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

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

EAP Patterns

EAP Patterns: Memory access and iteration patterns from the EAP code base with the physics removed. This is intended to be a serial app representing memory access patterns. We will populate the data structures from EAP output files to provide representative patterns of face and cell loops within the EAP code base The arguments to the program are the EAP output file and the number of MPI processors to emulate. Currently there is no MPI in the application and the number of processors represents a means of emulating the halo (clone) cells around the domain of the given processor. An optional argument `processor_ID` can be provided to specify the processor to emulate. In the future we plan to include the ability to run multiple MPI ranks to more accurately represent the on-node demands on memory bandwidth.

Swaminarayan, Sriram↗
DOE OSTI2024

A framework for studying the effects of offshore wind energy development on birds and bats in the Eastern United States

Offshore wind energy development (OWED), while a key strategy for reducing carbon emissions, has potential negative effects to wildlife that should be examined to inform decision making and adaptive management as the industry expands. We present a conceptual framework to guide the long-term study of potential effects to birds and bats from OWED. This framework includes a focus on exposure and vulnerability as key determinants of risk. For birds and bats that are exposed to OWED, there are three main effects of interest that may impact survival and productivity: 1) collision mortality, 2) behavioral responses, including avoidance, displacement, and attraction, and 3) habitat-mediated effects to prey populations. If these OWED effects cause changes in survival and/or breeding success (e.g., fitness), they have the potential for population-level consequences, including changes in population size and structure. Understanding the influence of ecological drivers on exposure and effect parameters can help to disentangle the potential impacts of OWED from other stressors. We use this theoretical framework to summarize existing relevant knowledge and identify current priority research questions (n=22) for the eastern United States, where largescale development of OWED is primarily in the planning and early construction phase. We also identify recommendations for study design and further prioritization of research topics.

17 WIND ENERGY↗
DOE OSTI2021

New Determination of Fundamental Properties of Palomar 5 Using Deep DESI Imaging Data

The legacy imaging surveys for the Dark Energy Spectroscopic Instrument project provides multiple-color photometric data, which are about 2 mag deeper than those from the SDSS. In this study, we redetermine the fundamental properties for an old halo globular cluster of Palomar 5 based on these new imaging data, including structure parameters, stellar population parameters, and luminosity and mass functions. These characteristics, together with its tidal tails, are key for dynamical studies of the cluster and constraining the mass model of the Milky Way. By fitting the King model to the radial surface density profile of Palomar 5, we derive the core radius of [[Formula]], tidal radius of [[Formula]], and concentration parameter of c = 0.78 ± 0.04. We apply a Bayesian analysis method to derive the stellar population properties and get an age of 11.508 ± 0.027 Gyr, metallicity of [Fe/H] = −1.798 ± 0.014, reddening of E(B − V) = 0.0552 ± 0.0005, and distance modulus of (m−M){sub 0} = 16.835±0.006. The main-sequence luminosity and mass functions for both the cluster center and tidal tails are investigated. The luminosity and mass functions at different distances from the cluster center suggest that there is obvious spatial mass segregation. Many faint low-mass stars have been evaporated at the cluster center, and the tidal tails are enhanced by low-mass stars. Both the concentration and relaxation times suggest that Palomar 5 is a totally relaxed system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

The Binary–Host Connection: Astrophysics of Gravitational-Wave Binaries from Host Galaxy Properties

Gravitational waves from the merger of binary neutron stars (BNSs) are accompanied by electromagnetic counterparts, making it possible to identify the associated host galaxy. In this work, we explore how properties of the hosts relate to the astrophysical processes leading to the mergers. It is thought that the BNS merger rate within a galaxy at a given epoch depends primarily on the galaxy's star formation history, as well as the underlying merger time-delay distribution of the binary systems. The stellar history of a galaxy, meanwhile, depends on the cosmological evolution of the galaxy through time, and is tied to the growth of structure in the universe. We study the hosts of BNS mergers in the context of structure formation by populating the UniverseMachine simulations with gravitational wave (GW) events, based on a simple time-delay model. We find that different time-delay distributions predict different properties of the associated host galaxies, including the distributions of stellar mass, star formation rate, halo mass, and local and large-scale clustering of hosts. Moreover, BNSs merging today with short delay times occur preferentially in hosts with high star formation rates, while those with long delay times live in dense regions within massive halos that have low star formation. Here, we show that with ${ \mathcal O }(10)$ events from current GW detector networks, it is possible to make preliminary distinctions between formation channels which trace stellar mass, halo mass, or star formation rate. We also find that strategies to follow-up GW events with electromagnetic telescopes can be significantly optimized using the clustering properties of their hosts.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

DELVE 6: An Ancient, Ultra-faint Star Cluster on the Outskirts of the Magellanic Clouds

Abstract We present the discovery of DELVE 6, an ultra-faint stellar system identified in the second data release of the DECam Local Volume Exploration (DELVE) survey. Based on a maximum-likelihood fit to its structure and stellar population, we find that DELVE 6 is an old ( τ > 9.8 Gyr at 95% confidence) and metal-poor ([Fe/H] < −1.17 dex at 95% confidence) stellar system with an absolute magnitude of M V = − 1.5 − 0.6 + 0.4 mag and an azimuthally averaged half-light radius of r 1 / 2 = 10 − 3 + 4 pc. These properties are consistent with the population of ultra-faint star clusters uncovered by recent surveys. Interestingly, DELVE 6 is located at an angular separation of ∼10° from the center of the Small Magellanic Cloud (SMC), corresponding to a 3D physical separation of ∼20 kpc given the system’s observed distance ( D ⊙ = 80 kpc). This also places the system ∼35 kpc from the center of the Large Magellanic Cloud (LMC), lying within recent constraints on the size of the LMC’s dark matter halo. We tentatively measure the proper motion of DELVE 6 using data from Gaia, which we find supports a potential association between the system and the LMC/SMC. Although future kinematic measurements will be necessary to determine its origins, we highlight that DELVE 6 may represent only the second or third ancient ( τ > 9 Gyr) star cluster associated with the SMC, or one of fewer than two dozen ancient clusters associated with the LMC. Nonetheless, we cannot currently rule out the possibility that the system is a distant Milky Way halo star cluster.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A Deep and Wide Twilight Survey for Asteroids Interior to Earth and Venus

We are conducting a survey using twilight time on the Dark Energy Camera with the Blanco 4 m telescope in Chile to look for objects interior to Earth's and Venus' orbits. To date we have discovered two rare Atira/Apohele asteroids, 2021 LJ4 and 2021 PH27, which have orbits completely interior to Earth's orbit. We also discovered one new Apollo-type Near Earth Object (NEO) that crosses Earth's orbit, 2022 AP7. Two of the discoveries have diameters ≳1 km. 2022 AP7 is likely the largest Potentially Hazardous Asteroid (PHA) discovered in about eight years. To date we have covered 624 square degrees of sky near to and interior to the orbit of Venus. The average images go to 21.3 mag in the r band, with the best images near 22nd mag. Our new discovery 2021 PH27 has the smallest semimajor axis known for an asteroid, 0.4617 au, and the largest general relativistic effects (53 arcsec/century) known for any body in the solar system. The survey has detected ~15% of all known Atira NEOs. We put strong constraints on any stable population of Venus co-orbital resonance objects existing, as well as the Atira and Vatira asteroid classes. These interior asteroid populations are important to complete the census of asteroids near Earth, including some of the most likely Earth impactors that cannot easily be discovered in other surveys. Comparing the actual population of asteroids found interior to Earth and Venus with those predicted to exist by extrapolating from the known population exterior to Earth is important to better understand the origin, composition, and structure of the NEO population.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Social network structure and the spread of complex contagions from a population genetics perspective

Ideas, behaviors, and opinions spread through social networks. If the probability of spreading to a new individual is a non-linear function of the fraction of the individuals’ affected neighbors, such a spreading process becomes a “complex contagion”. This non-linearity does not typically appear with physically spreading infections, but instead can emerge when the concept that is spreading is subject to game theoretical considerations (e.g. for choices of strategy or behavior) or psychological effects such as social reinforcement and other forms of peer influence (e.g. for ideas, preferences, or opinions). Here we study how the stochastic dynamics of such complex contagions are affected by the underlying network structure. Motivated by simulations of complex contagions on real social networks, we present a framework for analyzing the statistics of contagions with arbitrary non-linear adoption probabilities based on the mathematical tools of population genetics. The central idea is to use an effective lower-dimensional diffusion process to approximate the statistics of the contagion. This leads to a tradeoff between the effects of ”selection” (microscopic tendencies for an idea to spread or die out), random drift, and network structure. Our framework illustrates intuitively several key properties of complex contagions: stronger community structure and network sparsity can significantly enhance the spread, while broad degree distributions dampen the effect of selection compared to random drift. Finally, we show that some structural features can exhibit critical values that demarcate regimes where global contagions become possible for networks of arbitrary size. Our results draw parallels between the competition of genes in a population and memes in a world of minds and ideas. Our tools provide insight into the spread of information, behaviors, and ideas via social influence, and highlight the role of macroscopic network structure in determining their fate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Accumulation of Large Ion Populations with High Ion Densities and Effects Due to Space Charge in Traveling Wave-Based Structures for Lossless Ion Manipulations (SLIM) IMS-MS

The accumulation of very large ion populations in traveling wave (TW)-based Structures for Lossless ion Manipulations (SLIM) has been studied to better understand aspects of ‘in-SLIM’ ion accumulation, and particularly its use in conjunction with ion mobility spectrometry (IMS). A linear SLIM ion path was implemented that had a ‘gate’ for blocking and accumulating ions for arbitrary time periods. Removing the gate potential caused ions to exit and the spatial distributions of accumulated ions were examined. The ion populations for a set of peptides were observed to increase with increased accumulation times until space change effects became significant, after which the peptide precursor ion populations decreased due to growing space charge-related ion activation, reactions, and losses. Ions closest to the gate were preferentially activated, and increasingly so with added storage times, TW amplitude, and the size of the total ion population. For analytical applications, we found that relatively weak TWs in the accumulation/storage region should be utilized to prevent or minimize ion losses and/or ion heating effects that can also lead to fragmentation. Our results further indicate that an accumulation region close to the SLIM entrance is advantageous for both speeding accumulation, minimizing ion heating, and avoiding ion population profiles that result in IMS peak tailing. Importantly, space charge-driven separations were observed for large populations of accumulated species and attributed to the opposing effects of space charge and the TW. In these separations, ion species form distributions or peaks, sometimes moving against the TW, and ordered in the SLIM based on their mobilities. Such separations may offer utility for ion pre-fractionation of ions and increasing the dynamic range measurements, increasing the resolving power of IMS separations by decreasing peak widths for accumulated ion populations, and other purposes benefitting from separations of extremely large ion populations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Generating synthetic occupants for use in building performance simulation

Occupant behaviour simulation frameworks can employ synthetic populations to characterize occupancy and behavioural patterns in buildings based on observed demographic data at a certain geographical location. For buildings, very few synthetic occupant populations have been generated. This paper uses a Bayesian Networks (BN) structural learning approach to synthesize populations of occupants in a multi-family housing case study. Two additional cases of office occupants and senior housing residents are considered as a cross-case comparison. Furthermore, we draw upon the extended version of drivers-needs-actions-systems (DNAS) framework to guide the selection of variables and data imputation. Our results show that the BN approach is powerful in learning the structure of data sets. The synthetic data sets successfully match the joint distributions of the underlying combined data sets. Experiments on the multi-family housing particularly show better performance than the office and senior housing cases.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

The Melampsora americana Population on Salix purpurea in the Great Lakes Region Is Highly Diverse with a Contributory Influence of Clonality

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal lands in New York State and surrounding areas. Willow rust, caused by members of the genus Melampsora, is the most limiting disease of shrub willow in this region and remains extremely understudied. In this study, genetic diversity, genetic structure, and pathogen clonality were examined in Melampsora americana over two growing seasons via genotyping-by-sequencing to identify single-nucleotide polymorphism markers. In conjunction with this project, a reference genome of rust isolate R15-033-03 was generated to aid in variant discovery. Sampling between years allowed regional and site-specific investigation into population dynamics, in the context of both wild and cultivated hosts within high-density plantings. This work revealed that this pathogen is largely panmictic over the sampled areas, with few sites showing moderate genetic differentiation. These data support the hypothesis of sexual recombination between growing seasons because no genotype persisted across the two years of sampling. Additionally, clonality was determined as a driver of pathogen populations within cultivated fields and single shrubs; however, there is also evidence of high genetic diversity of rust isolates in all settings. This work provides a framework for M. americana population structure in the Great Lakes region, providing crucial information that can aid in future resistance breeding efforts.

Plant Sciences↗
DOE OSTI2021

The kinematic properties of Milky Way stellar halo populations

ABSTRACT In the Gaia era, stellar kinematics are extensively used to study Galactic halo stellar populations, to search for halo structures, and to characterize the interface between the halo and hot disc populations. We use distribution function-based models of modern data sets with 6D phase space data to qualitatively describe a variety of kinematic spaces commonly used in the study of the Galactic halo. Furthermore, we quantitatively assess how well each kinematic space can separate radially anisotropic from isotropic halo populations. We find that scaled action space (the ‘action diamond’) is superior to other commonly used kinematic spaces at this task. We present a new, easy to implement selection criterion for members of the radially anisotropic Gaia–Enceladus merger remnant. Assuming a 1:1 ratio of Gaia–Enceladus stars to more isotropic halo, we find our selection achieves a sample purity of 86 per cent in our models with respect to contamination from the more isotropic halo. We compare this criterion to literature criteria, finding that it produces the highest purity in the resulting samples, at the expense of a modest reduction in completeness. We also show that selection biases that underlie nearly all contemporary spectroscopic data sets can noticeably impact the E−Lz distribution of samples in a manner that may be confused for real substructure. We conclude by providing recommendations for how authors should use stellar kinematics in the future to study the Galactic stellar halo.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Gaia EDR3 Reveals the Substructure and Complicated Star Formation History of the Greater Taurus-Auriga Star-forming Complex

The Taurus-Auriga complex is the prototypical low-mass star-forming region, and provides a unique testbed of the star formation process, which left observable imprints on the spatial, kinematic, and temporal structure of its stellar population. Taurus’s rich observational history has uncovered peculiarities that suggest a complicated star-forming event, such as members at large distances from the molecular clouds and evidence of an age spread. With Gaia, an in-depth study of the Taurus census is possible, to confirm membership, identify substructure, and reconstruct its star formation history. We have compiled an expansive census of the greater Taurus region, identifying spatial subgroups and confirming that Taurus is substructured across stellar density. There are two populations of subgroups: clustered groups near the clouds and sparse groups spread throughout the region. The sparse groups comprise Taurus’s distributed population, which is on average older than the population near the clouds, and hosts subpopulations up to 15 Myr old. The ages of the clustered groups increase with distance, suggesting that the current star formation was triggered from behind. Still, the region is kinematically coherent, and its velocity structure reflects an initial turbulent spectrum similar to Larson’s Law that has been modified by dynamical relaxation. Overall, Taurus has a complicated star formation history, with at least two epochs of star formation featuring both clustered and distributed modes. Given the correlations between age and spatial distribution, Taurus might be part of a galaxy-scale star-forming event that can only begin to be understood in the Gaia era.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion

NMR relaxation dispersion measurements report on conformational changes occurring on the μs-ms timescale. Chemical shift information derived from relaxation dispersion can be used to generate structural models of weakly populated alternative conformational states. Current methods to obtain such models rely on determining the signs of chemical shift changes between the conformational states, which are difficult to obtain in many situations. Here, we use a “sample and select” method to generate relevant structural models of alternative conformations of the C-terminal-associated region of Escherichia coli dihydrofolate reductase (DHFR), using only unsigned chemical shift changes for backbone amides and carbonyls ( 1 H, 15 N, and 13 C'). We find that CS-Rosetta sampling with unsigned chemical shift changes generates a diversity of structures that are sufficient to characterize a minor conformational state of the C-terminal region of DHFR. The excited state differs from the ground state by a change in secondary structure, consistent with previous predictions from chemical shift hypersurfaces and validated by the x-ray structure of a partially humanized mutant of E. coli DHFR (N23PP/G51PEKN). The results demonstrate that the combination of fragment modeling with sparse chemical shift data can determine the structure of an alternative conformation of DHFR sampled on the μs-ms timescale. Such methods will be useful for characterizing alternative states, which can potentially be used for in silico drug screening, as well as contributing to understanding the role of minor states in biology and molecular evolution.

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

Projected Urban Morphology of the Los Angeles Area by the Year 2100

This dataset provides projections of urban building morphologies for the Los Angeles urban area at 30-meter spatial resolution. It contains 192 raster files that detail two primary building attributes: building footprint fractions (ranging from 0 to 1) and average building heights (ranging from 0 to 75 meters). The projections account for a wide range of future pathways, covering two Shared Socioeconomic Pathway (SSP) scenarios (SSP3 and SSP5), two population scenarios, two developed land intensification scenarios, and four distinct levels of intensification. The dataset was created using dual Generative Adversarial Networks (GANs) trained on 2015 land cover and building properties from the National Land Cover Database (NLCD) and Model America datasets. Supporting information on the dataset has been described in the LAUrbanAreaMorphologyProjections2100_README.txt file.

Pandey, Bhartendu↗