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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 1,801 records · Page 100
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

EMPDF : inferring the Milky Way mass with data-driven distribution function in phase space

We introduce the emPDF (empirical distribution function), a novel dynamical modelling method that infers the gravitational potential from kinematic tracers with optimal statistical efficiency under the minimal assumption of steady state. emPDF determines the best-fitting potential by maximizing the similarity between instantaneous kinematics and the time-averaged phase-space distribution function (DF), which is empirically constructed from observation upon the theoretical foundation of oPDF (Han et al. 2016). This approach eliminates the need for presumed functional forms of DFs or orbit libraries required by conventional DF- or orbit-based methods. emPDF stands out for its flexibility, efficiency, and capability in handling observational effects, making it preferable to the popular Jeans equation or other minimal assumption methods, especially for the Milky Way (MW) outer halo where tracers often have limited sample size and poor data quality. We apply emPDF to infer the MW mass profile using Gaia DR3 data of satellite galaxies and globular clusters, obtaining enclosed masses of M (,r) = 26±8, 46±8, 90±13⁠, and 149±40 x 10 10 M ⊙ at r = 30, 50, 100⁠, and 200 kpc, respectively. These are consistent with the updated constraints from simulation-informed DF fitting (Li et al. 2020). While the simulation-informed DF offers superior precision owing to the additional information extracted from simulations, emPDF is independent of such supplementary knowledge and applicable to general tracer populations. emPDF is currently implemented for tracers with complete 6D kinematics within spherical potentials, but it can potentially be extended to address more general problems.

Astrophysics of Galaxies (astro-ph.GA)↗
DOE OSTI2020

CoreCruncher : Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

CasDinG is a 5′-3′ dsDNA and RNA/DNA helicase with three accessory domains essential for type IV CRISPR immunity

Abstract CRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. Here, we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP-dependent 5′-3′ DNA translocase that unwinds double-stranded (ds)DNA and RNA/DNA hybrids. The crystal structure of CasDinG reveals a superfamily 2 helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these domains, we identified the preferred PAM sequence for the type IV-A system (5′-GNAWN-3′ on the 5′-side of the target) with a plasmid library and performed plasmid clearance assays with domain deletion mutants. Plasmid clearance assays demonstrated that all three domains are essential for type IV-A immunity. Protein expression and biochemical assays suggested the vFeS domain is needed for protein stability and the arch for helicase activity. However, deletion of the N-terminal domain did not impair ATPase, ssDNA binding, or helicase activities, indicating a role distinct from canonical helicase activities that structure prediction tools suggest involves interaction with dsDNA. This work demonstrates CasDinG helicase activity is essential for type IV-A CRISPR immunity as well as the yet undetermined activity of the CasDinG N-terminal domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

In silico λ-dynamics predicts protein binding specificities to modified RNAs

Abstract RNA modifications shape gene expression through a variety of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Empirical evaluation of all unique Cas9 protospacers in E. coli reveal widespread functionality and rules for gRNA design

The Cas9 nuclease has become central to modern methods and technologies in synthetic biology, largely due to the ease with which it can be targeted to specific DNA loci via guide RNAs (gRNAs). Reports vary widely on the actual specificity of this targeting, with some studies observing 60% of gRNAs possessing no activity against the genome, yet an assumption persists within the E. coli community that inactive gRNAs are rare. To resolve these contradictions, we evaluated the activity of 463 000 unique gRNAs in the E. coli K12 MG1655 genome. We show that the overwhelming majority (at least 93%) of unique gRNAs are functional while only 0.3% are nonfunctional. These nonfunctional gRNAs exhibit strong spacer self-interaction, which can either be excluded using a simple design rule or “repaired” during library design. Finally, this work provides the greater microbial synthetic biology community both a set of nearly half a million empirically evaluated E. coli gRNAs as well as a thoroughly evaluated experimental procedure, complete with appropriate controls for Cas9 activity, for conducting Cas9 assays in E. coli specifically and bacteria more generally. Lastly, we have produced a webapp to allow users to easily browse and extract gRNA sequences from the E. coli genome, which can be accessed at https://grna.ornl.gov.

Kammerdiener, Elise K. [Oak Ridge National Laborat↗
DOE OSTI2026

Cas3-Mediated Genome Reduction: Demonstration in Cupriavidus Necator H16 Improves Growth on Heterotrophic and Autotrophic Carbon Sources

Genome reduction is widely used to improve microbial bioprocessing hosts by reducing the burden of inessential physiology. Rationally identifying genomic regions that are dispensable or even detrimental to bioprocessing is challenged by our inability to map genome sequence to function across complex regulation and physiology. Thus, there is a need for tools that rapidly generate reduced genome strains with improved performance in process-relevant conditions. Here, we report a Cascade-Cas3-enabled method called TRIM3 that generates large deletions by targeting a randomly integrated transposon, enabling facile generation of a genome-reduced mutant library. Mutants with improved performance were isolated following growth-coupled selection and analyzed by long-read DNA sequencing to identify deletions in their genomes. We deploy this system iteratively in the industrial host Cupriavidus necator H16 on fructose and on formate. After two rounds of TRIM3, we isolate a strain containing a total reduction of 1.4 Mb (18.4% of the genome) that grows 25% faster in a bioreactor on fructose and a strain with a total reduction of 0.5 Mb (7.3% of the genome) that grows 14% faster on formate. This work demonstrates a method for random, iterative, growth-selectable genome reduction that represents a new avenue for large-scale genome modifications and the development of improved bioprocessing hosts.

09 BIOMASS FUELS↗
DOE OSTI2022

Metal-organic frameworks as effective sensors and scavengers for toxic environmental pollutants

Abstract Metal-organic frameworks (MOFs) constructed from a rich library of organic struts and metal ions/clusters represent promising candidates for a wide range of applications. The unique structure, porous nature, easy tunability and processability of these materials make them an outstanding class of materials for tackling serious global problems relating to energy and environment. Among them, environmental pollution is one aspect that has increased at an alarming rate in the past decade or so. With rapid urbanization and industrialization, toxic environmental pollutants are constantly released and accumulated leading to serious contamination in water bodies and thereby having adverse effects on human health. Recent studies have shown that many toxic pollutants, as listed by the World Health Organization and the US Environmental Protection Agency, can be selectively detected, captured, sequestered and removed by MOFs from air and aquatic systems. Most of these sensing/capture processes in MOFs are quantifiable and effective for even a trace amount of the targeted chemical species. The functional sites (ligands and metals) play a critical role in such recognition processes and offer an extensive scope of structural tunability for guest (pollutants, toxic entities) recognition. Whereas on the one hand, the underlying mechanisms governing such sensing and capture are important, it is also crucial to identify MOFs that are best suited for commercial applications for the future. In this review article, we provide an overview of the most recent progress in the sensing, capture and removal of various common toxic pollutants, including neutral and ionic, inorganic and organic species, with brief discussions on the mechanism and efficacy of selected MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

tonalli : an asexual genetic code to characterize APOGEE-2 stellar spectra. I. Validation with synthetic and solar spectra

ABSTRACT We present tonalli, a spectroscopic analysis python code that efficiently predicts effective temperature, stellar surface gravity, metallicity, $\alpha$-element abundance, and rotational and radial velocities for stars with effective temperatures between 3200 and 6250 K, observed with the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2). tonalli implements an asexual genetic algorithm to optimize the finding of the best comparison between a target spectrum and the continuum-normalized synthetic spectra library from the Model Atmospheres with a Radiative and Convective Scheme (MARCS), which is interpolated in each generation. Using simulated observed spectra and the APOGEE-2 solar spectrum of Vesta, we study the performance, limitations, accuracy, and precision of our tool. Finally, a Monte Carlo realization was implemented to estimate the uncertainties of each derived stellar parameter.

Adame, Lucía (ORCID:0000000263286099)↗
DOE OSTI2020

Building a custom high-throughput platform at the Joint Genome Institute for DNA construct design and assembly—present and future challenges

Abstract The rapid design and assembly of synthetic DNA constructs have become a crucial component of biological engineering projects via iterative design–build–test–learn cycles. In this perspective, we provide an overview of the workflows used to generate the thousands of constructs and libraries produced each year at the U.S. Department of Energy Joint Genome Institute. Particular attention is paid to describing pipelines, tools used, types of scientific projects enabled by the platform and challenges faced in further scaling output.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Conversion of Site-Specific Meteorological Data for use in CAP-88 PC

CAP-88 PC is a commonly used radiological atmospheric dispersion model. This US EPA-approved model is used to demonstrate compliance with atmospheric emission regulations for radionuclides. While the model includes a large library of meteorological data for use across the United States, there are applications when users may wish to use onsite meteorological data as an input to the CAP-88 PC model. Here, in this work, we present a work-around process for preparing and converting onsite data for use in CAP-88 PC. However, the use of local data should provide a more realistic estimate of doses to members of the public in the immediate vicinity of a facility, although the regulatory agency having jurisdiction may not accept the use of local data for compliance. Additionally, the historical meteorological records from 20+ years ago (at a site many kilometers away) might not be representative of current local weather patterns, highlighting another benefit of using local meteorological data.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Output-weighted sampling for multi-armed bandits with extreme payoffs

We present a new type of acquisition function for online decision-making in multi-armed and contextual bandit problems with extreme payoffs. Specifically, we model the payoff function as a Gaussian process and formulate a novel type of upper confidence bound acquisition function that guides exploration towards the bandits that are deemed most relevant according to the variability of the observed rewards. This is achieved by computing a tractable likelihood ratio that quantifies the importance of the output relative to the inputs and essentially acts as an attention mechanism that promotes exploration of extreme rewards. Our formulation is supported by asymptotic zero-regret guarantees, and its performance is demonstrated across several synthetic benchmarks, as well as two realistic examples involving noisy sensor network data. Finally, we provide a JAX library for efficient bandit optimization using Gaussian processes.

Science & Technology - Other Topics↗
DOE OSTI2020

The parallelism motifs of genomic data analysis

Genomic datasets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share these data with the research community, but some of these genomic data analysis problems require large-scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high-end parallel systems today and place different requirements on programming support, software libraries and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high-performance genomics analysis, including alignment, profiling, clustering and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or ‘motifs’ that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Philympics 2021: Prophage Predictions Perplex Programs

Most bacterial genomes contain integrated bacteriophages—prophages—in various states of decay. Many are active and able to excise from the genome and replicate, while others are cryptic prophages, remnants of their former selves. Over the last two decades, many computational tools have been developed to identify the prophage components of bacterial genomes, and it is a particularly active area for the application of machine learning approaches. However, progress is hindered and comparisons thwarted because there are no manually curated bacterial genomes that can be used to test new prophage prediction algorithms. Here, we present a library of gold-standard bacterial genome annotations that include manually curated prophage annotations, and a computational framework to compare the predictions from different algorithms. We use this suite to compare all extant stand-alone prophage prediction algorithms to identify their strengths and weaknesses. We provide a FAIR dataset for prophage identification, and demonstrate the accuracy, precision, recall, and f 1 score from the analysis of seven different algorithms for the prediction of prophages. We discuss caveats and concerns in this analysis and how those concerns may be mitigated.

Roach, Michael J.↗
DOE OSTI2025

Structural stability, elemental ordering, and transport properties of layered ScTaN 2

Ternary transition metal (TM) nitrides have gained significant attention in thin film research due to their promising properties for a broad range of applications. Particularly, some of the ternary TM nitrides have been predicted to adopt layered structures that make them interesting for thermoelectric conversion and quantum materials applications. Unfortunately, synthesis of TM ternary nitride films by physical vapor deposition often favors disordered 3D structures rather than the predicted 2D-like layered structure. In this study, we investigate the structural interplay in the Sc-Ta-N ternary system using a combinatorial approach. Combinatorial libraries S⁢c 𝑥 ⁢T⁢a 1−𝑥 ⁢N are synthesized following a two-step method: First, deposit film precursors by cosputtering and then process the resulting 3D-structured samples with rapid thermal annealing. Synchrotron grazing-incidence wide-angle x-ray scattering on films annealed at 1200 ⁢°⁢C for 20 min leads to the nucleation of ScTaN 2 layered structure (𝑃⁢6 3 /𝑚⁢𝑚⁢𝑐) near stoichiometry. We find that the layered structure can accommodate large off-stoichiometry in the Ta-rich region (𝑥 < 0.5), facilitated by the alloying with quasi-isostructural Ta 5 ⁢N 6 compound that exists on a composition tie line at 𝑥 = 0. While focusing on ScTaN 2 , we estimate the long-range order parameter in near-stoichiometric films to be 0.86, corresponding to a fraction of Sc/Ta antisites of 7%. Transport measurements on ScTaN 2 reveal a nearly temperature-independent high carrier density (10 21 c⁢m −3 ), suggesting a heavily doped semiconductor or semimetallic character, consistent with a small positive Seebeck coefficient of +19 µV/K. The carrier mobility at 2 K is relatively small (9.5c⁢m 2 V −1 s −1 ) and the residual-resistivity ratio is minor, suggesting that electrical conduction is dominated by defects or disorder. Measured magnetoresistance suggests possible weak antilocalization at 2 K. This paper highlights the interplay between ScTaN 2 and Ta 5 ⁢N 6 crystal structures in stabilizing layered materials, emphasizes the importance of cation order/disorder for potential tunable alloys, and suggests that ScTaN 2 is a promising platform for exploring electronic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Low-energy 17 O(𝑛,𝛾)⁢ 18 O reaction within the microscopic potential model and its role for the weak 𝑟 process

The neutron radiative capture reaction 17 O ⁡(𝑛,𝛾) ⁢18 O plays a pivotal role in both nuclear structure studies and astrophysical nucleosynthesis, particularly in the formation of elements during hydrostatic and explosive stellar environments. We calculated the 17 O ⁡(𝑛,𝛾) ⁢18 O cross section within the Skyrme Hartree-Fock potential model and analyzed electric dipole 𝐸⁢1 transitions to both positive- and negative-parity states below the α-decay threshold in 18 O. Our cross sections are significantly different from the data available in commonly used libraries. We further investigate the impact of the new calculated cross section on weak 𝑟-process nucleosynthesis using large-scale reaction network calculations across a wide range of electron fractions and entropies. Our results show that the 17 O ⁡(𝑛,𝛾) ⁢18 O reaction rate significantly influences the production of first 𝑟-process peak elements, such as strontium, under specific astrophysical conditions. This study highlights the importance of accurate nuclear data for light isotopes in modeling heavy-element synthesis and provides updated reaction rates for future nucleosynthesis simulations.

6 ≤ A ≤ 19↗
DOE OSTI2025

Harnessing ionic complexity: A modeling approach for hierarchical ionic circuit design

Since the 1950s, soft ionic devices have evolved from individual components to an expanding library of sensors, actuators, signal transmitters, and processors. However, integrating these components into complex, multifunctional systems remains challenging due to the nonintuitive and nonlinear interactions between ionic elements. In this work, we address these fundamental challenges by developing a lumped element model that enables interrogation of the physics that governs ionic circuits, as well as rapid design and optimization. Our model captures features specific to ionic charge carriers, while preserving the hierarchical design flexibility and computational efficiency of traditional circuit modeling. We demonstrate that our model can not only fit individual device behavior but also accurately predict the behavior of larger circuits formed by combining those devices. Additionally, we show how our tool utilizes the intrinsic nonlinearities of ionic systems to enable extended functionality, revealing how factors such as ion enrichment, ion leakage, and polymer charge density influence performance. Lastly, we present a fully ionic power supply, sensor, control system, and actuator for a soft robot that adapts its motion in response to environmental salt, illustrating the tool’s potential to accelerate advancements in chemical sensing, biointerfacing, biomimetic systems, and adaptive materials.

42 ENGINEERING↗
DOE OSTI2020

Consistency of $^{16}O(n,α)$ cross sections

The evaluated $^{16}O(n,α)$ cross sections in the ENDF/B-VIII.0 nuclear data library remain uncertain because of systematic discrepancies in the measured data. In the energy region below the first excited state, R-matrix analyses rely heavily on the inverse reaction, and in particular, they rely on the measured $^{13}C(α,n)^{16}O$ cross sections reported by Bair et al. in 1973 and Harissopulos et al. in 2005. The Harissopulos cross section values are systematically lower than those previously reported by Bair. Here, drawing on the available experimental information, this paper briefly describes and demonstrates that the two sets of measured cross sections are consistent.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

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