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At least 757 records · Page 42

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Abstract Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

60 APPLIED LIFE SCIENCES↗

Unlocking Metamaterials At The Macro Scale (CRADA Final Report)

This project was part of the Cyclotron Road program, which supports scientific entrepreneurs in their efforts to commercialize novel technologies with potential to address energy, manufacturing and climate related issues. The participants' technology is a lightweight cellular material system which could be applied to a range of products and markets and offer benefits of reduced weight, cost, waste, and carbon footprint. The objective of the project was to investigate potential opportunities and de-risk technical and market barriers in pursuit of successful commercialization. This project’s purpose was to find market pathways and technical roadmaps for commercializing the lightweight cellular material technology. The main problems to overcome are the risks in both tech and market. On the technical side, performance, weight, cost and speed of manufacturing, and other scaleup problems needed to be addressed. On the market side, the challenges included finding product/market fit, developing business models and go to market strategies, and developing commercial relationships within various industries. Our approach typically started with market analysis, in order to identify potential applications where our technology could solve problems and address pain points. To do this, we performed customer discovery, interviewing hundreds of industry stakeholders along all parts of the value chain for a given product or industry. From here, we would develop technoeconomic models which combined aspects of numerical modeling for structural and mechanical performance based on criteria from customers or industry guidelines such as stiffness, strength, weight, and other physical properties. Then, this would be combined with detailed cost models to translate the engineering solution into a manufacturable, scalable product. The challenge here was to have equal or better performance at lower cost and higher speed than existing solutions.

36 MATERIALS SCIENCE↗

Modular Autonomous Experimentation for Biological Applications (Full Report)

The Modular Autonomous Research System (MARS) was developed to address the pressing need for faster, more reliable, and more adaptable scientific discovery. Traditional experimentation is limited by manual labor, long cycle times, and fragmented data streams, which constrain the ability to explore complex chemical and materials design spaces. To overcome these limitations, we created an integrated, modular platform that combines laboratory robotics, diverse measurement instruments, and a central data infrastructure with artificial intelligence–driven decision-making. The system links liquid handling robots, robotic arms, and optical plate readers into a closed loop where experiments are executed automatically, data is analyzed in real time, and subsequent experimental conditions are adaptively chosen to maximize information gain. Over the course of the project, MARS was validated on two primary test cases—spectroscopic metal–ligand binding assays and peptide-directed mineralization—which highlighted the system’s ability to handle uncertainty and variability in experimental measurements. To further demonstrate modularity and extensibility, we also established additional testbeds in electrochemistry for catalyst discovery and electrolyte formulation for advanced batteries. The results show that MARS can reliably conduct autonomous campaigns with minimal human intervention, adapt to distinct scientific domains, and provide a scalable model for future self-driving laboratories. This work establishes new capabilities for modular, uncertainty-aware automation and directly supports the need for advanced, data-driven research platforms capable of accelerating discovery across a wide range of scientific and national security missions.

59 BASIC BIOLOGICAL SCIENCES↗

Interpretable Deep Learning for Advancing Field-Enhanced Catalysis

This DOE Early Career project developed a physics-informed, interpretable AI-and-modeling framework to understand and exploit electric-field effects in heterogeneous catalysis, with ammonia cracking and synthesis as a representative pathway. The team built and validated methods to map local electric fields on metal surfaces and nanoparticles, showing that low-coordination features (tips/edges/corners) can concentrate fields by several-fold relative to flat facets. Using DFT-generated datasets, the project created physics-guided machine learning models that rapidly predict local electric fields and field-dependent adsorption energetics with near-DFT accuracy while reducing computational cost by orders of magnitude. These predictions were integrated with microkinetic modeling to quantify how field-dipole interactions reshape reaction energetics and mechanisms, enabling large increases in predicted catalytic rates and substantial reductions in operating temperature under favorable field conditions. To accelerate discovery of earth-abundant catalysts, the project combined interpretable ML screening (with electronic-structure descriptors identified as key drivers) with a generative inverse-design workflow based on diffusion models and physics constraints. The resulting closed-loop approach, linking simulation, mechanistic modeling, and AI, provides reusable tools and datasets for designing catalysts and operating conditions in field-enhanced catalysis, with broad relevance to electrostatic catalysis, plasma catalysis, electrocatalysis, and other energy-related chemical transformations.

30 DIRECT ENERGY CONVERSION↗

Quantum-inspired weight-constrained neural network: Reducing variable numbers by 100× compared to standard neural networks

Although quantum machine learning has shown great promise, the practical application of quantum computers remains constrained in the noisy intermediate-scale quantum era. To take advantage of quantum machine learning, we investigate the underlying mathematical principles of these quantum models and find that the quantum neural network with amplitude encoding is equivalent to a weight-constrained neural network. Motivated by this discovery, we develop a classical weight-constrained neural network. We find that this approach can reduce the number of variables in a classical neural network by a factor of 135 while preserving its accuracy. In addition, we develop a dropout method to enhance the robustness of quantum machine learning models, which are highly susceptible to adversarial attacks. This technique can also be applied to improve the adversarial robustness of the classical weight-constrained neural network, which is essential for industry applications, such as self-driving vehicles. Our work offers an approach to reduce the complexity of large classical neural networks, addressing a critical challenge in machine learning.

quantum algorithms & computation↗

Machine Learning Models for Predicting Molecular UV–Vis Spectra with Quantum Mechanical Properties

Accurate understanding of Ultraviolet–visible (UV–Vis) spectra is critical for highthroughput design of compounds for drug discovery. Experimentally determining UV–Vis spectra can become expensive when dealing with a large quantity of novel molecules. This provides us an opportunity to drive computational advances in molecular property predictions using quantum mechanics and machine learning. In this work, we use both Quantum Mechanically (QM) predicted and measured UV–Vis spectra as input to modify four different machine learning architectures: UVvis-SchNet, UVvis- DTNN, UVvis-Transformer, and UVvis-MPNN. Here we find that the UVvis-MPNN model outperforms the other models when using optimized 3D coordinates and QM predicted spectra as input features. This model has the highest performance for predicting UVVisible spectra with a training RMSE of 0.06 and validation RMSE of 0.08.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA's Orbital Debris Optical Program: MCAT Operational on Ascension

The Orbital Debris Program Office at NASA Johnson Space Center has a long history of an optical observational program. The Meter Class Autonomous Telescope, MCAT, was dedicated to Eugene Stansbery (now also known as ES-MCAT) in 2017. MCAT, a 1.3m DFM telescope, has a proven capability for tracking known objects from Low-Earth Orbits (LEO) out to Geosynchronous (GEO) orbits. Monitoring the population of the GEO belt is accomplished through surveys. A GEO survey statistically samples the GEO belt (0 to ~15 deg orbital inclinations) to detect both correlated and uncorrelated targets. A GEO survey, the initial focus for MCAT, will commence in 2019 to map out the current state of the GEO population as input for the ORbital Debris Engineering Model (ORDEM 4.x). If a break-up occurs, surveys of the break-up field can be followed for discovery and investigations of daughter debris fragments from the parent satellite. Discovery can be accomplished by surveying orbits near to and including the parent object’s orbit. Targeted observations of debris can be taken with a suite of broadband filters for characterizing individual objects by rate-tracking their known or calculated orbital elements (Two-Line Element sets, TLEs). These observations can be used in conjunction with NASA’s Standard Satellite Break-up Model (SSBM). In 2018, MCAT’s primary mirror was realuminized with a high-end protected, enhanced silver ZeCoat and the CCD chip was replaced in the Spectral Instruments camera. With these updates completed, MCAT is now well on track to reach Full Operational Capability (FOC) in 2019 for its survey and rate-track capabilities. A full overview of MCAT’s operational state, capabilities, and mission will be discussed.

Orbital Debris Program↗

Are 100 Ensemble Members Enough to Capture the Remote Atmospheric Response to +2°C Arctic Sea Ice Loss?

This study presents results from the Polar Amplification Multimodel Intercomparison Project (PAMIP) single-year time-slice experiments that aim to isolate the atmospheric response to Arctic sea ice loss at global warming levels of +2°C. Using two general circulation models (GCMs), the ensemble size is increased up to 300 ensemble members, beyond the recommended 100 members. After partitioning the response in groups of 100 ensemble members, the reproducibility of the results is evaluated, with a focus on the response of the midlatitude jet streams in the North Atlantic and North Pacific. Both atmosphere-only and coupled ocean–atmosphere PAMIP experiments are analyzed. Substantial differences in the midlatitude response are found among the different experiment subsets, suggesting that 100-member ensembles are still significantly influenced by internal variability, which can mislead conclusions. Despite an overall stronger response, the coupled ocean–atmosphere runs exhibit greater spread due to additional ENSO-related internal variability when the ocean is interactive. The lack of consistency in the response is true for anomalies that are statistically significant according to Student’s t and false discovery rate tests. This is problematic for the multimodel assessment of the response, as some of the spread may be attributed to different model sensitivities whereas it is due to internal variability. Here, we propose a method to overcome this consistency issue that allows for more robust conclusions when only 100 ensemble members are used.

58 GEOSCIENCES↗

An artificial intelligence accelerated virtual screening platform for drug discovery

Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we develop a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screen multi-billion compound libraries against two unrelated targets, a ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel Na V 1.7. For both targets, we discover hit compounds, including seven hits (14% hit rate) to KLHDC2 and four hits (44% hit rate) to Na V 1.7, all with single digit micromolar binding affinities. Screening in both cases is completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.

Science & Technology - Other Topics↗

Summarizing experimental sensitivities of collider experiments to dark matter models and comparison to other experiments

Comparisons of the coverage of current and proposed dark matter searches can help us to understand the context in which a discovery of particle dark matter would be made. In some scenarios, a discovery could be reinforced by information from multiple, complementary types of experiments; in others, only one experiment would see a signal, giving only a partial, more ambiguous picture; in still others, no experiment would be sensitive and new approaches would be needed. In this whitepaper, we present an update to a similar study performed for the European Strategy Briefing Book performed within the dark matter at the Energy Frontier (EF10) Snowmass Topical Group We take as a starting point a set of projections for future collider facilities and a method of graphical comparisons routinely performed for LHC DM searches using simplified models recommended by the LHC Dark Matter Working Group and also used for the BSM and dark matter chapters of the European Strategy Briefing Book. These comparisons can also serve as launching point for cross-frontier discussions about dark matter complementarity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Rheology of dense fiber suspensions: Origin of yield stress, shear thinning, and normal stress differences

We use high-fidelity computational model of fiber suspension to investigate suspension rheology. We investigate the interplay between the hydrodynamic, noncontact attractive and repulsive, and interfiber contact interactions. The shear-thinning viscosity and finite yield stress obtained from the Immerse Boundary Method simulations align quantitatively with experimental findings from the literature. The study demonstrates that attractive interactions lead to both yield stress and shear thinning behavior in rigid fiber suspensions. This discovery holds significance as it contributes to the ongoing debate on the source of yield stress in fiber suspensions. The proposed model is used to quantify normal stresses in addition to shear thinning and yield stress.

Ardekani, Arezoo↗

Identification and expression of small multidrug resistance transporters in early‐branching anaerobic fungi

Abstract Membrane‐embedded transporters impart essential functions to cells as they mediate sensing and the uptake and extrusion of nutrients, waste products, and effector molecules. Promiscuous multidrug exporters are implicated in resistance to drugs and antibiotics and are highly relevant for microbial engineers who seek to enhance the tolerance of cell factory strains to hydrophobic bioproducts. Here, we report on the identification of small multidrug resistance (SMR) transporters in early‐branching anaerobic fungi (Neocallimastigomycetes). The SMR class of transporters is commonly found in bacteria but has not previously been reported in eukaryotes. In this study, we show that SMR transporters from anaerobic fungi can be produced heterologously in the model yeast Saccharomyces cerevisiae , demonstrating the potential of these proteins as targets for further characterization. The discovery of these novel anaerobic fungal SMR transporters offers a promising path forward to enhance bioproduction from engineered microbial strains.

59 BASIC BIOLOGICAL SCIENCES↗

Quark-universal U(1) breaking scalar at the LHC

If the quarks or leptons are charged under a new U(1) gauge symmetry, then besides a Z′ boson there must exist at least one new boson whose decay products include Standard Model particles. In the case of a minimal symmetry breaking sector, that new boson is a scalar ϕ that couples to the Z′ boson as well as to the new fermions required to cancel the U(1) gauge anomalies. The scalar may be produced at the Large Hadron Collider (LHC) in association with a Z′ boson, or through Z′ boson fusion, while its decays are typically into four jets or two photons. We analyze in detail the case where the Z′ boson is leptophobic, and all the quarks have the same charge under the new U(1). If ϕ mixes with the Standard Model Higgs boson, then the new scalar can also be produced via gluon fusion, and the discovery mode is likely to be a diphoton resonance.

Armbruster, Lorin [Mainz U., Inst. Phys.; U. Mainz↗

Co-simulation of transactive energy markets: A framework for market testing and evaluation

The proliferation of distributed energy resources (DER)—and the ability to intelligently control these assets—is re-defining the electrical distribution system. As the number of controllable devices rapidly expands, grid operators must determine how to incorporate these assets while delivering reliable, equitable, and affordable electricity. One possible approach is to establish distribution-level electricity markets and allow devices/aggregations of devices to participate in price establishment. While this approach purports some of the same benefits as the highly successful wholesale electricity markets (i.e., open competition, efficient price discovery, reduced communication overhead), this needs to be researched and quantified via an analysis platform that models distribution-level markets at the appropriate fidelity. Specifically, the simultaneous evaluation of market performance, DER performance, DER bidding approaches, and distribution feeder power quality requires modeling that spans multiple technical areas. Co-simulation has emerged as a powerful tool in addressing this type of problem, where outputs depend on a range of underlying areas of expertise and associated models. In this paper we describe a solution, as implemented in the HELICS co-simulation platform, where we include (1) high fidelity house models, (2) intelligent bidding agents, (3) a modular market integration/design, and (4) a distribution feeder model. We then present a case study where we test two different market designs: (1) a pseudo-wholesale double-blind auction, and (2) an asynchronous matching market. In this work, the markets are run under two DER penetration levels and economic results are compared to full retail net energy metering and avoided cost net metering scenarios that bookend current approaches to remuneration of DER participation. We show the potential for transactive markets to provide increased value for most customers relative to net metering (and all customers relative to avoided cost scenarios) while decreasing costs for the utility.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Thin film combinatorial sputtering of Al-Ce alloys: Investigating the phase separation of as-deposited solid solutions and determining the coefficient of thermal expansion

Al x Ce 100–x thin films with a composition range of ~75.0 < x < 99.5 at% (36.5 < x < 97.5 wt%) were synthesized via combinatorial co-sputtering from an Al and an Al 50 Ce 50 target. The crystal structure, phase fraction, film morphology, electrical resistivity, and temperature-dependent coefficients of thermal expansion (CTE) are all correlated to the Al x Ce 100–x composition. The as-deposited films form a metastable solid-solution, and annealing leads to the formation of the thermodynamically stable two-phase system of Al and the α-Al 11 Ce 3 intermetallic. Temperature dependent x-ray diffraction (XRD) reveals that the two phases expand independently of one another, and the thin film Al temperature-dependent CTE is similar to bulk Al. The thin film Al 11 Ce 3 intermetallic phase has a nearly constant CTE of ~1.5 × 10 –5 /°C within the temperature range studied (25–550 °C). To confirm the thin film Al 11 Ce 3 results, bulk stoichiometric Al 11 Ce 3 and +/- 1 wt% Ce samples were prepared and the CTE of each was measured with the same conditions. A Rietveld analysis of the bulk data enabled an estimation of the CTE in each of the 3 orthorhombic lattice parameters, which displayed anisotropic behavior. The thin film and bulk CTE measurements were in very good agreement. Estimations of the temperature dependent CTE of the two-phase alloys are made via the Reuss and Voigt models. Finally, by demonstrating the efficacy of the approach, more complex multi-component rapid materials discovery of low CTE Al-alloys can be pursued via the combinatorial thin film synthesis and XRD measurement.

36 MATERIALS SCIENCE↗

Parallel evaluation of alternative skin barrier models and excised human skin for dermal absorption studies in vitro

Skin permeation is a primary consideration in the safety assessment of cosmetic ingredients, topical drugs, and human users handling veterinary medicinal products. While excised human skin (EHS) remains the ‘gold standard’ for in vitro permeation testing (IVPT) studies, unreliable supply and high cost motivate the search for alternative skin barrier models. In this study, a standardized dermal absorption testing protocol was developed to evaluate the suitability of alternative skin barrier models to predict skin absorption in humans. Under this protocol, side-by-side assessments of a commercially available reconstructed human epidermis (RhE) model (EpiDerm-200-X, MatTek), a synthetic barrier membrane (Strat-M, Sigma-Aldrich), and EHS were performed. The skin barrier models were mounted on Franz diffusion cells and the permeation of caffeine, salicylic acid, and testosterone was quantified. Transepidermal water loss (TEWL) and histology of the biological models were also compared. EpiDerm-200-X exhibited native human epidermis-like morphology, including a characteristic stratum corneum, but had an elevated TEWL as compared to EHS. The mean 6 h cumulative permeation of a finite dose (6 nmol/cm2) of caffeine and testosterone was highest in EpiDerm-200-X, followed by EHS and Strat-M. Salicylic acid permeated most in EHS, followed by EpiDerm-200-X and Strat-M. Altogether, evaluating novel alternative skin barrier models in the manner outlined herein has the potential to reduce the time from basic science discovery to regulatory impact.

60 APPLIED LIFE SCIENCES↗

Multiple fermion scattering in the weakly coupled spin-chain compound YbAlO 3

The Heisenberg antiferromagnetic spin-1/2 chain, originally introduced almost a century ago, is one of the best studied models in quantum mechanics due to its exact solution, but nevertheless it continues to present new discoveries. Its low-energy physics is described by the Tomonaga-Luttinger liquid of spinless fermions, similar to the conduction electrons in one-dimensional metals. In this work we investigate the Heisenberg spin-chain compound YbAlO3 and show that the weak interchain coupling causes Umklapp scattering between the left- and right-moving fermions and stabilizes an incommensurate spin-density wave order at q = 2k F under finite magnetic fields. These Umklapp processes open a route to multiple coherent scattering of fermions, which results in the formation of satellites at integer multiples of the incommensurate fundamental wavevector Q = nq. Our work provides surprising and profound insight into bandstructure control for emergent fermions in quantum materials, and shows how neutron diffraction can be applied to investigate the phenomenon of coherent multiple scattering in metals through the proxy of quantum magnetic systems.

36 MATERIALS SCIENCE↗

Subterahertz collective dynamics of polar vortices

The collective dynamics of topological structures are of interest from both fundamental and applied perspectives. For example, studies of dynamical properties of magnetic vortices and skyrmions have not only deepened our understanding of many-body physics but also offered potential applications in data processing and storage. Topological structures constructed from electrical polarization, rather than electron spin, have recently been realized in ferroelectric superlattices, and these are promising for ultrafast electric-field control of topological orders. However, little is known about the dynamics underlying the functionality of such complex extended nanostructures. In this study, using terahertz-field excitation and femtosecond X-ray diffraction measurements, we observe ultrafast collective polarization dynamics that are unique to polar vortices, with orders-of-magnitude higher frequencies and smaller lateral size than those of experimentally realized magnetic vortices. A previously unseen tunable mode, hereafter referred to as a vortexon, emerges in the form of transient arrays of nanoscale circular patterns of atomic displacements, which reverse their vorticity on picosecond timescales. Its frequency is considerably reduced (softened) at a critical strain, indicating a condensation (freezing) of structural dynamics. We use first-principles-based atomistic calculations and phase-field modelling to reveal the microscopic atomic arrangements and corroborate the frequencies of the vortex modes. The discovery of subterahertz collective dynamics in polar vortices opens opportunities for electric-field-driven data processing in topological structures with ultrahigh speed and density.

36 MATERIALS SCIENCE↗