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DOE OSTI2024

Drugging the entire human proteome: Are we there yet?

Each of the ~20 000 proteins in the human proteome is a potential target for compounds that bind to it and modify its function. The 3D structures of most of these proteins are now available. Here, we discuss the prospects for using these structures to perform proteome-wide virtual HTS (VHTS). Furthermore, we compare physics-based (docking) and AI VHTS approaches, some of which are now being applied with large databases of compounds to thousands of targets. Although preliminary proteome-wide screens are now within our grasp, further methodological developments are expected to improve the accuracy of the results.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Toward a Smart Metaverse City: Immersive Realism and 3D Visualization of Digital Twin Cities

Metaverse and its related extended reality technologies can enable immersive, realistic, and participatory visualization of 3D data, and their use and the potential within a smart city can be effective for supporting urban research and urban operations management. This book chapter describes a vision for prototyping a “Smart Metaverse City” to combine the unique advantage of the Metaverse technology with the two-way connectivity of a digital twin city application. This synergy aims to create a virtual environment for immersive geovisualization to help researchers and the public understand the complex urban system through science-based and data-driven approaches. This book chapter selectively reviews past technological and paradigm advancements for collecting, analyzing, and visualizing 3D urban big data. Then we present a prototyping Geographic Information System (GIS) framework, together with some relevant data sources and open-source web technologies, to help researchers create a smart Metaverse city. We demonstrate our vision and discuss its application opportunities through a real-world example, a digital twin city developed at the Oak Ridge National Laboratory, to facilitate participatory, smart, and sustainable campus management.

Xu, Haowen↗

DOE OSTI2026

Smart Planning for Radioactive Source Transport Advanced Tools for Increased Safety and Efficiency

End-of-life (EOL) management of high-activity radioactive sources is made uniquely challenging by the inherent risks associated with storage and transportation of these sources, the complex logistics involved, and the strict requirements for regulatory compliance. Traditional methods lack comprehensive tools for accurate site assessments and precision planning for the transportation of radioactive sources. They also frequently fail to provide the adaptability required to consider diverse operational environments, resulting in inefficiencies and potential safety concerns. This paper introduces a novel software solution developed to address these issues by integrating advanced technologies such as light detection and ranging (LiDAR)-based 3D environment modeling, smart dynamic route planning, and customizable measurement functionalities. This software enables detailed terrain visualizations, facilitating thorough environmental assessments and enabling users to virtually navigate, analyze, and plan site-specific operations. Among the key features are a user-centric interface for virtual navigation, precise site measurement tools for site evaluations, interactive visualizations that highlight potential operational hazards, dynamic route planning capabilities, and real-time collision detection to promote safe workflows. By demonstrating the effectiveness of this tool through real-world application, the present work underscores the tool’s potential to revolutionize radioactive source EOL management by improving operational efficiencies, minimizing risk, and advancing the state of practice to achieve suitable and secure radioactive material handling.

99 - GENERAL AND MISCELLANEOUS↗

DOE OSTI2021

Harmonic generation predominantly from a single spin channel in a half metal

Harmonic generation in atoms and molecules has reshaped our understanding of ultrafast phenomena beyond the traditional nonlinear optics and has launched attosecond physics. Harmonics from solids represent a new frontier, where both majority and minority spin channels contribute to harmonics. This is true even in a ferromagnet whose electronic states are equally available to optical excitation. In this work, we demonstrate that harmonics can be generated {mostly} from a single spin channel in half metallic chromium dioxide. An energy gap in the minority channel greatly reduces the harmonic generation, so harmonics predominantly emit from the majority channel, with a small contribution from the minority channel. However, this is only possible when the incident photon energy is well below the energy gap in the minority channel, so all the transitions in the minority channel are virtual. The onset of the photon energy is determined by the transition energy between the dipole-allowed transition between the O-$2p$ and Cr-$3d$ states. Harmonics mainly from a single spin channel can be detected, regardless of laser field strength, as far as the photon energy is below the minority band energy gap. This prediction should be tested experimentally

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

CO 2 Injection Monitoring with a Scalable, Automated Sparse Seismic Array

Conference presentation at American Institute of Chemical Engineers (AIChE) Annual Meeting, Virtual, November 16–20, 2020. The scalable, automated sparse seismic array (SASSA) method has been ideated as a cost-effective alternative or complementary to conventional 3D seismic methods. Based on a sparse array of receivers deployed strategically on Earth’s surface and one or more fixed seismic sources, the SASSA method can be used to study specific portions of the subsurface to detect the movement of CO 2 in a reservoir with lower environmental footprint and shorter turnaround time to deliver results than conventional 3D seismic methods. Energy & Environmental Research Center (EERC) carried out seismic monitoring of an oilfield undergoing CO 2 enhanced oil recovery in Montana, USA, using the SASSA method.

02 PETROLEUM↗

DOE OSTI2020

3D micromechanical simulation of PBX composites

Previous research studied the constitutive response and interface strength of a bonded bicrystal system containing two HMX explosive grains bound with a HTPB polymer binder by performing FE simulations on real geometry imaged with micro Computed Tomography (µCT). The parameters generated from this past study were successfully applied to 2D mesoscale simulations of µCT imaged HMX-HTPB polycrystal samples. Presently, the mechanical response of PBXs containing a Nitro-Plasticized Estane (NPE) binder with similar microstructural geometry to the HMX-HTPB polycrystal samples were studied. Imaging of a HMX-NPE bicrystal sample allowed for simulation of the new material pairing. However, imaging using µCT techniques on the new polycrystal samples was difficult due to the decrease in contrast between the HMX grains and the NPE binder. Mesoscale polycrystal simulations utilizing a single µCT imaged microstructure were performed on a 3D representative volume element (RVE) comparing the delamination behavior and mechanical response of both HMX-HTPB and HMX-NPE PBXs. Furthermore, this technique shows the ability to virtually explore the mechanical response of a range of hypothetical materials that share common microstructural geometric characteristics in addition to studying numerically altered geometries.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Three-dimensional topological magnetic monopoles and their interactions in a ferromagnetic meta-lattice

Topological magnetic monopoles (TMMs), also known as hedgehogs or Bloch points, are three-dimensional (3D) nonlocal spin textures that are robust to thermal and quantum fluctuations due to the topology protection. Although TMMs have been observed in skyrmion lattices, spinor Bose–Einstein condensates, chiral magnets, vortex rings and vortex cores, it has been difficult to directly measure the 3D magnetization vector field of TMMs and probe their interactions at the nanoscale. Here, we report the creation of 138 stable TMMs at the specific sites of a ferromagnetic meta-lattice at room temperature. We further develop soft x-ray vector ptycho-tomography to determine the magnetization vector and emergent magnetic field of the TMMs with a 3D spatial resolution of 10 nm. This spatial resolution is comparable to the magnetic exchange length of transition metals, enabling us to probe monopole-monopole interactions. We find that the TMM and anti-TMM pairs are separated by 18.3±1.6 nm, while the TMM and TMM, anti-TMM and anti-TMM pairs are stabilized at comparatively longer distances of 36.1±2.4 nm and 43.1±2.0 nm, respectively. We also observe virtual TMMs created by magnetic voids in the meta-lattice. This work demonstrates that ferromagnetic meta lattices could be used as a platform to create and investigate the interactions and dynamics of TMMs. Furthermore, we expect that soft x-ray vector ptycho-tomography can be broadly applied to quantitatively image 3D vector fields in magnetic and anisotropic materials at the nanoscale.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2021

PPPL Laboratory Directed Research and Development (Project Final Reports, FY2018 - FY2020)

The U.S. Department of Energy’s (DOE) Princeton Plasma Physics Laboratory (PPPL) is a collaborative national center for fusion energy science, basic sciences, and advanced technology. The Laboratory has three major missions: (1) to develop the scientific knowledge and advanced engineering to enable fusion to power the U.S. and the world; (2) to advance the science of nanoscale fabrication for technologies of tomorrow; and (3) to further the development of the scientific understanding of the plasma universe from laboratory to astrophysical scales. PPPL’s Laboratory Directed Research and Development (LDRD) program supports and encourages creativity and innovation and contributes to its long-term viability. New scientific and technical research areas emerge and are nurtured through the program. Furthermore, new capabilities are developed to enable the Laboratory to meet its and DOE’s missions. The program is used to systematically diversify the Laboratory’s programs and mission. In the last few years, the program has started projects in nanomaterial synthesis, microelectronics, advanced x-ray spectroscopy, high-energy-density physics, superconducting magnet technology, machine learning and artificial intelligence, 3D magnetic fields to optimize fusion plasmas, integration of permanent magnets with simple high-field magnets to reduce the cost of producing complex 3D magnetic fields, advanced computational methods for predictive understanding and control of fusion plasma, development of quantum computing algorithms for plasma physics, liquid metal plasma-facing components for fusion reactors, virtual engineering, and plasma-based space propulsion. The program is also the vehicle to recruit and train talented scientists and engineers with the new skills needed to perform the Laboratory’s mission. Many of the new hires through the program go on to become world-class scientists and engineers in their fields. This report provides descriptions and accomplishments of those LDRD projects that were completed during fiscal years 2018 through 2020.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Exploring baryon resonances with transition generalized parton distributions: status and perspectives

QCD gives rise to a rich spectrum of excited baryon states. Understanding their internal structure is important for many areas of nuclear physics, such as nuclear forces, dense matter, and neutrino-nucleus interactions. Generalized parton distributions (GPDs) are an established tool for characterizing the QCD structure of the ground-state nucleon. They are used to create 3D tomographic images of the quark/gluon structure and quantify the mechanical properties such as the distribution of mass, angular momentum, and forces in the system. Transition GPDs extend these concepts to N → N* transitions and can be used to characterize the 3D structure and mechanical properties of baryon resonances. They can be probed in high-momentum-transfer exclusive electroproduction processes with resonance transitions e + N → e' + M + N*, such as deeply-virtual Compton scattering (M = γ) or meson production (M = π, K, etc.), and in related photon/hadron-induced processes. This White Paper describes a research program aiming to explore baryon resonance structure with transition GPDs. This includes the properties and interpretation of the transition GPDs, theoretical methods for structures and processes, first experimental results from JLab 12 GeV, future measurements with existing and planned facilities (JLab detector and energy upgrades, COMPASS/AMBER, EIC, EicC, J-PARC, LHC ultraperipheral collisions), and the theoretical and experimental developments needed to realize this program.

Experimental Nuclear Physics↗

DOE OSTI2022

Radiographic Imaging and Tomography

Radiographic imaging and tomography (RadIT) come in many flavors such as X-ray imaging and tomography (IT), proton IT, neutron IT, muon IT, neutrino IT, etc. We identify five RadIT themes: Physics, Sources, Detectors, Methods, and Data Science, which are integral parts of image interpretation and three-dimensional (3D) tomographic reconstruction. Traditionally, RadIT have been driven by medicine, non-destructive testing, material sciences, and security applications. The latest thrusts of growth come from automation, machine vision, additive manufacturing and virtual reality (‘metaverse’). The five RadIT themes parallel their counterparts in optical IT. Synergies among different forms of RadIT and with optical IT motivate further advances towards multi-modal IT and quantum IT.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Evaluating the pressure dependence of PZT structures using a virtual reality environment

Pb–Zr–Ti–O (PZT) perovskites span a large solid-solution range and have found widespread use due to their piezoelectric and ferroelectric properties that also span a large range. Crystal structure analysis via Rietveld refinement facilitates materials analysis via the extraction of the structural parameters. These parameters, often obtained as a function of an additional dimension (e.g., pressure), can help to diagnose materials response within a use environment. Often referred to as “ in-situ ” studies, these experiments provide an abundance of data. Viewing structural changes due to applied pressure conditions can give much-needed insight into materials performance. However, challenges exist for viewing/presenting results when the details are inherently three-dimensional (3D) in nature. For PZT perovskites, the use of polyhedra (e.g., Zr/Ti–O 6 octahedra) to view bonding/connectivity is beneficial; however, the visualization of the octahedra behavior with pressure dependence is less easily demonstrated due to the complexity of the added pressure dimension. We present a more intuitive visualization by projecting structural data into virtual reality (VR). We employ previously published structural data for Pb 0.99 (Zr 0.95 Ti 0.05 ) 0.98 Nb 0.02 O 3 as an exemplar for VR visualization of the PZT R3c crystal structure between ambient and 0.62 GPa pressure. This is accomplished via our in-house CAD2VR™ software platform and the new CrystalVR plugin. The use of the VR environment enables a more intuitive viewing experience, while enabling on-the-fly evaluation of crystal data, to form a detailed and comprehensive understanding of in-situ datasets. Discussion of methodology and tools for viewing are given, along with how recording results in video form can enable the viewing experience.

Rodriguez, Mark A. (ORCID:0000000269405044)↗

DOE OSTI2025

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Pxl

The code consists of several scripts. The image is fetched from a predefined URL, downloaded, and is displayed in the virtual environment at a predefined location. The image is also dynamically scaled to fit in the virtual environment depending on its size. The image is sent to have each pixel's value written to a CSV file. While the CSV is being written, a dictionary is populated with values that map each pixel to a temperature reading. The image's height, width, position and references to its corners are sent to make a button that is the same size as the image and placed right behind the image in the virtual scene. The button defines behavior that should be triggered when the user pushes the image. Unity provides visual cues that alert the user when they are about to touch something in the virtual environment. The code holds references to the cues for the left and right hands. The button queries the cue tracker and receives the position of the active cue in the form of a 3D vector. The 3D vector is compared to the bottom left corner of the image to transform the world space coordinates of the cue to the pixel space of the image. The specific pixel is approximated relative to how far left and up the user touched from the bottom left corner of the image. The approximated pixel value, which is represented as a coordinate in 2D space, is used to retrieve the temperature value associated with the approximated pixel. A window of text is then updated to display the temperature reading.

. Otis, KrystianeS [Idaho National Laboratory (INL↗

DOE OSTI2024

DASSH-F: Subchannel Based Thermal Analysis

The DASSH thermal analysis code is designed to rapidly allow a reactor design engineer to obtain flow rates requirements that satisfy peak temperature constraints in the domain. The advantage of using DASSH over a hand calculation is that it has a more rigorous treatment of the pin power distribution and coolant heat transfer within an assembly and between assemblies. The advantage of using DASSH over a conventional 3D subchannel code or a computational fluid dynamics code (CFD) is that it can obtain the desired solution in a matter of minutes in serial with minor computer memory needs. The DASSH methodology is virtually identical to SUPERENERGY-2 with additional functionalities taken from follow on work to SUPERENERGY-2 done at ANL in the 1980s. DASSH today is an integral component of the Argonne Fast Reactor analysis suite for reactor design work. DASSH obtains the power distribution from a coupled neutron-gamma heating calculation in GAMSOR (including DIF3D) at each time point of a companion fuel cycle analysis calculation with REBUS. The domain in DASSH assumes a hexagonal grid typical for fast reactors with much of the geometry information taken from the DIF3D model. DASSH assumes the assemblies that are loaded into each grid position are ducted to control the coolant flow. Considerable detail is given on the subchannel formulation of DASSH in this document. Much of the formulation and design of the code builds upon research done by previous authors with little new investigation. Thus the decisions made in developing the subchannel model used in DASSH have their origins over 50 years ago. Much of the heat transfer methodology in DASSH is built upon correlations for both the coolant mixing and heat transfer coefficients for pins and ducts. DASSH is thus not a rigorous treatment of a given problem, but a rapid assessment of the temperature field that has known limitations with respect to an experimental measurement or CFD calculation. The DASSH input and output are detailed along with usage of the software. The DASSH output provides tables of evaluated material properties and key coolant and pin temperature results. DASSH can create Python scripts that generate domain summary pictures. DASSH can also generate assembly temperature maps and VTK output files which allow the DASSH solution to be visualized. As the primary purpose of the DASSH software is to compute the coolant and fuel pin temperature distribution for a given model of a reactor, much of the output focus is giving the user quick summary tables needed to assess the performance of a given orifice flow specification. The present version of DASSH has a crude orifice search capability and an efficient orifice flow search capability. The flow search tries to meet user specified constraints for 1) peak 2-sigma clad midwall temperature, 2) peak coolant temperature, and 3) desired bulk outlet temperature. There are many development shortcomings in DASSH detailed in this document, but this version is functional for modern analysis needs. This document serves as the manual for the Fortran based DASSH software that was developed to replace the Python version of DASSH developed as part of the VTR program.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Numerical integration in the virtual element method with the scaled boundary cubature scheme

Abstract The virtual element method (VEM) is a stabilized Galerkin method on meshes that consist of arbitrary (convex and nonconvex) polygonal and polyhedral elements. A crucial ingredient in the implementation of low‐ and high‐order VEM is the numerical integration of monomials and nonpolynomial functions over such elements. In this article, we apply the recently proposed scaled boundary cubature (SBC) scheme to compute the weak form integrals in various virtual element formulations over polygonal and polyhedral meshes. In doing so, we demonstrate the flexibility of the approach and the accuracy that it delivers on a broad suite of boundary‐value problems in 2D and 3D over polytopes with affine faces as well as on elements with curved boundaries. In addition, the use of the SBC scheme is exemplified in an enriched Poisson formulation of the VEM in which weakly singular functions are required to be integrated. This study establishes the SBC method as a simple, accurate and efficient integration scheme for use in the VEM.

Chin, Eric B.↗

DOE OSTI2026

DASSH-F: Subchannel Based Thermal Analysis

The DASSH thermal analysis code is designed to rapidly allow a reactor design engineer to obtain flow rates requirements that satisfy peak temperature constraints in the domain. The advantage of using DASSH over a hand calculation is that it has a more rigorous treatment of the pin power distribution and coolant heat transfer within an assembly and between assemblies. The advantage of using DASSH over a conventional 3D subchannel code or a computational fluid dynamics code (CFD) is that it can obtain the desired solution in a matter of minutes in serial with minor computer memory needs. The DASSH methodology for pin lattice models is virtually identical to SUPERENERGY-2 with additional functionalities taken from follow on work to SUPERENERGY-2 done at ANL in the 1980s. DASSH today is an integral component of the Argonne Fast Reactor analysis suite for reactor design work. DASSH obtains the power distribution from a coupled neutron-gamma heating calculation in GAMSOR (including DIF3D) at each time point of a companion fuel cycle analysis calculation with REBUS. The domain in DASSH assumes a hexagonal grid typical for fast reactors with much of the geometry information taken from the DIF3D model. DASSH assumes the assemblies that are loaded into each grid position are ducted to control the coolant flow. The user can alternatively provide their own geometry and power profile instead of inheriting it from DIF3D. Considerable detail is given on the subchannel formulation of DASSH in this document. Much of the formulation and design of the code builds upon research done by previous authors with little new investigation. Thus the decisions made in developing the subchannel model used in DASSH have their origins over 50 years ago. Much of the heat transfer methodology in DASSH is built upon correlations for both the coolant mixing and heat transfer coefficients for pins and ducts. DASSH is thus not a rigorous treatment of a given problem, but a rapid assessment of the temperature field that has known limitations with respect to an experimental measurement or CFD calculation. The DASSH input and output are detailed along with usage of the software. The DASSH output provides tables of evaluated material properties and key coolant and pin temperature results. DASSH can create Python scripts that generate domain summary pictures. DASSH can also generate assembly temperature maps and VTK output files which allow the DASSH solution to be visualized. As the primary purpose of the DASSH software is to compute the coolant and fuel pin temperature distribution for a given model of a reactor, much of the output focus is giving the user quick summary tables needed to assess the performance of a given orifice flow specification. The present version of DASSH has a crude orifice search capability and a sufficient orifice flow search capability. The flow search tries to meet user specified constraints for 1) peak 2-sigma clad temperature, 2) peak coolant temperature, and 3) desired bulk outlet temperature. This document serves as the manual for the Fortran based DASSH software that was developed to replace the Python version of DASSH developed as part of the VTR program.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Exploring the 3D nucleon structure with CLAS and CLAS12 at JLAB

Exploring the 3 dimensional structure of the nucleon can help to understand several fundamental questions of nature, such as the origin of the nucleon spin and the charge and density distributions inside the nucleon. In QCD, the 3-dimensional structure of the nucleon is described by Wigner functions. However, experimentally momentum and coordinate space have to be assessed independently. The momentum distribution can be accessed by transverse momentum dependent distribution functions (TMDs) measured in semi-inclusive deep inelastic scattering (SIDIS) or Drell-Yan processes while the distribution in transverse coordinate and longitudinal momentum space is described by generalized parton distributions (GPDs) which can be accessed for example by deeply virtual Compton scattering (DVCS) and hard exclusive meson production (DVMP). Based on the high quality data of CLAS and the recently upgraded CLAS12 detector at Jefferson Laboratory (JLAB), a detailed study of these distribution functions is being performed. With the new CLAS12 data, multidimensional, high precision studies in an extended kinematic range become possible for the first time. The talk will present the results of recent SIDIS, DVCS and DVMP studies with CLAS and CLAS12 and their impact on the understanding of the 3D nucleon structure.

Diehl, Stefan↗

DOE OSTI2022

Novel light field imaging device with enhanced light collection for cold atom clouds

We present a light field imaging system that captures multiple views of an object with a single shot. The system is designed to maximize the total light collection by accepting a larger solid angle of light than a conventional lens with equivalent depth of field. This is achieved by populating a plane of virtual objects using mirrors and fully utilizing the available field of view and depth of field. Simulation results demonstrate that this design is capable of single-shot tomography of objects of size $\mathcal{O}$(1 mm 3 ), reconstructing the 3-dimensional (3D) distribution and features not accessible from any single view angle in isolation. In particular, for atom clouds used in atom interferometry experiments, the system can reconstruct 3D fringe patterns with size $\mathcal{O}$(100 μm). We also demonstrate this system with a 3D-printed prototype. The prototype is used to take images of $\mathcal{O}$(1 mm 3 ) sized objects, and 3D reconstruction algorithms running on a single-shot image successfully reconstruct $\mathcal{O}$(100 μm) internal features. The prototype also shows that the system can be built with 3D printing technology and hence can be deployed quickly and cost-effectively in experiments with needs for enhanced light collection or 3D reconstruction. Imaging of cold atom clouds in atom interferometry is a key application of this new type of imaging device where enhanced light collection, high depth of field, and 3D tomographic reconstruction can provide new handles to characterize the atom clouds.

47 OTHER INSTRUMENTATION↗