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At least 415 records · Page 23

AIMSim : An accessible cheminformatics platform for similarity operations on chemicals datasets

The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Further, most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a Graphical User Interface for code-free utilization with fully interactive plots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The SENSEI Generic In Situ Interface: Tool and Processing Portability at Scale [Book Chapter]

One key challenge when doing in situ processing is the investment required to add code to numerical simulations needed to take advantage of in situ processing. Such instrumentation code is often specialized, and tailored to a specific in situ method or infrastructure. Then, if a simulation wants to use other in situ tools, each of which has its own bespoke API [4], then the simulation code team will quickly become overwhelmed with having a different set of instrumentation APIs, one per in situ tool or method. In an ideal situation, such instrumentation need happen only once, and then the instrumentation API provides access to a large diversity of tools. In this way, a data producer’s instrumentation need not be modified if the user desires to take advantage of a different set of in situ tools. The SENSEI generic in situ interface addresses this challenge, which means that SENSEI-instrumented codes enjoy the benefit of being able to use a diversity of tools at scale, tools that include Libsim, Catalyst, Ascent, as well as user-defined methods written in C++ or Python. SENSEI has been shown to scale to greater than 1M-way concurrency on HPC platforms, and provides support for a rich and diverse collection of common scientific data models. Furthermore, this chapter presents the key design challenges that enable tool and processing portability at scale, some performance analysis, and example science applications of the methods.

Bethel, E. Wes↗

MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry

Modern mass spectrometry-based workflows employing hybrid instrumentation and orthogonal separations collect multidimensional data, potentially allowing deeper understanding in omics studies through adoption of artificial intelligence methods. However, the large volume of these rich data challenges existing data storage and access technologies, therefore precluding informatics advancements. Here we present MZA™ (pronounced m-za), the mass-to-charge (m/z) generic data storage and access tool designed to facilitate software development and artificial intelligence research in multidimensional mass spectrometry measurements. Composed by a data conversion tool and a simple file structure based on the HDF5 format, MZA provides easy, cross-platform and efficient programmatic access to raw MS-data, enabling fast development of new tools in data science programming languages such as Python and R. The software executable and example Python and R scripts are freely available at https://github.com/PNNL-m-q/mza.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct Correlation of Charge Carrier Transport to Local Crystal Quality in Lead Halide Perovskites

Although solution processing methods provide an attractive route toward development of low-cost functional materials, these accessible fabrication approaches can engender high concentrations of microscopic structural defects that are detrimental to performance. In lead halide perovskites, structural disorder derived from solution processing has been implicated as an important determiner of photophysical properties. However, a direct correlation between the functional properties of these materials and the local crystal structure in which non-equilibrium states evolve has remained elusive, in part because structural heterogeneities occur on length scales that defy conventional characterization techniques. To address this knowledge gap, in this work we have combined ultrafast pump–probe microscopy and electron backscattering diffraction to directly correlate charge carrier transport with the local diffraction pattern contrast, an indicator of crystal quality. Spatial correlation of these measurements strongly suggests that even on individual single crystal CsPbBr3 domains, microscopic variability in the crystal quality profoundly impacts the efficiency of charge carrier transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Benchmarking Guanidinium Organosulfonate Hydrogen-Bonded Frameworks for Structure Determination of Encapsulated Guests

Single crystal X-ray diffraction (SCXRD) is arguably the most definitive method for molecular structure determination, but it is often challenged by compounds that are liquids or oils at room temperature or do not form crystals adequate for analysis. Our laboratory previously reported a simple, cost-effective, single-step crystallization method based on guanidinium organosulfonate (GS) hydrogen bonded frameworks for structure determination of a wide range of encapsulated guest molecules, including assignment of the absolute configuration of chiral centers. Herein, we expand on those results and report a head-to-head comparison of the GS method with adamantoid “molecular chaperones”, which have been reported to be useful hosts for structure determination. Inclusion compounds limited to only two GS hosts are characterized by low R1 values and Flack parameters, infrequent disorder of the host and guest, and manageable disorder when it does exist. The structures of some target molecules that were not included or resolved using the adamantoid chaperones were successfully included and resolved by the GS hosts, and vice versa. Of the 32 guests attempted by the GS method, 31 inclusion compounds afforded successful guest structure solutions, a 97% success rate. The GS hosts and adamantoid chaperones are complementary with respect to guest inclusion, arguing that both should be employed in the arsenal of methods for structure determination. Furthermore, the low cost of organosulfonate host components promises an accessible route to molecular structure determination for a wide range of users.

36 MATERIALS SCIENCE↗

Dissolved Inorganic Carbon and Dissolved Organic Carbon Data for the East River Watershed, Colorado (2015-2025)

This data package contains mean values for dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) for water samples taken from the East River Watershed in Colorado. The East River is part of the Watershed Function Scientific Focus Area (WFSFA) located in the Upper Colorado River Basin, United States. DOC and DIC concentrations in water samples were determined using a TOC-VCPH analyzer (Shimadzu Corporation, Japan). DOC was analyzed as non-purgeable organic carbon (NPOC) by purging HCl-acidified samples with carbon-free air to remove DIC prior to measurement. After the acidified sample has been sparged, it is injected into a combustion tube filled with oxidation catalyst heated to 680 oC. The DOC in samples is combusted to CO2 and measured by a non-dispersive infrared (NDIR) detector. The peak area of the analog signal produced by the NDIR detector is proportional to the DOC concentration of the sample. DIC was determined by acidifying the samples with HCl first, and then purging with carbon-free air to release CO2 for analysis by NDIR detector. Total dissolved nitrogen (TDN) was analyzed using a Shimadzu Total Nitrogen Module (TNM-L) combined with the TOC-L analyzer (Shimadzu Corporation, Japan). TNM-L is a non-specific measurement of total nitrogen (TN). All nitrogen species in samples are combusted to nitrogen monoxide and nitrogen dioxide, then reacted with ozone to form an excited state of nitrogen dioxide. Upon returning to ground state, light energy is emitted. Then, TDN is measured using a chemiluminescence detector. All data reported are the mean values upon minimum of three replicate measurements, with a relative standard deviation < 3%. All samples were analyzed under a rigorous quality assurance and quality control (QA/QC) process. This data package contains (1) a zip file (dic_npoc_data_2014-2025.zip) containing a total of 337 files: 336 data files of DIC and NPOC data from across the Lawrence Berkeley National Laboratory (LBNL) Watershed Function Scientific Focus Area (SFA) which is reported in .csv files per location and a locations.csv (1 file) with latitude and longitude for each location; (2) a file-level metadata (v6_20250901_flmd.csv) file that lists each file contained in the dataset with associated metadata; (3) a data dictionary (v6_20250901_dd.csv) file that contains terms/column_headers used throughout the files along with a definition, units, and data type; and (4) PDF and docx files for the determiniation of Method Detection Limits (MDLs) for DIC and NPOC data, which has been updated in 2026-08. Missing values within the anion data files are noted as either "-9999" or "0.0" for not detectable (N.D.) data. There are a total of 113 locations containing DIC/NPOC data. Update on 2020-10-07: Updated the data files to remove times from the timestamps, so that only dates remain. The data values have not changed. Update on 2021-04-11: Added Determination of Method Detection Limits (MDLs) for DIC, NPOC and TDN Analyses document, which can be accessed as a PDF or with Microsoft Word.Update on 6/10/2022: versioned updates to this dataset was made along with these changes: (1) updated dissolved inorganic carbon and dissolved organic carbon data for all locations up to 2021-12-31, (2) removal of units from column headers in datafiles, (3) added row underneath headers to contain units of variables, (4) restructure of units to comply with CSV reporting format requirements, (5) added -9999 for empty numerical cells, and (6) the addition of the file-level metadata (flmd.csv) and data dictionary (dd.csv) were added to comply with the File-Level Metadata Reporting Format. Update on 2022-09-09: Updates were made to reporting format specific files (file-level metadata and data dictionary) to correct swapped file names, add additional details on metadata descriptions on both files, add a header_row column to enable parsing, and add version number and date to file names (v2_20220909_flmd.csv and v2_20220909_dd.csv). Update on 2023-08-08: Updates were made to both the data files and reporting format specific files. New available anion data was added, up until 2023-01-05. The file level metadata and data dictionary files were updated to reflect the additional data added. Update on 2024-03-11: Updates were made to both the data files and reporting format specific files. New available anion data was added, up until 2023-11-21. Further, revisions to the data files were made to remove incorrect data points (from 1970 and 2001). The reporting format specific files were updated to reflect the additional data added. Revised versions of the PDF and docx files for determination of MDLs for DIC and NPOC were added to replace previous versions. Update on 2025-05-15: Updates were made to both the data files and reporting format specific files. New available DIC and NPOC data was added, up until the end of WY2024 (September 30, 2024). International Generic Sample Numbers (IGSNs), when registered, were added to the data files. The reporting format specific files were updated to reflect the additional data added. Update on 2026-09-01: Updates were made to both the data files and reporting format specific files. New available DIC and NPOC data was added, up until the end of WY2025 (September 30, 2025). Updated versions, as of 2026-08-10, of the PDF and docx files for determination of MDLs for DIC and NPOC data were added to this dataset.

54 ENVIRONMENTAL SCIENCES↗

Nanostructures for Electrical Energy Storage (NEES) (2020 Final Technical Report)

Nanostructures for Electrical Energy Storage (NEES, www.efrc.umd.edu) was an Energy Frontier Research Center supported by the DOE Office of Science, Basic Energy Sciences, from 8/1/2009 to 7/31/2020. Led by the University of Maryland, NEES enjoyed extensive collaborations with its funded partners, including two DOE Laboratories and six universities. The NEES vision has been to reveal a set of scientific insights and design principles that can underpin a next-generation electrical energy storage approach, building on advances in nanoscale science and technology to achieve simultaneous high power and high energy over extended charge/discharge cycling. The vision is motivated by the recognition that scaling into the nano regime opens the door to new physical phenomena and that the tools enlisted in nanoscale research provide major new opportunities for the synthesis not only of materials at molecular scale but for structures at nano scale and above. NEES has translated this vision into its research program based on two observations. First, while the behavior of ions and electrons in electrolytes and in electrode materials is crucial to electrical energy storage (or more appropriately electrochemical energy storage), it is the transport of ion and electron charge between different structural components of a storage device that ultimately determine its performance. With it well recognized that the choice of electrode materials typically constrain ion transport kinetics as well as maximum ion concentration, the search for better electrode materials has been a primary driver of battery research. At the same time the synthesis of electrodes is typically based on aggregation of particles with varying size, shape, and orientation in the electrode. Together with the presence of additional materials to impart electrical conductivity and cohesion to the composite electrode, change in electrode materials is necessarily accompanied by structural changes at the nano/micro scale that are difficult to categorize and manage. From the beginning, NEES’ vision has been to create and study simpler, highly controlled spatial arrangements of known materials as battery components (electrodes, current collectors, and electrolyte) and to understand how design and structure above the molecular scale determines the energy storage performance available from known materials. Second, advances in nanoscience dramatically expanded the portfolio of synthesis methods, structural motifs, and new phenomena available for research. Some of these gave rapid access to new building blocks at the deep nanoscale (e.g., carbon nanotubes grown by self-assembly, nanoscale arrays formed by electrochemical self-alignment, monolayer films controlled by self-limiting reaction). Such advances served as the enabler for the NEES vision to be pursued experimentally through study of 3D structures created and controlled at the nano, micro, and meso scales. Here, we use meso as in the BES MESO Report, implying not only intermediate or varying length scales, but very much the way behavior is influenced by other factors including aggregation of nanocomponents at different densities and spatial configurations, statistical variations in the aggregates, hierarchical architectures in which they can be assembled, or local 3D configurations that result from the architectures. Over its life cycle, NEES has pursued two overarching goals: (1) to understand the scientific fundamentals of electrochemical storage from the nanoscale to the mesoscale; and (2) to create and learn from innovative, controlled, heterogeneous nanostructures, where such nanostructures can enable the first goal and serve as models for future paradigms in energy storage. Specific goals have included: Synthesize heterogeneous nanostructures comprised of multiple materials arranged in controlled fashion and characterize their behavior; Demonstrate and elucidate design principles for achieving simultaneous high power and high energy; Develop materials processes which enable precision control of thin layers and 3D structures; Investigate the impact of artificial interphases on electrode stability during ion insertion/deinsertion; Create dense arrays of nanostructures to understand how the architecture of these assemblies, along with nanostructure design, influences energy storage behavior at the mesoscale; Identify and understand the consequences of nanoconfinement and local inhomogeneities in 3D mesoscale arrays; Develop and apply computational models to stimulate, guide and interpret experiments.

25 ENERGY STORAGE↗

Harnessing the Quantum Zeno Effect in superconducting qubits for particle detection

Superconducting qubits, originally developed for quantum computing, are emerging as a potentially powerful tool for detecting low-energy particle interactions, such as dark matter and neutrinos. These devices can register energy deposits as small as a few meV, dramatically lowering the detection threshold compared to conventional sensors. However, their deployment in rare-event searches is hampered by a critical and unresolved background: Two-Level Systems (TLSes). TLSes are material defects that can scramble qubit frequencies and coherence times in a way that resembles particle energy deposits. Such false signals can critically limit the sensitivity and extend experimental runtimes for qubit-based sensors by years. This talk introduces a novel method to eliminate TLSes as a background source in superconducting qubit-based detectors. By harnessing the Quantum Zeno Effect (QZE), a well-established quantum phenomenon where frequent observation inhibits system evolution, I will discuss the possibility of “freezing” these TLS defects in place. This effectively suppresses their interference, stabilizes qubit behavior, and opens the door to using TLSes themselves as auxiliary sensors. I have already identified target TLSes and observed early signs of QZE-like dynamics in Fermilab-fabricated devices. The method builds on my existing collaborations at Fermilab’s Quantum Information Testbed (QUIET), with access to low muon flux cryogenic facilities 100 meters underground, control electronics, and expert mentors across multiple institutions. By removing a key bottleneck to superconducting sensor deployment, this research targets advancing the development of a general-purpose technique to enhance sensitivity, reduce false positives, and accelerate discovery in searches for dark matter, neutrinos, and other rare phenomena.

Seidel, Olivia [Texas U., Arlington]↗

Systems and methods for locating and imaging proppant in an induced fracture

Born Scattering Inversion (BSI) systems and methods are disclosed. A BSI system may be incorporated in a well system for accessing natural gas, oil and geothermal reserves in a geologic formation beneath the surface of the Earth. The BSI system may be used to generate a three-dimensional image of a proppant-filled hydraulically-induced fracture in the geologic formation. The BSI system may include computing equipment and sensors for measuring electromagnetic fields in the vicinity of the fracture before and after the fracture is generated, adjusting the parameters of a first Born approximation model of a scattered component of the surface electromagnetic fields using the measured electromagnetic fields, and generating the image of the proppant-filled fracture using the adjusted parameters.

03 NATURAL GAS↗

Direct photopatterning of robust and diverse materials

The present invention relates to methods of metathesizing olefins using catalysts previously considered to be practically inactive. The present invention further relates to novel photosensitive compositions, their use as photoresists, and methods related to patterning polymer layers on substrates. Further, modifications to the compositions and method provide for an unprecedented functionalization of the compositions, useful for example in the preparation of sensors, drug delivery systems, and tissue scaffolds. The novel compositions and associated methods also provide for the opportunity to prepare 3-dimensional objects which provide new access to critically dimensioned devices, including for example photonic devices.

36 MATERIALS SCIENCE↗

Systems and methods for locating and imaging proppant in an induced fracture

Born Scattering Inversion (BSI) systems and methods are disclosed. A BSI system may be incorporated in a well system for accessing natural gas, oil and geothermal reserves in a geologic formation beneath the surface of the Earth. The BSI system may be used to generate a three-dimensional image of a proppant-filled hydraulically-induced fracture in the geologic formation. The BSI system may include computing equipment and sensors for measuring electromagnetic fields in the vicinity of the fracture before and after the fracture is generated, adjusting the parameters of a first Born approximation model of a scattered component of the surface electromagnetic fields using the measured electromagnetic fields, and generating the image of the proppant-filled fracture using the adjusted parameters.

Aldridge, David F.↗

Machine learning model explanation apparatus and methods

Explanation apparatus and methods are described. In one aspect, an explanation apparatus includes processing circuity configured to access a source instance which has been classified by a machine learning model; create associations of the source instance with a plurality of training instances; and process the associations of the source instance and the training instances to identify a first subset of the training instances which have less relevance to the classification decision of the source instance by the machine learning model compared with a second subset of the training instances; and an interface configured to communicate information to a user, and wherein the processing circuitry is configured to control the user interface to communicate the second subset of the training instances to the user as evidence to explain the classification of the source instance by the machine learning model.

Arendt, Dustin↗

EXAGRAPH: Graph and combinatorial methods for enabling exascale applications

Combinatorial algorithms in general and graph algorithms in particular play a critical enabling role in numerous scientific applications. However, the irregular memory access nature of these algorithms makes them one of the hardest algorithmic kernels to implement on parallel systems. With tens of billions of hardware threads and deep memory hierarchies, the exascale computing systems in particular pose extreme challenges in scaling graph algorithms. The codesign center on combinatorial algorithms, ExaGraph, was established to design and develop methods and techniques for efficient implementation of key combinatorial (graph) algorithms chosen from a diverse set of exascale applications. Algebraic and combinatorial methods have a complementary role in the advancement of computational science and engineering, including playing an enabling role on each other. In this paper, we survey the algorithmic and software development activities performed under the auspices of ExaGraph from both a combinatorial and an algebraic perspective. In particular, we detail our recent efforts in porting the algorithms to manycore accelerator (GPU) architectures. We also provide a brief survey of the applications that have benefited from the scalable implementations of different combinatorial algorithms to enable scientific discovery at scale. We believe that several applications will benefit from the algorithmic and software tools developed by the ExaGraph team.

97 MATHEMATICS AND COMPUTING↗

Signatures of Thermal and Electrical Crosstalk in a Microwave Multiplexed Hard X-ray Transition Edge Sensor Array

We investigate the crosstalk between Transition-Edge Sensor (TES) pixels in a 24-pixel hard X-ray spectrometer array fabricated at the Advanced Photon Source, Argonne National Laboratory. Analysis shows thermal cross talk, possibly associated with insufficient thermalization, and rare but larger in magnitude electrical crosstalk between specific perpetrator-victim pixel combinations, potentially due to defects in the bias wiring or microwave multiplexing circuit. We use a method based on group-triggering and averaging to isolate the crosstalk response despite only having access to X-ray photon illumination uniform across the entire array. This allows us to identify thermal and electrical crosstalk between pixel pairs in repeated measurements to the level of 1 part in 1000 or better. In the array under study, the magnitude of observed crosstalk is small but comparable to the resolving power of this pixel design (E/Delta E similar to\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$E/\Delta {}E \sim$$\end{document} 1000 at 20 keV) and so potentially responsible for a degradation in energy resolution of the array at high incident photon rates. Having proven the methods to identify and quantify crosstalk in our setup, we can now consider mitigations.

Triamkitsawat, Panthita↗

Intact mass spectrometry screening to optimize hydroxyl radical dose for protein footprinting

Hydroxyl radical protein footprinting (HRPF) using synchrotron radiation is a well-validated method to assess protein structure in the native solution state. In this method, X-ray radiolysis of water generates hydroxyl radicals that can react with solvent accessible side chains of proteins, with mass spectrometry used to detect the resulting labeled products. An ideal footprinting dose provides sufficient labeling to measure the structure but not so much as to influence the results. The optimization of hydroxyl radical dose is typically performed using an indirect Alexa488 fluorescence assay sensitive to hydroxyl radical concentration, but full evaluation of the experiment's outcome relies upon bottom-up liquid chromatography mass spectrometry (LC-MS) measurements to directly determine sites and extent of oxidative labeling at the peptide and protein level. A direct evaluation of the extent of labeling to provide direct and absolute measurements of dose and “safe” dose ranges in terms of, for example, average numbers of labels per protein, would provide immediate feedback on experimental outcomes prior to embarking on detailed LC-MS analyses. To this end, we describe an approach to integrate intact MS screening of labeled samples immediately following exposure, along with metrics to quantify the extent of observed labeling from the intact mass spectra. Intact MS results on the model protein lysozyme were evaluated in the context of Alexa488 assay results and a bottom-up LC-MS analysis of the same samples. In conclusion, this approach provides a basis for placing delivered hydroxyl radical dose metrics on firmer technical grounds for synchrotron X-ray footprinting of proteins, with explicit parameters to increase the likelihood of a productive experimental outcome. Further, the method directs approaches to provide absolute and direct dosimetry for all types of labeling for protein footprinting.

59 BASIC BIOLOGICAL SCIENCES↗

Hybrid RANS-LES of the Atmospheric Boundary Layer for Wind Farm Simulations: Preprint

Wind farm simulations often do not accurately represent wake-atmospheric boundary layer (ABL) interactions, blade boundary layer (BL) dynamics, and turbine-turbine interactions. In this work, we use Active Model Split (AMS), a new hybrid Reynolds-Averaged Navier Stokes (RANS)-large eddy simulation (LES) model, which is well suited to capture these effects because the model can (i) accurately simulate the ABL with the Coriolis effect, (ii) is accurate in adverse pressure gradients such as those near wind turbine blades, and (iii) has sufficiently low computational cost to simulate multiple turbines while resolving the blade BL. For simplicity and consistency we develop AMS to be used throughout the domain rather than in a zonal method. We implement our work in the massively parallel flow solver, Nalu-Wind, so that our model can access the compute resources needed for blade-resolved simulations of multiple wind turbines. To accomplish these aims, we modify the baseline AMS by changing the RANS contribution to SST k - omega with a length scale limiter, adding the Coriolis effect, and developing an appropriate wall treatment. We show that AMS of the ABL with the Coriolis effect matches LES reference results better than those obtained with RANS. We describe our plans to add buoyancy effects and wind turbines to our AMS simulations.

atmospheric boundary layer↗

Forensic characterization of surrogate nuclear explosion debris: radiochemical and spectroscopic strategies for method validation

Surrogate nuclear explosion debris (SNED) has emerged as a critical platform for advancing post-detonation nuclear forensic analysis in the absence of readily accessible historic materials. SNED enables controlled investigation and validation of analytical methodologies used to interrogate the chemical, isotopic, radiological, and microstructural signatures preserved in nuclear explosion debris. This review presents an integrated assessment of destructive and non-destructive analytical techniques commonly employed within decision-driven nuclear forensic workflows. Each technique is discussed individually while highlighting how it contributes to different stages of post-detonation analysis. Core methods – including gamma and alpha spectrometry, ICP-MS, TIMS, SIMS, SEM-EDS, XRF, LIBS, vibrational spectroscopy, and X-ray absorption spectroscopy – are critically evaluated with respect to forensic maturity, information content, and matrix limitations. Emphasis is placed on the role of SNED in benchmarking multi-modal workflows and identifying gaps in reproducing heterogeneity, fractionation, and radiation-driven evolution relevant to forensic attribution.

X-ray spectroscopic methods↗