Digital Commons Network^™

Conditional Decoupling Of Quantum Information, Mario Berta, Fernando G.S.L. Brandão, Christian Majenz, Mark M. Wilde

Faculty Publications

Insights from quantum information theory show that correlation measures based on quantum entropy are fundamental tools that reveal the entanglement structure of multipartite states. In that spirit, Groisman, Popescu, and Winter [Phys. Rev. A 72, 032317 (2005)PLRAAN1050-294710.1103/PhysRevA.72.032317] showed that the quantum mutual information I(A;B) quantifies the minimal rate of noise needed to erase the correlations in a bipartite state of quantum systems AB. Here, we investigate correlations in tripartite systems ABE. In particular, we are interested in the minimal rate of noise needed to apply to the systems AE in order to erase the correlations between A and B given …

Hiv-1 Integrase-Targeted Short Peptides Derived From A Viral Protein R Sequence, Xue Zhi Zhao, Mathieu Métifiot, Evgeny Kiselev, Jacques Kessl, Kasthuraiah Maddali, Christophe Marchand, Mamuka Kvaratskhelia, Yves Pommier, Terrence R. Burke Jr.

Faculty Publications

HIV-1 integrase (IN) inhibitors represent a new class of highly effective anti-AIDS therapeutics. Current FDA-approved IN strand transfer inhibitors (INSTIs) share a common mechanism of action that involves chelation of catalytic divalent metal ions. However, the emergence of IN mutants having reduced sensitivity to these inhibitors underlies efforts to derive agents that antagonize IN function by alternate mechanisms. Integrase along with the 96-residue multifunctional accessory protein, viral protein R (Vpr), are both components of the HIV-1 pre-integration complex (PIC). Coordinated interactions within the PIC are important for viral replication. Herein, we report a 7-mer peptide based on the shortened Vpr …

Lightweight Multilingual Software Analysis, Damian Lyons, Anne Marie Bogar, David Baird

Faculty Publications

Large software systems can often be multilingual – that is, software systems are written in more than one language. However, many popular software engineering tools are monolingual by nature. Nonetheless, companies are faced with the need to manage their large, multilingual codebases to address issues with security, efficiency, and quality metrics. This paper presents a novel lightweight approach to multilingual software analysis – MLSA. The approach is modular and focused on efficient static analysis computation for large codebases. One topic is addressed in detail – the generation of multilingual call graphs to identify language boundary problems in multilingual code. The …

Responses Of Non-Native Earthworms To Experimental Eradication Of Garlic Mustard And Implications For Native Vegetation, Kristina A. Stinson, Serita D. Frey, M. R. Jackson, E. Coates-Connor, Mark A. Anthony, K. Martinez

Faculty Publications

Recent studies in invasion biology suggest that positive feedback among two or more introduced organisms facilitate establishment within a new range and drive changes in native plant communities. Here, we experimentally tested for relationships between native plants and two non-native organisms invading forest habitats in North America: garlic mustard (Alliaria petiolata, Brassicaceae) and earthworms. In two forested sites, we compared understory vegetation and earthworm biomass in plots where garlic mustard was removed for three years, plots without garlic mustard invasion, and plots invaded by garlic mustard that was not removed. Earthworm biomass was highest in the plots with garlic mustard, …

Unraveling Substituent Effects On The Glass Transition Temperatures Of Biorenewable Polyesters, Xiaopeng Yu, Junteng Jia, Shu Xu, Ka Un Lao, Maria J. Sanford, Ramesh K. Ramakrishnan, Sergei I. Nazarenko, Thomas R. Hoye, Geoffrey W. Coates, Robert A. Distasio Jr.

Faculty Publications

Converting biomass-based feedstocks into polymers not only reduces our reliance on fossil fuels, but also furnishes multiple opportunities to design biorenewable polymers with targeted properties and functionalities. Here we report a series of high glass transition temperature (T_g up to 184 °C) polyesters derived from sugar-based furan derivatives as well as a joint experimental and theoretical study of substituent effects on their thermal properties. Surprisingly, we find that polymers with moderate steric hindrance exhibit the highest T_g values. Through a detailed Ramachandran-type analysis of the rotational flexibility of the polymer backbone, we find that additional steric hindrance does …

Ip Preparedness For Outbreak Diseases, Ana Santos Rutschman

Faculty Publications

Outbreaks of infectious diseases will worsen in the coming decades, as illustrated by the recent back-to-back Ebola and Zika epidemics. The development of innovative drugs, especially in the form of vaccines, is key to minimizing the scale and impact of future outbreaks, yet current intellectual property (IP) regimes are ineffective in supporting this goal.

Scholarship has not adequately addressed the role of IP in the development of vaccines for outbreak diseases. This Article fills that void. Through case studies on the recent Ebola and Zika outbreaks, it provides the first descriptive analysis of the role of IP from the pre- …

Erepo-Orp: Exploring The Opportunity Space To Combat Orphan Diseases With Existing Drugs, Michal Brylinski, Misagh Naderi, Rajiv Gandhi Govindaraj, Jeffrey Lemoine

Faculty Publications

© 2017 About 7000 rare, or orphan, diseases affect more than 350 million people worldwide. Although these conditions collectively pose significant health care problems, drug companies seldom develop drugs for orphan diseases due to extremely limited individual markets. Consequently, developing new treatments for often life-threatening orphan diseases is primarily contingent on financial incentives from governments, special research grants, and private philanthropy. Computer-aided drug repositioning is a cheaper and faster alternative to traditional drug discovery offering a promising venue for orphan drug research. Here, we present eRepo-ORP, a comprehensive resource constructed by a large-scale repositioning of existing drugs to orphan diseases …

An Ensemble Stacked Convolutional Neural Network Model For Environmental Event Sound Recognition, Shaobo Li, Yong Yao, Jie Hu, Guokai Liu, Xuemei Yao, Jianjun Hu

Faculty Publications

Convolutional neural networks (CNNs) with log-mel audio representation and CNN-based end-to-end learning have both been used for environmental event sound recognition (ESC). However, log-mel features can be complemented by features learned from the raw audio waveform with an effective fusion method. In this paper, we first propose a novel stacked CNN model with multiple convolutional layers of decreasing filter sizes to improve the performance of CNN models with either log-mel feature input or raw waveform input. These two models are then combined using the Dempster–Shafer (DS) evidence theory to build the ensemble DS-CNN model for ESC. Our experiments over three …

Large And Realistic Models Of Amorphous Silicon, Dale Ingram, Bishal Bhattarai, Parthapratim Biswas, David A. Drabold

Faculty Publications

Amorphous silicon (a-Si) models are analyzed for structural, electronic and vibrational characteristics. Several models of various sizes have been computationally fabricated for this analysis. It is shown that a recently developed structural modeling algorithm known as force-enhanced atomic refinement (FEAR) provides results in agreement with experimental neutron and X-ray diffraction data while producing a total energy below conventional schemes. We also show that a large model (∼ 500 atoms) and a complete basis is necessary to properly describe vibrational and thermal properties. We compute the density for a-Si, and compare with experimental results.

Evolving Paradigms In Biological Carbon Cycling In The Ocean, Chuanlun Zhang, Hongyue Dang, Farooq Azam, Ronald Benner, Louis Legendre, Uta Passow, Luca Polimene, Carol Robinson, Curtis A. Suttle, Nianzhi Jiao

Faculty Publications

Carbon is a keystone element in global biogeochemical cycles. It plays a fundamental role in biotic and abiotic processes in the ocean, which intertwine to mediate the chemistry and redox status of carbon in the ocean and the atmosphere. The interactions between abiotic and biogenic carbon (e.g. CO₂, CaCO₃, organic matter) in the ocean are complex, and there is a half-century-old enigma about the existence of a huge reservoir of recalcitrant dissolved organic carbon (RDOC) that equates to the magnitude of the pool of atmospheric CO₂. The concepts of the biological carbon pump (BCP) …

The Performance Of Syngas-Fueled Sofcs Predicted By A Reduced Order Model (Rom): Temperature And Fuel Composition Effects, Xinfang Jin, Anthony Ku, Atul Verma, Brandon Ohara, Kevin Huang, Surinder Singh

Faculty Publications

An electrochemical reduced order model (ROM) has been developed in this study to simulate the performance of syngas-fueled anode-supported SOFCs with coupled bulk chemical reactions and multi-species gas diffusion in the electrodes. Experimental V-I curves with syngas fuel were used to validate the model to ensure its high fidelity. The model was used to investigate the effects of fuel composition and temperature on the electrochemical performance of the cell, chemical reaction rate and concentration distributions of gaseous species across the anode. The results show that H₂ electro-oxidation dominates the overall cell performance, and that CO contributes to the performance …

Securing Zigbee Commercial Communications Using Constellation Based Distinct Native Attribute Fingerprinting, Christopher M. Rondeau, J. Addison Betances, Michael A. Temple

Faculty Publications

This work provides development of Constellation Based DNA (CB-DNA) Fingerprinting for use in systems employing quadrature modulations and includes network protection demonstrations for ZigBee offset quadrature phase shift keying modulation. Results are based on 120 unique networks comprised of seven authorized ZigBee RZSUBSTICK devices, with three additional like-model devices serving as unauthorized rogue devices. Authorized network device fingerprints are used to train a Multiple Discriminant Analysis (MDA) classifier and Rogue Rejection Rate (RRR) estimated for 2520 attacks involving rogue devices presenting themselves as authorized devices. With MDA training thresholds set to achieve a True Verification Rate (TVR) of TVR = …

A 3.5 Million Solar Masses Black Hole In The Centre Of The Ultracompact Dwarf Galaxy Fornax Ucd3, Anton Afanasiev, Igor Chilingarian, Steffen Mieske, Karina Voggel, Arianna Picotti, Michael Hilker, Anil Seth, Nadine Neumayer, Matthias Frank, Aaron Romanowsky, George Hau, Holger Baumgardt, Christopher Ahn, Jay Strader, Mark Den Brok, Richard Mcdermid, Lee Spitler, Jean Brodie, Jonelle Walsh

Faculty Publications

The origin of ultracompact dwarfs (UCDs), a class of compact stellar systems discovered two decades ago, still remains a matter of debate. Recent discoveries of central supermassive black holes in UCDs likely inherited from their massive progenitor galaxies provide support for the tidal stripping hypothesis. At the same time, on statistical grounds, some massive UCDs might be representatives of the high luminosity tail of the globular cluster luminosity function. Here we present a detection of a 3.3+1.4−1.2×106M⊙ black hole (1σ uncertainty) in the centre of the UCD3 galaxy in the Fornax cluster, which corresponds to 4 per cent of its …

Non-Gnss Smartphone Pedestrian Navigation Using Barometric Elevation And Digital Map-Matching, Daniel J. Broyles, Kyle J. Kauffman, John F. Raquet, Piotr Smagowski

Faculty Publications

Pedestrian navigation in outdoor environments where global navigation satellite systems (GNSS) are unavailable is a challenging problem. Existing technologies that have attempted to address this problemoften require external reference signals or specialized hardware, the extra size,weight, power, and cost of which are unsuitable for many applications. This article presents a real-time, self-contained outdoor navigation application that uses only the existing sensors on a smartphone in conjunction with a preloaded digital elevation map. The core algorithm implements a particle filter, which fuses sensor data with a stochastic pedestrian motion model to predict the user’s position. The smartphone’s barometric elevation is then …

Sediment Characteristics And Methane Ebullition In Three Subarctic Lakes, Martin Wik, Joel E. Johnson, Patrick M. Crill, Joel P. Destasio, Lance Erickson, Madison J. Halloran, Maria Florencia Fahnestock, Maurice K. Crawford, Stephen C. Phillips, Ruth K. Varner

Faculty Publications

Ebullition (bubbling) from climate‐sensitive northern lakes remains an unconstrained source of atmospheric methane (CH4). Although the focus of many recent studies, ebullition is rarely linked to the physical characteristics of lakes. In this study we analyze the sediments of subarctic postglacial lakes and investigate how sediment properties relate to the large spatial variation in CH4 bubble flux, quantified over multiple years using bubble traps. The results show that the sediments from our lakes are rich in total organic carbon, containing 37 kg/m3 on average. This number is roughly 40% higher than the average for yedoma deposits, which have been identified …

Annotated Bibliography Of The Global Literature On The Secondary Transportation Of Raw And Comminuted Forest Products (2000-2015), Anil Koirala, Anil Raj Kizha, Cornelis F. De Hoop, Brian E. Roth, Han Sup Han, Patrick Hiesl, Dalia Abbas, Shuva Gautam, Srijana Baral, Steve Bick, Kamalakanta Sahoo

Faculty Publications

Secondary transportation of raw and comminuted forest products is a major component in forest harvesting operations in terms of economics, public perception, and safety. Consequently, there is a substantial amount of literature on this topic. The existing literature has dealt with many of the technical aspects of transportation with a majority of them focusing on improving supply chain issues; however, there are only few specific to secondary transportation issues in general. This annotated bibliography will help practitioners, researchers, and stakeholders gain a better understanding of the existing literature from 2000 to 2015. To this end, we began by classifying the …

Litter Identity Affects Assimilation Of Carbon And Nitrogen By A Shredding Caddisfly, Adam C. Siders, Zacchaeus G. Compson, Bruce A. Hungate, Paul Dijkstra, George W. Koch, Adam S. Wymore, A. Stuart Grandy, Jane C. Marks

Faculty Publications

Ecologists often equate litter quality with decomposition rate. In soil and sediments, litter that is rapidly decomposed by microbes often has low concentrations of tannin and lignin and low C:N ratios. Do these same traits also favor element transfer to higher trophic levels in streams, where many insects depend on litter as their primary food source? We test the hypothesis that slow decomposition rates promote element transfer from litter to insects, whereas rapid decomposition favors microbes. We measured carbon and nitrogen fluxes from four plant species to a leaf-shredding caddisfly using isotopically labeled litter. Caddisflies assimilated a higher percentage of …

Aerosol Microdroplets Exhibit A Stable Ph Gradient, Haoran Wei, Eric P. Vejerano, Weinan Leng, Qishen Haung, Marjorie R. Willner, Linsey C. Marr, Peter J. Vikesland

Faculty Publications

Suspended aqueous aerosol droplets (<50 μm) are microreactors for many important atmospheric reactions. In droplets and other aquatic environments, pH is arguably the key parameter dictating chemical and biological processes. The nature of the droplet air/ water interface has the potential to significantly alter droplet pH relative to bulk water. Historically, it has been challenging to measure the pH of individual droplets because of their inaccessibility to conventional pH probes. In this study, we scanned droplets containing 4-mercaptobenzoic acid–functionalized gold nanoparticle pH nanoprobes by 2D and 3D laser confocal Raman microscopy. Using surface-enhanced Raman scattering, we acquired the pH distribution inside approximately 20-μm-diameter phosphate-buffered aerosol droplets and found that the pH in the core of a droplet is higher than that of bulk solution by up to 3.6 pH units. This finding suggests the accumulation of protons at the air/water interface and is consistent with recent thermodynamic model results. The existence of this pH shift was corroborated by the observation that a catalytic reaction that occurs only under basic conditions (i.e., dimerization of 4-aminothiophenol to produce dimercaptoazobenzene) occurs within the high pH core of a droplet, but not in bulk solution. Our nanoparticle probe enables pH quantification through the cross-section of an aerosol droplet, revealing a spatial gradient that has implications for acid-base–catalyzed atmospheric chemistry.

Sub-Shot-Noise-Limited Phase Estimation Via Su(1,1) Interferometer With Thermal States, Xiaoping Ma, Chenglong You, Sushovit Adhikari, Elisha S. Matekole, Ryan T. Glasser, Hwang Lee, Jonathan P. Dowling

Faculty Publications

We theoretically study the phase sensitivity of an SU(1,1) interferometer with a thermal state and a squeezed vacuum state as inputs and parity detection as the measurement. We find that the phase sensitivity can beat the shot-noise limit and approaches the Heisenberg limit, with increasing input photon number, in an ideal situation. We also consider the e ect of various noises, including photon loss, dark counts, and thermal photon noise. Our results show that the phase sensitivity is below the shot-noise limit with photon loss and dark counts, but cannot beat the shot-noise limit in the presence of thermal noise.

Modeling Soot Formation From Solid Complex Fuels, Alexander J. Josephson, Rod R. Linn, David O. Lignell

Faculty Publications

A detailed model is proposed for predicting soot formation from complex solid fuels. The proposed model resolves two particle size distributions, one for soot precursors and another for soot particles. The precursor size distribution is represented with a sectional approach while the soot particle-size distribution is represented with the method of moments and an interpolative closure method is used to resolve fractional methods. Based on established mechanisms, this model includes submodels for precursor coagulation, growth, and consumption, as well as soot nucleation, surface growth, agglomeration, and consumption. The model is validated with comparisons to experimental data for two …

An Implementation Strategy To Quantify The Marine Microbial Carbon Pump And Its Sensitivity To Global Change, Carol Robinson, Douglas Wallace, Jung-Ho Hyun, Luca Polimene, Ronald Benner, Yao Zhang, Ruanhong Cai, Rui Zhang, Nianzhi Jiao

Faculty Publications

No abstract provided.

Commentary: Plastic Waste Associated With Disease On Coral Reefs, Gorka Bidegain, Ika Paul-Pont

Faculty Publications

No abstract provided.

Asynchronous Execution Of Python Code On Task-Based Runtime Systems, R. Tohid, Bibek Wagle, Shahrzad Shirzad, Patrick Diehl, Adrian Serio, Alireza Kheirkhahan, Parsa Amini, Katy Williams, Kate Isaacs, Kevin Huck, Steven Brandt, Hartmut Kaiser

Faculty Publications

Despite advancements in the areas of parallel and distributed computing, the complexity of programming on High Performance Computing (HPC) resources has deterred many domain experts, especially in the areas of machine learning and artificial intelligence (AI), from utilizing performance benefits of such systems. Researchers and scientists favor high-productivity languages to avoid the inconvenience of programming in low-level languages and costs of acquiring the necessary skills required for programming at this level. In recent years, Python, with the support of linear algebra libraries like NumPy, has gained popularity despite facing limitations which prevent this code from distributed runs. Here we present …

Lightweight Multilingual Software Analysis, Damian Lyons, Anne Marie Bogar, David Baird

Faculty Publications

Developer preferences, language capabilities and the persistence of older languages contribute to the trend that large software codebases are often multilingual – that is, written in more than one computer language. While developers can leverage monolingual software development tools to build software components, companies are faced with the problem of managing the resultant large, multilingual codebases to address issues with security, efficiency, and quality metrics. The key challenge is to address the opaque nature of the language interoperability interface: one language calling procedures in a second (which may call a third, or even back to the first), resulting in a …

A Building Permit System For Smart Cities: A Cloud-Based Framework, Magdalini Eirinaki, Subhankar Dhar, Shishir Mathur, Adwait Kaley, Arpit Patel, Akshar Joshi, Dhvani Shah

Faculty Publications

In this paper we propose a novel, cloud-based framework to support citizens and city officials in the building permit process. The proposed framework is efficient, user-friendly, and transparent with a quick turn-around time for homeowners. Compared to existing permit systems, the proposed smart city permit framework provides a pre-permitting decision workflow, and incorporates a data analytics and mining module that enables the continuous improvement of both the end user experience and the permitting and urban planning processes. This is enabled through a data mining-powered permit recommendation engine as well as a data analytics process that allow a gleaning of key …

Glimpses Of Space-Time Beyond The Singularities Using Supercomputers, Parampreet Singh

Faculty Publications

A fundamental problem of Einsteins theory of classical general relativity is the existence of singularities such as the big bang. All known laws of physics end at these boundaries of classical space-time. Thanks to recent developments in quantum gravity, supercomputers are now playing an important role in understanding the resolution of big bang and black hole singularities. Using supercomputers, explorations of the very genesis of space and time from quantum geometry are revealing a novel picture of what lies beyond classical singularities and the new physics of the birth of our universe.

Measurement Of Inclusive Double-Differential Νμ Charged-Current Cross Section With Improved Acceptance In The T2k Off-Axis Near Detector, K. Abe, J. Amey, C. Andreopoulos, L. Anthony, M. Antonova, S. Aoki, A. Ariga, Y. Ashida, Y. Azuma, S. Ban, M. Barbi, G. J. Barker, G. Barr, C. Barry, M. Batkiewicz, V. Berardi, S. Berkman, R. M. Berner, S. Bhadra, S. Bienstock, A. Blondel, S. Bolognesi, S. Bordoni, B. Bourguille, S. B. Boyd, D. Brailsford, A. Bravar, C. Bronner

Faculty Publications

We report a measurement of the flux-integrated cross section for inclusive muon neutrino charged-current interactions on carbon. The double-differential measurements are given as a function of the muon momentum and angle. Relative to our previous publication on this topic, these results have an increased angular acceptance and higher statistics. The data sample presented here corresponds to 5.7×1020 protons on target. The total flux-integrated cross section is measured to be (6.950±0.662)×10-39 cm2 nucleon-1 and is consistent with our simulation.

Estimating Epidemiological Parameters Of A Stochastic Differential Model Of Hiv Dynamics Using Hierarchical Bayesian Statistics, Renee Dale, Bei Bei Guo

Faculty Publications

Current estimates of the HIV epidemic indicate a decrease in the incidence of the disease in the undiagnosed subpopulation over the past 10 years. However, a lack of access to care has not been considered when modeling the population. Populations at high risk for contracting HIV are twice as likely to lack access to reliable medical care. In this paper, we consider three contributors to the HIV population dynamics: at-risk population exhaustion, lack of access to care, and usage of anti-retroviral therapy (ART) by diagnosed individuals. An extant problem in the mathematical study of this system is deriving parameter estimates …

Discrete Bethe–Sommerfeld Conjecture, Rui Han, Svetlana Jitomirskaya

Faculty Publications

In this paper, we prove a discrete version of the Bethe–Sommerfeld conjecture. Namely, we show that the spectra of multi-dimensional discrete periodic Schrödinger operators on Zd lattice with sufficiently small potentials contain at most two intervals. Moreover, the spectrum is a single interval, provided at least one of the periods is odd, and can have a gap whenever all periods are even.

On-Orbit Operations And Offline Data Processing Of Calet Onboard The Iss, Y. Asaoka, S. Ozawa, S. Torii, O. Adriani, Y. Akaike, K. Asano, M. G. Bagliesi, G. Bigongiari, W. R. Binns, S. Bonechi, M. Bongi, P. Brogi, J. H. Buckley, N. Cannady, G. Castellini, C. Checchia, M. L. Cherry, G. Collazuol, V. Di Felice, K. Ebisawa, H. Fuke, T. G. Guzik, T. Hams, M. Hareyama, N. Hasebe, K. Hibino, M. Ichimura, K. Ioka, W. Ishizaki, M. H. Israel, A. Javaid, K. Kasahara, J. Kataoka

Faculty Publications

The CALorimetric Electron Telescope (CALET), launched for installation on the International Space Station (ISS) in August, 2015, has been accumulating scientific data since October, 2015. CALET is intended to perform long-duration observations of high-energy cosmic rays onboard the ISS. CALET directly measures the cosmic-ray electron spectrum in the energy range of 1 GeV to 20 TeV with a 2% energy resolution above 30 GeV. In addition, the instrument can measure the spectrum of gamma rays well into the TeV range, and the spectra of protons and nuclei up to a PeV. In order to operate the CALET onboard ISS, JAXA …