Search NASA⌕ Search

SEARCH · Search NASA

Results for “EBIS”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Enriched Background Isotope Study (EBIS): Analysis of 14C-Enriched Carbon Cycle in Soils and Litter at Forested Oak Ridge and AmeriFlux Sites, 2001-2011

These data provide a record of the multi-year, multi-institutional Enriched Background Isotope Studies (EBIS) projects that ran from 2000 through 2011. Elevated levels of 14C enriched CO2 in the air and soil atmosphere as well as leaf, stem, and root tissues were observed on the Oak Ridge Reservations (ORR) during the summer of 1999, and were attributed to local incinerator activities on and/or near the ORR (Trumbore et al. 2002). The isolated enrichment of the background levels of 14C in local forest ecosystem represented a unique opportunity to study unresolved carbon cycling processes such as the contribution of leaf versus root litter contributions to soil carbon accumulation, the rate of vertical transport of carbon into deep soil storage pools, and the differential contribution of physicochemical versus faunal driven processes to soil carbon cycling and sequestration. Leaf litter from the local enriched forest was transplanted to selected sites on the ORR and to selected AmeriFlux study sites to study soil C cycling across a range of soils and climates. The EBIS research projects provide data on C flux from litter sources to mineral soil sinks for United States eastern hardwood forests necessary for testing process hypotheses and judging efficacy of soil C cycling models. Experimental results from this study are being used to parameterize and refine existing carbon dynamics models, the quantification of the long-term fate of ecosystem carbon inputs and as a means to judge the potential for ecosystem carbon sequestration via enhance litter inputs to soil. EBIS observations support conclusions that intra- and inter-annual soil carbon cycling in hardwood forest soils should be characterized as a least a two-compartment system where surface leaf-litter and belowground root turnover represent primary carbon sources for organic-layer and mineral-soil carbon cycles, respectively. EBIS experiments were conducted to complete enriched litterfall maniplations in upland forests on Ultisol and Inceptisol soils of the Oak Ridge Reservation, Oak Ridge, Tennessee. We also collected additional14C-enriched materials for new experimental applications, and applied those materials to multiple AmeriFlux sites over a range of climatic, edaphic and biological conditions. The research provided data for addressing DOE's goal of understanding mechanisms controlling C flux, and for the improvement of models to be applied to policy discussions regarding the safe levels of greenhouse gases for the earth's system. There are 5 data files provided in comma separated (*.csv) format for vegetation, field litter, soil and air [C] and C isotope data from the EBIS studies and associated environmental data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

EBIS Beam Intensity Online Optimization with GPTune and Offline Analysis with XGBoost

The application of machine learning techniques to accelerator research has led to significant breakthroughs in optimization strategies. This paper presents a pioneering study using a novel machine learning algorithm, GPTune, to optimize beam intensity by adjusting parameters in the EBIS injection and extraction beam lines. Our research demonstrates substantial improvements, achieving a remarkable 22% and 70% increase in beam intensity at two separate measurement locations.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

The 2023 Gold Run in the Injectors

RHIC Run 23 used Gold beam from Tandem with an AGS extraction energy of 9.8 GeV. The same basic setup, 8 single bunch transfers from the Booster and a 12-6 merge in the AGS to provide 4 bunches at extraction, had been used before to deliver Tandem Au to RHIC. But in those cases, it was used for low energy runs (3.85 GeV in 2021 and 5.75 GeV in 2020) where extraction was below transition energy (7.9 GeV). Tandem beam was used for this run because the intensity and stability of EBIS Au did not meet the requirements for RHIC. Physics was first declared in RHIC on May 22 nd and on August 1 st the run was cut short by about 2 months due to a major failure in RHIC. Prior to the advent of EBIS as the preinjector in 2012, 9.8 GeV Tandem Au was regularly delivered to RHIC but the setup in the Booster and AGS was quite different: Four Booster transfers of 6 bunches each were merged into 4 bunches using a 24-12-4 merge scheme. The supercycle length was 6.0 sec before June 29 th when it was extended to 6.6 sec to accommodate EBIS commissioning. The Tandem, Booster, and AGS were on user 1 for the 9.8 GeV setup. Some work with EBIS Au 32+ took place on EBIS, Booster, and AGS user 5 using the standard 9.8 GeV injector setup with a 4 to 1 merge in Booster and a 6-3-1 type merge in AGS. The Siemens motor generator was used for the entire run. An intensity limit of 8.0e9 Au 77+ ions in the AGS was in effect during the run to protect the J7 plunging stripping foil and the Copper absorber of the AGS beam dump. This corresponds to a merged bunch intensity limit of 2.0e9 Au 77+ ions for 4 equal intensity bunches. The per bunch intensity limit can be increased to 2.67e9 by reducing the number of BtA transfers from 8 to 6. There was also a Booster Late intensity limit of 16e9 Au ions in effect to protect the BtA stripping foil from damage due to overheating. Lowering the number of transfers also makes this limit less of a constraint. BtA foil 5, which was installed in 2020 and had not been used regularly prior to this run was used all run and showed no obvious signs of deterioration. In May, a Tandem Au 3.85 GeV setup from 2021 was also re-established on AGS user 2. It was used for APEX on May 24 and July 26. Initial work with 3.85 GeV beam was on May 19. Proton beam was also set up during the run and extracted to W dump on July 10. It was used for APEX on July 12. Although the OPPIS source was used the AGS setup was without snakes.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Optically pumped polarized 3 He ++ ion source development for RHIC/EIC

The proposed polarized 3 He ++ acceleration in RHIC and the future Electron-Ion Collider will require about 2×10 11 ions in the source pulse. A new technique had been proposed for production of high intensity polarized 3 He ++ ion beams. It is based on ionization and accumulation of the 3 He gas (polarized by metastability-exchange optical pumping and in the 5T high magnetic field) in the existing Electron Beam Ion Source (EBIS). A novel 3 He cryogenic purification and storage technique was developed to provide the required gas purity. An original gas refill and polarized 3 He gas injection to the EBIS long drift tubes, (which serves as the storage cell) were developed to ensure polarization preservation. An infrared laser system for optical pumping and polarization measurements in the high 3–5 T field has been developed. The 3 He polarization 80–85% (and sufficiently long ~30 min relaxation time) was obtained in the “open” cell configuration with refilling valve tube inlet and isolation valve closed. The development of the spin-rotator and 3 He 4 He absolute nuclear polarimeter at 6 MeV 3 He ++ beam energy is also presented here in this work.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Progress of the laser ion source upgrade (LION2) for RHIC and NSRL program at Brookhaven National Laboratory

At Brookhaven National Laboratory (BNL), the LION2 ion source is being constructed to replace an existing laser ion ablation ion source (LIS) at the EBIS facility, which provides heavy ion beams of multiple ion species for the operation of NASA Space Radiation Laboratory (NSRL) and Relativistic Heavy Ion Collider (RHIC). The LION1 ion source currently provides singly charged ions of Li, B, C, O, Al, Si, Ca, Ti, Fe, Cu, Zr, Nb, Ag, Tb, Ta, W, Au, Bi, and Th with a rapid-species-change capability. An electron beam ion source, Extended-EBIS captures, confines, and ionizes the ions to high charge state, suitable for injection and acceleration by an RFQ accelerator. Typically, single pulses of the LIS ion species for NSRL are changed sequentially during Galactic Cosmic Ray experiments, while multiple pulses of a given ion beam are provided quasi-simultaneously for RHIC. LION2 will have the same capability of the rapid-species-change with improved beam performance and reliability. LION2 is being constructed in a remote assembly location and is expected to finish in December 2023. The removal of LION1 and installation of LION2 is planned during the December 2023 or summer 2024 shutdown.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗
DOE OSTI2024

In situ effective pumping speed measurements as a tool for non-evaporable getter activation and saturation monitoring

We have developed method of in situ effective pumping speed measurements based on injecting finite gas pulse into a vacuum volume and subsequent recording of pressure response using a Residual Gas Analyzer (RGA). The pressure burst caused by injected gas pulse falls exponentially in time and the exponential coefficient of such pressure decay is proportional to total effective pumping speed of all vacuum pumps acting on vacuum chamber volume. The effective pumping speed can be extracted from the dependence of injected gas species pressure vs time recorded by an RGA. Non-Evaporable Getters (NEGs) are widely used in multiple ultra and extremely high vacuum devices and applications during the last several decades. Areas of NEG applications were recently expanded into vacuum devices with relatively high-pressure levels (up to 10 -7 Torr) by the invention of high capacity ZAO NEG which can be operated at elevated temperatures. The intrinsic property of all NEG-based vacuum pumps is the reduction of their pumping speed, called “NEG saturation”, after an extended period of operation. Typical time interval for such process can span from about a month and up to a few years depending on NEG type, vacuum level of NEG pump operation, and residual gas content. After that, the NEG pump will require a re-activation cycle to restore its pumping speed close to the initial value. For many applications it is difficult to realize what is the current pumping speed of NEG pump is and when the pump should be re-activated. A method for in situ effective pumping speed measurements developed in this study can be used as a tool for NEG-based pump activation and saturation monitoring. Application of such an approach to monitor pumping status of NEG pumps was utilized and will be continually used at Extended EBIS which was recently developed and commissioned for Relativistic Heavy Ion Collider (RHIC) and future Electron Ion Collider (EIC). The results obtained during commissioning are presented and discussed.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

Community recommendations on cryoEM data archiving and validation

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2023

Stripping Foils at the RHIC Injectors: A History

Stripping foils are used throughout Collider-Accelerator Department to strip ions of unwanted electrons. This is done in stages throughout the complex to optimize the transmission of particles. For polarized protons, they are injected into the AGS Booster as H-, and then stripped to H+. For ions from the tandem source, there are two stripping foils: one at the center and the other at the end of the tandem. The tandem foils will not be covered in this document. For ions out of the EBIS source, there is no use of stripping foils upstream of injection into the Booster. All ions that are not fully stripped in Booster are stripped further in the Booster to AGS (BTA) transfer line stripping foil assembly. Finally, any ions that are not fully stripped in the AGS are either stripped in the AGS to RHIC transfer line stripping foil, or as they are being dumped in the AGS by the plunging stripping foil (PSF) dependent on the particles intensity and charge. The BTA foil is the workhorse of the complex, having to provide the desired charge state of ions as light as O, and as heavy as Uranium. Optimizing the stripping efficiency to the desired charge state, while minimizing the energy lost and emittance growth from transiting the foil, requires careful consideration of the foil materials and thicknesses. This paper serves an overview of stripping foils at C-AD, with a review of foils from the construction of the AGS Booster to now.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Helions below |Gγ| = 10.5 in AGS

Polarized helion collisions are part of the Electron Ion Collider physics program. The required intensity at collision is 1.2×10 11 at 70% polarization. The EBIS source is expected to provide 2×10 11 helions/bunch at 80% polarization. To reach the EIC requirements, the AGS at extraction will need 1.5×10 11 helions/bunch and negligible polarization loss. A critical point for polarization loss in the injectors is the AGS injection energy, which can occur at either |Gγ| = 7.5 or |Gγ| = 10.5. Injection at |Gγ| = 7.5 will result in 80% beam loss and 2.5% polarization up to |Gγ| = 10.5.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

The 2024 Run in the Injectors

The injectors provided polarized protons to RHIC for most of Run 24. That was followed by 3 weeks of Gold at 9.8 GeV/n using Tandem. Physics with PP was first declared on May 1 st and the PP portion of the run ended on Sept. 30 th . The standard BU4/AU4 setup was used for most of it. Although, from Sept. 7 th to 30 th the AGS skew quad setup (BU4/AU6) was used instead. More work was done on the Split/Merge setup (BU3/AU3) initially developed in Run 22. A two Linac pulse setup was also developed this run (BU4/AU2). As far as PP work in the injectors goes this note will focus on the standard, Split/Merge, and Two Linac pulse setups. The 9.8 GeV/n Tandem Au setup was essentially the same as in Run 23. The injector setup for Helium-3 from EBIS (BU7/AU7), which was used for an APEX study in RHIC on August 7 th , will be covered as well.

43 PARTICLE ACCELERATORS↗
DOE OSTI2026

Estimating Residual Gas Beam Loss in the BNL AGS Booster:Model, Numerical Tools, and Implications for a Polarimeter Chamber

Beamloss from residual gas scattering is calculated for a storage ring of circumference C = 200m, covering a linear magnetic rigidity ramp from B ρ inj = 1.25Tm to B ρ ext = 9.50Tm over tramp = 1.00s. Three loss mechanisms are considered: nuclear inelastic reactions, single Coulomb scattering beyond the acceptance angle of the machine, and charge-state exchange for heavy ions. Calculations are performed for protons and Au 32+ ions, the latter being the charge state delivered by the EBIS pre-injector into the BNL AGS Booster. At a baseline vacuum of P 0 = 5 × 10 −11 mbar the integrated fractional beam loss over the full ramp is negligible for protons (< 0.001%) and 33.1% for Au 32+ . The impact of a 1m polarimeter section at elevated pressure P s = 5 × 10 −9 mbar is evaluated: the proton loss remains negligible, while the Au 32+ loss rises to 45.1%, establishing the vacuum requirement for the polarimeter chamber. In the present compact approximate model, Au 32+ losses are dominated by charge exchange at injection, while proton losses are dominated by single Coulomb scattering. The design, outgassing budget, pumping strategy, and commissioning sequence for a UHV polarimeter chamber housing silicon detectors and ASICs are described in detail.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics↗
DOE OSTI2026

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.

Nextflow↗
DOE OSTI2025

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format

Advances in mass spectrometry (MS) instrumentation, such as higher resolution, faster scan speeds, and improved sensitivity, have significantly increased the volume and complexity of data. The growing adoption of imaging and ion mobility further amplifies these challenges across MS-based omics fields, including proteomics, metabolomics, and lipidomics. While these technologies unlock new possibilities, they also present significant challenges in data management, storage, and accessibility. Existing open formats, such as the XML-based community standards mzML and imzML, struggle to meet the demands of modern MS workflows due to their large file sizes, slow data access, and limited metadata support. Vendor-specific formats, while optimized for proprietary instruments, lack interoperability, comprehensive metadata support and long-term archival reliability. This white paper lays the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multi-dimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will enable enhanced interoperability across platforms, seamless support for complex workflows including ion mobility and MS imaging, and faster data access compared to existing community formats such as mzML. Its design will ensure data is managed in compliance with regulatory standards, essential for applications such as precision medicine and chemical safety, where long-term data integrity and accessibility are critical. For vendors, mzPeak provides a streamlined, open alternative to proprietary formats, reducing the burden of regulatory compliance while aligning with the industry's push for transparency and standardization. By offering a high-performance, interoperable solution, mzPeak positions vendors to meet customer demands for sustainable data management tools which will be able to handle emerging and future data types and workflows. mzPeak aspires to become the cornerstone of MS data management, empowering researchers, vendors, and developers to innovate and collaborate more effectively.

data formats↗