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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 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

TU-H-CAMPUS-JeP2-02: Interobserver Variability of CT, PET-CT and MRI Based Primary Tumor Delineation for Lung Cancer

Purpose: Target delineation in lung cancer radiotherapy has, in general, large variability. MRI has so far not been investigated in detail for lung cancer delineation variability. The purpose of this study is to investigate delineation variability for lung tumors using MRI and compare it to CT alone and PET-CT based delineations. Methods: Seven physicians delineated the primary tumor volumes of nine patients for the following scenarios: (1) CT only; (2) post-contrast T1-weighted MRI registered with diffusion-weighted MRI; and (3) PET-CT fusion images. To compute interobserver variability, the median surface was generated from all observers’ contours and used as the reference surface. A single physician labeled the interface types (tumor to lung, atelectasis (collapsed lung), hilum, mediastinum, or chest-wall) on the median surface. Volume variation (normalized to PET-CT volume), minimum distance (MD), and bidirectional local distance (BLD) between individual observers’ contours and the reference contour were measured. Results: CT- and MRI-based normalized volumes were 1.61±0.76 (mean±SD) and 1.38±0.44, respectively, both significantly larger than PET-CT (p<0.05, paired t-test). The overall uncertainty (root mean square of SD values over all points) of both BLD and MD measures of the observers for the interfaces were not significantly different (p>0.05, two-samples t-test) for all imaging modalities except between tumor-mediastinum and tumor-atelectasis in PET-CT. The largest mean overall uncertainty was observed for tumor-atelectasis interface, the smallest for tumor-mediastinum and tumor-lung interfaces for all modalities. The whole tumor uncertainties for both BLD and MD were not significantly different between any two modalities (p>0.05, paired t-test). Overall uncertainties for the interfaces using BLD were similar to using MD. Conclusion: Large volume variations were observed between the three imaging modalities. Contouring variability appeared to depend on the interface type. This study will be useful for understanding the delineation uncertainty for radiotherapy planning of lung cancer using different imaging modalities. Disclosures: Research agreement with Phillips Healthcare (GH and EW), National Institutes of Health Licensing agreement with Varian Medical Systems (GH and EW), research grants from the National Institute of Health (GH and EW), UpToDate royalties (EW), and none (others). Authors have no potential conflicts of interest to disclose.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Hyperdimensional visualization tool

A method and apparatus for displaying data. Independent data in the data is displayed by a computer system in a two-dimensional graph in a graphical user interface on a display system. Dimensions of dependent data in the data that are dependent on the independent data are displayed by the computer system in the two-dimensional graph using graphical indicators.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Cross-scale efficient tensor contractions for coupled cluster computations through multiple programming model backends

Coupled-cluster methods provide highly accurate models of molecular structure through explicit numerical calculation of tensors representing the correlation between electrons. These calculations are dominated by a sequence of tensor contractions, motivating the development of numerical libraries for such operations. While based on matrix–matrix multiplication, these libraries are specialized to exploit symmetries in the molecular structure and in electronic interactions, and thus reduce the size of the tensor representation and the complexity of contractions. The resulting algorithms are irregular and their parallelization has been previously achieved via the use of dynamic scheduling or specialized data decompositions. We introduce our efforts to extend the Libtensor framework to work in the distributed memory environment in a scalable and energy-efficient manner. We achieve up to 240× speedup compared with the optimized shared memory implementation of Libtensor. We attain scalability to hundreds of thousands of compute cores on three distributed-memory architectures (Cray XC30 and XC40, and IBM Blue Gene/Q), and on a heterogeneous GPU-CPU system (Cray XK7). As the bottlenecks shift from being compute-bound DGEMM's to communication-bound collectives as the size of the molecular system scales, we adopt two radically different parallelization approaches for handling load-imbalance, tasking and bulk synchronous models. Nevertheless, we preserve a unified interface to both programming models to maintain the productivity of computational quantum chemists.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Understanding the Solid-State Electrode–Electrolyte Interface of a Model System Using First-Principles Statistical Mechanics and Thin-Film X-ray Characterization

Intermixing of atomic species at the electrode-electrolyte boundaries can impact the properties of the interfaces in solid-state batteries. Herein, this work uses first-principles statistical mechanics along with experimental characterization to understand intermixing at the electrode-electrolyte interface. For the model presented in this work, lithium manganese oxide (LiMn 2 O 4 , LMO) and lithium lanthanum titanate (Li 3x La 2/3-x TiO 3 , LLTO) are employed as the cathode and electrolyte, respectively. The results of the computational work show that Ti-Mn intermixing at the interface is significant at synthesis temperatures. The experimental results in this work find that, at some critical temperatures between 600 and 700 degrees C for material preparation, the interface of LLTO-LMO becomes blurred. Calculations predict that the interface is unstable with regard to Ti-Mn intermixing starting at 0 K, suggesting that the critical temperature found in the experiment is related to kinetics. The work overall suggests that, in designing a solid-state battery, the fundamental reactions such as intermixing need to be considered.

25 ENERGY STORAGE↗
DOE OSTI2023

A MultiGPU Performance-Portable Solution for Array Programming Based on Kokkos

Today, multiGPU nodes are widely used in high-performance computing and data centers. However, current programming models do not provide simple, transparent, and portable support for automatically targeting multiple GPUs within a node on application areas of array programming. In this paper, we describe a new application programming interface based on the Kokkos programming model to enable array computation on multiple GPUs in a transparent and portable way across both NVIDIA and AMD GPUs. We implement different variations of this technique to accommodate the exchange of stencils (array boundaries) among different GPU memory spaces, and we provide autotuning to select the proper number of GPUs, depending on the computational cost of the operations to be computed on arrays, that is completely transparent to the programmer. We evaluate our multiGPU extension on Summit (#5 TOP500), with six NVIDIA V100 Volta GPUs per node, and Crusher that contains identical hardware/software as Frontier (#1 TOP500), with four AMD MI250X GPUs, each with 2 Graphics Compute Dies (GCDs)for a total of 8 GCDs per node. We also compare the performance of this solution against the use of MPI + Kokkos, which is the cur-rent de facto solution for multiple GPUs in Kokkos. Our evaluation shows that the new Kokkos solution provides good scalability for many GPUs and a faster and simpler solution (from a programming productivity perspective) than MPI + Kokkos.

Valero Lara, Pedro↗
DOE OSTI2019

Understanding data motion in the modern HPC data center

The utilization and performance of storage, compute, and network resources within HPC data centers have been studied extensively, but much less work has gone toward characterizing how these resources are used in conjunction to solve larger scientific challenges. To address this gap, we present our work in characterizing workloads and workflows at a data-center-wide level by examining all data transfers that occurred between storage, compute, and the external network at the National Energy Research Scientific Computing Center over a three-month period in 2019. Using a simple abstract representation of data transfers, we analyze over 100 million transfer logs from Darshan, HPSS user interfaces, and Globus to quantify the load on data paths between compute, storage, and the wide-area network based on transfer direction, user, transfer tool, source, destination, and time. We show that parallel I/O from user jobs, while undeniably important, is only one of several major I/O workloads that occurs throughout the execution of scientific workflows. We also show that this approach can be used to connect anomalous data traffic to specific users and file access patterns, and we construct time-resolved user transfer traces to demonstrate that one can systematically identify coupled data motion for individual workflows.

Lockwood, GK↗
DOE OSTI2022

Enabling Modular Autonomous Feedback‐Loops in Materials Science through Hierarchical Experimental Laboratory Automation and Orchestration

Abstract Materials acceleration platforms (MAPs) operate on the paradigm of integrating combinatorial synthesis, high‐throughput characterization, automatic analysis, and machine learning. Within a MAP, one or multiple autonomous feedback loops may aim to optimize materials for certain functional properties or to generate new insights. The scope of a given experiment campaign is defined by the range of experiment and analysis actions that are integrated into the experiment framework. Herein, the authors present a method for integrating many actions within a hierarchical experimental laboratory automation and orchestration (HELAO) framework. They demonstrate the capability of orchestrating distributed research instruments that can incorporate data from experiments, simulations, and databases. HELAO interfaces laboratory hardware and software distributed across several computers and operating systems for executing experiments, data analysis, provenance tracking, and autonomous planning. Parallelization is an effective approach for accelerating knowledge generation provided that multiple instruments can be effectively coordinated, which the authors demonstrate with parallel electrochemistry experiments orchestrated by HELAO. Efficient implementation of autonomous research strategies requires device sharing, asynchronous multithreading, and full integration of data management in experimental orchestration, which to the best of the authors’ knowledge, is demonstrated for the first time herein.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Valence : A Massively Parallel Implementation of the Variational Subspace Valence Bond Method

This work describes the software package, Valence, for the calculation of molecular energies using the variational subspace valence bond (VSVB) method. VSVB is an ab initio electronic structure method based on nonorthogonal orbitals. Important features of practical value include high parallel scalability, wave functions that can be constructed automatically by combining orbitals from previous calculations, and ground and excited states that can be modeled with a single configuration or determinant. Here, the open-source software package includes tools to generate wave functions, a database of generic orbitals, example input files, and a library build intended for integration with other packages. We also present the interface to an external software package, enabling the computation of optimized molecular geometries and vibrational frequencies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Information or resolution: Which is required from an SEM to study bulk inorganic materials?: Evaluate SEMs’ practical performance

Significant technological advances in scanning electron microscopy (SEM) have been achieved over the past years. Different SEMs can have significant differences in functionality and performance. This work presents the perspectives on selecting an SEM for research on bulk inorganic materials. Understanding materials demands quantitative composition and orientation information, and informative and interpretable images that reveal subtle differences in chemistry, orientation/structure, topography, and electronic structure. The capability to yield informative and interpretable images with high signal-to-noise ratios and spatial resolutions is an overall result of the SEM system as a whole, from the electron optical column to the detection system. The electron optical column determines probe performance. The roles of the detection system are to capture, filter or discriminate, and convert signal electrons to imaging information. The capability to control practical operating parameters including electron probe size and current, acceleration voltage or landing voltage, working distance, detector selection, and signal filtration is inherently determined by the SEM itself. As a platform for various accessories, e.g. an energydispersive spectrometer and an electron backscatter diffraction detector, the properties of the electron optical column, specimen chamber, and stage greatly affect the performance of accessories. Ease-of-use and ease-of-maintenance are of practical importance. It is practically important to select appropriate test specimens, design suitable imaging conditions, and analyze the specimen chamber geometry and dimensions to assess the overall functionality and performance of an SEM. Finally, for an SEM that is controlled/operated with a computer, the stable software and user-friendly interface significantly affect the usability of the SEM.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Elucidating the Onset of Plasticity in Sliding Contacts Using Differential Computational Orientation Tomography

Abstract Depending on the mechanical and thermal energy introduced to a dry sliding interface, the near-surface regions of the mated bodies may undergo plastic deformation. In this work, we use large-scale molecular dynamics simulations to generate “differential computational orientation tomographs” (dCOT) and thus highlight changes to the microstructure near tribological FCC alloy surfaces, allowing us to detect subtle differences in lattice orientation and small distances in grain boundary migration. The analysis approach compares computationally generated orientation tomographs with their undeformed counterparts via a simple image analysis filter. We use our visualization method to discuss the acting microstructural mechanisms in a load- and time-resolved fashion, focusing on sliding conditions that lead to twinning, partial lattice rotation, and grain boundary-dominated processes. Extracting and laterally averaging the color saturation value of the generated tomographs allows us to produce quantitative time- and depth-resolved maps that give a good overview of the progress and severity of near-surface deformation. Corresponding maps of the lateral standard deviation in the color saturation show evidence of homogenization processes occurring in the tribologically loaded microstructure, frequently leading to the formation of a well-defined separation between deformed and undeformed regions. When integrated into a computational materials engineering framework, our approach could help optimize material design for tribological and other deformation problems. Graphic Abstract .

36 MATERIALS SCIENCE↗
DOE OSTI2019

Recognition of a Key Anchor Residue by a Conserved Hydrophobic Pocket Ensures Subunit Interface Integrity in DNA Clamps

Sliding clamp proteins encircle duplex DNA and are involved in processive DNA replication and the DNA damage response. Clamp proteins are ring-shaped oligomers (dimers or trimers) and are loaded onto DNA by an ATP-dependent clamp loader complex that ruptures the interface between two adjacent subunits. Here we measured the solution dynamics of the human clamp protein, proliferating cell nuclear antigen, by monitoring the change in the fluorescence of a site-specifically labeled. To unravel the origins of clamp subunit interface stability, we carried out comprehensive comparative analysis of the interfaces of seven sliding clamps. Here, we used computational modeling (molecular dynamic simulations and MM/GBSA binding energy decomposition analyses) to identify conserved networks of hydrophobic residues critical for clamp stability and ring-opening dynamics. The hydrophobic network is shared among clamp proteins and exhibits a “key in a keyhole” pattern where a bulky aromatic residue from one clamp subunit is anchored into a hydrophobic pocket of the opposing subunit. Bioinformatics and dynamic network analyses showed that this oligomeric latch is conserved across DNA sliding clamps from all domains of life and dictates the dynamics of clamp opening and closing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Deformation and fracture of explosion-welded Ti/Al plates: A synchrotron-based study

Here, explosion-welded Ti/Al plates are characterized with energy dispersive spectroscopy and x-ray computed tomography, and exhibit smooth, well-jointed, interface. We perform dynamic and quasi-static uniaxial tension experiments on Ti/Al with the loading direction either perpendicular or parallel to the Ti/Al interface, using a mini split Hopkinson tension bar and a material testing system in conjunction with time-resolved synchrotron x-ray imaging. X-ray imaging and strain-field mapping reveal different deformation mechanisms responsible for anisotropic bulk-scale responses, including yield strength, ductility and rate sensitivity. Deformation and fracture are achieved predominantly in Al layer for perpendicular loading, but both Ti and Al layers as well as the interface play a role for parallel loading. The rate sensitivity of Ti/Al follows those of the constituent metals. For perpendicular loading, single deformation band develops in Al layer under quasi-static loading, while multiple deformation bands nucleate simultaneously under dynamic loading, leading to a higher dynamic fracture strain. For parallel loading, the interface impedes the growth of deformation and results in increased ductility of Ti/Al under quasi-static loading, while interface fracture occurs under dynamic loading due to the disparity in Poisson's contraction.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Integrating Ab Initio Simulations and X-ray Photoelectron Spectroscopy: Toward A Realistic Description of Oxidized Solid/Liquid Interfaces

Many energy storage and conversion devices rely on processes that take place at complex interfaces, where structural and chemical properties are often difficult to probe under operating conditions. A primary example is solar water splitting using high-performance photoelectrochemical cells, where surface chemistry, including native oxide formation, affects hydrogen generation. In this Perspective, we discuss some of the challenges associated with interrogating interface chemistry, and how they may be overcome by integrating high-level first-principles calculations of explicit interfaces with ambient pressure X-ray photoelectron spectroscopy and direct spectroscopic simulations. We illustrate the benefit of this combined approach toward insights into native oxide chemistry at prototypical InP/water and GaP/water interfaces. Lastly, this example suggests a more general roadmap for obtaining a realistic and reliable description of the chemistry of complex interfaces by combining state-of-the-art computational and experimental techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Feature engineering descriptors, transforms, and machine learning for grain boundaries and variable-sized atom clusters

Abstract Obtaining microscopic structure-property relationships for grain boundaries is challenging due to their complex atomic structures. Recent efforts use machine learning to derive these relationships, but the way the atomic grain boundary structure is represented can have a significant impact on the predictions. Key steps for property prediction common to grain boundaries and other variable-sized atom clustered structures include: (1) describing the atomic structure as a feature matrix, (2) transforming the variable-sized feature matrix to a fixed length common to all structures, and (3) applying a machine learning algorithm to predict properties from the transformed matrices. We examine how these steps and different combinations of engineered features impact the accuracy of grain boundary energy predictions using a database of over 7000 grain boundaries. Additionally, we assess how different engineered features support interpretability, offering insights into the physics of the structure-property relationships.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Comprehensive characterization of protein–protein interactions perturbed by disease mutations

Technological and computational advances in genomics and interactomics have made it possible to identify how disease mutations perturb protein–protein interaction (PPI) networks within human cells. Here, we show that disease-associated germline variants are significantly enriched in sequences encoding PPI interfaces compared to variants identified in healthy participants from the projects 1000 Genomes and ExAC. Somatic missense mutations are also significantly enriched in PPI interfaces compared to noninterfaces in 10,861 tumor exomes. We computationally identified 470 putative oncoPPIs in a pan-cancer analysis and demonstrate that oncoPPIs are highly correlated with patient survival and drug resistance/sensitivity. Further, we experimentally validate the network effects of 13 oncoPPIs using a systematic binary interaction assay, and also demonstrate the functional consequences of two of these on tumor cell growth. In summary, this human interactome network framework provides a powerful tool for prioritization of alleles with PPI-perturbing mutations to inform pathobiological mechanism- and genotype-based therapeutic discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes

Abstract Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES’s primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fixed-target serial crystallography at the Structural Biology Center

Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Multi-Line Superconducting Waveguides Based on YBCO-on-Kapton Technology

Coplanar (with the ground) and stripline 25 cm long waveguides are manufactured from the YBCO-Kapton material. The waveguides are intended as the key components of a scalable signal delivery for large quantum computing systems and detectors. The waveguide is coupled with an integrated power divider that replaces the standard attenuator. The divider is designed to return most of the power to the previous thermalization stage. The method is projected to reduce the active dissipation by ≈10. We investigate the effect of internal strain in YBCO layer on the device's mechanical stability. Here, we show that adhesives with high stiffness are essential for the reliability of YBCO-Kapton devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗