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Machine learning approaches for crystallographic classification from synthetic 2D X-ray diffraction data

Crystallographic structure identification is crucial for understanding material properties; however, current methodologies often depend on labor-intensive and time-consuming analyses of 2D X-ray diffraction (XRD) patterns. To address these limitations, this study employs synthetic 2D XRD patterns combined with deep learning (DL) techniques to enable automated and high-throughput classification of the seven crystal systems and 230 space groups. We introduce the novel Auto Diffraction Pipeline, designed to generate synthetic 2D XRD spot patterns from crystallographic information files under diverse conditions, including varying zone axes, atomic substitution, atomic depletion and mechanical loading. These conditions enhance the realism of synthetic data, mitigating the scarcity of experimental datasets and enabling the creation of large representative training sets. Convolutional neural networks were trained and validated on these synthetic datasets to classify crystallographic structures across multiple scenarios. Our results demonstrate that integrating synthetic 2D XRD patterns with DL facilitates rapid, accurate and automated crystallographic classification, promoting the wider adoption of data-driven approaches in materials science.

Shahnazari, Ayoub [Univ. of Rochester, NY (United ↗

Observational constraints on early dark energy

In this paper, we review and update constraints on the Early Dark Energy (EDE) model from cosmological data sets, in particular Planck PR3 and PR4 cosmic microwave background (CMB) data and large-scale structure (LSS) data sets including galaxy clustering and weak lensing data from the Dark Energy Survey, Subaru Hyper Suprime-Cam and KiDS+VIKING-450, as well as BOSS/eBOSS galaxy clustering and Lyman-[Formula: see text] forest data. We detail the fit to CMB data, and perform the first analyses of EDE using the CAMSPEC and Hillipop likelihoods for Planck CMB data, rather than Plik, both of which yield a tighter upper bound on the allowed EDE fraction than that found with Plik. We then supplement CMB data with LSS data in a series of new analyses. All these analyses are concordant in their Bayesian preference for [Formula: see text]CDM over EDE, as indicated by marginalized posterior distributions. We perform a series of tests of the impact of priors in these results, and compare with frequentist analyses based on the profile likelihood, finding qualitative agreement with the Bayesian results. All these tests suggest prior volume effects are not a determining factor in analyses of EDE. This work provides both a review of existing constraints and several new analyses.

Astronomy & Astrophysics↗

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Experiment Level 2 Sensor Data v2-1

This is the version v2-1 Level 2 (L2) data release for COMPASS-FME environmental sensors located at our Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental site. This manipulative, ecosystem-scale TEMPEST experiment addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in MD, USA. The experiment uses a large-unit (2000 m2), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments. Level 2 (L2) data consist of sensor observations from the COMPASS-FME synoptic sites, TEMPEST, and DELUGE. Compared to the L1 data, these are more consistent (always 15-minute timestamps for the entire year); better QA/QC’d (out of bounds, out of service, and extreme outlier values are removed); and more complete, with a gap-filled time series available alongside the main observations, and additional derived (calculated) variables. L2 data are intended to be rapidly and easily usable in analyses and simulations. However, algorithmic outlier identification always carries the risk of removing valid data, and Level 1 data may be more suitable for analyses that focus on variability or extreme events. This dataset includes: - An overall dataset README file that describes the current version, gives citation and contact information, etc. - Site- and year-specific folders, each holding variable-specific Parquet (a high performance, space efficient format; see https://parquet.apache.org) data files for each site and plot in that year. - Metadata files within each site-year folder provide full information on data units, expected ranges, contact information, detailed flood times, as well as a general description of the site. - Environmental sensor types that appear in the data files include weather (ClimaVUE50, CS, RM Young, and LI instruments in the graphs below); soil conditions (TEROS12); soil redox state (Redox); groundwater variables (AquaTROLL200 and AquaTROLL600); open water sondes (Exo); tree sap velocity (Sapflow); and system voltage and state (Datalogger). Data are reported every 15 minutes. Please see v2-1 TEMPEST L2 Sensor Package Quick Start.pdf for detailed information on data package structure, temporal coverage, and versioning. Data files are in Apache Parquet, a high performance, space efficient format for tabular data. These files can be read using R's `arrow` package (https://arrow.apache.org/docs/r/), with similar tools available in other languages. The TEMPEST flood events occurred on the following dates. They lasted for ~10 hours each day and delivered ~80,000 gallons to each plot; many data streams are available at 1 or 5 minute frequency during these periods. * Tests: Aug 25 (fresh plot) and Sep 9 (salt plot), 2021 * TEMPEST 1: June 22, 2022 * TEMPEST 2: June 6-7, 2023 * TEMPEST 3: June 11-13, 2024

EARTH SCIENCE > ATMOSPHERE > ATMOSPHERIC TEMPERATU↗

Terrestrial laser scanning data (Levels 0 and 1) for Pasoh, Malaysia, Sep 2024

This data package contains data from terrestrial laser scanning (TLS) at the Pasoh Forest Reserve, Malaysia. The Pasoh Forest Reserve is a facility of the Forest Research Institute Malaysia, and contains evergreen lowland dipterocarp forest. The Next-Generation Ecosystem Experiments Tropics (NGEE-Tropics) study areas at Pasoh were established to study how different species respond to climatic variation and soil water availability. Two study areas were chosen representing different topography and species. The TLS data archived here were collected to provide detailed, three-dimensional information about forest structure. Specifically, data were collected to allow tree-level characterization of woody structure and leaf area for 12 focal trees with FloraPulse and sap flux sensors, facilitating estimation of woody biomass and leaf area to allow upscaling of water content and transpiration data to the tree-level. Scan positions were not selected to provide consistent data for non-focal trees with the study areas. This data package contains the following data: - High-level files document further details of the campaign and data package: 1_CampaignSummary.csv provides details about the campaign and study site, 2_ScanAreasDetail.csv provides details about each separate scan area (groups of scans post-processed into a single point cloud), 3_TerrestrialLidarSensor.csv provides further technical details about the Riegl VZ-400i TLS sensor, TLS_CSV_dd.csv is a CSV Data Dictionary providing information about the fields in CSV files following the ESS-DIVE CSV File Formatting Guidelines Reporting Format, TLS_flmd.csv is a File Level Metadata file providing information about each file in the data package following the ESS-DIVE File Level Metadata Reporting Format, and README.txt is a text file describing the overall project and file structure. - Level 0 data are the raw data (.PROJ folders) as recorded by the Riegl VZ-400i TLS instrument before scan co-registration and post-processing with the Riegl's proprietary RiSCAN PRO software, which requires a license. - Level 1 data contain post-processed, co-registered data from each scan area. The "PointClouds" folder for each scan area contains a .las file with 1 cm resolution point cloud data exported from RiSCAN PRO. These are the main files likely to be of interest to most users and can be further processed with any software capable of manipulating .las files (e.g. Python, R CloudCompare). The "Project Information" folder contains log files from post-processing in RiSCAN PRO that may be of interest to users who want to see detailed records of post-processing, including all PDF reports generated by RiSCAN PRO. The "ScanPositions" folder contains information about the final position of all TLS scans, after post-processing, in multiple formats. The file ScanPositions_*.csv provides final geo-referenced scan positions, and the file SOP_backup_*.csv can be used in RiSCAN PRO to restore the co-registered scan positions if users wish to re-process raw data (Level 0 .PROJ folders) with RiSCAN PRO software (e.g., subsample to a different resolution, exclude a certain scan position, or apply different filters on reflectance or deviation values) without redoing time-consuming co-registration steps.

54 ENVIRONMENTAL SCIENCES↗

Terrestrial laser scanning data (Levels 0 and 1) from Urban Biogeochemistry Pilot Project sites, Knoxville, Tennessee, Jul 2024 - Jul 2025

This data package contains data from terrestrial laser scanning (TLS) at five urban park sites in Knoxville, Tennessee, USA. All parks include open-grown and/or closed-canopy trees and mixed nearby land use. These study sites were established as part of the Urban Biogeochemistry Pilot Project, which has an overall goal of better understanding how hydrobiogeochemical cycling is altered within the human environment. These five sites represent a gradient of urbanization, and were instrumented to understand hydrological and biogeochemical cycling (e.g., soil moisture, soil physical properties and biogeochemistry, tree transpiration, species type). The TLS data archived here were collected to provide detailed, three-dimensional information about forest structure. Specifically, data were collected to allow tree- and stand-level characterization of woody structure and leaf area. TLS scans were placed to capture the area around trees with sap flow sensors, and as much of a 50 m radius area around the meteorological station as possible given site property limits. Derived products will allow upscaling of water content and transpiration data. This data package contains the following data: - High-level files document further details of the campaign and data package: 1_CampaignSummary.csv provides details about the campaign and study site, 2_ScanAreasDetail.csv provides details about each separate scan area (groups of scans post-processed into a single point cloud), 3_TerrestrialLidarSensor.csv provides further technical details about the Riegl VZ-400i TLS sensor, TLS_CSV_dd.csv is a CSV Data Dictionary providing information about the fields in CSV files following the ESS-DIVE CSV File Formatting Guidelines Reporting Format, TLS_flmd.csv is a File Level Metadata file providing information about each file in the data package following the ESS-DIVE File Level Metadata Reporting Format, and README.txt is a text file describing the overall project and file structure. - Level 0 data are the raw data (.PROJ folders) as recorded by the Riegl VZ-400i TLS instrument before scan co-registration and post-processing with the Riegl's proprietary RiSCAN PRO software, which requires a license. - Level 1 data contain post-processed, co-registered data from each scan area. The "PointClouds" folder for each scan area contains a .las file with 1 cm resolution point cloud data exported from RiSCAN PRO. These are the main files likely to be of interest to most users and can be further processed with any software capable of manipulating .las files (e.g. Python, R CloudCompare). The "Project Information" folder contains log files from post-processing in RiSCAN PRO that may be of interest to users who want to see detailed records of post-processing, including all PDF reports generated by RiSCAN PRO. The "ScanPositions" folder contains information about the final position of all TLS scans, after post-processing, in multiple formats. The file ScanPositions_*.csv provides final geo-referenced scan positions, and the file SOP_backup_*.csv can be used in RiSCAN PRO to restore the co-registered scan positions if users wish to re-process raw data (Level 0 .PROJ folders) with RiSCAN PRO software (e.g., subsample to a different resolution, exclude a certain scan position, or apply different filters on reflectance or deviation values) without redoing time-consuming co-registration steps.

54 ENVIRONMENTAL SCIENCES↗

Final technical report for DE-SC0022255: Discovering Physically Meaningful Structures from Climate Extreme Data

The past two decades have witnessed natural disasters and extreme weather events that affect millions of people. At the same time, the data volume from high-resolution climate models, satellite, in-situ and ground-based measurements have substantially increased to petabyte scales. These new and readily accessible datasets create the previously missing pipeline required for scientific machine learning (ML) and therefore new opportunities for improved understanding and prediction capability of climate extreme events. This project developed a deep latent variable model framework to discover physically meaningful hidden structures from high-dimensional, spatiotemporal climate extreme data.

97 MATHEMATICS AND COMPUTING↗

Discovering Physically Meaningful Structures from Climate Extreme Data

The original proposal described an interdisciplinary team spanning UC San Diego (lead), Columbia University, and UC Irvine, with Columbia investigators including Pierre Gentine, Elias Bareinboim, and Marcus van Lier-Walqui. The proposal further specified a leadership structure in which Columbia co-investigators contributed across the three aims, with Co-PI Gentine serving as a point of contact with science teams and with responsibilities distributed across aims.

42 ENGINEERING↗

Calcium is associated with specific soil organic carbon decomposition products at Blodgett Forest Research Center, Georgetown, California as analysed with scanning transmission X-ray microscopy carbon near-edge X-ray absorption fine structure spectroscopy

This data is from the paper calcium is associated with specific soil organic carbon decomposition products, published in SOIL. DOI: https://doi.org/10.5194/soil-11-381-2025, 2025.This file contains CSVs with spectral data and bulk soil data and there is no specific program required to open this data. The data includes Scanning transmission X-ray microscopy carbon near-edge X-ray absorption fine structure spectroscopy. data from the measurement of samples from the Whole-soil Warming project, run by the Belowground Biogeochemistry team at Blodgett Forest Research Center, Georgetown, California run by the University of California, Berkeley. It also includes bulk soil chemical properties. The University of California's Blodgett Forest Research Station (Forest) is situated in the Sierra Nevada foothills (1370 m a.s.l.) near Georgetown, California. The samples were collected from here: 38.912013, -120.661469, https://maps.app.goo.gl/291bCJ1zVqUhgktz6. The Forest soils were characterised as Alfisols, which are equivalent to Dystric Cambisols (IUSS Working Group WRB, 2015), and formed in granitic parent materials, in a temperate climate, under thinned, mixed-coniferous forest (Fig. S3; Gaudinski et al., 2009). With these analyses we aimed to answer the question, is calcium associated with a specific type of organic matter enriched in aromatic and phenolic carbon at the microscale in samples from Blodgett Forest Research Center? and how does this specific type of carbon respond to experiments targetted at removing and adding calcium to the soils, specifically cation exchange and incubation after calcium addition? Abstract from the paper can be found below: Calcium (Ca) may contribute to the preservation of soil organic carbon (SOC) in more ecosystems than previously thought. Here we provide evidence that Ca is co-located with SOC compounds that are enriched in aromatic and phenolic groups, across different acidic soil-types and locations with different ecosystem properties, differing in terms of climate, parent material, soil type, and vegetation. In turn, this co-localised fraction of Ca-SOC is removed through cation-exchange, and the association is then only re-established during decomposition in the presence of Ca (Ca addition incubation). Thus, highlighting a causative link between decomposition and the co-location of Ca with a characteristic fraction of SOC. Decomposition increases the relative proportion of negatively charged functional groups, which can increase the propensity for the association between SOC and Ca, and in turn, this association inhibits dissolved organic carbon export or further decomposition. We propose that this mechanism could be driven by Ca hotspots on the microscale shifting local decomposition processes and thereby explaining the colocation of Ca with SOC of a specific composition across different acidic soil environments. Incorporating this biogeochemical process into Earth System Models could improve our understanding, predictions, and management of carbon dynamics in soils, and account for their response to Ca-rich amendments.

54 ENVIRONMENTAL SCIENCES↗

GeoThermalCloud: Cloud Fusion of Big Data and Multi-Physics Models using Machine Learning for Discovery, Exploration, and Development of Hidden Geothermal Resources

The primary goals of this project are exploring hidden geothermal resources in the U.S.A. and designing profitable enhanced geothermal systems (EGS). Many processes and parameters control geothermal exploration and energy production from geothermal fields. Diverse datasets (e.g., geology, geochemistry, geophysics, satellite, airborne geophysics) are available to help characterize subsurface geothermal conditions. Sparse and multi-scale characteristics of these datasets prohibit properly leveraging these datasets for geothermal exploration and profitable EGS design. Recent advancements in machine learning (ML) promise to resolve these issues. The tremendous challenges and risks of geothermal exploration and production bring the demand for novel ML methods and tools that can (1) analyze large field datasets, (2) assimilate model simulations (large inputs and outputs), (3) process sparse datasets, (4) perform transfer learning (between sites with different exploratory levels), (5) extract hidden geothermal signatures in the field and simulation data, (6) label geothermal resources and processes, (7) identify high-value data acquisition targets, and (8) guide geothermal exploration and production by selecting optimal exploration, production, and drilling strategies. To address these necessities, ML-based geothermal resources exploration and enhanced geothermal systems (EGS) design tools have been developed. The exploration tool is called GeoThermalCloud and EGS design tool is called GeoDT-ML. GeoThermalCloud (https://github.com/SmartTensors/GeoThermalCloud.jl) utilizes a LANL unsupervised ML platform called SmartTensors (https://tensors.lanl.gov/) to automate data analyses and interpretations by extracting hidden signatures to identify geothermal prospects. Also, it enables the identification of critical measurements needed to identify geothermal resource signatures. Alternatively, GeoDT-ML (https://github.com/SmartTensors/GeoThermalCloud.jl/tree/master/EGS) is an ML-based alternative to GeoDT (https://github.com/GeoDesignTool/GeoDT.git), a fast, simplified multi-physics solver to evaluate EGS project designs in uncertain geologic systems. GeoDT-ML leverages recent advances in deep learning and high-performance computing. It is a faster and simpler version of GeoDT. To make this project a success, we used capabilities of LANL, PNNL, Google, Stanford, and Julia Computing. We analyzed eight datasets of the U.S.A. using GeothermalCloud and demonstrated potential highly prospective geothermal resources and identified key factors defining highly prospective sites. The first data set includes 44 locations in southwest New Mexico and 18 geological, hydrogeological, geophysical, geothermal, geochemical attributes. We defined low- and medium-temperature hydrothermal systems and discovered a new highly prospective site. The second data set analyzed 18 shallow water chemistry attributes at 14,342 locations in the Great Basin. It demarcated modestly, moderately, and highly prospective sites including key attributes for each type of prospectivity. The third data set analyzed Utah FORGE data including satellite (InSAR), geophysical (gravity, seismic), geochemical, and geothermal attributes. Here, we performed prospectivity analysis to identify future drilling locations using geological, geochemical, and geophysical attributes. Maps of temperature at depth and heat flow are constructed based on the available data. Prospectivity maps were generated, and drilling locations were proposed for future geothermal field exploration. The fourth data set analyzed 21 attributes at 120 locations in Tularosa Basin, New Mexico; data comes from past play fairway analyses in this region. ML analyses identified geothermal signatures associated with modestly, moderately, and highly hydrothermal systems. We also defined dominant attributes and spatial distribution of the geothermal signatures. The fifth, sixth, seventh, and eighth datasets include Tohatchi Springs, New Mexico, Hawaii, Brady site, Nevada, and EGS Collab, respectively. Moreover, we coupled GeothermalCloud and magnetotellurics data to pinpoint drilling locations for developing geothermal projects in the Tularosa Basin, New Mexico. GeothermalCloud found potential prospective locations for geothermal resources near White Sands Missile Range and McGregor Range at Fort Bliss. Magnetotellurics data determined the potential depth (~1800m) of geothermal prospects at McGregor Range based on apparent resistivity structures/layers in the subsurface. The McGregor Range consists of three resistivity layers and two resistivity structures. Magnetotellurics data also helps identify that the western portion of the McGregor Range has thick and low-resistivity earth materials. The low resistivity to the west is most likely for a fault system. Assuming temperature is consistent with a geothermal reservoir, the west-central part of the McGregor Range has the highest geothermal potential because of the increase in porosity and associated permeability attributed to the interpreted fault system. Also, we devised a coupling strategy between a process model and GeothermalCloud to characterize hydrogeological conditions and geothermal conditions, respectively. The process model characterizes hydrogeological and geothermal conditions on highly prospective geothermal sites provided by GeothermalCloud. We developed a physics-informed neural network (PINN) version of the Burns equation that can be easily coupled with GeothermalCloud. Furthermore, we performed an optimal design decision maximizing the economic value of an EGS power plant. This study optimized the range of well spacing between injection and production wells maximizing net present value in dollars (NPV). For this task, we used the GeoDT to simulate the Utah FORGE EGS development cycle from the initial well design to the end of production. Next, we accomplished another crucial task, which is predicting permeability of geothermal reservoirs. Predicting permeability of geothermal reservoirs is a non-trivial task because of huge computational runtime of simulation and lack of measurements. To avoid these limitations, we used easy-to-measure chemical concentrations in the subsurface as measurement data and convolutional neural network based ML model of a high-fidelity model. Next, we predicted permeability using Markov chain Monte Carlo simulation. We found that Markov chain Monte Carlo simulation predicts permeability with a high certainty if the prediction zone in the simulation area has chemical concentration data. Finally, we analyzed the DOE funded INGENIOUS and GeoDAWN projects data. For discovering hidden geothermal systems in the Great Basin, the INGENIOUS project accumulated old data, collected new data, and released them in 2022. The dataset includes a total of 24 geological, geophysical, and geochemical attributes. Data resolution and scale significantly vary prohibiting an appropriate usage. To avoid such limitations, we brought all data in the same resolution and scale by applying the inverse distance weighting interpolation technique for predicting data in unsampled locations. Subsequently, we analyzed LiDAR data of the GeoDAWN project. We received data in tiles format. The DOE’s overarching goal is to use ML on LiDAR data for finding favorable geological structures (e.g., step up faults in Brady, Nevada). To serve the purpose, we need to label favorable geologic structures that correspond to LiDAR data. We wrote an algorithm to label the LiDAR data with the favorable geologic structures.

15 GEOTHERMAL ENERGY↗

Code for the manuscript "Mori-Zwanzig Modal Decomposition"

We would like to create an open source repository in LANL's github on code written in Julia, in which we implement and extend the data-driven Mori-Zwanzig method for extracting large-scale spatio-temporal structures from data, which we call MZMD. This method is an extension of Dynamic Mode Decomposition (DMD) in which Mori-Zwanzig memory kernels are included into the associated companion matrix. In the code we would like to release, we apply MZMD to a flow over a cylinder with Reynolds number 100 rather than the much larger data set used in the associated manuscript. DMD is used extensively in the fluid dynamics community mainly for extracting large scale spatio-temporal structures (patters) from flow data. This is useful for understanding the key mechanisms that generate certain complex dynamical process relevant in engineering design. In MZMD, we improve upon DMD by adding the Mori-Zwanzig memory kernels, and show this improvement is especially important in strongly nonlinear regions of the flow.

Woodward, Michael↗

Hyper Spectral Anomaly Detection

The HSA is a statistics based anomaly detection model. The model performs unsupervised anomaly detection, based on a datapoint's density and similarity within a dataset. Density and similarity data are encoded into an affinity matrix. The affinity matrix is evolved to summarize the data's structure on greater topographical scales within the data's function space. The set of evolved affinity matrices and an anomaly score vector are passed to a user defined penalized objective function. The penalized objective function of anomaly scores is then minimized. Data points where the absolute value of the z-scores of anomaly scores greater than a specified threshold are predicted as anomalies. A novel multi-filter feature has also been implemented. To reduce false positive rates, the multi-filter records the indexes of the HSA predictions. A new dataset and data loader are instantiated consisting of all the initial HSA predictions and non-anomalous data points in a 10% and 90% split respectively. The HSA is then run through this data set and a count of number of times a data point is predicted is kept. In this way the initial predictions may be compared with data spanning the entire dataset. After the multi-filter is complete, all datapoints will have an associated anomaly score, as well as a multi-filter prediction count to further filter the anomalous predictions.

Rogers, DempseyD [Idaho National Laboratory (INL),↗

Data for: Subsurface Interface Structure Controlling Local Electronic Properties of Epitaxial Graphene on SiC(0001)

Recently realized high-mobility semiconducting epitaxial graphene on silicon carbide, provided an important step towards integration of the graphene-based system into active components in post-silicon micro- and nano-electronics. However, the exact atomic-scale structure and the complex bonding configurations of the first epitaxial graphene carbon layer remain an open problem. Our recent report has shed new light on understanding this interface, where the external transverse electric field-dependent dynamic switching behavior of the Cbuffer-SiC bonds was observed. Here, using scanning tunneling microscopy and spectroscopy (STM and STS), we present the direct evidence of silicon (Si) vacancies at the interface and provide their distribution at the topmost reconstructed SiC(0001) layer. Experimental STM and density functional theory modeling data were used in the preparation of figures in a published article in the Journal of Physical Chemistry Letters. Files related to the figures and supplementary materials in the article are present in this dataset in .txt format.

Condensed matter imaging↗

Data for: Subsurface Interface Structure Controlling Local Electronic Properties of Epitaxial Graphene on SiC(0001)

Recently realized high-mobility semiconducting epitaxial graphene on silicon carbide, provided an important step towards integration of the graphene-based system into active components in post-silicon micro- and nano-electronics. However, the exact atomic-scale structure and the complex bonding configurations of the first epitaxial graphene carbon layer remain an open problem. Our recent report has shed new light on understanding this interface, where the external transverse electric field-dependent dynamic switching behavior of the Cbuffer-SiC bonds was observed. Here, using scanning tunneling microscopy and spectroscopy (STM and STS), we present the direct evidence of silicon (Si) vacancies at the interface and provide their distribution at the topmost reconstructed SiC(0001) layer. Experimental STM and density functional theory modeling data were used in the preparation of figures in a published article in the Journal of Physical Chemistry Letters. Files related to the figures and supplementary materials in the article are present in this dataset in .txt format.

Condensed matter imaging↗

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗

Data for: Miscanthus × giganteus changes soil structure and increases maximum water holding capacity

The data provided include results from a comparative study evaluating the impact of Miscanthus × giganteus (miscanthus) versus maize on soil structural properties and maximum water holding capacity (MWHC) across two Iowa sites. The dataset includes MWHC values determined using the Funnel Filter Paper Drainage (FFPD) method, as well as additional measurements of MWHC following structural disruption of the soil to isolate the effect of aggregation. It also contains three-dimensional micro-computed tomography (microCT) data used to quantify total porosity and pore size distribution (PSD) of soil aggregates at a 5 µm resolution. All data are provided as raw replicate-level measurements, organized by site, crop, and depth, along with processed summary files in table form in CSV (.csv) format to support reproducibility and downstream analysis.

Misanthus x giganteus↗

Learning of networked spreading models from noisy and incomplete data

Recent years have seen a lot of progress in algorithms for learning parameters of spreading dynamics from both full and partial data. Some of the remaining challenges include model selection under the scenarios of unknown network structure, noisy data, missing observations in time, as well as an efficient incorporation of prior information to minimize the number of samples required for an accurate learning. Here, in this work, we introduce a universal learning method based on a scalable dynamic message-passing technique that addresses these challenges often encountered in real data. The algorithm leverages available prior knowledge on the model and on the data, and reconstructs both network structure and parameters of a spreading model. We show that a linear computational complexity of the method with the key model parameters makes the algorithm scalable to large network instances.

97 MATHEMATICS AND COMPUTING↗