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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Characterization of Heparin’s Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy

Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin’s solution conformational dynamics and structure–function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule’s underlying conformational ensemble, which then provides important information necessary for understanding structure–function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin’s conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. In this work, the anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.

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

Toward Computation-Guided Design of Tunable Organic-Inorganic CdS Quantum Dot Binary Superlattices

Combining the advantages of structural programmability in sequence-defined biomimetic molecules and the controllable packing geometry in nanoparticle superlattices, we demonstrate a self-assembled organic-inorganic superlattice whose structure can be altered with the slightest change in the sequence of the organic counterpart. Here, oleate-coated CdS quantum dots (QDs) form a square-packed superlattice with a 1:1 molar equivalence of a di-block amphiphilic peptoid (Nbrpe6Dig) in chloroform. In contrast, no apparent structure is observed in the organic solvent alone. Based on theoretical evidence, we show that the assembly is a binary superlattice where both the CdS QDs and the peptoids serve as building blocks and further predict a correlation between the superlattice structure and the peptoid sequence. The computationally guided prediction is validated by experiments where superlattice transformation is observed with modified peptoids. The mechanism identified in our work inspires new ways to control and tune organic-inorganic hybrid nanomaterial self-assembly.

Qi, Xin↗
DOE OSTI2024

Modularization of EDGE Workflows Using Nextflow: Improving the Efficiency and Maintainability of Bioinformatics Software

EDGE is a bioinformatics platform developed in 2016 by researchers at Los Alamos National Laboratory (LANL) to facilitate the analysis of next-generation sequencing data by researchers with varying levels of experience in bioinformatics (Li et al., 2017). Users with single-end, paired-end or long-read sequencing data can provide their reads as input to EDGE and select the combination of workflows to run that are most useful for their research (e.g., quality control of reads, genome assembly, or the taxonomic classification of input reads). Table 1 summarizes the modules available in EDGE. EDGE is available as a web platform at https://edgebioinformatics.org, as installable source code maintained on GitHub under a GPLv3 license, and as a publicly hosted Docker image.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function

Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses seven times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2022

Dipolar Heteronuclear Correlation Solid-State NMR Experiments between Half-Integer Quadrupolar Nuclei: The Case of 11 B– 17 O

With 73% of all NMR-active nuclei being quadrupolar, there is great interest in the development of NMR experiments that can probe the proximity of quadrupolar spins. Here, pulse sequences for magic-angle spinning (MAS) 11 B– 17 O resonance-echo saturation-pulse double-resonance (RESPDOR) and dipolar heteronuclear multiple quantum correlation (D-HMQC) solid-state NMR experiments were investigated. In these pulse sequences, rotational-echo double-resonance (REDOR) recoupling was used with central transition (CT)-selective π-pulses applied to either the 11 B or 17 O spins to recouple 11 B– 17 O dipolar interactions. 11 B{ 17 O} RESPDOR experiments on 17 O-enriched boric acid and benzene diboronic acid showed that application of dipolar recoupling on the 11 B channel yielded more signal dephasing than when recoupling is applied on the 17 O channel; however, short effective 11 B transverse relaxation time constants (T 2 ') hinder the acquisition of dephasing curves out to long recoupling durations. Application of REDOR recoupling to 17 O spins was found to produce significant dephasing without compromising the 11 B T 2 '. Comparison of experimental 11 B{ 17 O} RESPDOR curves to those of numerical simulations enabled the 17 O isotopic enrichment to be estimated. 2D 11 B{ 17 O} D-HMQC spectra were recorded with either 11 B or 17 O REDOR recoupling under a variety of radio frequency field conditions. Lastly, 2D 11 B{ 17 O} and 23 Na{ 17 O} D-HMQC spectra of an 17 O-enriched sodium borate glass were acquired to demonstrate the practical application of these heteronuclear correlation experiments to probe structural connectivity between two quadrupolar spins. Importantly, the high-field 2D 11 B– 17 O D-HMQC NMR spectrum revealed two unique 17 O sites correlating to 4-coordinate BO 4 ( [4] B), which were attributed to the [3] B–O– [4] B and [4] B–O– [4] B bridging O atoms. Furthermore, the heteronuclear correlation experiments outlined here should be applicable to a variety of quadrupolar spin pairs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chronic drought differentially alters the belowground microbiome of drought tolerant and drought susceptible genotypes of Populus trichocarpa

Populus trichocarpa is an ecologically important tree species and economically important biofeedstock. Belowground, P. trichocarpa interacts with diverse microorganisms in the rhizosphere and root endosphere. These plant-microbial interactions can bolster a variety of plant processes, ranging from pathogen suppression to drought tolerance, yet we know little about the impact of chronic drought stress on P. trichocarpa’s belowground microbiomes. To investigate the interactive effect of chronic drought on belowground microbial communities across genetically different P. trichocarpa hosts, we assessed archaeal/bacterial and fungal communities within the root endosphere, rhizosphere, and surrounding bulk soil of selected genotypes in a long-term drought experiment in Boardman, OR, USA. We sequenced the 16S rRNA and ITS2 gene region on samples collected from 16 distinct P. trichocarpa genotypes in plots with full or reduced irrigation. Eight of these genotypes have been previously identified as drought tolerant while the other eight genotypes were drought susceptible. While reduced irrigation influenced the composition of every archaeal/bacterial microbiome compartment, fungal communities were only affected in the rhizosphere and bulk soil compartments. Drought-tolerant bacteria, such as Actinobacteria, were differentially abundant in reduced irrigation across all belowground microbiomes. Host drought-tolerance influenced plant-associated microbiome compartments but had little impact on the bulk soil compartment. Drought-tolerant trees were enriched for potential growth-promoting microorganisms in the root endosphere and rhizosphere, including Sphingomonas bacteria and ectomycorrhizal fungi. Overall, associations of growth-promoting microbes in drought resistant P. trichocarpa genotypes can be leveraged to improve biofeedstock productivity in regions prone to periodic drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Impact of Load Tap Changer Control Operation Under Microgrid Conditions

Every microgrid is unique in its diversity of assets, operation, and network structure. This uniqueness presents challenges for each microgrid implementation that need to be understood and addressed to prevent power quality concerns, stability issues, and blackouts. In this research work, we present one challenge faced during microgrid operation that could potentially cause a blackout in some microgrid configurations. Through the incorrect operation of the load tap changer controller during an islanding event for a microgrid with generation present on both primary and secondary busses, the primary voltage will increase or decrease beyond allowable bounds, causing a cascading failure. This work presents the issue first with simulation results to demonstrate the phenomenon and then presents results of load tap changer controller operation using a controller-hardware-in-the-loop experiment. Finally, details of the complete sequence of operation and the blackout scenarios are presented and summarized.

blackout↗
DOE OSTI2023

Conservation of beneficial microbes between the rhizosphere and the cyanosphere

Summary Biocrusts are phototroph‐driven communities inhabiting arid soil surfaces. Like plants, most photoautotrophs (largely cyanobacteria) in biocrusts are thought to exchange fixed carbon for essential nutrients like nitrogen with cyanosphere bacteria. Here, we aim to compare beneficial interactions in rhizosphere and cyanosphere environments, including finding growth‐promoting strains for hosts from both environments. To examine this, we performed a retrospective analysis of 16S rRNA gene sequencing datasets, host–microbe co‐culture experiments between biocrust communities/biocrust isolates and a model grass ( Brachypodium distachyon ) or a dominant biocrust cyanobacterium ( Microcoleus vaginatus ), and metabolomic analysis. All 18 microbial phyla in the cyanosphere were also present in the rhizosphere, with additional 17 phyla uniquely found in the rhizosphere. The biocrust microbes promoted the growth of the model grass, and three biocrust isolates ( Bosea sp._L1B56, Pseudarthrobacter sp. _ L1D14 and Pseudarthrobacter picheli_ L1D33) significantly promoted the growth of both hosts. Moreover, pantothenic acid was produced by Pseudarthrobacter sp._L1D14 when grown on B . distachyon exudates, and supplementation of plant growth medium with this metabolite increased B . distachyon biomass by over 60%. These findings suggest that cyanobacteria and other diverse photoautotrophic hosts can be a source for new plant growth‐promoting microbes and metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Sensitivity of 44 Ti and 56 Ni Production in Core-collapse Supernova Shock-driven Nucleosynthesis to Nuclear Reaction Rate Variations

Recent observational advances have enabled high resolution mapping of 44 Ti in core-collapse supernova (CCSN) remnants. Comparisons between observations and models provide stringent constraints on the CCSN mechanism. However, past work has identified several uncertain nuclear reaction rates that influence 44 Ti and 56 Ni production in postprocessing model calculations. We evolved one-dimensional models of 15 M ⊙ , 18 M ⊙ , 22 M ⊙ , and 25 M ⊙ stars from zero age main sequence through CCSN using Modules for Experiments in Stellar Astrophysics and investigated the previously identified reaction rate sensitivities of 44 Ti and 56 Ni production. In this work, we tested the robustness of our results by making various assumptions about the CCSN explosion energy and mass cut. We found a number of reactions that have a significant impact on the nucleosynthesis of 44 Ti and 56 Ni, particularly for lower progenitor masses. Notably, the reaction rates ${}^{13}{\rm{N}}{(\alpha ,p)}^{16}{\rm{O}}$, ${}^{17}{\rm{F}}{(\alpha ,p)}^{20}\mathrm{Ne}$, ${}^{52}\mathrm{Fe}{(\alpha ,p)}^{55}\mathrm{Co}$, ${}^{56}\mathrm{Ni}{(\alpha ,p)}^{59}\mathrm{Cu}$, ${}^{57}\mathrm{Ni}{(n,p)}^{57}\mathrm{Co}$, ${}^{56}\mathrm{Co}{(p,n)}^{56}\mathrm{Ni}$, ${}^{39}{\rm{K}}{(p,\gamma )}^{40}\mathrm{Ca}$, ${}^{47}{\rm{V}}{(p,\gamma )}^{48}\mathrm{Cr}$, ${}^{52}\mathrm{Mn}{(p,\gamma )}^{53}\mathrm{Fe}$, ${}^{57}\mathrm{Co}{(p,\gamma )}^{58}\mathrm{Ni}$, and ${}^{39}{\rm{K}}{(p,\alpha )}^{36}\mathrm{Ar}$ are influential for a large number of model conditions. Furthermore, we found the list of influential reactions identified by previous postprocessing studies of CCSN shock-driven nucleosynthesis is likely incomplete, motivating future larger-scale sensitivity studies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Impedance Scan of Inverter-Based Resources and Diesel Generator for Stability Analysis: Preprint

Impedance-based methods are widely used for power system stability analysis with inverter-based resources (IBRs), e.g., assessing dynamic interactions between the power grid and an IBR, control interactions between multiple IBRs, and the sub-synchronous oscillation and damping phenomenon. Since it is difficult to get a numerical model 100% matching with the hardware IBR, using the hardware inverter directly to obtain its output impedance has become a prominent approach nowadays. Therefore, this article presents the impedance scan using hardware IBRs, and also a hardware diesel generator as it still stays with the grid before the grid completely goes to renewable. The devices under test (DuTs) for the impedance scan includes two 3-..phi.., 480 V, 60 Hz commercial grid-forming IBRs (one of 250 kVA and another of 125 kVA rating) in series with ..delta..-Y transformers, one 3-..phi.., 480 V, 60 Hz commercial grid-following IBR (of 125 kVA rating), and a 3-..phi.., 480 V, 60 Hz commercial diesel generator (of 187.5 kVA rating). Using voltage signals perturbed with sub-, inter-, and higher harmonic components, and measuring the current response, the positive-sequence impedances are computed via an offline- based post-analysis. Moreover, best-fit transfer functions are estimated that closely resemble the measured data points of the positive-sequence impedances. Based on the observations from various outcomes of the hardware experiments, this article also provides some fundamental insights on the equivalent positive- sequence impedance of a combination of multiple hardware components by comparing the estimated and the empirically computed impedances. A comparative insight on the damping capability of the DuTs using the positive-sequence impedances of the hardware is also discussed.

grid following inverter↗
DOE OSTI2024

Impedance Scan of Inverter-Based Resources and Diesel Generator for Stability Analysis

Impedance-based methods are widely used for power system stability analysis with inverter-based resources (IBRs), e.g., assessing dynamic interactions between the power grid and an IBR, control interactions between multiple IBRs, and the sub-synchronous oscillation and damping phenomenon. Since it is difficult to get a numerical model 100% matching with the hardware IBR, using the hardware inverter directly to obtain its output impedance has become a prominent approach nowadays. Therefore, this article presents the impedance scan using hardware IBRs, and also a hardware diesel generator as it still stays with the grid before the grid completely goes to renewable. The devices under test (DuTs) for the impedance scan includes two 3-..phi.., 480 V, 60 Hz commercial grid-forming IBRs (one of 250 kVA and another of 125 kVA rating) in series with ..delta..-Y transformers, one 3-..phi.., 480 V, 60 Hz commercial grid-following IBR (of 125 kVA rating), and a 3-..phi.., 480 V, 60 Hz commercial diesel generator (of 187.5 kVA rating). Using voltage signals perturbed with sub-, inter-, and higher harmonic components, and measuring the current response, the positive-sequence impedances are computed via an offline-based post-analysis. Moreover, best-fit transfer functions are estimated that closely resemble the measured data points of the positive-sequence impedances. Based on the observations from various outcomes of the hardware experiments, this article also provides some fundamental insights on the equivalent positive-sequence impedance of a combination of multiple hardware components by comparing the estimated and the empirically computed impedances. A comparative insight on the damping capability of the DuTs using the positive-sequence impedances of the hardware is also discussed.

current measurement↗
DOE OSTI2020

Ultra-short-period Planets Are Stable against Tidal Inspiral

It has been unambiguously shown both in individual systems and at the population level that hot Jupiters experience tidal inspiral before the end of their host stars’ main-sequence lifetimes. Ultra-short-period (USP) planets have orbital periods P < 1 day, rocky compositions, and are expected to experience tidal decay on similar timescales to hot Jupiters if the efficiency of tidal dissipation inside their host stars parameterized as Q{sub ∗}{sup ′} is independent of P and/or secondary mass M {sub p}. Any difference between the two classes of systems would reveal that a model with constant Q{sub ∗}{sup ′} is insufficient. If USP planets experience tidal inspiral, then USP planet systems will be relatively young compared to similar stars without USP planets. Because it is a proxy for relative age, we calculate the Galactic velocity dispersions of USP planet candidate host and non-host stars using data from Gaia Data Release 2 supplemented with ground-based radial velocities. We find that main-sequence USP planet candidate host stars have kinematics consistent with similar stars in the Kepler field without observed USP planets. This indicates that USP planet hosts have similar ages to field stars and that USP planets do not experience tidal inspiral during the main-sequence lifetimes of their host stars. The survival of USP planets requires that Q{sub ∗}{sup ′} ≳ 10{sup 7} at P ≈ 0.7 day and M{sub p}≈2.6 M{sub ⊕}. This result demands that Q{sub ∗}{sup ′} depend on the orbital period and/or mass of the secondary in the range 0.5 day≲P≲5 days and 1 M{sub ⊕}≲M{sub p}≲1000 M{sub ⊕}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Applying Waveform Correlation to Aftershock Sequences Using a Global Sparse Network

Agencies that monitor for underground nuclear tests are interested in techniques that automatically characterize earthquake aftershock sequences to reduce the human analyst effort required to produce high-quality event bulletins. Waveform correlation is effective in detecting similar seismic waveforms from repeating earthquakes, including aftershock sequences. We report the results of an experiment that uses waveform templates recorded by multiple stations of the Comprehensive Nuclear-Test-Ban Treaty International Monitoring System during the first twelve hours after a mainshock to detect and identify aftershocks that occur during the subsequent week. We discuss approaches for station and template selection, threshold setting, and event detection that are specialized for aftershock processing for a sparse, global network. We apply the approaches to three aftershock sequences to evaluate the potential for establishing a set of standards for aftershock waveform correlation processing that can be effective for operational monitoring systems with a sparse network. We compare candidate events detected with our processing methods to the Reviewed Event Bulletin of the International Data Center to develop an intuition about potential reduction in analyst workload.

58 GEOSCIENCES↗
DOE OSTI2018

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach for discovering the functions of bacterial genes. However, the development of a suitable TnSeq strategy for a given bacterium can be costly and time-consuming. To meet this challenge, we describe a part-based strategy for constructing libraries of hundreds of transposon delivery vectors, which we term “magic pools.” Within a magic pool, each transposon vector has a different combination of upstream sequences (promoters and ribosome binding sites) and antibiotic resistance markers as well as a random DNA barcode sequence, which allows the tracking of each vector during mutagenesis experiments. To identify an efficient vector for a given bacterium, we mutagenize it with a magic pool and sequence the resulting insertions; we then use this efficient vector to generate a large mutant library. We used the magic pool strategy to construct transposon mutant libraries in five genera of bacteria, including three genera of the phylum Bacteroidetes .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Test methodology for validation of multi-frequency models of renewable energy generators using small-signal perturbations

Providing trustworthy and accurate multi-frequency (or harmonic) models for renewable energy generators (REG) is an ongoing challenge for harmonic studies. There have been effective attempts to propose and design a test device to validate the harmonic models, mainly based on shunt current perturbations. However, using additional devices for perturbations is costly for converter-based test sites. This paper provides the test specifications to extend the application of the grid emulators for voltage perturbations and appropriate harmonic model validation. Besides, the effects of the sequence couplings, initial emissions, and power set-points on the test results have been overlooked in the literature. Considering these effects, this paper proposes a generic test methodology to obtain more accurate models in the sequence domain. The experimental verification of the proposed methodology is demonstrated using a 7 MVA grid emulator for testing of a 2 MVA photo-voltaic converter and a 2 MVA Type 3 wind turbine. This way, the test challenges, specifications, and recommendations are presented using the MW-scale experiments on different REGs. Furthermore, the effects of sequence couplings and initial emissions on the calculation results are investigated and compared. The proposed methodology is applicable for harmonic model validation as well as empirical modelling.

24 POWER TRANSMISSION AND DISTRIBUTION↗