of the obvious approach to evading such detection. We implement a simplified version of the detection algorithm and study whether the attack may be in progress on the current Tor network. Our preliminary measurements indicate that the attack was probably not implemented …

Soliton Perturbation Theory For A Higher-Order Hirota Equation, Tim Marchant

Tim Marchant

Solitary wave evolution for a higher order Hirota equation is examined. For the higher order Hirota equation resonance between the solitary waves and linear radiation causes radiation loss. Soliton perturbation theory is used to determine the details of the evolving wave and its tail. An analytical expression for the solitary wave tail is derived and compared to numerical solutions. An excellent comparison between numerical and theoretical solutions is obtained for both right- and left-moving waves. Also, a two-parameter family of higher order asymptotic embedded solitons is identified.

Polymorphic Ros Scavenging Revealed By Cccp In A Lizard, Mats Olsson, Mark Wilson, Caroline Isaksson, Tobias Uller

Mark R Wilson

Ingestion of antioxidants has been argued to scavenge circulating reactive molecules (e.g., free radicals), play a part in mate choice (by mediating access to this important resource), and perhaps increase life span. However, recent work has come to question these relationships. We have shown elsewhere in the polychromatic lizard, Ctenophorus pictus, that diet supplementation of carotenoids as antioxidants does not depress circulating natural reactive oxygen species (ROS) levels and leads to no corresponding improvement of color traits. However, a much stronger test would be to experimentally manipulate the ROS levels themselves and assess carotenoid-induced ROS depression. Here, we achieve this …

Modulation Analysis Of Boundary Induced Motion Of Optical Solitary Waves In A Nematic Liquid Crystal, Tim Marchant

Tim Marchant

We consider the motion of a solitary wave, a nematicon, in a finite cell filled with a nematic liquid crystal. A modulation theory is developed to describe the boundary-induced bouncing of a nematicon in a one-dimensional cell and it is found to give predictions in very good agreement with numerical solutions. The boundary-induced motion is then considered numerically for a two-dimensional cell and a simple extension of the modulation theory from one to two space dimensions is then made, with good agreement being found with numerical solutions for the nematicon trajectory. The role of nematicon shape and relative position to …

The Effect Of Catalyst Of The Reaction Of P-Hydroxybenzaldehyde With Acetic Anhydride: A Discovery-Oriented Green Laboratory Experiment, Ram Mohan, Matthew Huddle, Michael Devore

Ram S. Mohan

No abstract provided.