Physical Sciences and Mathematics Commons^™

Hash-Map-Eradicator: Filtering Non-Target Sequences From Next Generation Sequencing Reads, Jonathon Brenner, Catherine Putonti

Catherine Putonti

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and …

A Polyglot Approach To Bioinformatics Data Integration: A Phylogenetic Analysis Of Hiv-1, Steven Reisman, Thomas Hatzopoulous, Konstantin Läufer, George K. Thiruvathukal, Catherine Putonti

Catherine Putonti

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 …

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Catherine Putonti

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Proton Transfer And Esterification Reactions In Emimoac-Based Acidic Ionic Liquids, Anh T. Tran, Phuoc H. Lam, Alexandra M. Miller, Dustin J. Walczyk, Jay Tomlin, Timothy D. Vaden, Lei Yu

Lei Yu

Acetate-based ionic liquids (such as 1-ethyl-3-methylimidazolium acetate, EMIMOAc) have potential applications for CO2 absorption and electrochemical reduction, chemical separations and extractions, and Fischer esterification of alcohols, amines, and starch. Both strong and weak organic acids can be dissolved in EMIMOAc and yield interesting proton-rich acidic ionic liquid solutions. We have used GCMS vapor pressure measurements, spectroscopic methods, calorimetry, and viscosity/conductivity measurements to investigate the properties and reactions of various acids dissolved in EMIMOAc. Unique proton transfer and esterification reactions are observed in many of these acidic solutions with carboxylic acids or sulfonic acids as solutes. Some acids react with the …

Intramolecular Glycosylation, Alexei Demchenko, Xiao G. Jia

Alexei Demchenko

Oligomers Of Cyclopentadithiophene-Vinylene In Aromatic And Quinoidal Versions And Redox Species With Intermediate Forms, Paula Mayorga Burrezo, Rocío Domínguez, José L. Zafra, Ted M. Pappenfus, Pilar De La Cruz, Lorena Welte, Daron E. Janzen, Juan T. López Navarrete, Fernando Langa, Juan Casado

Daron E Janzen, Ph.D.

No abstract provided.

Vetcompass Australia: A National Big Data Collection System For Veterinary Science, Paul Mcgreevy, Peter Thomson, Navneet K. Dhand, David Raubenheimer, Sophie Masters, Caroline S. Mansfield, Timothy Baldwin, Ricardo J. Soares Magalhaes, Jacquie Rand, Peter Hill, Anne Peaston, James Gilkerson, Martin Combs, Shane Raidal, Peter Irwin, Peter Irons, Richard Squires, David Brodbelt, Jeremy Hammond

Paul McGreevy, PhD

Non-Hermitian Engineering Of Single Mode Two Dimensional Laser Arrays, M. H. Teimourpour, Li Ge, Demetrios N. Christodoulides, Ramy El-Ganainy

Ramy El-Ganainy

A new scheme for building two dimensional laser arrays that operate in the single supermode regime is proposed. This is done by introducing an optical coupling between the laser array and lossy pseudo-isospectral chains of photonic resonators. The spectrum of this discrete reservoir is tailored to suppress all the supermodes of the main array except the fundamental one. This spectral engineering is facilitated by employing the Householder transformation in conjunction with discrete supersymmetry. The proposed scheme is general and can in principle be used in different platforms such as VCSEL arrays and photonic crystal laser arrays.

Non-Hermitian Engineering Of Synthetic Saturable Absorbers For Applications In Photonics, M. H. Teimourpour, A. Rahman, K. Srinivasan, Ramy El-Ganainy

Ramy El-Ganainy

We explore a type of synthetic saturable absorber based on quantum-inspired photonic arrays. We demonstrate that the interplay between optical Kerr nonlinearity, interference effects, and non-Hermiticity through radiation loss leads to a nonlinear optical filtering response with two distinct regimes of small and large optical transmissions. More interestingly, we show that the boundary between these two regimes can be very sharp. The threshold optical intensity that marks this abrupt “phase transition” and its steepness can be engineered by varying the number of the guiding elements. The practical feasibility of these structures as well as their potential applications in laser systems …

Supersymetric Laser Arrays, Ramy El-Ganainy, Li Ge, M. Khajavikhan, Demetrios N. Christodoulides

Ramy El-Ganainy

We introduce the concept of supersymmetric laser arrays that consist of a main optical lattice and its superpartner structure, and we investigate the onset of their lasing oscillations. Due to the coupling of the two constituent lattices, their degenerate optical modes form doublets, while the extra mode associated with unbroken supersymmetry forms a singlet state. Singlet lasing can be achieved for a wide range of design parameters, either by introducing stronger loss in the partner lattice or by pumping only the main array. Our findings suggest the possibility of building single-mode, high-power laser arrays and are also important for understanding …

Topological Tight-Binding Models From Nontrivial Square Roots, J. Arkinstall, M. H. Teimourpour, L. Feng, Ramy El-Ganainy, H. Schomerus

Ramy El-Ganainy

We describe a versatile mechanism that provides tight-binding models with an enriched, topologically nontrivial band structure. The mechanism is algebraic in nature, and leads to tight-binding models that can be interpreted as a nontrivial square root of a parent lattice Hamiltonian—in analogy to the passage from a Klein-Gordon equation to a Dirac equation. In the tight-binding setting, the square-root operation admits to induce spectral symmetries at the expense of broken crystal symmetries. As we illustrate in detail for a simple one-dimensional example, the emergent and inherited spectral symmetries equip the energy gaps with independent topological quantum numbers that control the …

Notes On Eryx, Omega, And Ata, Victor Fet

Victor Fet

Observations on several Nabokov’s works (Pale Fire, Lolita) where geographic or zoological names provide sources for puns and hidden parallels.

Creating An Experimental Learning And Research Driven Spacesuit Lab For Erau, Ryan L. Kobrick, Erik Seedhouse

Ryan L. Kobrick

This paper evaluates key functional data parameters that must be considered for suborbital spaceflight participants wearing pressurized suits for intravehicular activity (IVA). Data parameters of an analog spacesuit worn in an analog flight environment were obtained from 40 civilian participants using the Suborbital Space Flight Simulator (SSFS) at Embry-Riddle Aeronautical University (ERAU) while donning Final Frontier Design’s (FFD) fully pressurized third-generation spacesuit as part of their training for Project PoSSUM (the Polar Suborbital Science in the Upper Mesosphere Project). The physiological data collected included: blood pressure, electrocardiograms, heart rate, grip strength, and skin temperature. These parameters were measured using a …

Initial Experience In Moving Key Academic Department Functions To Social Networking Sites, David Dennis, George K. Thiruvathukal, Konstantin Läufer

David B. Dennis

We discuss our initial experience with the transition from conventional technology to social networking sites and other cloud-backed sites for three core business functions of an academic computer science department at a mid-size private university: course management, research collaboration, and community engagement. We first discuss the social/cultural context that informs our technology choices, as well as the evolution of the technology choices themselves. Then, we identify the targeted department functions and their actors. Next, we describe the past and present technical architectures used to support these functions. We conclude with a discussion of our preliminary experience with this transition and …

History Of Computing, George K. Thiruvathukal, David B. Dennis

David B. Dennis

The social and organizational history of humanity is intricately entangled with the history of technology in general and the technology of information in particular. Advances in this area have often been closely involved in social and political transformations. While the contemporary period is often referred to by such names as the Computing and Information Age, this is the culmination of a series of historical transformations that have been centuries in the making. This course will provide a venue for students to learn about history through the evolution of number systems and arithmetic, calculating and computing machines, and advanced communication technology …

Moving Academic Department Functions To Social Networks And Clouds: Initial Experiences, George K. Thiruvathukal, Konstantin Läufer, David Dennis

David B. Dennis

The ability to move locally hosted services to cloud-based technologies is a key element in the scientific programming toolbox.

Architecture-Based Self-Adaptation For Moving Target Defense (Cmu-Isr-14-109), Bradley Schmerl, Javier Camara, Gabriel Moreno, David Garlan, Andrew O. Mellinger

Gabriel A. Moreno

The fundamental premise behind Moving Target Defense (MTD) is to create a dynamic and shifting system that is more difficult to attack than a static system because a constantly changing attack surface at least reduces the chance of an attacker finding and exploiting the weakness. However, MTD approaches are typically chosen without regard to other qualities of the system, such as performance or cost. This report explores the use of self-adaptive systems, in particular those based on the architecture of the running system. A systems software architecture can be used to trade off different quality dimensions of the system. In …

Vr Usability From Elderly Cohorts: Preparatory Challenges In Overcoming Technology Rejection, George Coldham, David M. Cook

Dr. David M Cook

Optimizing Synthesis Of Substituted Oxadiazole Based Liquid Crystal Compounds.Pptx, Blake Bordokas

Blake Bordokas

Fractal Holography: A Geometric Re-Interpretation Of Cosmological Large Scale Structure, Jonas R. Mureika

Jonas Mureika

The fractal dimension of large-scale galaxy clustering has been demonstrated to be roughly D_F∼2 from a wide range of redshift surveys. If correct, this statistic is of interest for two main reasons: fractal scaling is an implicit representation of information content, and also the value itself is a geometric signature of area. It is proposed that the fractal distribution of galaxies may thus be interpreted as a signature of holography (``fractal holography''), providing more support for current theories of holographic cosmologies. Implications for entropy bounds are addressed. In particular, because of spatial scale invariance in the matter distribution, …

Differentiating Unparticles From Extra Dimensions Via Mini Black Hole Thermodynamics, Jonas R. Mureika

Jonas Mureika

A thermodynamics-based method is presented for differentiating mini black hole creation mechanisms in high energy parton collisions, including scenarios with large compactified extra dimensions and unparticle-enhanced gravity with real scaling dimension dU. Tensor unparticle interactions are shown to mimic the physics of (2dU−2) noninteger extra spatial dimensions. This yields unique model-dependent production rates, Hawking temperature profiles, and decay multiplicities for black holes of mass MBH∼1–15  TeV that may be created at the LHC and other future colliders.

Vector Unparticle Enhanced Black Holes: Exact Solutions And Thermodynamics, Jonas R. Mureika, Euro Spallucci

Jonas Mureika

Tensor and scalar unparticle couplings to matter have been shown to enhance gravitational interactions and provide corrections to the Schwarzschild metric and associated black hole structure. We derive an exact solution to the Einstein equations for vector unparticles, and conclusively demonstrate that these induce Riessner–Nordström (RN)-like solutions where the role of the “charge” is defined by a composite of unparticle phase space parameters. These black holes admit double-horizon structure, although unlike the RN metric these solutions have a minimum inner horizon value. In the extremal limit, the Hawking temperature is shown to vanish. As with the scalar/tensor case, the (outer) …

Self-Completeness And Spontaneous Dimensional Reduction, Jonas R. Mureika, Piero Nicolini

Jonas Mureika

A viable quantum theory of gravity is one of the biggest challenges physicists are facing. We discuss the confluence of two highly expected features which might be instrumental in the quest of a finite and renormalizable quantum gravity —spontaneous dimensional reduction and self-completeness. The former suggests the spacetime background at the Planck scale may be effectively two-dimensional, while the latter implies a condition of maximal compression of matter by the formation of an event horizon for Planckian scattering. We generalize such a result to an arbitrary number of dimensions, and show that gravity in higher than four dimensions remains self-complete, …

The Effects Of Temperature, Humidity, And Barometric Pressure On Short-Sprint Race Times, Jonas R. Mureika

Jonas Mureika

A numerical model of 100 m and 200 m world class sprinting performances is modified using standard hydrodynamic principles to include effects of air temperature, pressure, and humidity levels on aerodynamic drag. The magnitude of the effects are found to be dependent on wind speed. This implies that differing atmospheric conditions can yield slightly different corrections for the same wind gauge reading. In the absence of wind, temperature is found to induce the largest variation in times (0.01 s per 10◦C increment in the 100 m), while relative humidity contributes the least (under 0.01 s for all realistic conditions for …

Multifractal Structure In Nonrepresentational Art, Jonas R. Mureika, C. C. Dyer, G. C. Cupchik

Jonas Mureika

Multifractal analysis techniques are applied to patterns in several abstract expressionist artworks, painted by various artists. The analysis is carried out on two distinct types of structures: the physical patterns formed by a specific color (“blobs”) and patterns formed by the luminance gradient between adjacent colors (“edges”). It is found that the multifractal analysis method applied to “blobs” cannot distinguish between artists of the same movement, yielding a multifractal spectrum of dimensions between about 1.5 and 1.8. The method can distinguish between different types of images, however, as demonstrated by studying a radically different type of art. The data suggest …

Does Entropic Gravity Bound The Masses Of The Photon And Graviton?, Jonas R. Mureika, R. B. Mann

Jonas Mureika

If the information transfer between test particle and holographic screen in entropic gravity respects both the uncertainty principle and causality, a lower limit on the number of bits in the universe relative to its mass may be derived. Furthermore, these limits indicate particles that putatively travel at the speed of light -- the photon and/or graviton -- have a non-zero mass m≥10−68 kg. This result is found to be in excellent agreement with current experimental mass bounds on the graviton and photon, suggesting that entropic gravity may be the result of a (recent) softly-broken local symmetry. Stronger bounds emerge from …

Self-Completeness And The Generalized Uncertainty Principle, Maximiliano Isi, Jonas Mureika, Piero Nicolini

Jonas Mureika

The generalized uncertainty principle discloses a self-complete characteristic of gravity, namely the possibility of masking any curvature singularity behind an event horizon as a result of matter compression at the Planck scale. In this paper we extend the above reasoning in order to overcome some current limitations to the framework, including the absence of a consistent metric describing such Planck-scale black holes. We implement a minimum-size black hole in terms of the extremal configuration of a neutral non-rotating metric, which we derived by mimicking the effects of the generalized uncertainty principle via a short scale modified version of Einstein gravity. …

Primordial Black Hole Evaporation And Spontaneous Dimensional Reduction, Jonas R. Mureika

Jonas Mureika

Several different approaches to quantum gravity suggest the effective dimension of spacetime reduces from four to two near the Planck scale. In light of such evidence, this Letter re-examines the thermodynamics of primordial black holes (PBHs) in specific lower-dimensional gravitational models. Unlike in four dimensions, (1 + 1)-D black holes radiate with power P ∼ M²_BH, while it is known no (2+1)-D (BTZ) black holes can exist in a non-anti-de Sitter universe. This has important relevance to the PBH population size and distribution, and consequently on cosmological evolution scenarios. The number of PBHs that have evaporated to …

Unparticle-Enhanced Black Holes At The Lhc, Jonas R. Mureika

Jonas Mureika

Based on the idea that tensor unparticles can enhance the gravitational interactions between standard model particles, potential black hole formation in high energy collisions is examined. Modifications to the horizon radius rH are derived, and the corresponding geometric cross-sections of such objects are calculated. It is shown that rH increases dramatically to the electroweak scale for masses MBH∼1–10 TeV, yielding a geometric cross-section σBH=πr2H on the order of ⩽50 pb. This suggests that unparticle physics provides a mechanism for black hole formation in future accelerators, without the requirement of extra spatial dimensions.

Gravitationally Induced Quantum Superposition Reduction With Large Extra Dimensions, Jonas R. Mureika

Jonas Mureika

A gravity-driven mechanism (``objective reduction'') proposed to explain quantum state reduction is analyzed in light of the possible existence of large extra dimensions in the ADD scenario. By calculating order-of-magnitude estimates for nucleon superpositions, it is shown that if the mechanism at question is correct, constraints may be placed on the number and size of extra dimensions. Hence, measurement of superposition collapse times ({\it e.g.} through diffraction or reflection experiments) could represent a new probe of extra dimensions. The influence of a time-dependent gravitational constant on the gravity-driven collapse scheme with and without the presence of extra dimensions is also …