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Chemical Detection using Electrically Open Circuits having no Electrical Connections
This paper presents investigations to date on chemical detection using a recently developed method for designing, powering and interrogating sensors as electrically open circuits having no electrical connections. In lieu of having each sensor from a closed circuit with multiple electrically connected components, an electrically conductive geometric pattern that is powered using oscillating magnetic fields and capable of storing an electric field and a magnetic field without the need of a closed circuit or electrical connections is used. When electrically active, the patterns respond with their own magnetic field whose frequency, amplitude and bandwidth can be correlated with the magnitude of the physical quantities being measured. Preliminary experimental results of using two different detection approaches will be presented. In one method, a thin film of a reactant is deposited on the surface of the open-circuit sensor. Exposure to a specific targeted reactant shifts the resonant frequency of the sensor. In the second method, a coating of conductive material is placed on a thin non-conductive plastic sheet that is placed over the surface of the sensor. There is no physical contact between the sensor and the electrically conductive material. When the conductive material is exposed to a targeted reactant, a chemical reaction occurs that renders the material non-conductive. The change in the material s electrical resistance within the magnetic field of the sensor alters the sensor s response bandwidth and amplitude, allowing detection of the reaction without having the reactants in physical contact with the sensor.
Applications of Anomaly Detection and Precursor Identification in Airspace Operations
As we continue to advance the U.S. National Airspace into the next generation of air traffic, we face challenges in both increase in complexity, as well as, a significant growth in traffic volume. Addressing these challenges, while maintaining the same level of safety is an important application of data mining. Because of these significant shifts in airspace design and usage there is a need to identify current and emergent safety risks along with their potential precursors. In recent years NASA has made advancements in developing scalable methods to address this effort in the Big Data paradigm. Multiple kernel anomaly detection approaches have been employed on both surveillance radar data and flight operational quality assurance data to identify operationally significant safety risks. Additionally, events have been explored with a recently developed precursor identification tool to discover states that reveal an increased probability of a safety event. These tools can be used to discover emerging safety risks that may not be currently monitored, which allows for mitigation tactics to be employed and ultimately make the overall airspace safer. This talk will discuss an overview of these methods and a discussion of the findings.
OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data
Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.
Ubiquity and Causes of Soil Water Preferential Flow Across 17 Ecoregions
Abstract Preferential flow (PF) in soil causes the rapid transport of water, nutrients, and contaminants into the subsurface, influencing groundwater recharge and streamflow. Data scarcity has hindered the quantification of PF occurrence and the identification of its drivers across diverse ecoregions. We address this gap by analyzing high‐frequency, multi‐depth soil moisture data across 17 ecoregions in the USA, using ∼1,500 sensors at 40 sites. We discovered that PF is widespread, with sites experiencing PF in up to 60% of rainfall events ≥2 mm. Multiple approaches consistently show that PF is more likely to occur with increased peak rainfall intensity, finer textured material, low soil moisture variability, humid climate, and higher net primary productivity. This suggests that PF patterns could shift with projected climate changes, increasing uncertainty in predictions of groundwater recharge, water quality, and streamflow generation. Plain Language Summary Water can bypass part of the soil's matrix through a process called preferential flow (PF). This quick transport of water through the soil brings with it nutrients and contaminants and eventually makes it to groundwater and streams. To ensure ample amounts of good quality groundwater and surface water we need to understand when and where PF occurs. We inferred when PF occurred at 40 different sites across 17 ecoregions in the USA using soil moisture and rainfall data. We found that PF happened at all sites and in up to 60% of rainfall events ≥2 mm. Preferential flow was most likely at sites with high rainfall intensities, high clay content in soils, low variability in soil moisture, and high vegetation productivity. As rainfall intensities are predicted to increase due to climate change and vegetation becomes more productive, PF occurrence becomes more important for predicting groundwater recharge, water quality, and streamflow generation. Key Points Preferential flow (PF) is ubiquitous across the USA and occurs in up to 60% of all rainfall events ≥2 mm Rainfall intensity, soil texture, and antecedent soil moisture emerge as critical in generating PF across diverse ecoregions Two different PF detection approaches show similar relationships between key drivers and occurrence of PF
InSAR-based detection method for mapping and monitoring slow-moving landslides in remote regions with steep and mountainous terrain: An application to Nepal
Mapping and monitoring landslides in remote areas with steep and mountainous terrain is logistically challenging, expensive, and time consuming. Yet, in order to mitigate hazards and prevent loss of life in these areas, and to better understand landslide processes, high-resolution measurements of landslide activity are necessary. Satellite-based synthetic aperture radar interferometry (InSAR) provides millimeter-scale measurements of ground surface deformation that can be used to identify and monitor landslides in remote areas where ground-based monitoring techniques are not feasible. Here we present a novel InSAR deformation detection approach, which uses double difference time-series with local and regional spatial filters and pixel clustering methods to identify and monitor slow-moving landslides without making a priori assumptions of the location of landslides. We apply our analysis to freely available Copernicus Sentinel-1 satellite data acquired between 2014 and 2017 centered on the Trishuli River drainage basin in Nepal. We found a minimum of 6 slow-moving landslides that all occur within the Ranimatta lithologic formation (phyllites, metasandstones, meta basics). These landslides have areas ranging from 0.39 to 1.66 sq.km and long-term dry-season displacement rates ranging from 2.1 to 8.8 cm/yr. Due to periods of low coherence during the monsoon season (June – September) each year, and following the 25 April 2015 Mw7.8 Gorkha earthquake, our time series analysis is limited to the 2014-2015 and 2016-2017 dry seasons (September - May). We found that each of the landslides displayed slightly higher rates during the 2014 period, likely as a result of higher cumulative rainfall that fell during the 2014 monsoon season. Although we do not have high quality InSAR data to show the landslide evolution directly following the Gorkha earthquake, the similar rates of movement before (2014-2015) and after (2016-2017) Gorkha suggest the earthquake had negligible long-term impact on these landslides. Our findings highlight the potential for region-wide mapping of slow-moving l and slides using freely available remote sensing data in remote areas such as Nepal and future work will benefit from expanding our methodology to other regions around the world.
Revisiting the SGTE lattice stability of bcc aluminum
The CALPHAD framework rests on the ability to assign well-defined free energies to all phases, including mechanically unstable ones. Given the experimental difficulties associated with the latter, researchers have turned to computational methods to obtain a theoretically justified definition of the free energy of mechanically unstable phases. Recently, a method called “inflection detection” has been shown to yield free energies that are broadly consistent with the current SGTE (Scientific Group Thermodata Europe) standard for pure elements, which were obtained through an extrapolation of stable solid solutions free energies towards unstable end members. Despite this general agreement, apparent failures for a few elements stand out, notably for the bcc–fcc enthalpy difference for the common element Al. Furthermore we revisit the definition of the bcc Al enthalpy and show that a careful CALPHAD-based analysis of enthalpy trends in five different mechanically stable binary solid solutions in fact does agree very well with the inflection-detection approach.
Octupole moment driven free charge generation in partially chlorinated subphthalocyanine for planar heterojunction organic photodetectors
In this study, high-performance organic photodetectors are presented which utilize a pristine chlorinated subphthalocyanine photoactive layer. Optical and optoelectronic analyses indicate that the device photocurrent is primarily generated through direct charge generation within the chlorinated subphthalocyanine layer, rather than exciton separation at layer interfaces. Molecular modelling suggests that this direct charge generation is facilitated by chlorinated subphthalocyanine high octupole moment (-80 DÅ 2 ), which generates a 200 meV shift in molecular energetics. Increasing the thickness of chlorinated subphthalocyanine leads to faster response time, correlated with a decrease in trap density. Notably, photodetectors with a 50 nm thick chlorinated subphthalocyanine photoactive layer exhibit detectivities approaching 10 13 Jones, with a dark current below 10 -7 A cm -2 up to -5 V. Based on these findings, we conclude that high octupole moment molecular semiconductors are promising materials for high-performance organic photodetectors employing single-component photoactive layer.
Spin-informed universal graph neural networks for simulating magnetic ordering
The screening and discovery of magnetic materials are hindered by the computational cost of first-principles density-functional theory (DFT) calculations required to find the ground state magnetic ordering. Although universal machine-learning interatomic potentials (uMLIPs), also known as atomistic foundation models, offer high-fidelity models of many atomistic systems with significant speedup, they currently lack the inputs required for predicting magnetic ordering. In this work, we present a data-efficient, spin-informed graph neural network framework that incorporates spin degrees of freedom as inputs and preserves physical symmetries, extending the functionality of uMLIPs to simulate magnetic orderings. This framework speeds up DFT calculations through better initial guesses for magnetic moments, determines the ground-state ordering of bulk materials and even generalizes to magnetic ordering in surfaces. Furthermore, we implement a closed-loop anomaly detection approach that effectively addresses the classic "chicken-and-egg" problem of creating a high-quality dataset while developing a uMLIP, unearthing anomalies in large benchmark datasets and boosting model accuracy.
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, for this work, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.
Search for new physics in final states with semivisible jets or anomalous signatures using the ATLAS detector
A search is presented for hadronic signatures of beyond the Standard Model (BSM) physics, with an emphasis on signatures of a strongly coupled hidden dark sector accessed via resonant production of a 𝑍′ mediator. The ATLAS experiment dataset collected at the Large Hadron Collider from 2015 to 2018 is used, consisting of proton-proton collisions at $\sqrt{𝑠}$ = 13 TeV and corresponding to an integrated luminosity of 140 fb −1 . The 𝑍′ mediator is considered to decay to two dark quarks, which each hadronize and decay to showers containing both dark and Standard Model particles, producing a topology of interacting and noninteracting particles within a jet known as “semivisible.” Machine learning methods are used to select these dark showers and reject the dominant background of mismeasured multijet events, including an anomaly detection approach to preserve broad sensitivity to a variety of BSM topologies. A resonance search is performed by fitting the transverse mass spectrum based on a functional form background estimation. No significant excess over the expected background is observed. Results are presented as limits on the production cross section of semivisible jet signals, parametrized by the fraction of invisible particles in the decay and the 𝑍′ mass, and by quantifying the significance of any generic Gaussian-shaped mass peak in the anomaly region.
A High-Fidelity Cyber-Physical Testbed-Based Benchmarking Dataset For Testing Operational Technology Specific Intrusion Detection Systems
Quality datasets serve a critical purpose in cyber security research. Data is needed to understand system behavior and develop security controls to protect critical systems. However, for critical infrastructure operational environments there is a lack of available datasets to study because of the high cost and specialized capabilities necessary to generate them. This paper documents the development of a dataset of high fidelity hardware in the loop laboratory simulated models of electric and natural gas distribution systems with real cyber attack test cases. A deep dive discussion for the experimental setup and controls for generating the data is provided along with observations from using the data in evaluating intrusion detection approaches.
2020 IEEE PES Innovative Smart Grid Technologies Europe (ISGT-Europe)
Recent proliferation of distributed energy sources in distribution or sub-transmission systems necessitates close monitoring of these three-phase power grids which typically operate under unbalanced loading conditions. Unlike the transmission systems where the network equations are commonly based on the positive sequence component models, a detailed three phase model will have to be used in implementing network applications for these systems. In the specific case of the state estimator, where measurement and parameter errors may bias the solution, bad data and parameter error detection algorithms should also be incorporated. Implementing the state estimator and error detection algorithms for three-phase systems impose additional computational burden and modifications to the state estimation code. This paper proposes a practical solution to avoid these issues by using synchronized phasor measurements and modal decoupling. The previously developed parameter error detection algorithm based on the normalized Lagrange multipliers (NLM) test is applied to the measurements independently in each mode in parallel, not only saving CPU time but also avoiding new code development for a three-phase estimator. Different parameter error scenarios are created and tested to verify the effectiveness of the proposed error detection approach.
Toward Polydisperse Flows With MFIX-EXA
In the presence of large size disparities, single-grid neighbor search algorithms lead to inflated neighbor lists that significantly degrade the performance of Lagrangian particle solvers. If Eulerian–Lagrangian (EL) frameworks are to remain performant when simulating realistic systems, improved neighbor detection approaches must be adopted. To this end, we consider the application of a multigrid neighbor search (MGNS) algorithm in the mfix-exa software package, an exascale EL solver built upon the AMReX library. Here, details regarding the implementation and verification of MGNS are provided along with speedup curves for a bidisperse mixing layer. MGNS is shown to yield up to 15$\times$ speedup on CPU and 6$\times$ speedup on GPU for the problems considered here. The mfix-exa software is then validated for a variety of polydisperse flows. Finally, a brief discussion is given for how dynamic MGNS may be completed, with application to spatially varying particle size distributions.
Multi-Artifact Analysis of Self-Admitted Technical Debt in Scientific Software
Context: Self-admitted technical debt (SATD) occurs when developers acknowledge shortcuts in code. In scientific software (SSW), such debt poses unique risks to the validity and reproducibility of results. Objective: This study aims to identify, categorize, and evaluate scientific debt, a specialized form of SATD in SSW, and assess the extent to which traditional SATD categories capture these domain-specific issues. Method: We conduct a multi-artifact analysis across code comments, commit messages, pull requests, and issue trackers from 23 open-source SSW projects. We construct and validate a curated dataset of scientific debt, develop a multi-source SATD classifier to guide SATD management, and conduct a practitioner validation to assess the practical relevance of scientific debt. Results: Our classifier performs strongly across 900,358 artifacts from 23 SSW projects. SATD is most prevalent in pull requests and issue trackers, underscoring the value of multi-artifact analysis. Models trained on traditional SATD often miss scientific debt, emphasizing the need for its explicit detection in SSW. Practitioner validation confirmed that scientific debt is both recognizable and useful in practice. Conclusions: Scientific debt represents a unique form of SATD in SSW that that is not adequately captured by traditional categories and requires specialized identification and management. Our dataset, classification analysis, and practitioner validation results provide the first formal multi-artifact perspective on scientific debt, highlighting the need for tailored SATD detection approaches in SSW.
Blocking Simulations in GFDL GCMs for CMIP5 and CMIP6
Abstract The frequency of atmospheric blocking has been largely underestimated by general circulation models (GCMs) participating in the Coupled Model Intercomparison Project (CMIP). Errors in the onset, persistence, barotropicity, geographical preference, seasonality, intensity, and moving speed of global blocking were diagnosed in 10 Geophysical Fluid Dynamics Laboratory (GFDL) GCMs for recent CMIP5 and CMIP6 using a detection approach that combines zonal eddies and the reversal of zonal winds. The blocking frequency, similar at 500 and 250 hPa, is underestimated by 50% in the Atlantic–Europe region during December–February but is overestimated by 60% in the Pacific–North America region during that season and by 70% in the southwest Pacific during July–August. These blocking biases at 500 hPa were investigated in the five CMIP6 models that showed improvements over the CMIP5 versions. The Atlantic–Europe underestimate corresponds to lower instantaneous blocking rates, lower persistent blocking rates, and higher persistent stationary ridge rates; the number of blocks with a duration of 4–5 days is only 40%–65% of that in observations. In contrast, the overestimate consists of excessive blocks with a duration longer than 12 days in the Pacific–North America and up to twice as many 4–6-day events in the southwest Pacific. Simulated December–February blocks up to 12 days in the Pacific–North America region tend to be stronger and to move more slowly than those in observations. Diagnostic sensitivity tests indicated that the zonal mean and zonal eddy components of the mean state play a key role, as replacing each with that of observations substantially reduced many of the outstanding biases in these GCMs.
Frequency-bin photonic quantum information
Discrete frequency modes, or bins, present a blend of opportunities and challenges for photonic quantum information processing. Frequency-bin-encoded photons are readily generated by integrated quantum light sources, naturally high-dimensional, stable in optical fiber, and massively parallelizable in a single spatial mode. Yet quantum operations on frequency-bin states require coherent and controllable multifrequency interference, making them significantly more challenging to manipulate than more traditional spatial degrees of freedom. In this mini-review, we describe recent developments that have transformed these challenges and propelled frequency bins forward. Focusing on sources, manipulation schemes, and detection approaches, we introduce the basics of frequency-bin encoding, summarize the state of the art, and speculate on the field’s next phases. Given the combined progress in integrated photonics, high-fidelity quantum gates, and proof-of-principle demonstrations, frequency-bin quantum information is poised to emerge from the lab and leave its mark on practical quantum information processing—particularly in networking where frequency bins offer unique tools for multiplexing, interconnects, and high-dimensional communications.
PIPER: Performance Insight for Programmers and Exascale Runtimes (Final Technical Report)
This project concentrated on the development of novel performance tools and analysis techniques for large scale parallel systems and applications, eventually targeting exascale platforms. Activities conducted included work to novel root cause detection approaches and an auto-tuning framework for parallel systems. The work has led to several software solutions, which are available as open source.