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At least 865 records · Page 48

Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge

The continually expanding distributed global compendium of biomedical knowledge is diffuse, heterogeneous and huge, posing a serious challenge for biomedical researchers in knowledge harvesting: accessing, compiling, integrating and interpreting data, information and knowledge. In order to accelerate research towards effective medical treatments and optimizing health, it is critical that efficient and automated tools for identifying key research concepts and their experimentally discovered interrelationships are developed. As an activity within the feasibility phase of a project called “Translator” (https://ncats.nih.gov/translator) funded by the National Center for Advancing Translational Sciences (NCATS) to develop a biomedical science knowledge management platform, we designed a Representational State Transfer (REST) web services Application Programming Interface (API) specification, which we call a Knowledge Beacon. Knowledge Beacons provide a standardized basic API for the discovery of concepts, their relationships and associated supporting evidence from distributed online repositories of biomedical knowledge. This specification also enforces the annotation of knowledge concepts and statements to the NCATS endorsed the Biolink Model data model and semantic encoding standards (https://biolink.github.io/biolink-model/). Implementation of this API on top of diverse knowledge sources potentially enables their uniform integration behind client software which will facilitate research access and integration of biomedical knowledge.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Integrated Research Infrastructure Architecture Blueprint Activity (Final Report 2023)

The complexity of scientific pursuits is increasing rapidly with aspects that require dynamic integration of experiment, observation, theory, modeling, simulation, visualization, machine learning (ML), artificial intelligence (AI), and analysis. Research projects across the Department of Energy (DOE) are increasingly data and compute intensive. Innovative research teams are accelerating the pace of discovery by using high-performance computational and data tools in their research workflows and leveraging multiple research infrastructures. Additionally, several recent high-level U.S. government reports underscore the necessity of a new advanced computing ecosystem for international competitiveness and national security. International competitors are moving forward with major research infrastructure integration efforts that seek to capture a competitive advantage in the global innovation race. Owing to its unparalleled constellation of world-class experimental and observational facilities and high-performance and extreme-scale computational, data, and networking infrastructure, DOE is positioned to be a global leader in this new era of integrated science. However, this new integration paradigm will demand continuing evolution to ensure the U.S. remains a global leader in research and innovation. The DOE Office of Science (SC) has seized on the strategic importance of integration and has adopted a vision for Integrated Research Infrastructure (IRI): To empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation. To respond to the evolving computational requirements of research and the competitive international innovation landscape, experimental facilities could be connected with high performance computing resources for near real-time analysis, and resources should be provided for merging enormous and diverse data for AI/ML techniques and analysis.

97 MATHEMATICS AND COMPUTING↗

Informed Critical Mineral Recovery from Fossil Energy Waste Feedstocks

Critical minerals (CM), such as rare earth elements (REE), cobalt, nickel, and lithium, have important uses in modern energy and technologies, yet are vulnerable to potential supply chain disruptions. One potential domestic CM source is fossil energy wastes, such as coal combustion ash, acid mine drainage (AMD) and treatment solids (AMD solids), and Oil and Gas (O&G) drilling wastes (drill cuttings and produced waters). CM recovery from these feedstocks is promising due to their abundant quantity and fast availability as waste products. To develop informed and effective CM recovery, DOE’s National Energy Technology Laboratory (NETL) have collected and analyzed CM data for aforementioned fossil energy wastes, and utilized advanced geochemical characterization (e.g., synchrotron microprobe, sequential extraction and geochemical modeling) to identify the CM speciation and binding environments. Novel methods that recover multiple CMs while co-producing other valuable byproducts from these feedstocks have been developed. Successful examples include: (1) the discovery of easily mobile REE phases in Ca-rich coal combustion ash resulted in a patented REE recovery process from the ash feedstock while producing zeolite sorbents from the extraction wastes; (2) the successful identification of REE/Co/Ni/Zn hosting phases in acid mine drainage treatment solids (AMD solids) has informed the sequential CM recovery from AMD solids and has inspired lithium sorbent development from the extraction wastes; (3) the recovery potential of Li and other CMs in O&G produced waters and drill cuttings has been explored while the extraction residuals have been demonstrated to support plant growth as soil supplements. The innovations driven by characterization information have the potential to maximize CM recovery revenue, offset the cost of waste management and wastewater treatments while reducing the cost and environmental footprint of CM extraction.

characterization and extraction of rare earth elem↗

Uncovering Structure–Conductivity Relationships in Anion Exchange Membranes (AEMs) Using Interpretable Machine Learning

Anion exchange membranes (AEMs) play a vital role in the performance of water electrolyzers and fuel cells, yet their discovery and optimization remain challenging due to the complexity of structure–property relationships. In this study, we introduce a machine learning framework that leverages conditional graph neural networks (cGNNs) and descriptor-based models and a hybrid graph neural network (HGARE) to predict and interpret ionic conductivity. The descriptor-based pipeline employs principal component analysis (PCA), ablation, and SHAP analysis to identify factors governing anion conductivity, revealing electronic, topological, and compositional descriptors as key contributors. Beyond prediction, dimensionality reduction and clustering are performed by employing t-SNE and KMeans as well as SOM, which reveal distinct membranes clusters, some of which were enriched with high anion conductivity. Among graph-based approaches, the graph convolutional (GCN) achieved strong predictive performance, while the Hybrid Graph Autoencoder-Regressor Ensemble (HGARE) achieved the highest accuracy. Additionally, atom-level saliency maps from GCN provide spatial explanations for conductive behavior, revealing the importance of polarizable and flexible regions. This work contributes to the accelerated and data-driven design of high-performance AEMs.

Naghshnejad, Pegah [Department of Chemical Enginee↗

Suspended and Restored Activities of a Nearby Supermassive Black Hole

The discovery of spectral type transition of active galactic nuclei (AGNs), the so-called “changing-look” (CL) phenomenon, challenges the widely accepted AGN paradigm, not only in the orientation-based unified model, but also in the standard disk model. In past decades, only a couple of nearby repeat changing-look active galactic nuclei (CL-AGNs) have been identified. Here we report spectroscopic observations of UGC 3223 over the course of 18 yr, from 2001 onwards. Combining the spectrum taken in 1987 by Stirpe, we have witnessed its type transitions from 1.5→2.0→1.8 over 32 yr, and captured a long-lived (at least 10 yr) thorough “turn-off” state with a spectrum typical of a Seyfert 2 galaxy. The long-term thorough turn-off state probably suggests a once-dormant and an awakening central engine in UGC 3223. We argue that the (dis)appearance of the broad Balmer emission lines can be explained by the disk–wind broad-line region model given the evolution of the calculated Eddington ratio of accretion of the supermassive black hole.

79 ASTRONOMY AND ASTROPHYSICS↗

A New Way to Discover Strong Gravitational Lenses: Pairwise Spectroscopic Search from DESI DR1

We present a new method to search for strong gravitational-lensing systems by pairing spectra that are close together on the sky in a spectroscopic survey. We visually inspect 26,621 spectra in the Dark Energy Spectroscopic Instrument (DESI) Data Release 1 that are selected in this way. We further inspect the 11,848 images corresponding to these spectra in the DESI Legacy Imaging Surveys Data Release 10, and obtain 2046 conventional strong gravitational lens candidates, of which 1906 are new. This constitutes the largest sample of lens candidates identified to date in spectroscopic data. Besides the conventional candidates, we identify a new class of systems that we term “dimple lenses.” These systems have a low-mass foreground galaxy as a lens, typically smaller in angular extent and fainter compared with the lensed background source galaxy, producing subtle surface brightness indentations in the latter. We report the discovery of 318 of these “dimple lens” candidates. We suspect that these represent dwarf galaxy lensing. With follow-up observations, they could offer a new avenue to test the cold dark matter model by probing their mass profiles, stellar mass–halo mass relation, and halo mass function for M Halo ≲ 10 13 M ⊙ . Thus, in total, we report 2164 new lens candidates. Our method demonstrates the power of pairwise spectroscopic analysis and provides a pathway complementary to imaging-based and single-spectrum lens searches.

Hsu, Yuan-Ming 許淵明 [National Taiwan University, Ta↗

Discovery and characterization of five new eclipsing AM CVn systems

ABSTRACT AM CVn systems are ultra-compact, hydrogen-depleted, and helium-rich, accreting binaries with degenerate or semidegenerate donors. We report the discovery of five new eclipsing AM CVn systems with orbital periods of 61.5, 55.5, 53.3, 37.4, and 35.4 min. These systems were discovered by searching for deep eclipses in the Zwicky Transient Facility (ZTF) light curves of white dwarfs selected using Gaia parallaxes. We obtained phase-resolved spectroscopy to confirm that all systems are AM CVn binaries, and we obtained high-speed photometry to confirm the eclipse and characterize the systems. The spectra show double-peaked H e lines but also show metals, including K and Zn, elements that have never been detected in AM CVn systems before. By modelling the high-speed photometry, we measured the mass and radius of the donor star, potentially constraining the evolutionary channel that formed these AM CVn systems. We determined that the average mass of the accreting white dwarf is ≈0.8 M⊙, and that the white dwarfs in long-period systems are hotter than predicted by recently updated theoretical models. The donors have a high entropy and are a factor of ≈2 more massive compared to zero-entropy donors at the same orbital period. The large donor radius is most consistent with H e-star progenitors, although the observed spectral features seem to contradict this. The discovery of five new eclipsing AM CVn systems is consistent with the known observed AM CVn space density and estimated ZTF recovery efficiency.

79 ASTRONOMY AND ASTROPHYSICS↗

Advancing AI-Driven Analysis in X-ray Absorption Spectroscopy: Spectral Domain Mapping and Universal Models

In recent years, rapid progress has been made in developing artificial intelligence (AI) and machine learning (ML) methods for X-ray absorption spectroscopy (XAS) analysis. Compared to traditional XAS analysis methods, AI/ML approaches offer dramatic improvements in efficiency and help eliminate human bias. To advance this field, we advocate an AI-driven XAS analysis pipeline that features several interconnected key building blocks: benchmarks, workflows, databases, and AI/ML models. Specifically, we present two case studies for XAS ML. In the first study, we demonstrate the importance of reconciling the discrepancies between simulation and experiment using spectral domain mapping (SDM). Our ML model, which is trained solely on simulated spectra, predicts an incorrect oxidation state trend for Ti atoms in a combinatorial zinc titanate film. After transforming the experimental spectra into a simulation-like representation using SDM, the same model successfully recovers the correct oxidation state trend. In the second study, we explore the development of universal XAS ML models that are trained on the entire periodic table, which enables them to leverage common trends across elements. Looking ahead, we envision that an AI-driven pipeline can unlock the potential of real-time XAS analysis to accelerate scientific discovery.

36 MATERIALS SCIENCE↗

Multiwavelength study of OT 081: broadband modelling of a transitional blazar

ABSTRACT OT 081 is a well-known, luminous blazar that is remarkably variable in many energy bands. We present the first broadband study of the source, which includes very high energy (VHE, $E\gt $ 100 GeV) $\gamma$-ray data taken by the MAGIC (Major Atmospheric Gamma-ray Imaging Cherenkov telescopes) and H.E.S.S. (High Energy Stereoscopic System) imaging Cherenkov telescopes. The discovery of VHE $\gamma$-ray emission happened during a high state of $\gamma$-ray activity in July 2016, observed by many instruments from radio to VHE $\gamma$-rays. We identify four states of activity of the source, one of which includes VHE $\gamma$-ray emission. Variability in the VHE domain is found on daily time-scales. The intrinsic VHE spectrum can be described by a power law with index $3.27\pm 0.44_{\rm stat}\pm 0.15_{\rm sys}$ (MAGIC) and $3.39\pm 0.58_{\rm stat}\pm 0.64_{\rm sys}$ (H.E.S.S.) in the energy range of 55–300 and 120–500 GeV, respectively. The broadband emission cannot be successfully reproduced by a simple one-zone synchrotron self-Compton model. Instead, an additional external Compton component is required. We test a lepto-hadronic model that reproduces the data set well and a proton-synchrotron-dominated model that requires an extreme proton luminosity. Emission models that are able to successfully represent the data place the emitting region well outside of the broad-line region to a location at which the radiative environment is dominated by the infrared thermal radiation field of the dusty torus. In the scenario described by this flaring activity, the source appears to be a flat spectrum radio quasar (FSRQ), in contrast with past categorizations. This suggests that the source can be considered to be a transitional blazar, intermediate between BL Lac and FSRQ objects.

Abe, H.↗

The confluence of machine learning and multiscale simulations

Multiscale modeling has a long history of use in structural biology, as computational biologists strive to overcome the time- and length-scale limits of atomistic molecular dynamics. Contemporary machine learning techniques, such as deep learning, have promoted advances in virtually every field of science and engineering and are revitalizing the traditional notions of multiscale modeling. Deep learning has found success in various approaches for distilling information from fine-scale models, such as building surrogate models and guiding the development of coarse-grained potentials. However, perhaps its most powerful use in multiscale modeling is in defining latent spaces that enable efficient exploration of conformational space. In conclusion, this confluence of machine learning and multiscale simulation with modern high-performance computing promises a new era of discovery and innovation in structural biology.

59 BASIC BIOLOGICAL SCIENCES↗

Interwoven magnetic kagome metal overcomes geometric frustration

Magnetic kagome materials provide a platform for exploring magneto-transport phenomena, symmetry breaking and charge ordering driven by the intricate interplay among electronic structure, topology and magnetism. Yet geometric frustration in conventional kagome magnets limits their tunability. Here we propose a design strategy for interweaving quasi-one-dimensional magnetic Tb zigzag chains with non-magnetic Ti-based kagome bilayers in TbTi 3 Bi 4 . Comprehensive spectroscopic analyses reveal coexisting elliptical-spiral magnetic and spin-density-wave orders accompanied by a large ~90 meV band-folding gap. The combined magnetic and electronic state leads to a giant anomalous Hall conductivity of 10 5 Ω −1 cm −1 , which exceeds that observed in frustrated kagome analogues. These results establish TbTi 3 Bi 4 as a model system of magnetic kagome metals with strong electron–magnetism interactions and underscore the necessity of interweaving designed magnetic and charge layers separately to achieve tunable transport properties. This design strategy will enable the discovery of emergent quantum states and next-generation electronic materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Inverse methods for design of soft materials

Functional soft materials, comprising colloidal and molecular building blocks that self-organize into complex structures as a result of their tunable interactions, enable a wide array of technological applications. Inverse methods provide a systematic means for navigating their inherently high-dimensional design spaces to create materials with targeted properties. Furthermore, while multiple physically motivated inverse strategies have been successfully implemented in silico, their translation to guiding experimental materials discovery has thus far been limited to a handful of proof-of-concept studies. In this perspective, we discuss recent advances in inverse methods for design of soft materials that address two challenges: (1) methodological limitations that prevent such approaches from satisfying design constraints and (2) computational challenges that limit the size and complexity of systems that can be addressed. Strategies that leverage machine learning have proven particularly effective, including methods to discover order parameters that characterize complex structural motifs and schemes to efficiently compute macroscopic properties from the underlying structure. We also highlight promising opportunities to improve the experimental realizability of materials designed computationally, including discovery of materials with functionality at multiple thermodynamic states, design of externally directed assembly protocols that are simple to implement in experiments, and strategies to improve the accuracy and computational efficiency of experimentally relevant models.

36 MATERIALS SCIENCE↗

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a–RNA–DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.

59 BASIC BIOLOGICAL SCIENCES↗

Entanglement transitions from restricted Boltzmann machines

The search for novel entangled phases of matter has lead to the recent discovery of a new class of “en- tanglement transitions,” exemplified by random tensor networks and monitored quantum circuits. Most known examples can be understood as some classical ordering transitions in an underlying statistical mechanics model, where entanglement maps onto the free-energy cost of inserting a domain wall. In this paper we study the possibility of entanglement transitions driven by physics beyond such statistical mechanics mappings. Motivated by recent applications of neural-network-inspired variational Ansätze, we investigate under what conditions on the variational parameters these Ansätze can capture an entanglement transition. We study the entanglement scaling of short-range restricted Boltzmann machine (RBM) quantum states with random phases. For uncorrelated random phases, we analytically demonstrate the absence of an entanglement transition and reveal subtle finite-size effects in finite-size numerical simulations. Introducing phases with correlations decaying as 1/r α in real space, we observe three regions with a different scaling of entanglement entropy depending on the exponent α. We study the nature of the transition between these regions, finding numerical evidence for critical behavior. Furthermore, our work establishes the presence of long-range correlated phases in RBM-based wave functions as a required ingredient for entanglement transitions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

FiXR : a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

Ab initio reconstruction methods have revolutionized the capabilities of small-angle X-ray scattering (SAXS), allowing the data-driven discovery of previously unknown molecular conformations, exploiting optimization heuristics and assumptions behind the composition of globular molecules. While these methods have been successful for the analysis of small particles, their impact on fibrillar assemblies has been more limited. The micrometre-range size of these assemblies and the complex interaction of their periodicities in their scattering profiles indicate that the discovery of fibril structures from SAXS measurements requires novel approaches beyond extending existing tools for molecular discovery. In this work, it is proposed to use SAXS measurements, together with diffraction theory, to infer the electron distribution of the average cross-section of a fiber. This cross-section is modeled as a discrete electron density with continuous support, allowing representations beyond binary distributions. Additional constraints, such as non-negativity or smoothness/connectedness, can also be added to the framework. The proposed approach is tested using simulated SAXS data from amyloid β fibril models and using measured data of Tobacco mosaic virus from SAXS experiments, recovering the geometry and density of the cross-sections in all cases. The approach is further tested by analyzing SAXS data from different amyloid β fibril assemblies, with results that are in agreement with previously proposed models from cryo-EM measurements. The limitations of the proposed method, together with an analysis of the robustness of the method and the combination with different experimental sources, are also discussed.

Biochemistry & Molecular Biology↗

Review of Landscaping Equipment Vibration Risk Exposure, LLNL Site 200 (Various Locations), Whole Body Vibration Seated and Standing Mowers

WBV (Whole-Body Vibration) for operators of seated and standing lawn mowers was conducted during landscape activities from April 2019 through August 2019 at various locations around LLNL Site 200. Mowing is generally performed by each landscaper for 2-3 days every other week with a maximum duration of 3-5 hours each day. On mowing days, other tasks are performed for the remainder of the day that do not expose the worker to WBV such as irrigation, blowing, or sweeping. The mowing terrain at LLNL is variable with typical reported conditions such as gopher holes, exposed tree roots, quick turns, normal and high growth, weeds, and mushy/wet ground that can result in jolts to the mower operator. The Larson Davis HVM200 seat pad with tri-axial accelerometer was used for monitoring workers. For the seated mowers, the HVM200 seat pad with tri-axial accelerometer was placed on the seat between the user and seat pan of the mower. For standing mowers, the seat pad with tri-axial accelerometer was wrapped with Dycem (for seat pad protection) and placed directly on top of the mower deck and underneath the end-user’s right foot. Monitoring for WBV was conducted while operators used different types, makes, and models of mowers. A total of sixteen samples were collected from the operators of seated mower and 6 samples were collected from operators of standing mower. This initial data sampling was part of a discovery phase to identify if WBV exposure met the 2016 ACGIH TLVs (Threshold Limit Values). This initial data identified that workers operating the mowers do not exceed either the TLV or Action Level (AL) for Weighted Acceleration Levels (A(8)) but typically exceed the Vibration Dose Value (VDV) lower boundary for the standing mowers.

59 BASIC BIOLOGICAL SCIENCES↗

RAVEN User Manual

RAVEN is a generic software framework to perform parametric and probabilistic analysis based on the response of complex system codes. The initial development was aimed to provide dynamic risk analysis capabilities to the Thermo-Hydraulic code RELAP-7, currently under development at the Idaho National Laboratory (INL). Although the initial goal has been fully accomplished, RAVEN is now a multi-purpose probabilistic and uncertainty quantification platform, capable to agnostically communicate with any system code. This agnosticism includes providing Application Programming Interfaces (APIs). These APIs are used to allow RAVEN to interact with any code as long as all the parameters that need to be perturbed are accessible by inputs files or via python interfaces. RAVEN is capable of investigating the system response, and investigating the input space using Monte Carlo, Grid, or Latin Hyper Cube sampling schemes, but its strength is focused to- ward system feature discovery, such as limit surfaces, separating regions of the input space leading to system failure, using dynamic supervised learning techniques. The development of RAVEN has started in 2012, when, within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the need to provide a modern risk evaluation framework became stronger. RAVEN principal assignment is to provide the necessary software and algorithms in order to employ the concept developed by the Risk Informed Safety Margin Characterization (RISMC) program. RISMC is one of the pathways defined within the Light Water Reactor Sustainability (LWRS) program. In the RISMC approach, the goal is not just the individuation of the frequency of an event potentially leading to a system failure, but the closeness (or not) to key safety-related events. Hence, the approach is interested in identifying and increasing the safety margins related to those events. A safety margin is a numerical value quantifying the probability that a safety metric (e.g. for an important process such as peak pressure in a pipe) is exceeded under certain conditions. The initial development of RAVEN has been focused on providing dynamic risk assessment capability to RELAP-7, currently under development at the INL and, likely, future replacement of the RELAP5-3D code. Most the capabilities that have been implemented having RELAP-7 as principal focus are easily deployable for other system codes. For this reason, several side activates are currently ongoing for coupling RAVEN with soft- ware such as RELAP5-3D, etc. The aim of this document is the explanation of the input requirements, focalizing on the input structure.

97 MATHEMATICS AND COMPUTING↗

The HST See Change Program. I. Survey Design, Pipeline, and Supernova Discoveries*

The See Change survey was designed to make z > 1 cosmological measurements by efficiently discovering high-redshift Type Ia supernovae (SNe Ia) and improving cluster mass measurements through weak lensing. This survey observed twelve galaxy clusters with the Hubble Space Telescope (HST) spanning the redshift range z = 1.13–1.75, discovering 57 likely transients and 27 likely SNe Ia at z ~ 0.8–2.3. As in similar previous surveys, this proved to be a highly efficient use of HST for supernova observations; the See Change survey additionally tested the feasibility of maintaining, or further increasing, the efficiency at yet higher redshifts, where we have less detailed information on the expected cluster masses and star formation rates. Furthermore, we find that the resulting number of SNe Ia per orbit is a factor of ~8 higher than for a field search, and 45% of our orbits contained an active SN Ia within 22 rest-frame days of peak, with one of the clusters by itself yielding 6 of the SNe Ia. We present the survey design, pipeline, and supernova discoveries. Novel features include fully blinded supernova searches, the first random forest candidate classifier for undersampled IR data (with a 50% detection threshold within 0.05 mag of human searchers), real-time forward-modeling photometry of candidates, and semi-automated photometric classifications and follow-up forecasts. We also describe the spectroscopic follow-up, instrumental in measuring host galaxy redshifts. The cosmology analysis of our sample will be presented in a companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗