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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Outcomes of WPEC SG47 on "Use of Shielding Integral Benchmark Archive and Database for Nuclear Data Validation"

The Working Party on International Nuclear Data Evaluation Co-operation Subgroup 47 (WPECSG47) entitled "Use of Shielding Integral Benchmark Archive and Database for Nuclear Data Validation" was organised from 2019 and 2022 with the objectives to promote more systematic and wider use of shielding benchmark experiments in nuclear data (ND) and transport code validation and development, to provide feedback on the Shielding Integral Benchmark Archive and Database (SINBAD), and to promote its further development in coordination with the Expert Group on Physics of Reactor Systems (EGPRS). Altogether 9 meetings, the large majority (8) held remotely, were organised during the past 3 years to discuss the experience on the use of SINBAD, evaluation of new benchmarks and improvements to be contributed to the database which was severely neglected and lacking maintenance over the past ← 10+ years. Several proposals for new or updated benchmark evaluation were presented and discussed, such as FNG copper, LLNL pulsed spheres, CIAE iron sphere, KFK 1977 gamma measurements, Rez Fe sphere, ASPIS, ORNL Oxygen broomstick, TIARA and others. Complementing the database with new features was also discussed, for example providing the nuclear data sensitivity profiles more systematically would facilitate and better guide the use of data. Information on the geometry, (radiation source) and materials available in CAD format is expected to allow an easier and less error prone reference for computational model preparation and a potential input to CAD based workflows. Inputs for various transport codes and other benchmark data from participants have been shared via the NEA GitLab which could hopefully in the future evolve and form a bases for critically checked and validated benchmark data. Future development of SINBAD will be monitored by EGPRS and the newly created SINBAD Task Force.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

WPEC SG50: Developing an Automatically Readable, Comprehensive and Curated Experimental Nuclear Reaction Database

The Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) Working Party on International Nuclear Data Evaluation Co-operation (WPEC) subgroup (SG) 50 was formed in 2020 to develop an automatically readable, comprehensive and curated experimental nuclear reaction database. This database is called MEDUSAL (Machine-readable Experimental Data User Application & Library), and will draw from EXFOR. The EXFOR database preserves experimental nuclear reaction data true to its original documentation and information from the authors of the data. MEDUSAL will deviate from EXFOR by storing additional information from users of the data for their fields of work (evaluation, model development, validation, etc.). This includes expert judgment on the data sets, identification of data points as outliers, renormalization of the data to the newest monitor reactions, and estimations of missing uncertainty sources. The format for MEDUSAL is being developed to enable easy automatic parsing of large amounts of data. Here, we will summarize the use cases, high-level requirements and first steps towards developing the database MEDUSAL and the API to access it.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

Parallel database search and prime factorization with magnonic holographic memory devices

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Quantum computing without quantum computers: Database search and data processing using classical wave superposition

Quantum computers are proven to be more efficient at solving a specific class of problems compared to traditional digital computers. Superposition of states and quantum entanglement are the two key ingredients that make quantum computing so powerful. However, not all quantum algorithms require quantum entanglement (e.g., search through an unsorted database). Is it possible to utilize classical wave superposition to speed up database searching as much as by using quantum computers? There were several attempts to mimic quantum computers using classical waves. It was concluded that the use of classical wave superposition comes with the cost of an exponential increase in resources. In this work, we consider the feasibility of building classical wave-based devices able to provide fundamental speedup over digital counterparts without the exponential overhead. We present experimental data on database searching through a magnetic database using spin wave superposition. The results demonstrate the same speedup as expected for quantum computers. Also, we present examples of numerical modeling demonstrating classical wave interference for period finding. This approach may not compete with quantum computers with efficiency but outperform classical digital computers. We argue that classical wave-based devices can perform some of the quantum algorithms with the same efficiency as quantum computers as long as quantum entanglement is not required.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

A database and meta-analysis on the performance of exploding pusher implosions conducted at OMEGA

A database of 222 exploding pusher implosions conducted at the OMEGA Laser Facility is presented. The dataset consists of glass-shell capsules filled with varying pressures of D 2 , T 2 , and 3 He, which were imploded using square laser pulses with intensities ranging from 1 to 1 × 10 15 W/cm 2 . The database includes measurements of bang times, ion temperatures, and yields from the DD, D 3 He, and DT fusion reactions. A semi-analytic exploding pusher model is introduced, which effectively captures the observed trends in the data. This model predicts that the measurements scale according to a power-law relation based on the initial capsule and laser conditions. A generalized power-law scaling relation is directly fit to each dataset, providing a useful interpolation of the entire database. Overall, the database provides a valuable resource to estimating bang times, temperatures, and yields for the design of future experiments. Additionally, it provides a diverse set of data for validating more advanced implosion physics models.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

SMALL-SCALE AND GLOBAL DYNAMOS AND THE AREA AND FLUX DISTRIBUTIONS OF ACTIVE REGIONS, SUNSPOT GROUPS, AND SUNSPOTS: A MULTI-DATABASE STUDY

In this work, we take advantage of 11 different sunspot group, sunspot, and active region databases to characterize the area and flux distributions of photospheric magnetic structures. We find that, when taken separately, different databases are better fitted by different distributions (as has been reported previously in the literature). However, we find that all our databases can be reconciled by the simple application of a proportionality constant, and that, in reality, different databases are sampling different parts of a composite distribution. This composite distribution is made up by linear combination of Weibull and log-normal distributions—where a pure Weibull (log-normal) characterizes the distribution of structures with fluxes below (above) 10{sup 21}Mx (10{sup 22}Mx). Additionally, we demonstrate that the Weibull distribution shows the expected linear behavior of a power-law distribution (when extended to smaller fluxes), making our results compatible with the results of Parnell et al. We propose that this is evidence of two separate mechanisms giving rise to visible structures on the photosphere: one directly connected to the global component of the dynamo (and the generation of bipolar active regions), and the other with the small-scale component of the dynamo (and the fragmentation of magnetic structures due to their interaction with turbulent convection)

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

THE NASA AMES PAH IR SPECTROSCOPIC DATABASE VERSION 2.00: UPDATED CONTENT, WEB SITE, AND ON(OFF)LINE TOOLS

A significantly updated version of the NASA Ames PAH IR Spectroscopic Database, the first major revision since its release in 2010, is presented. The current version, version 2.00, contains 700 computational and 75 experimental spectra compared, respectively, with 583 and 60 in the initial release. The spectra span the 2.5-4000 μm (4000-2.5 cm{sup -1}) range. New tools are available on the site that allow one to analyze spectra in the database and compare them with imported astronomical spectra as well as a suite of IDL object classes (a collection of programs utilizing IDL's object-oriented programming capabilities) that permit offline analysis called the AmesPAHdbIDLSuite. Most noteworthy among the additions are the extension of the computational spectroscopic database to include a number of significantly larger polycyclic aromatic hydrocarbons (PAHs), the ability to visualize the molecular atomic motions corresponding to each vibrational mode, and a new tool that allows one to perform a non-negative least-squares fit of an imported astronomical spectrum with PAH spectra in the computational database. Finally, a methodology is described in the Appendix, and implemented using the AmesPAHdbIDLSuite, that allows the user to enforce charge balance during the fitting procedure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Empirical scaling of the L–H threshold power for metal wall tokamaks using a multi-device database

The empirical scaling for the H-mode power threshold in tokamaks has been revisited using a database with threshold data from machines with a metallic first wall as part of International Tokamak Physics Activity (ITPA) task TC-26. The database contains discharges from ASDEX Upgrade (AUG) (W), JET (Be/W) and Alcator C-Mod (Mo). This was motivated by reports that in like-for-like discharges the power threshold was reduced by approximately 30% after the change from carbon based to metallic first wall materials on AUG (Ryter et al 2013 Nucl. Fusion 53 113003) and JET (Maggi et al 2014 Nucl. Fusion 54 023007). The database contains L–H transition data for all hydrogen isotopes and mixtures, including T and DT from the recent JET campaigns. Compared to the ITPA 2008 scaling (Martin et al 2008 J. Phys.: Conf. Ser. 123 012033), the metal wall scaling has a smaller magnetic field exponent but a larger density exponent. We present an additional parameter to capture the strong dependence of the L–H power threshold (approx. factor 2) on the magnetic configuration in the divertor on JET. The scaling recovers the approximate inverse isotope mass scaling of the threshold power. Alternative scalings involving the plasma current and poloidal magnetic field are explored. Despite the reduction in threshold observed earlier, the scalings based on the metal wall database do not necessarily extrapolate to a lower threshold for ITER compared to the ITPA 2008 scaling, especially at high density. The divertor configuration effect induces the largest uncertainty in the extrapolation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2018

Belle II Conditions Database

The Belle II experiment at KEK is preparing for taking first collision data in early 2018. For the success of the experiment it is essential to have information about varying conditions available to systems worldwide in a fast and efficient manner that is straightforward for both the user and maintainer. The Belle II Conditions Database was designed to make maintenance as easy as possible. To this end, a HTTP REST service was developed with industry-standard tools such as Swagger for the API interface development, Payara for the Java EE application server, and the Hazelcast in-memory data grid for support of scalable caching as well as transparent distribution of the service across multiple sites. On the client side, the online and offline software has to be able to obtain conditions data from the Belle II Conditions Database in a robust and reliable way under very different situations. As such the client side interface to the Belle II Conditions Database has been designed with a variety of access mechanisms which allow the software to be used with and without an internet connection. Different methods to access the payload information are implemented to allow for a high level of customization per site and to simplify testing of new payloads locally. Changes to the conditions data are usually handled transparently but users can actively check whether an object has changed or register callback functions to be called whenever a conditions data object is updated. In addition a command line user interface has been developed to simplify inspection and modification of the database contents.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Sipros Ensemble improves database searching and filtering for complex metaproteomics

Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics. Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch & MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers. Freely available under the GNU GPL license at http://sipros.omicsbio.org.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acid complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Prevalence of gp160 polymorphisms known to be related to decreased susceptibility to temsavir in different subtypes of HIV-1 in the Los Alamos National Laboratory HIV Sequence Database

Fostemsavir, a prodrug of the gp120-directed attachment inhibitor temsavir, is indicated for use in heavily treatment-experienced individuals with MDR HIV-1. Reduced susceptibility to temsavir in the clinic maps to discrete changes at amino acid positions in gp160: S375, M426, M434 and M475.To query the Los Alamos National Laboratory (LANL) HIV Sequence Database for the prevalence of polymorphisms at gp160 positions of interest. Full-length gp160 sequences (N = 7560) were queried for amino acid polymorphisms relative to the subtype B consensus at positions of interest; frequencies were reported for all sequences and among subtypes/circulating recombinant forms (CRFs) with ≥10 isolates in the database. Among 239 subtypes in the database, the 5 most prevalent were B (n = 2651, 35.1%), C (n = 1626, 21.5%), CRF01_AE (n = 674, 8.9%), A1 (n = 273, 3.6%) and CRF02_AG (n = 199, 2.6%). Among all 7560 sequences, the most prevalent amino acids at positions of interest (S 375 , 73.5%; M 426 , 82.1%; M 434 , 88.2%; M 475 , 89.9%) were the same as the subtype B consensus. Specific polymorphisms with the potential to decrease temsavir susceptibility (S 375 H/I/M/N/T/Y, M 426 L/P, M 434 I/K and M475I) were found in <10% of isolates of subtypes D, G, A6, BC, F1, CRF07_BC, CRF08_BC, 02A, CRF06_cpx, F2, 02G and 02B. S 375 H and M 475 I were predominant among CRF01_AE (S375H, 99.3%; M 475 I, 76.3%; consistent with previously reported low temsavir susceptibility of this CRF) and 01B (S 375 H, 71.7%; M 475 I, 49.5%). Analysis of the LANL HIV Sequence Database found a low prevalence of gp160 amino acid polymorphisms with the potential to reduce temsavir susceptibility overall and among most of the common subtypes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

eQuilibrator 3.0: a database solution for thermodynamic constant estimation

Abstract eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts around 1,000 distinct monthly users, its design could not accommodate larger compound databases and it lacked a scalable Application Programming Interface (API) for integration into other tools developed by the systems biology community. Here, we report on the recent updates to the database as well as the addition of a new Python-based interface to eQuilibrator that adds many new features such as a 100-fold larger compound database, the ability to add novel compounds, improvements in speed and memory use, and correction for Mg2+ ion concentrations. Moreover, the new interface can compute the covariance matrix of the uncertainty between estimates, for which we show the advantages and describe the application in metabolic modelling. We foresee that these improvements will make thermodynamic modelling more accessible and facilitate the integration of eQuilibrator into other software platforms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.gov), a database of transgenic enhancer assays conducted in developing mouse embryos in vivo. Since the original publication in 2007, the database grew nearly 20-fold from 250 to over 4500 experiments and currently harbors over 23 500 images. The updated database provides structured information on experiments conducted at different stages of embryonic development, including enhancer activities of human pathogenic and synthetic variants and sequences derived from a variety of species. In addition to manually curated results of thousands of individual experiments, the new database also features hundreds of manually curated comparisons between alleles. The VISTA Enhancer Browser provides a crucial resource for study of human genetic variation, gene regulation and developmental biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns

The discovery and engineering of new enzymes is important across the bioeconomy, with diverse applications from foods to pharmaceuticals, sensors to agriculture. However, enzyme engineering, in particular machine learning-guided engineering, is hampered by a lack of data. Currently there exists no database designed to capture and interpret datasets created in this domain, nor are there easy analysis and visualisation tools. We developed the Enzyme Engineering Database to provide a centralized resource and an online analysis tool to consolidate sequence-function data from enzyme engineering campaigns, thereby making three contributions: (i) a database into which researchers can deposit public data, (ii) visualisation and analysis tools for protein engineers to analyse their own data or compare enzyme variants to other engineering campaigns, and (iii) a gold-standard dataset for benchmarking automated extraction along with the first large language model extraction pipeline specific for enzyme engineering campaigns. The Enzyme Engineering Database is accessible at http://enzengdb.org/.

Long, Yueming [California Institute of Technology ↗
DOE OSTI2014

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Tallo: A global tree allometry and crown architecture database

Abstract Data capturing multiple axes of tree size and shape, such as a tree's stem diameter, height and crown size, underpin a wide range of ecological research—from developing and testing theory on forest structure and dynamics, to estimating forest carbon stocks and their uncertainties, and integrating remote sensing imagery into forest monitoring programmes. However, these data can be surprisingly hard to come by, particularly for certain regions of the world and for specific taxonomic groups, posing a real barrier to progress in these fields. To overcome this challenge, we developed the Tallo database, a collection of 498,838 georeferenced and taxonomically standardized records of individual trees for which stem diameter, height and/or crown radius have been measured. These data were collected at 61,856 globally distributed sites, spanning all major forested and non‐forested biomes. The majority of trees in the database are identified to species (88%), and collectively Tallo includes data for 5163 species distributed across 1453 genera and 187 plant families. The database is publicly archived under a CC‐BY 4.0 licence and can be access from: https://doi.org/10.5281/zenodo.6637599 . To demonstrate its value, here we present three case studies that highlight how the Tallo database can be used to address a range of theoretical and applied questions in ecology—from testing the predictions of metabolic scaling theory, to exploring the limits of tree allometric plasticity along environmental gradients and modelling global variation in maximum attainable tree height. In doing so, we provide a key resource for field ecologists, remote sensing researchers and the modelling community working together to better understand the role that trees play in regulating the terrestrial carbon cycle.

Jucker, Tommaso↗