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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗
DOE OSTI2025

Antipodal self-duality of square fishnet graphs

In strongly deformed planar 𝒩 = 4 super-Yang-Mills theory, or fishnet theory, a point-split single-trace correlation function of four dimension-𝑚 scalar operators is given by a single Feynman integral, which involves integrating over locations of a 𝑚 × 𝑚 grid of points. We show that for any integer 𝑚 this square fishnet graph is invariant under the combined action of a kinematic map and the antipode map of the Hopf algebra on multiple polylogarithms; i.e. it possesses an antipodal self-duality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Progress with the 5D full-F continuum gyrokinetic code COGENT

COGENT is an Eulerian gyrokinetic code being developed for edge plasma modelling. The code is distinguished by the use of a high-order finite-volume (conservative) discretization combined with mapped multi-block grid technology. Our recent work is focused on the development of a 5D full-F COGENT version.Anumerical algorithm utilizing locally a field-aligned multi-block coordinate system is implemented to facilitate simulations of highly anisotropic microturbulence in the presence of a strong magnetic shear. In this approach, the toroidal direction is divided into blocks such that,within each block, the cells are field-aligned and a non-matching (non-conformal) grid interface is allowed at the block boundaries. In this paper we report on details of the numerical implementation and present preliminary results of verification studies performed for the case of the ion temperature gradient (ITG) instability in a sheared toroidal annulus geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Understanding Binder–Silicon Interactions during Slurry Processing

The conformation of poly(acrylic acid) (PAA) as a function of shear during slurry processing to construct silicon-based anodes is elucidated via rheology-coupled ultra-small-angle neutron scattering (rheo-USANS). Rheo-USANS shows that PAA with encapsulated silicon exists as discrete aggregates that do not interact with one another. As a result, a well-connected matrix of silicon and carbon black dispersed in PAA does not exist; thus, the electrode is inhomogeneous. Raman mapping and X-ray photoelectron spectroscopy were used to confirm the electrode heterogeneity and further understand the cycling properties. These results are correlated to silicon surface chemistry to provide a pathway to making better electrodes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A duality in string theory on AdS 3

We consider bosonic string theory on AdS 3 supported by Kalb-Ramond flux. It is well known that the α' exact worldsheet theory is described by the SL(2,R) WZW model. In this note we perform checks of an α' exact dual description proposed in [arXiv:2104.07233] involving a winding condensate on a free theory background. We give the explicit map of vertex operators for normalizable states on both sides of the duality and demonstrate the equivalence of their two and three point functions by direct computation. The duality is of strong-weak nature in α' .

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies

HIV-1 and its SIV precursors share a broadly neutralizing antibody (bNAb) epitope in variable loop 2 (V2) at the envelope glycoprotein (Env) trimer apex. Here, we tested the immunogenicity of germ line-targeting versions of a chimpanzee SIV (SIVcpz) Env in human V2-apex bNAb heavy-chain precursor-expressing knock-in mice and as chimeric simian-chimpanzee immunodeficiency viruses (SCIVs) in rhesus macaques (RMs). Trimer immunization of knock-in mice induced V2-directed NAbs, indicating activation of V2-apex bNAb precursor-expressing mouse B cells. SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. Antibody cloning from two of these animals identified multiple expanded lineages with long heavy chain third complementarity determining regions that cross-neutralized as many as 7 of 19 primary HIV-1 strains, but with low potency. Negative stain electron microscopy (NSEM) of members of the two most cross-reactive lineages confirmed V2 targeting but identified an angle of approach distinct from prototypical V2-apex bNAbs, with antibody binding either requiring or inducing an occluded-open trimer. Probing with conformation-sensitive, nonneutralizing antibodies revealed that SCIV-expressed, but not wild-type SIVcpz Envs, as well as a subset of primary HIV-1 Envs, preferentially adopted a more open trimeric state. These results reveal the existence of a cryptic V2 epitope that is exposed in occluded-open SIVcpz and HIV-1 Env trimers and elicits cross-neutralizing responses of limited breadth and potency.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

SARS-CoV2 Docking Dataset

Description: Small-molecule conformations and docking scores for 1.4 billion molecules docked against 6 protein targets from SARS-CoV2: MPro 5R84, MPro 6WQF, NSP15 6WLC, PLPro 7JIR, Spike 6M0J, and a hand-optimized model of the RNA-dependent RNA polymerase. Docking was carried out using the Autodock-GPU program performing 20 independent structure minimizations per dock - saving 3 results per molecule. Scores reported include the Autodock free energy estimate as well as RF3 and VS-DUD-E v2 machine-learned rescoring models. Protein structure files and maps in the format input to Autodock-GPU are included. Literature Ref: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19, J. Chem. Inf. Model. 2020, 60(12): 5832–5852.

36 MATERIALS SCIENCE↗
DOE OSTI2021

4-manifolds and topological modular forms

We build a connection between topology of smooth 4-manifolds and the theory of topological modular forms by considering topologically twisted compactification of 6d (1, 0) theories on 4-manifolds with flavor symmetry backgrounds. The effective 2d theory has (0, 1) supersymmetry and, possibly, a residual flavor symmetry. The equivariant topological Witten genus of this 2d theory then produces a new invariant of the 4-manifold equipped with a principle bundle, valued in the ring of equivariant weakly holomorphic (topological) modular forms. We describe basic properties of this map and present a few simple examples. As a byproduct, we obtain some new results on ’t Hooft anomalies of 6d (1, 0) theories and a better understanding of the relation between 2d (0, 1) theories and TMF spectra.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Integral Field Probe for Mapping of Curved Magnets

The Single Stretched Wire (SSW) method allows highly precise integral field measurements by recording voltage across a tensioned wire mounted to 2-axis linear stages at either end of the magnet aperture. However, traditional SSW probes are not well suited for curved accelerator magnets, which are essential for steering charged particles along arced trajectories in storage rings or beamlines. The tension required to eliminate sag demands a purely straight path, making them incompatible with non-linear magnet geometries. To address this limitation for curved magnets, a modified approach was developed using a segmented, 3D-printed support structure that incorporates a pre-shaped anti-sag curve. Under its own weight and that of the wire bundle, the structure deforms to lie flat while conforming to the curvature of the magnet in the horizontal plane. The optimal geometry of the probe was derived using an iterative process combining FEA simulations in Ansys Mechanical with testing of various carbon fiber-reinforced filaments. The printed and assembled probe was successfully used to measure the SDD-059 magnet at Fermilab, yielding promising results.

Jakopin, Alexander [Northern Illinois U.]↗
DOE OSTI2025

DOE Repository Metadata Profile (DRMP): A Metadata Framework for Advancing Interoperability and AI Readiness Across Scientific Repositories

The Department of Energy (DOE) funds a diverse and distributed ecosystem of repositories that steward scientific data, publications, and software across its research programs, user facilities, and national laboratories. While significant progress has been made in standardizing dataset-level metadata, the metadata describing repositories themselves (their identity, governance, access interfaces, policies, and technical capabilities) remains inconsistent and fragmented across DOE-funded systems. This variability limits discoverability, interoperability, automated validation, and AI-driven analysis, all of which are increasingly essential for modern scientific workflows. To address this gap, the DOE Data Curation Working Group (DCWG) developed the DOE Repository Metadata Profile (DRMP). The DRMP is a practical, community-driven framework that defines how repositories can describe themselves in a consistent, machine-actionable, and scalable manner. The DRMP is not a new metadata schema. Instead, it is a mapping profile and structured element set capturing the essential characteristics of DOE repositories. It harmonizes repository-level metadata across six widely adopted community schemas: RE3Data; DCAT-US v3; Schema.org; Dublin Core; DataCite 4.6; and PREMIS 3.0. This harmonization eliminates reinvention and enables interoperability within DOE and across the broader scientific ecosystem. A core objective of the DRMP is to reduce burden on repositories by allowing them to reuse their existing metadata through a Rosetta-style crosswalk rather than redesigning local implementations. The profile introduces a three-level conformance model that supports incremental adoption: • Level 1 – Minimum Viable Record (MVR): foundational identification elements required for workflows, project registration, and basic repository presence. • Level 2 – Interoperable: structured metadata enabling alignment with national and international discovery systems. • Level 3 – AI-Ready: enhanced provenance, policy transparency, fixity, semantic context, and capabilities that support automated reasoning, model training governance, and machine-assisted curation. To support implementation, the DRMP includes JSON Schema definitions, OpenAPI patterns, and MCP templates that allow repositories to publish machine-readable metadata directly within existing platforms. These resources are modular and lightweight, enabling adoption without major architectural change. Adopting the DRMP enables repositories to: • Enhance discoverability and interoperability by aligning identifiers, classifications, and descriptive elements across widely used schema standards. • Support federated discovery and cross-registration across DOE systems, Data.gov, and international catalogs. • Enable AI agents and workflow orchestration systems to interpret repository-level metadata within the American Science Cloud (AmSC) through Model Context Protocol (MCP)-based context publication. • Demonstrate alignment with DOE’s open science, stewardship, and FAIR data priorities. This guidance represents a community-driven step forward. Through voluntary adoption and continued feedback, the DRMP advances a cohesive, machine-actionable description of DOE repositories that supports FAIR data practices, preparing the infrastructure for AI-enabled research, and strengthening the discoverability and reuse of DOE’s scientific outputs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

Fast GPU-Based Generation of Large Graph Networks From Degree Distributions

Synthetically generated, large graph networks serve as useful proxies to real-world networks for many graph-based applications. The ability to generate such networks helps overcome several limitations of real-world networks regarding their number, availability, and access. Here, we present the design, implementation, and performance study of a novel network generator that can produce very large graph networks conforming to any desired degree distribution. The generator is designed and implemented for efficient execution on modern graphics processing units (GPUs). Given an array of desired vertex degrees and number of vertices for each desired degree, our algorithm generates the edges of a random graph that satisfies the input degree distribution. Multiple runtime variants are implemented and tested: 1) a uniform static work assignment using a fixed thread launch scheme, 2) a load-balanced static work assignment also with fixed thread launch but with cost-aware task-to-thread mapping, and 3) a dynamic scheme with multiple GPU kernels asynchronously launched from the CPU. The generation is tested on a range of popular networks such as Twitter and Facebook, representing different scales and skews in degree distributions. Results show that, using our algorithm on a single modern GPU (NVIDIA Volta V100), it is possible to generate large-scale graph networks at rates exceeding 50 billion edges per second for a 69 billion-edge network. GPU profiling confirms high utilization and low branching divergence of our implementation from small to large network sizes. For networks with scattered distributions, we provide a coarsening method that further increases the GPU-based generation speed by up to a factor of 4 on tested input networks with over 45 billion edges.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Directional Gateway to Metal Oxidation: 3D Chemical Mapping Unfolds Oxygen Diffusional Pathways in Rhodium Nanoparticles

The interaction of oxygen with a reactive metal is ubiquitous, yet the precise atomic-level mechanisms and pathways leading to the formation of a surface oxide are not well-understood. We report oxygen atom distributions inside Rh single nanoparticles using atom probe microscopy (APM) and demonstrate that mainly facets of the ?022¯? crystallographic directions act as oxygen-permeable gateways. The highly anisotropic spatial distribution of incorporated oxygen atoms is in agreement with video-field emission analyses according to which {113} facets of the ?022¯? zones act as portals for subsurface diffusion. In addition to providing a more fundamental understanding of the precursor states to metal corrosion, in particular for the case of nanosized metal particles, our studies are also relevant for heterogeneous catalysis where catalytic activity and selectivity conform to reaction-induced structural changes of metal nanoparticles.

Lambeets, Sten V M.↗
DOE OSTI2022

Dose Summation Strategies for External Beam Radiation Therapy and Brachytherapy in Gynecologic Malignancy: A Review from the NRG Oncology and NCTN Medical Physics Subcommittees

Definitive, nonsurgical management of gynecologic malignancies involves external beam radiation therapy (EBRT) and/or brachytherapy (BT). Summation of the cumulative dose is critical to assess the total biologic effective dose to targets and organs at risk. Cumulative dose calculation from EBRT and BT can be performed with or without image registration (IR) and biologic dose summation. Among these dose summation strategies, linear addition of dose-volume histogram (DVH) parameters without IR is the global standard for composite dose reporting. This approach stems from an era without image guidance and simple external beam and brachytherapy treatment approaches. With technological advances, EBRT and high-dose-rate BT have evolved to allow for volume-based treatment planning and delivery. Modern conformal therapeutic radiation involves volumetric or intensity modulated EBRT, capable of simultaneously treating multiple targets at different specified dose levels. Therefore, given the complexity of modern radiation treatment, the linear addition of DVH parameters from EBRT and high-dose-rate BT is challenging to represent the combined dose distribution. Deformable image registration (DIR) between EBRT and image guided brachytherapy (IGBT) data sets may provide a more nuanced calculation of multimodal dose accumulation. However, DIR is still nascent in this regard, and needs further development for accuracy and efficiency for clinical use. Biologic dose summation can combine physical dose maps from EBRT and each IGBT fraction, thereby generating a composite DVH from the biologic effective dose. However, accurate radiobiologic parameters are tissue-dependent and not well characterized. A combination of voxel-based DIR and biologic weighted dose maps may be the best approximation of dose accumulation but remains invalidated. The purpose of this report is to review dose summation strategies for EBRT and BT, including conventional equivalent dose in 2-Gy fractions dose summation without image registration, physical dose summation using 3-dimensional rigid IR and DIR, and biologic dose summation. We also provide general clinical workflows for IGBT with a focus on cervical cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

In-situ qualification and physics-based process design for aerosol jet printing via spatially correlated light scattering measurements

Aerosol jet printing is a contactless, digital, and additive technique broadly used for manufacturing flexible, hybrid, and conformal electronics. However, batch-to-batch variability has hindered widespread industry adoption and scaling to production volumes. Recently, light scattering measurements have emerged as a tool to measure aerosol volume fraction – a key parameter determining deposition rate – and have proven an effective feedback source for closed loop control on timescales ranging from minutes to hours. Here, the efficacy of light scattering measurements as a tool for in-situ qualification over shorter time durations is explored. To be the linear relationship between light scattering measurements and deposition rate was validated at 500 ms time intervals, allowing deposition rate to be mapped to positional coordinates and providing a new data stream to drive quality control assessments. Because light scattering measurements are indicative of a physical process parameter, they were substituted into equations for resistance and sheet resistance, resulting in predictions nominally within 10% of measured values for sets of printed devices. Finally, to highlight a more active utility, light scattering measurements were employed in a print repair framework, successfully repairing prints with randomly induced defects to within 5% of the measured resistance of a control set.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus

Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3'-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII 170-755 , as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH’s global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Experiences with SYCL on AMD GPUs with Kokkos

With the recent diversification of the hardware landscape in the high-performance computing (HPC) community, performance-portability solutions are becoming more and more important. One of the most popular choices is Kokkos, which recently became a Linux Foundation project. Most of its development is supported by the US Department of Energy and the French Alternative Energies and Atomic Energy Commission. Kokkos is implemented as a C++ library with multiple backends to support CPUs as well as various GPU architectures. These backends include OpenMP, CUDA, HIP, and also SCYL. This approach enables users to leverage the preferred vendor toolchain for the respective platform (e.g. CUDA, ROCm, OneAPI). The SYCL backend is used to target Intel GPUs, in particular to support the Aurora exascale supercomputer. However, SYCL itself also offers a large degree of portability, and in fact Kokkos’ CI for SYCL has been running on NVIDIA hardware due to a lack of access to Intel GPUs. In this report, we describe our experience with using Kokkos SYCL backend on AMD GPUs targeting the Frontier supercomputer at Oak Ridge National Laboratory. The two major SYCL implementations are DPC++ and AdaptiveCpp. While the Kokkos SYCL backend has been implemented using the former, the latter was the first implementation to target AMD GPUs. We will discuss the experience with both of these SYCL implementations in terms of functionality and performance. Using Kokkos to evaluate SYCL toolchains has a number of benefits. Kokkos’ use of SYCL is fairly complex, exercising features such as graphs, relocatable device functions, atomics – including for non-arithmetic types, as well as pinned and page migratable memory allocations. Kokkos also needs to implement capabilities such as Kokkos’ hierarchical parallelism that are not a straight-forward mapping to SYCL capabilities. Furthermore, a large number of libraries and applications that represent diverse use cases are implemented in Kokkos, providing readily available test cases for a toolchain evaluation. Preliminary results show that support for AMD GPUs in DPC++ is much less mature than for NVIDIA GPUs or Intel GPUs. While the situation has improved significantly over the last year, we still encounter many runtime failures, dispatching problems, and code generation issues. With AdaptiveCpp the challenges arise even earlier in the evaluation process. Since Kokkos’ SYCL implementation is largely focused on supporting Intel GPUs, we opted to leverage SYCL extensions which are available in DPC++ but not in AdaptiveCpp. Furthermore, AdaptiveCpp appears to be less conformant with the SYCL2020 standard which Kokkos relies on. In some cases, we are able to work around the lack of feature support, in other cases we have to disable certain Kokkos capabilities to evaluate the toolchain. Our evaluation will leverage Kokkos’ unit tests to establish basic functionality and feature completeness. We then use simple benchmarks for components of a CG implementation as a measure of usability and performance of the SYCL toolchains.

97 MATHEMATICS AND COMPUTING↗