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DOE OSTI2023

Multipoint Turbulence Analysis with HelioSwarm

Exploration of plasma dynamics in space, including turbulence, is entering a new era of multisatellite constellation measurements that will determine fundamental properties with unprecedented precision. Familiar but imprecise approximations will need to be abandoned and replaced with more-advanced approaches. We present a preparatory study of the evaluation of second- and third-order statistics, using simultaneous measurements at many points. Here, for specificity, the orbital configuration of the NASA Swarm mission is employed in conjunction with 3D magnetohydrodynamics numerical simulations of turbulence. The HelioSwarm nine-spacecraft constellation flies virtually through the turbulence to compare results with the exact numerical statistics. We demonstrate novel increment-based techniques for the computation of (1) the multidimensional spectra and (2) the turbulent energy flux. This latter increment-space estimate of the cascade rate, based on the third-order Yaglom–Politano–Pouquet theory, uses numerous increment-space tetrahedra. Our investigation reveals that HelioSwarm will provide crucial information on the nature of astrophysical turbulence.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Coronaviruses (Coronaviridae) such as SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus) and MERS‐CoV (Middle East respiratory syndrome coronavirus) have been the source of recent outbreaks and global health concerns. While vaccines have been essential for controlling the SARS‐CoV‐2 (COVID‐19) pandemic, it is uncertain whether they will be effective against future coronavirus strains. Therefore, identification or design of a broad‐spectrum drug that targets highly conserved regions of the main protease of multiple coronavirus strains is essential in the long term. As part of a virtual summer research experience with the RCSB PDB, bioinformatics tools were employed to predict and construct 3D models of the coronavirus main protease (MPro) using SARS‐CoV‐2 as the template, with a focus on mutational trends and active sites. This study focused on the active sites of MPro, a cysteine protease essential for viral assembly and replication. Sequence alignments and structure modeling of MPro structures has identified conserved regions across multiple coronavirus strains. Inhibition of MPro halts coronavirus replication, making it an ideal drug target, and studies of MPro may foster and accelerate the discovery of high affinity broad‐spectrum drugs.

Wu Wu, Amy↗

DOE OSTI2020

Performance Evaluation of Augmented Teleoperation of Contact Manipulation Tasks

At Argonne National Laboratory, an enhanced telerobotic concept has been suggested by providing augmented virtual fixtures for precise and dexterous manipulation. The proposed technology incorporated a human-robot interface that can assist personnel on the processes of Deactivation and Decommissioning in sites of high radiation. It has been implemented on a dual-arm robot system, known as Baxter, by integrating the Robotic Operating System (ROS) with 3D sensors and visual-haptic operator interface. However, what remained before its practical utilization is the capability for precisely placing the virtual fixtures. To this end, the objectives involved camera calibration, which required hardware fabrication and setup, as well as modification and implementation of ROS. The goal of this Research and Development is to develop an augmented-reality- based operator interface for human-inclusive, intelligent, and autonomous robotic system for the Deactivation and Decommissioning (D and D) of radioactive sites. The objectives are to develop: Collaborative Robot; Multi-modal Mixed-Reality Human-Robot Interface; Intelligent and Autonomous Behaviors. In order to achieve this, Baxter's Head-Kinect camera and Left-Hand camera need to be calibrated to overlap the real environment with the simulated environment. Camera calibration, which is crucial for precisely placing the virtual fixtures, was successful after running the simulations. The real and simulated environments overlapped, permitting the utilization of augmented teleoperation and the dexterous manipulation of Baxter for D and D applications in nuclear sites. Future steps: Performance evaluation of augmented teleoperation of contact manipulation tasks: Multiple-Camera 3D Reconstruction and Automation. Oculus Interface: Augmented reality and machine learning for enhanced telerobotic operation (Augmented Tele-autonomy): Machine-learning techniques for complex and flexible autonomous robotic behaviors. Interactive remote operation of robotic systems. Mesh cutting with simulation and real robot.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Radsource Mr: Mixed Reality Planning Tool For Radioactive Recovery

The RadSource MR system leverages Meta Quest 3's advanced mixed reality capabilities to create a comprehensive spatial planning platform for end-of-life sealed radioactive source recovery operations. The application utilizes the Quest 3's high-resolution passthrough cameras and spatial mapping algorithms to generate accurate 3D environmental models. Core technical components include: (1) Real-time spatial measurement algorithms calculating distances, angles, slopes, and surface areas with sub-centimeter accuracy; (2) Virtual object placement system allowing users to position digital representations of recovery equipment (trailers, containment vessels, protective barriers) within the real environment; (3) Voice recording and annotation system for hands-free documentation in protective equipment; (4) 3D mesh capture and storage capabilities for post-operation analysis and regulatory documentation. (5) Procedure documentation is available for viewing in Mixed Reality, providing an innovative and convenient way to access the information during pre-visit and inspection activities. (6) Support for screen capture for the view for real world and virtual objects together to use it later for planning. The system integrates computer vision techniques for environmental understanding, spatial mathematics for precise measurements, and human-computer interaction principles optimized for hazardous environment operations. Data persistence allows teams to save and share planning sessions across multiple stakeholders while maintaining operational security requirements.

Khadka, Rajiv [Idaho National Laboratory (INL), Id↗

DOE OSTI2024

Spin-Controllable Dynamics in Defect-Engineered Carbon Nanotubes as Single Photon Emitters: Data-Driven Modeling and Computations

Quantum technologies, such as quantum computing and sensing, require efficient single-photon emission (SPE) sources that operate at room temperature in telecom wavelengths. While several materials can serve as SPE sources, no single platform meets all the criteria for efficiency, ambient operation, and scalability. Single-walled carbon nanotubes (SWCNTs) with covalently attached molecules offer a promising solution. Their SPE can be easily tuned via modifications of the SWCNT's diameter, chirality, and bonded molecules, enabling emission across near-IR to telecom wavelengths at ambient conditions. However, to fully realize the potential of SWCNTs and unlock their quantum capabilities, a deeper understanding of how structural defects from molecular adducts affect their emission and competing photoexcited processes is essential. To address this gap in our knowledge, this project combined quantum chemistry calculations with data-driven methods of cheminformatics (QSAR) and machine learning (ML). The developed computational approaches have provided several design strategies for covalent functionalization of SWCNTs to improve their optical response. The collaboration with Los Alamos National Lab (LANL) enabled direct comparison of computational and experimental data, facilitating method validation. This partnership was enhanced through access to LANL's Center for Integrated Nanotechnologies (CINT) utilizing User Facility Program and summer internships, which provided three NDSU graduate students with hands-on experience at LANL. The outcomes of this project included (1) Advancing the current stage of computational methods in accurate modeling of non-adiabatic spin-dependent photoexcited dynamics and its applicability to nanosystems consisting of thousands of atoms, realized as open-access codes linked to existing DFT-based software; (2) Establishing the relationship between the structure of adducts and SWCNTs and intrinsic excitonic and spin properties of defect states for guiding novel synthetic strategies and experimental probes of chemically functionalized SWCNTs as near-IR emitting materials; (3) Generating virtual libraries of hypothetical functionalized SWCNTs for virtual screening of their chemical structures and optical properties, leveraging new functionalities of SWCNTs; (4) Offering a unique experience for NDSU graduate students that prepared them for future scientific careers related to materials modeling and big data processing. These results were summarized in 12 published journal papers and 3 recently submitted papers. One of a key finding is that the position of defect sites on the SWCNT surface primarily drives the emission redshift (up to 100 meV), while the polarity of the defect-inducing molecules has a much smaller effect (~10 meV). However, the electron-donating or withdrawing properties of a molecule influence selecting reactivity of defect sites. These insights important for optimizing synthetic protocols for desired emissions in SWCNTs. We also revealed that the interaction between two defects at various positions on the SWCNT enhances the redshift and optical activity of states, favoring strong near-IR emission. This suggests that manipulations in defect concentrations is a promising strategy for controlling efficient emission. Mostly important, the defect position was found controllable by the spin states of photoexcited intermediates: Excited aromatic molecules form ortho defects with SWCNTs at their singlet states in the presence of oxygen, while oxygen-free conditions favor para defects via the triplet-state mechanism. Additionally, a heat-activated [2+2] cycloaddition reaction facilitates divalent defect formation with fewer bonding positions that narrows emission bands. These groundbreaking findings have been experimentally validated and significantly advance our understanding of defect chemistry in SWCNTs. Using a novel encoding technique and 3D-MoRSE descriptors, we developed highly accurate ML/QSAR models to predict both the 3D structure and optical properties of SWCNTs with chemical defects. This model enabled the creation of a virtual library of 125,556 structures, providing new insights into the relationship between SWCNT-defect structure and emission.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

Microstructure-Based Estimation of Strength and Ductility Distributions for \(\alpha +\beta \) Titanium Alloys

Titanium alloys are processed to develop a wide range of microstructure configurations and therefore material properties. While these properties are typically measured experimentally, a framework for property prediction could greatly enhance alloy design and manufacturing. In this work, a microstructure-sensitive framework is presented for the prediction of strength and ductility as well as estimates of the bounds in variability for these properties. The framework explicitly considers distributions of microstructure via new approaches for instantiation of structure in synthetic samples. The parametric evaluation strategy, including the finite element simulation package FEpX, is used to create and test virtual polycrystalline samples to evaluate the variability bounds of mechanical properties in Ti-6Al-4V. Critical parameters for the property evaluation framework are provided by measurements of single crystal properties and advanced characterization of microstructure and slip system strengths in 2D and 3D. Property distributions for yield strength and ductility are presented, along with the validation and verification steps undertaken. Comparisons between strain localization and slip activity in virtual samples and in experimental grain-scale strain measurements are also discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Direct observation of 3D topological spin textures and their interactions using soft x-ray vector ptychography

Magnetic topological defects are energetically stable spin configurations characterized by symmetry breaking. Vortices and skyrmions are two well-known examples of 2D spin textures that have been actively studied for both fundamental interest and practical applications. However, experimental evidence of the 3D spin textures has been largely indirect or qualitative to date, due to the difficulty of quantitively characterizing them within nanoscale volumes. Here, we develop soft x-ray vector ptychography to quantitatively image the 3D magnetization vector field in a frustrated superlattice with 10 nm spatial resolution. By applying homotopy theory to the experimental data, we quantify the topological charge of hedgehogs and anti-hedgehogs as emergent magnetic monopoles and probe their interactions inside the frustrated superlattice. We also directly observe virtual hedgehogs and anti-hedgehogs created by magnetically inert voids. We expect that this new quantitative imaging method will open the door to study 3D topological spin textures in a broad class of magnetic materials. Our work also demonstrates that magnetically frustrated superlattices could be used as a new platform to investigate hedgehog interactions and dynamics and to exploit optimized geometries for information storage and transport applications.

Rana, A↗

DOE OSTI2023

Coupling of CTF and RELAP5-3D Within an Enhanced Fidelity Nuclear Power Plant Simulator

A robust and accurate multiphysics engineering simulator is being developed to model the core behavior and system response of pressurized water reactors. This simulator relies on the NESTLE and CTF computer codes to model the neutronics and thermal hydraulics (TH), respectively, inside the core on a nodal scale and on the Reactor Excursion and Leak Analysis Program—Three Dimensional (RELAP5-3D) to model the entire nuclear steam supply system. The RELAP5-3D model includes highly detailed nodalization and multidimensional flow modeling throughout the vessel. Previously, pin-resolved data generated via the Virtual Environment for Reactor Analysis core simulator were used to improve the accuracy of the NESTLE core predictions. The engineering simulator being developed as part of this work uses the 3KEYMASTER platform to couple the enhanced NESTLE model to a nodal-fidelity CTF model to balance run time with accuracy; NESTLE provides node-dependent powers to CTF, and CTF provides node-dependent coolant densities and fuel temperatures to NESTLE.An overlapping domain approach is used for the core TH in which RELAP5-3D provides core boundary conditions based on the system response and CTF provides a node-dependent coolant heating rate to the RELAP5-3D core solution. In the preliminary TH demonstration discussed in this paper, CTF and RELAP5-3D provided similar steady-state core predictions, indicating the hydraulic compatibility between the codes, as well as reasonable and expected behavior under hypothetical transient conditions. This provides an initial step in ongoing efforts toward a robust, multiscale TH/neutronics engineering simulator capability.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2025

Generating multi-scale Li-ion battery cathode particles with radial grain architectures using stereological generative adversarial networks

Abstract Understanding structure-property relationships of Li-ion battery cathodes is crucial for optimizing rate-performance and cycle-life resilience. However, correlating the morphology of cathode particles, such as in LiNi0.8Mn0.1Co0.1O2 (NMC811), and their inner grain architecture with electrode performance is challenging, particularly, due to the significant length-scale difference between grain and particle sizes. Experimentally, it is not feasible to image such a high number of particles with full granular detail. A second challenge is that sufficiently high-resolution 3D imaging techniques remain expensive and are sparsely available at research institutions. Here, we present a stereological generative adversarial network-based model fitting approach to tackle this, that generates representative 3D information from 2D data, enabling characterization of materials in 3D using cost-effective 2D data. Once calibrated, this multi-scale model can rapidly generate virtual cathode particles that are statistically similar to experimental data, and thus is suitable for virtual characterization and materials testing through numerical simulations. A large dataset of simulated particles with inner grain architecture has been made publicly available.

25 ENERGY STORAGE↗

DOE OSTI2024

Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures

Decades of drug development research have explored a vast chemical space for highly active compounds. The exponential growth of virtual libraries enables easy access to billions of synthesizable molecules. Computational modeling, particularly molecular docking, utilizes physics-based calculations to prioritize molecules for synthesis and testing. Nevertheless, the molecular docking process often yields docking poses with favorable scores that prove to be inaccurate with experimental testing. To address these issues, several approaches using machine learning (ML) have been proposed to filter incorrect poses based on the crystal structures. However, most of the methods are limited by the availability of structure data. Here, we propose a new pose classification approach, PECAN2 (Pose Classification with 3D Atomic Network 2), without the need for crystal structures, based on a 3D atomic neural network with Point Cloud Network (PCN). The new approach uses the correlation between docking scores and experimental data to assign labels, instead of relying on the crystal structures. We validate the proposed classifier on multiple datasets including human mu, delta, and kappa opioid receptors and SARS-CoV-2 Mpro. Our results demonstrate that leveraging the correlation between docking scores and experimental data alone enhances molecular docking performance by filtering out false positives and false negatives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Advanced two-phase subchannel method via non-linear iteration

A fast-running, robust two-phase flow, sub-channel model is presented based on non-linear solution of the steady-state subchannel fluid flow equations. The drift-flux model solves for conservation of liquid and vapor mass, mixture energy, and axial and transverse mixture momentum as part of an efficient planar marching scheme and nonlinear, nested outer and inner iteration. Here, models based on mechanistic subcooled boiling, two-phase turbulent void mixing, and drift are included. Solution verification and mesh convergence studies were performed for modern GE 10 × 10 fuel geometry and are shown to have excellent convergence behavior. Run time performance for a 50 axial mesh model showed 2.2 seconds on a single CPU core to tightly converge all 3D distributions (flow, void, pressure) for the GE 10 × 10 fuel geometry, supporting its efficient use within the Virtual Environment for Reactor Applications boiling water reactor framework.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Computing virtual dark-field X-ray microscopy images of complex discrete dislocation structures from large-scale molecular dynamics simulations

Dark-field X-ray microscopy (DFXM) is a novel diffraction-based imaging technique that non-destructively maps the local deformation from crystalline defects in bulk materials. While studies have demonstrated that DFXM can spatially map 3D defect geometries, it is still challenging to interpret DFXM images of the high-dislocation-density systems relevant to macroscopic crystal plasticity. This work develops a scalable forward model to calculate virtual DFXM images for complex discrete dislocation structure(s) (DDS) obtained from atomistic simulations. Our new DDS-DFXM model integrates a non-singular formulation for calculating the local strain from the DDS and an efficient geometrical optics algorithm for computing the DFXM image from the strain field. We apply the model to complex DDS obtained from a large-scale molecular dynamics simulation of compressive loading on single-crystal silicon. Simulated DFXM images exhibit prominent contrast for dislocation features between the multiple slip systems, demonstrating the potential of DFXM to resolve features from dislocation multiplication. In conclusion, the integrated DDS-DFXM model provides a toolbox for DFXM experimental design and image interpretation in the context of bulk crystal plasticity for a range of measurements across shock plasticity and the broader materials science community.

X-ray imaging↗

DOE OSTI2024

Unleashing the potential of waste: A supercharged high-performance 3D printing resin from discarded polylactic acid

In additive manufacturing/3D printing, the limitation no longer lies in people’s imagination but in the very materials that one can print with. While the additive manufacturing process can virtually create any geometry, available applications are often limited by factors like parts’ mechanical strength, glass transition temperature, and heat deflection temperature. These factors are especially critical for polymer-based printing. Here we introduce a simple formulation derived from the aminolysis of polylactic acid (PLA) plastic waste, namely the N-lactoyl ethanolamine (N-LEA). The N-LEA is next reacted with excess methacrylic anhydride, forming a photo-crosslinkable resin for MSLA 3D printing. The resulting 3D printed part has a set of impressive properties that is unrivaled amongst engineering grade 3D printing resins on the market and research literature. The 3D printed part has an ultrahigh tensile strength of 131.7 MPa, glass transition at ~190 °C, and heat deflection temperature at 162.6 °C. Furthermore, this work demonstrates a true upcycling approach for turning PLA waste into a value-added product in a simple and efficient manner while also expanding the high-performance material portfolio available for photocuring additive manufacturing.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Virtual prototyping of liquid metal blanket performance in fusion pilot plant

Liquid metal blanket is a dominant design option for the next step fusion devices responsible for harvesting energy from fusion reaction, and simultaneously producing fuel for the same reaction through tritium breeding. Liquid metal blankets introduce additional complexity to the design due to fluid motion, fluid structure interaction, and magnetohydrodynamic (MHD) effects arising from the motion of the conducting fluid through the magnetic field. They are also directly affected by the plasma heat flux and neutronic fluence. PPPL is currently developing a virtual prototyping system for numerical analysis of the liquid metal blankets for future fusion devices. The system has a customized 3D computational fluid dynamics (CFD) code in its core, allowing MHD flow and conjugate heat transfer analysis in blankets fluids and solids. The code was successfully used before for dual coolant blanket analysis [A. Khodak et al., Fusion Eng. and Des. 137 (2018)]. Recently the same code was modified to allow verified simulation of MHD flows at high Hartmann numbers of several thousand typical for blanket applications. CFD code receives volumetric heat source distribution from the neutronic analysis based on MCNP code. In addition, direct tritium breeding simulation will be performed allowing optimization of the blanket performance. 2D axisymmetric version of neutronics code will be used for rapid optimization, with 3D version employed for detailed analysis. The surface heat distribution on the plasma facing wall will be defined by the software HEAT allowing 3D modeling of the heat flux based on the magnetic field distribution including gyro-orbit effects. Results of thermal analysis are imported into structural analysis code also included in the system. Finally, direct import of CAD geometry will be used for analyzing all components and as a result design option can be efficiently optimized.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

SoLID Program at JLab

An overview of the Solenoidal Large Intensity Device (SoLID) and its scientific program will be given in this talk. SoLID is a spectrometer/detector system proposed to exploit the full potential of the Jefferson Lab (JLab) 12 GeV energy upgrade. SoLID will push the limit of luminosity frontier in hadronic physics with its unique capability to handle very high rates with large acceptance under high luminosity (1037-39/cm2/s). A rich and vibrant scientific program has been developed for SoLID, including but not limited to the precision study of the 3d nucleon structure in both momentum space using Semi-Inclusive Deep Inelastic Scattering (SIDIS) and coordinate space using Deep Virtual Exclusive Reactions (DVER), probing physics beyond the Standard Model with Parity Violating Deep Inelastic Scattering (PVDIS), and investigating the gluonic field contribution to the proton structure and proton mass via J/¿ threshold production. The SoLID collaboration has developed a robust, low risk and flexible conceptual design, with a base line design capable of accomplishing its scientific goals and flexibility to adopt the cutting-edge technology. Detector subsystems have been tested with prototypes in realistic high luminosity conditions and are demonstrated to function well under extremely challenging environment to satisfy the requirements of planned experiments.

Chen, Jian-Ping [Thomas Jefferson National Acceler↗

DOE OSTI2023

MATBOX, an Open-Source Microstructure Analysis Toolbox for Meshing, Generation, Segmentation, and Characterization of 3D Heterogenous Volumes

Battery performance is strongly correlated with electrode microstructural properties. To account for its impact, lithium-ion battery (LIB) models either abstract the microstructural heterogeneity of composite electrodes using effective macroscopic properties (macro- or meso- scale models) or directly solve the system of equations on the microstructure geometry or mesh (microstructure-scale models). Therefore, to be adequate, both families of models require information from the microstructure geometry, which can be provided by the numerical tool presented in this work. MATBOX is a MATLAB open-source application [1] developed by NREL for performing various microstructure-related tasks including microstructure numerical generation, image filtering and microstructure segmentation, microstructure characterization and correlation, visualization, and microstructure meshing. MATBOX was originally developed for the analysis of LIB electrode microstructures; however, the algorithms provided by the toolbox are widely applicable to other heterogeneous materials. The toolbox provides a user-friendly experience thanks to a Graphical-User Interface, requires no coding by the user, and is well documented. This presentation will illustrate various MATBOX features for the characterization of a LIB electrode, including a fully automated Representative Volume Element (RVE) analysis, the numerical generation of complex 'virtual' microstructure, including dual-layer electrodes and carbon-binder additive phase, and the meshing of a complex NMC/graphite full cell microstructure suitable for 3D finite-element modeling. Other modules (segmentation, visualization, and correlation) will be briefly presented. Thanks to its modular, open-source approach, MATBOX can easily incorporate third-party algorithms to eventually build a standard in the field that will benefit the whole scientific community. Effective diffusion coefficient [2], additive phase numerical generation [3], and meshing [4] third-party algorithms have been already integrated in the toolbox with more to come.

DIRECT ENERGY CONVERSION,MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Many-body expansion based machine learning models for octahedral transition metal complexes

Abstract Graph-based machine learning (ML) models for material properties show great potential to accelerate virtual high-throughput screening of large chemical spaces. However, in their simplest forms, graph-based models do not include any 3D information and are unable to distinguish stereoisomers such as those arising from different orderings of ligands around a metal center in coordination complexes. In this work we present a modification to revised autocorrelation descriptors, a molecular graph featurization method, for predicting spin state dependent properties of octahedral transition metal complexes (TMCs). Inspired by analytical semi-empirical models for TMCs, the new modeling strategy is based on the many-body expansion (MBE) and allows one to tune the captured stereoisomer information by changing the truncation order of the MBE. We present the necessary modifications to include this approach in two commonly used ML methods, kernel ridge regression and feed-forward neural networks. On a test set composed of all possible isomers of binary TMCs, the best MBE models achieve mean absolute errors (MAEs) of 2.75 kcal mol −1 on spin-splitting energies and 0.26 eV on frontier orbital energy gaps, a 30%–40% reduction in error compared to models based on our previous approach. We also observe improved generalization to previously unseen ligands where the best-performing models exhibit MAEs of 4.00 kcal mol −1 (i.e. a 0.73 kcal mol −1 reduction) on the spin-splitting energies and 0.53 eV (i.e. a 0.10 eV reduction) on the frontier orbital energy gaps. Because the new approach incorporates insights from electronic structure theory, such as ligand additivity relationships, these models exhibit systematic generalization from homoleptic to heteroleptic complexes, allowing for efficient screening of TMC search spaces.

Meyer, Ralf (ORCID:0000000322360261)↗

DOE OSTI2022

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

59 BASIC BIOLOGICAL SCIENCES↗