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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 199 records · Page 11

Ambient Mass Spectrometry Rapid Analysis Methods for Trace Inorganics

The ability to rapidly detect and characterize the chemistry of trace quantities of inorganic species has multiple potential applications, including nuclear safeguards, nuclear forensics, and environmental monitoring. Some mass spectrometric methods currently exist, but they are costly and time-intensive, often destroying chemical information in the process of ionization. Ambient mass spectrometry is a relatively new analytical method in which samples are introduced to the mass spectrometer from atmospheric pressure, rather than from high vacuum. Ambient MS can operate with gentler ionization methods such as electrospray ionization (ESI) and paper-spray ionization (PSI), reducing fragmentation and preserving the chemical information of the analyte. This may be useful for determining the intended purpose of material in a sample. Strontium, part of nuclear fallout, is analyzed here to test these new analytical methods for viability. Electrospray ionization mass spectrometry functions by spraying the sample as a solution through a needle charged to a few kV. A nebulizing gas flows out along with the sample to create the spray before droplets enter a drying chamber with heated drying gas to remove the solvent molecules. From there bare analyte ions enter the mass spectrometer. This method has the advantage of relatively fast sample preparation and stable ionization. More stable ionization produces higher-quality data. Paper-spray ionization mass spectrometry operates by applying sample to a paper triangle. The paper triangle is then electrified in a metal clamp to a few kV before spray solvent is applied. The spray solvent transports analyte in the sample to the tip, where it is ionized and enters the mass spectrometer. One advantage of this method is reduced sample preparation - an analyst can even swipe a surface and cut a triangle directly from the swipe. The data analysis serves to rapidly process tens of samples all at once. The mass spectrometer outputs a file containing a few hundred spectra for each sample. The pipeline processes each one to identify peaks of interest. A full palette of data analysis metrics are generated, including plots of the raw data and plots of calculated values such as isotopic ratios. The pipeline filters the raw data to remove noise and background peaks, as well as peaks representing detector saturation. A heat map is generated to show the overall spectrum in mass-time- intensity space. Post-processing, we obtained the desired calibration curves, demonstrating that both ESI-MS and PSI-MS are viable methods for quantifying trace amounts of inorganics while retaining their chemical speciation information. ESI-MS demonstrated a linear response region of 100 ppb to 20 ppm, with a limit-of-detection of around 100 ppb. At top left is an example spectrum with the {sup 88}SrNO{sub 3} peak identified to show the retention of chemical speciation. PSI-MS showed a linear response region of around 1 ppb to 1 ppm, with a limit-of-detection of near 1 ppb. PSI-MS produced more erratic results than ESI-MS, likely due to the variability in ionization resulting from manual positioning of the paper triangle near the MS inlet. Future efforts will focus on improving the repeatability of PSI-MS as well as analyzing other species of interest such as cerium and uranium. Improvements will also be made to create more reliable data extraction and intelligent data filtering.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Summer 2021 Internship Report

During this internship program, I was assigned with developing a Web application to robustify web resources referenced by links (URI-Rs) in PDFs. It was intended for use in LANL Research 2 Library systems such as RASSTI (Review and Approval System for Scientific and Technical Information), where users submit scholarly PDFs that may contain URI-Rs. For such PDFs, the application should, using Web Archives, create robust snapshots (i.e., Mementos) of the web resources referenced by URI-Rs, and notify this robustification to LANL Research Library systems. The Mementos were to be created using the Robust Links Service, and the notifications were to be sent using the Linked Data Notifications (LDN) Protocol.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Nuclear Physics Network Requirements Review Report

The Energy Sciences Network (ESnet) is the Office of Science’s high-performance network user facility, delivering highly reliable data transport capabilities optimized for the requirements of data-intensive science. In essence, ESnet is the circulatory system that enables the U.S. Department of Energy (DOE) science mission by connecting each and every DOE lab and its user facilities. ESnet is funded and stewarded by the Advanced Scientific Computing Research (ASCR) Program and managed and operated by the Scientific Networking Division at Lawrence Berkeley National Laboratory (LBNL). ESnet is widely regarded as a global leader in the research and education networking community. ESnet connects DOE national laboratories, user facilities, and major experiments so scientists can use remote instruments and computing resources as well as share data with collaborators, transfer large data sets, and access distributed data repositories. While ESnet provides network connectivity, it cannot be characterized as an internet service provider as it is specifically built to provide a range of network services that are tailored to meet the unique requirements of DOE’s data-intensive science.

97 MATHEMATICS AND COMPUTING↗

Trust Not Verify? The Critical Need for Data Curation Standards in Materials Informatics

The importance of data curation has been recognized in multiple areas of research; however, the discussion of this important issue is only beginning to emerge in materials science. In this Perspective, we highlight the benefits of using the standardized data curation protocols in materials science and discuss current gaps in accurate and reproducible data reporting using case studies drawn from high-impact materials science papers and well-known databases such as the Crystallography Open Database (COD) and the Cambridge Structural Database (CSD). We argue that both experimental and computational materials scientists need to embrace a culture of rigorous data curation as part of modern research data management. We propose a sample data curation pipeline for materials chemistry and illustrate its use by creating two new materials chemistry databases. Here, we hope that this perspective will serve to catalyze further discussion and promote the continuous development of rigorous data curation practices within the materials science research community. We posit that adherence to best practices of data curation will promote and enhance the reliability, reproducibility, and integrity of materials research and enable the development of reliable AI and machine learning models that critically depend on the use of quality data.

Chemical structure↗

Psychosocial drivers of land management behaviour: How threats, norms, and context influence deforestation intentions

Understanding how private landholders make deforestation decisions is of paramount importance for conservation. Behavioural frameworks from the social sciences have a lot to offer researchers and practitioners, yet these insights remain underutilised in describing what drives landholders' deforestation intentions under important political, social, and management contexts. Using survey data of private landholders in Queensland, Australia, we compare the ability of two popular behavioural models to predict future deforestation intentions, and propose a more integrated behavioural model of deforestation intentions. We found that the integrated model outperformed other models, revealing the importance of threat perceptions, attitudes, and social norms for predicting landholders' deforestation intentions. Social capital, policy uncertainty, and years of experience are important contextual moderators of these psychological factors. Here, we conclude with recommendations for promoting behaviour change in this deforestation hotspot and highlight how others can adopt similar approaches to illuminate more proximate drivers of environmental behaviours in other contexts.

54 ENVIRONMENTAL SCIENCES↗

Pseudonymization at Scale: OLCF’s Summit Usage Data Case Study

The analysis of vast amounts of data and the processing of complex computational jobs have traditionally relied upon high performance computing (HPC) systems, which offer reliable and efficient management of large-scale computational and data resources. Understanding these analyses’ needs is paramount for designing solutions that can lead to better science, and similarly, understanding the characteristics of the user behavior on those systems is important for improving user experiences on HPC systems. A common approach to gathering data about user behavior is to extract workload characteristics from system log data available only to system administrators. Recently at Oak Ridge Leadership Computing Facility (OLCF), however, we unveiled user behavior about the Summit supercomputer by collecting data from a user’s point of view with ordinary Unix commands.In this paper, we discuss the process, challenges, and lessons learned while preparing this dataset for publication and submission to an open data challenge. The original dataset contains personal identifiable information (PII) about the users of OLCF which needed be masked prior to publication, and we determined that anonymization, which scrubs PII completely, destroyed too much of the structure of the data to be interesting for the data challenge. We instead chose to pseudonymize the dataset, which reduced the linkability of the dataset to the users’ identities. Pseudonymization is significantly more computationally expensive than anonymization, and the size of our dataset, which is approximately 175 million lines of raw text, necessitated the development of a parallelized workflow that could be reused on different HPC machines. We demonstrate the scaling behavior of the workflow on two leadership class HPC systems at OLCF, and we show that we were able to bring the overall makespan time from an impractical 20+ hours on a single node down to around 2 hours. As a result of this work, we release the entire pseudonymized dataset and make the workflows and source code publicly available.

Maheshwari, Ketan↗

BOXKIT

SF-23-067 BoxKit is a library that provides building blocks to parallelize and scale data science, high performance computing, and machine learning applications for block-structured datasets. Spatial data from simulations and experiments can be accessed and managed using tools available in this library when working with more data analysis oriented packages like SciKit (https://github.com/scikit-learn/scikit-learn) and FlowNet (https://github.com/NVIDIA/flownet2-pytorch)

DHRUV, AKASH↗

NDMAS

Overview of Current ART-GCR Data: Fuel Fabrication, Irradiation Monitoring (Fuel & Graphite – near real-time for HDG-1), Post-Irradiation Examination (Fuel & Graphite), Graphite Characterization (Baseline and Irradiated), High Temperature Metals Mechanical Tests, Design, Methods, and Validation Data, Japan Atomic Energy Agency’s High Temperature Test Reactor (HTTR), Argonne National Laboratory’s Natural convection Shutdown heat removal Test Facility (NSTF), Oregon State University’s High Temperature Test Facility (HTTF), Generation IV International VHTR Materials Handbook, Additional related data, and Advanced Test Reactor operations (near real-time).

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Editorial: Achieving Water-Energy-Food Nexus Sustainability: A Science and Data Need or a Need for Integrated Public Policy?

The benefits of addressing the water, energy, and food sectors in an integrated manner is gaining significant recognition. An integrated approach can provide improved resource use efficiencies, more coherent environmental policies, and an overall strategy for achieving sustainability in the three sectors, as outlined in the United Nations Sustainable Development Goals (SDG) 2 (Food), 6 (Water), and 7 (Energy). Societies are concerned with ensuring food security, avoiding wars over water, and creating opportunity by ensuring access to energy. To be effective, however, this approach needs to be adopted at all levels of societies including government, private and civil society and reinforced by management and planning methods. This special issue identifies different approaches that are either being conceptualized or tested to support the Water-Energy-Food (WEF) Nexus approach. The articles contribute to answering the question, “Is achieving Water-Energy-Food (WEF) Nexus Sustainability a science and data need or an integrated public policy need?” In either case, both natural and social sciences will need to combine to support science issues or integrated policy issues. The papers explore the ways in which science, data, and policy development could help to define integrative principles and policies for the three sectors. This approach could expand beyond the water, energy, and food sectors to include health, environment, trade, commerce, and international assistance thereby providing broad support to the SDGs. Moreover, this issue demonstrates that data combined with new technologies (tools and models) can support better decision-making when adopted by governments and the sectors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Specifications and a Prototype Software to Demonstrate a Data Catalog for Hanford Datasets

Environmental management activities at the Hanford Site produce extensive data about site conditions, contaminants, and cleanup activities. Managing, archiving, and accessing that data requires a high degree of collaboration among site contractors and a high level of awareness by project managers and staff. The Hanford Site has a range of databases (e.g., Hanford Environmental Information System [HEIS]) and their associated user interfaces (e.g., Environmental Dashboard Application [EDA], Virtual Library [VL]), as well as other document management systems (e.g., Integrated Document Management System [IDMS]). However, Hanford lacks a single unified resource to find data (which itself comes in multiple formats) amongst the multiple disparate systems, not to mention ad hoc data not contained in an official repository/database.

54 ENVIRONMENTAL SCIENCES↗

Integrated Hydro-Terrestrial Modeling: Development of a National Capability

Water is one of our most important natural resources and is essential to our national economy and security. Multiple federal government agencies have mission elements that address national needs related to water. Each water-related agency champions a unique science and/or operational mission focused on advancing a portion of the nation’s ability to meet our water-related challenges. These diverse mission needs have engendered a rich and extensive base of water-related data and modeling capabilities. While useful for their intended purposes, these capabilities are not well integrated to address complex regional problems and overarching national problems. These major investments by a number of federal agencies, however, lay the foundation for an integrated hydro-terrestrial modeling and data infrastructure that will enhance knowledge, understanding, prediction, and management of the nation’s diverse water challenges. Creating a more seamless national hydro-terrestrial modeling and data capacity presents an enormous opportunity to advance operational as well as research capabilities leading to more effective water management. Advances are necessary not only in operational tools for forecasting but also in research to identify and resolve knowledge and data gaps that lead to unacceptable uncertainties in forecast outcomes. As such, close coordination across scientific, operational, and resource management communities is required. To this end, an interagency workshop on “Integrated Hydro-Terrestrial Modeling: Development of a National Capacity” was held at the National Science Foundation (NSF) headquarters in Alexandria, Virginia in September 2019, led jointly by the NSF, the U.S. Department of Energy (DOE) and the U.S. Geological Survey (USGS) and with broader interagency support provided through an interagency steering committee. This workshop provided a venue to bring together representatives of water-related agencies and their scientific partners (including university researchers) to initiate and refine a vision for a national Integrated Hydro-Terrestrial Modeling (IHTM) and data infrastructure and advance ideas towards its development. The workshop was designed to address three critical foci to advance the development of a national IHTM capacity: “Priority Water Challenges” around which to motivate and initiate development; Technical and methodological obstacles related to data and modeling; Organizational, structural, and cultural barriers that heretofore have impeded integration of capabilities across the federal and research landscapes. The following “Priority Water Challenge” domain areas represent targets for initiating development of the IHTM and were identified and selected in alignment with priorities of the administration’s Water Sub-Cabinet: (1) Nutrient loading, hypoxia, and harmful algal blooms; (2) Water availability in the western United States; and (3) Extreme weather-related water hazards. These water challenges span agency mission boundaries and encompass a broad range of geographies, complex system dynamics and feedbacks, and critical processes spanning hydrological, climatic, and biophysical systems as well as land-use/land-cover, agricultural, built infrastructure, societal, economic, and decisional environments. These three Priority Water Challenges cannot be fully addressed without leveraging complementary and synergistic capabilities across multiple agencies.

99 GENERAL AND MISCELLANEOUS↗

Data Archive and Portal (DAP) Platform for Solid Phase Processing Technologies

The scale and speed of data generated by modern scientific experiments have constantly challenged the research community to store, curate, manage and optimally use it to drive scientific discoveries. In this work, we have developed a data archive and portal (DAP) platform including analytics capabilities to collect, curate, and manage data and metadata stream for solid phase processing (SPP) techniques. We successfully hosted around ~347K files of data related to processing parameters, microscopic images, and spectroscopic data related to solid phase processing. The DAP platform for SPP will establish an enduring capability to support machine learning and grow collaboration at the intersection of materials science and data science.

36 MATERIALS SCIENCE↗

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is the premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It is jointly managed by the Worldwide Protein Data Bank (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is funded by the National Science Foundation, National Institutes of Health, and US Department of Energy and serves as the US data center for the wwPDB. RCSB PDB is also responsible for the security of PDB data in its role as wwPDB‐designated Archive Keeper. Every year, RCSB PDB serves tens of thousands of depositors of 3D macromolecular structure data (coming from macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction). The RCSB PDB research‐focused web portal ( RCSB.org ) makes PDB data available at no charge and without usage restrictions to many millions of PDB data consumers around the world. The RCSB PDB training, outreach, and education web portal ( PDB101.RCSB.org ) serves nearly 700 K educators, students, and members of the public worldwide. This invited Tools Issue contribution describes how RCSB PDB (i) is organized; (ii) works with wwPDB partners to process new depositions; (iii) serves as the wwPDB‐designated Archive Keeper; (iv) enables exploration and 3D visualization of PDB data via RCSB.org ; and (v) supports training, outreach, and education via PDB101.RCSB.org . New tools and features at RCSB.org are presented using examples drawn from high‐resolution structural studies of proteins relevant to treatment of human cancers by targeting immune checkpoints.

59 BASIC BIOLOGICAL SCIENCES↗

LANL Contributions to pyiron: An integrated development environment for computational materials science

To support and accelerate the development of simulation protocols in atomistic modelling, we introduce an integrated development environment (IDE) for computational materials science called pyiron (http://pyiron.org). The pyiron IDE combines a web based source code editor, a job management system for build automation, and a hierarchical data management solution. The core components of the pyiron IDE are pyiron objects based on an abstract class, which links application structures such as atomistic structures, projects, jobs, simulation protocols and computing resources with persistent storage and an interactive user environment. The simulation protocols within the pyiron IDE are constructed using the Python programming language. To highlight key concepts of this tool as well as to demonstrate its ability to simplify the implementation and testing of simulation protocols we discuss two applications. In these examples we show how pyiron supports the whole life cycle of a typical simulation, seamlessly combines ab initio with empirical potential calculations, and how complex feedback loops can be implemented. While originally developed with focus on ab initio thermodynamics simulations, the concepts and implementation of pyiron are general thus allowing to employ it for a wide range of simulation topics.

Janssen, Jan↗

Curifactory: A research experiment manager

Curifactory is a command line tool and framework for organizing Python experiment code, configuration parameters, and results. It is an opinionated and lightweight approach to workflow management infrastructure and is primarily intended to support researchers conducting experiments on one machine. This software was developed to support the reproducibility of results for several data science projects in the Nuclear Nonproliferation Division at Oak Ridge National Laboratory. Curifactory is intended to be a general framework and is not specific to machine learning or data science. It can aid in any field in which experiments are primarily computation-based studies and can be implemented in Python (e.g., high-energy physics, astronomy, computational chemistry). Here, the design emphasizes the automated caching of intermediate data analysis artifacts to speed up development involving computationally intensive tasks. It also allows for data provenance and experiment reproduction. Individual experiment runs are tracked through logs and their output reports, and entire copies of a run with all cached data and metadata can be exported for others to run using Curifactory on another machine. Curifactory experiments can either be integrated into a project from the beginning or can be written on top of an existing codebase without needing significant modification. A few important views of the Curifactory library can be seen in Figure 1.

97 MATHEMATICS AND COMPUTING↗

Publishing Environmental Assessment and Management Science: Crossing the Hurdles

Benefits accrue to scientists, resource managers, companies, and policymakers when environmental scientists publish in peer-reviewed journals. However, environmental scientists and practitioners face challenges, including the sometimes low value placed on journal articles, institutional vested interests in outcomes, and the changing priorities of employers and project sponsors. Confidentiality agreements can also lead scientists to assume publication is not an option. Case studies may be viewed by potential authors as too routine for peer-reviewed journals. On the basis of 30 years of experience, we suggest that publishing hurdles can be overcome and that environmental scientists have a range of options. The topics of manuscripts can include not only results from case studies and perspectives based on them but also byproducts of assessments, including definitions, plans, monitoring methods and models, and decision frameworks. Environmental scientists have unique opportunities to move science forward with their practical knowledge if they can move across the institutional, logistical, data-related, and content-related hurdles.

54 ENVIRONMENTAL SCIENCES↗

Machine learning enabling high-throughput and remote operations at large-scale user facilities

Imaging, scattering, and spectroscopy are fundamental in understanding and discovering new functional materials. Contemporary innovations in automation and experimental techniques have led to these measurements being performed much faster and with higher resolution, thus producing vast amounts of data for analysis. These innovations are particularly pronounced at user facilities and synchrotron light sources. Machine learning (ML) methods are regularly developed to process and interpret large datasets in real-time with measurements. However, there remain conceptual barriers to entry for the facility general user community, whom often lack expertise in ML, and technical barriers for deploying ML models. Herein, we demonstrate a variety of archetypal ML models for on-the-fly analysis at multiple beamlines at the National Synchrotron Light Source II (NSLS-II). We describe these examples instructively, with a focus on integrating the models into existing experimental workflows, such that the reader can easily include their own ML techniques into experiments at NSLS-II or facilities with a common infrastructure. The framework presented here shows how with little effort, diverse ML models operate in conjunction with feedback loops via integration into the existing Bluesky Suite for experimental orchestration and data management.

36 MATERIALS SCIENCE↗

Accelerating Scientific Workflows on HPC Platforms with In Situ Processing

Scientific workflows drive most modern large-scale science breakthroughs by allowing scientists to define their computations as a set of jobs executed in a given order based on their data dependencies. Workflow management systems (WMSs) have become key to automating scientific workflows-executing computational jobs and orchestrating data transfers between those jobs running on complex high-performance computing (HPC) platforms. Traditionally, WMSs use files to communicate between jobs: a job writes out files that are read by other jobs. However, HPC machines face a growing gap between their storage and compute capabilities. To address that concern, the scientific community has adopted a new approach called in situ, which bypasses costly parallel filesystem I/O operations with faster in-memory or in-network communications. When using in situ approaches, communication and computations can be interleaved. In this work, we leverage the Decaf in situ dataflow framework to accelerate task-based scientific workflows managed by the Pegasus WMS, by replacing file communications with faster MPI messaging. We propose a new execution engine that uses Decaf to manage communications within a sub-workflow (i.e., set of jobs) to optimize inter-job communications. We consider two workflows in this study: (i) a synthetic workflow that benchmarks and compares file- and MPI-based communication; and (ii) a realistic bioinformatics workflow that computes mu-tational overlaps in the human genome. Experiments show that in situ communication can improve the bioinformatics workflow execution time by 22% to 30% compared with file communication. Our results motivate further opportunities and challenges for bridging traditional WMSs with in situ frameworks.

Decaf↗