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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 1,369 records · Page 76
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural and functional insights into the interaction between the bacteriophage T4 DNA processing proteins gp32 and Dda

Abstract Bacteriophage T4 is a classic model system for studying the mechanisms of DNA processing. A key protein in T4 DNA processing is the gp32 single-stranded DNA-binding protein. gp32 has two key functions: it binds cooperatively to single-stranded DNA (ssDNA) to protect it from nucleases and remove regions of secondary structure, and it recruits proteins to initiate DNA processes including replication and repair. Dda is a T4 helicase recruited by gp32, and we purified and crystallized a gp32–Dda–ssDNA complex. The low-resolution structure revealed how the C-terminus of gp32 engages Dda. Analytical ultracentrifugation analyses were consistent with the crystal structure. An optimal Dda binding peptide from the gp32 C-terminus was identified using surface plasmon resonance. The crystal structure of the Dda–peptide complex was consistent with the corresponding interaction in the gp32–Dda–ssDNA structure. A Dda-dependent DNA unwinding assay supported the structural conclusions and confirmed that the bound gp32 sequesters the ssDNA generated by Dda. The structure of the gp32–Dda–ssDNA complex, together with the known structure of the gp32 body, reveals the entire ssDNA binding surface of gp32. gp32–Dda–ssDNA complexes in the crystal are connected by the N-terminal region of one gp32 binding to an adjacent gp32, and this provides key insights into this interaction.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Crystal structure of MutYX: a novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-oxoguanine recognition sphere

Abstract The [4Fe–4S] cluster is an important cofactor of the base excision repair (BER) adenine DNA glycosylase MutY to prevent mutations associated with 8-oxoguanine (OG). Several MutYs lacking the [4Fe–4S] cofactor have been identified. Phylogenetic analysis shows that clusterless MutYs are distributed in two clades suggesting cofactor loss has occurred in multiple independent evolutionary events. Herein, we determined the first crystal structure of a clusterless MutY complexed with DNA. On the basis of the dramatic structural divergence from canonical MutYs, we refer to this as representative of a clusterless MutY subgroup “MutYX.” Interestingly, MutYX compensates for the missing [4Fe–4S] cofactor to maintain positioning of catalytic residues by expanding a pre-existing α-helix and acquisition of a new α-helix. Surprisingly, MutYX also acquired a new C-terminal domain that uniquely recognizes OG using residues Gln201 and Arg209. Adenine glycosylase assays and binding affinity measurements indicate that Arg209 is the primary residue responsible for OG:A lesion specificity, while Gln201 assists by bridging OG and Arg209. Surprisingly, replacement of Arg209 and Gln201 with Ala increased activity toward G:A mismatches. The MutYX structure serves as an example of devolution, capturing structural features required to retain function in the absence of a metal cofactor considered indispensable.

Trasviña-Arenas, Carlos H [University of Californi↗
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 OSTI2025

Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella

Auxenochlorella spp. are diploid oleaginous green algae whose streamlined genomes can be readily manipulated by homologous recombination, making them highly amenable to discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity, and aneuploidy; however, studies of these forces have largely focused on yeasts. Here, we present a telomere-to-telomere phased diploid genome assembly of Auxenochlorella UTEX 250-A (haploid length 22 Mb) and introduce a genetic toolkit for site-specific manipulation of the nuclear genome in multiple strains, featuring several selectable markers, inducible promoters, and fluorescent reporters for protein localization. UTEX 250-A is an allodiploid hybrid of Auxenochlorella protothecoides and Auxenochlorella symbiontica, two species differentiated by extensive chromosomal rearrangements. UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic. Loss-of-heterozygosity events are pervasive across Auxenochlorella and can evolve rapidly in the laboratory. High-quality structural annotation yielded ∼7,500 genes per haplotype. Auxenochlorella have experienced gene family loss and reduction, including core photosynthesis genes, and exhibit periodic adenine and cytosine methylation at promoters and gene bodies, respectively. Approximately 10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, which may participate in a regulatory mechanism. We demonstrate the utility of Auxenochlorella for fundamental research by knockout of a chlorophyll biosynthesis enzyme, and confirm one trisomy by allele-specific transformation. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy and provide a foundation for the use of Auxenochlorella as a reference organism.

CHL27↗
DOE OSTI2023

Chloroplast phosphate transporter CrPHT4-7 regulates phosphate homeostasis and photosynthesis in Chlamydomonas

Abstract In eukaryotic cells, phosphorus is assimilated and utilized primarily as phosphate (Pi). Pi homeostasis is mediated by transporters that have not yet been adequately characterized in green algae. This study reports on PHOSPHATE TRANSPORTER 4-7 (CrPHT4-7) from Chlamydomonas reinhardtii, a member of the PHT4 transporter family, which exhibits remarkable similarity to AtPHT4;4 from Arabidopsis (Arabidopsis thaliana), a chloroplastic ascorbate transporter. Using fluorescent protein tagging, we show that CrPHT4-7 resides in the chloroplast envelope membrane. Crpht4-7 mutants, generated by the CRISPR/Cas12a-mediated single-strand templated repair, show retarded growth, especially in high light, reduced ATP level, strong ascorbate accumulation, and diminished non-photochemical quenching in high light. On the other hand, total cellular phosphorous content was unaffected, and the phenotype of the Crpht4-7 mutants could not be alleviated by ample Pi supply. CrPHT4-7-overexpressing lines exhibit enhanced biomass accumulation under high light conditions in comparison with the wild-type strain. Expressing CrPHT4-7 in a yeast (Saccharomyces cerevisiae) strain lacking Pi transporters substantially recovered its slow growth phenotype, demonstrating that CrPHT4-7 transports Pi. Even though CrPHT4-7 shows a high degree of similarity to AtPHT4;4, it does not display any substantial ascorbate transport activity in yeast or intact algal cells. Thus, the results demonstrate that CrPHT4-7 functions as a chloroplastic Pi transporter essential for maintaining Pi homeostasis and photosynthesis in C. reinhardtii.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DNA adducts form in mouse lung and liver after oral naphthalene exposure

Naphthalene is a ubiquitous combustion product and environmental contaminant with known human exposure. Chronic exposure to naphthalene vapor leads to respiratory tumor formation in rodents. Naphthalene forms DNA adducts (precursors to genotoxicity) in tissue explants but it is unclear if this occurs in vivo. Wild-type C57BL/6 mice were orally exposed to 50 mg/kg 14 C-naphthalene. Naphthalene-DNA adducts were detected by accelerator mass spectrometry at 2- to 72-h post-exposure in both lung and liver, with decreasing abundance over time. Adducts persisted even at 72-h after exposure, which indicates possible evasion of DNA repair and potential to contribute to mutagenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

State densities of heavy nuclei in the static-path plus random-phase approximation

We report that nuclear state densities are important inputs to statistical models of compound-nucleus reactions. State densities are often calculated with self-consistent mean-field approximations that do not include important correlations and must be augmented with empirical collective enhancement factors. Here, we benchmark the static-path plus random-phase approximation (SPA + RPA) to the state density in a chain of samarium isotopes 148–155 Sm against exact results (up to statistical errors) obtained with the shell-model Monte Carlo (SMMC) method. The SPA + RPA method incorporates all static fluctuations beyond the mean field together with small-amplitude quantal fluctuations around each static fluctuation. Using a pairing plus quadrupole interaction, we show that the SPA + RPA state densities agree well with the exact SMMC densities for both the even- and odd-mass isotopes. For the even-mass isotopes, we also compare our results with mean-field state densities calculated with the finite-temperature Hartree-Fock-Bogoliubov (HFB) approximation. We find that the SPA + RPA repairs the deficiencies of the mean-field approximation associated with broken rotational symmetry in deformed nuclei and with the violation of particle-number conservation in the pairing condensate. In particular, in deformed nuclei the SPA + RPA reproduces the rotational enhancement of the state density relative to the mean-field state density.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase

Nanobodies (VHHs) are single-domain antibodies with three antigenic CDR regions and are used in diverse scientific applications. Here, an ∼14 kDa nanobody (A5) specific for the endonuclease VIII (Nei)-like 1 or NEIL1 DNA glycosylase involved in the first step of the base-excision repair pathway was crystallized and its structure was determined to 2.1 Å resolution. The crystals posed challenges due to potential twinning and anisotropic diffraction. Despite inconclusive twinning indicators, reprocessing in an orthorhombic setting and molecular replacement in space groupP2 1 2 1 2 enabled the successful modeling of 96% of residues in the asymmetric unit, with finalR work andR free values of 0.199 and 0.229, respectively.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Thermal modeling of directed energy deposition additive manufacturing using graph theory

Purpose: The purpose of this paper is to develop, apply and validate a mesh-free graph theory–based approach for rapid thermal modeling of the directed energy deposition (DED) additive manufacturing (AM) process. Design/methodology/approach: Here, the authors develop a novel mesh-free graph theory–based approach to predict the thermal history of the DED process. Subsequently, the authors validated the graph theory predicted temperature trends using experimental temperature data for DED of titanium alloy parts (Ti-6Al-4V). Temperature trends were tracked by embedding thermocouples in the substrate. The DED process was simulated using the graph theory approach, and the thermal history predictions were validated based on the data from the thermocouples. Findings: The temperature trends predicted by the graph theory approach have mean absolute percentage error of approximately 11% and root mean square error of 23°C when compared to the experimental data. Moreover, the graph theory simulation was obtained within 4 min using desktop computing resources, which is less than the build time of 25 min. By comparison, a finite element–based model required 136 min to converge to similar level of error. Research limitations/implications: This study uses data from fixed thermocouples when printing thin-wall DED parts. In the future, the authors will incorporate infrared thermal camera data from large parts. Practical implications: The DED process is particularly valuable for near-net shape manufacturing, repair and remanufacturing applications. However, DED parts are often afflicted with flaws, such as cracking and distortion. In DED, flaw formation is largely governed by the intensity and spatial distribution of heat in the part during the process, often referred to as the thermal history. Accordingly, fast and accurate thermal models to predict the thermal history are necessary to understand and preclude flaw formation. Originality/value: This paper presents a new mesh-free computational thermal modeling approach based on graph theory (network science) and applies it to DED. The approach eschews the tedious and computationally demanding meshing aspect of finite element modeling and allows rapid simulation of the thermal history in additive manufacturing. Although the graph theory has been applied to thermal modeling of laser powder bed fusion (LPBF), there are distinct phenomenological differences between DED and LPBF that necessitate substantial modifications to the graph theory approach.

42 ENGINEERING↗
DOE OSTI2020

Quantitative Evaluation of Reliability Improvement: Case Study on a Self-healing Distribution System

In this work, we develop a methodology and tool to quantitatively evaluate the reliability of a self-healing system that considers practical distribution system features such as the distributed energy resources, microgrids, and service restoration strategies. Also, this paper addresses various practical issues when being applied to an actual Duke Energy distribution system, including the design of feasible and practical service restoration strategies that are used to identify the customer interruptions after a fault, and the incorporation of the utility’s historical reliability indices that are used to calibrate the failure rate and repair time of distribution system components such as overhead lines and underground cables. This case study demonstrates the effectiveness of the proposed method.

Dong, Jiaojiao↗
DOE OSTI2020

Q-Learning-Based Impact Assessment of Propagating Extreme Weather on Distribution Grids

The increasing number of power outage events due to extreme weather conditions is hampering us socioeconomically. Preparing in advance for the extreme weather event is critical. It can help utility operators to reduce grid damages, restore grid service quickly, allocate energy resources and repair crews strategically, and hence dramatically increase grid resilience. In this paper, we propose a method to identify the sequence of worst impact zones in the power grid caused by extreme weather events based on Q-learning (a reinforcement learning algorithm). To quantity the weather severity and its effect on the grid, we model the impact of extreme weather on the grid as a function of intensity, vulnerability, and exposure. A modified IEEE 123-node distribution feeder is presented in a mesh grid and experimented for sequences of zones identification. Finally, simulation results present the identified sequences and their associated impacts on the grid caused by extreme weather events.

distribution system↗
DOE OSTI2020

Magnetic Field Optimization of an In-Vacuum Undulator at NSLS-II Transactions on Applied Superconductivity

A 3.0 m long In-Vacuum Undulator (IVU) is employed at the National Synchrotron Light Source II (NSLS-II) for the Hard X-ray Nanoprobe (HXN) beamline providing structural and X-ray fluorescence imaging with world-leading spatial resolution. On July 1 st 2018 a gearbox shaft in the gap drive train assembly sheared due to corrosion fatigue caused by stress due to mechanical misalignment. Furthermore, the device was extracted from the storage ring and measured. The magnetic field measurements detected a degradation of the magnetic performance as well as a localized demagnetization of the magnetic modules of the first 3 upstream periods. We describe here the mechanical repairs and the magnetic phase shimming optimization implemented to restore the spectral performance of the device.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

DIII-D Electron Cyclotron Heating and Current Drive System Status and Plans

The DIII-D 110 GHz Electron Cyclotron Heating and Current Drive (ECH/ECCD) System supports a wide range of experiments at the DIII-D National Fusion Facility and is pioneering innovative new techniques for future fusion reactors. Here, the system currently includes 8 sockets with 4 installed gyrotrons, 31.75 mm circular corrugated transmission lines, four dual real time steerable launchers plus two Top Launchers. After the successful testing of the first Top Launcher, that injects the EC waves downward nearly parallel to the resonance layer with double current drive efficiency and a long absorption path, a second new Top Launcher was designed and installed with an upgraded design. Some of the operational limitations encountered for the 110 GHz X-mode second harmonic resonance scenario launched in over-dense plasmas were overcome with the alternative use of O-mode second harmonic launch. Two new gyrotrons in a new series manufactured by CPI were installed and tested, bringing up the total installed power to 3 MW. The installation of repaired and new gyrotrons will increase the number of installed gyrotrons to 7 in 2023. An addition to the DIII-D building will be completed in early 2022 to provide the space to expand the ECH/ECCD system to ten gyrotron systems, plus an extra gyrotron test socket.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Power System Resilience Enhancement in Typhoons Using a Three-Stage Day-Ahead Unit Commitment

In this work, we propose a three-stage resilient unit commitment model which considers uncertain typhoon paths and line outages to improve the power system resilience against typhoon events. The proposed solution coordinates resources in response to the worst-case scenario for each possible typhoon path. The optimal decision is based on the characterization of the power system schedule into three stages of preventive control, emergency control, and restoration. Preventive control is performed before the typhoon occurs by quickly adjusting the three-stage resilient unit commitment schedule; emergency control is conducted during the typhoon by shedding local loads to meet the power balance, while other control strategies are assumed to be unavailable due to possible interruptions in the communication system; restoration is realized after the typhoon, when resources are optimally dispatched to repair the outages of critical devices and recover the normal operation state of the power system quickly. Considering the typhoon path uncertainty, we have introduced a stochastic model for possible typhoon paths where all possible affected lines along each typhoon path are assumed to be on outage during the typhoon. Accordingly, we explore the strategy for co-optimizing the three stages in unit commitment. The proposed model is tested on the IEEE 118-bus system and the real-world provincial system to verify its effectiveness.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Towards Optimal and Executable Distribution Grid Restoration Planning With a Fine-Grained Power-Communication Interdependency Model

Distribution service restoration (DSR) under natural disasters is always a critical and challenging problem for utility companies. An effective solution must not ignore the power-communication interdependency as various systems are getting increasingly connected in the Smart Grid era. In this paper, we propose a two-layer distribution system model with both power and communication components. Based on this model, we formulate the restoration process as a routing problem that schedules the path and action sequence of utility crews that involves repairing damaged components, closing power switches, and enabling communication paths between the control center and remote field devices. Further, we develop a simulation-based method to quantitatively evaluate the restoration process with public reference models of large-scale power systems. The experimental results show that our method improves the total restored energy up to 57.6% and reduces the recovery time up to 63% by considering the power-communication interdependency.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

A Practical Solver for Scalar Data Topological Simplification

This paper presents a practical approach for the optimization of topological simplification, a central pre-processing step for the analysis and visualization of scalar data. Given an input scalar field f and a set of “signal” persistence pairs to maintain, our approaches produces an output field g that is close to f and which optimizes (i) the cancellation of “non-signal” pairs, while (ii) preserving the “signal” pairs. In contrast to pre-existing simplification algorithms, our approach is not restricted to persistence pairs involving extrema and can thus address a larger class of topological features, in particular saddle pairs in three-dimensional scalar data. Our approach leverages recent generic persistence optimization frameworks and extends them with tailored accelerations specific to the problem of topological simplification. Extensive experiments report substantial accelerations over these frameworks, thereby making topological simplification optimization practical for real-life datasets. Our approach enables a direct visualization and analysis of the topologically simplified data, e.g., via isosurfaces of simplified topology (fewer components and handles). We apply our approach to the extraction of prominent filament structures in three-dimensional data. Specifically, we show that our pre-simplification of the data leads to practical improvements over standard topological techniques for removing filament loops. Here, we also show how our approach can be used to repair genus defects in surface processing. Finally, we provide a C++ implementation for reproducibility purposes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Multi-Agent Simulation Based Framework for Power Restoration Time Estimation at Distribution Level

The growing frequency of power outages has prompted increased interest in developing a more resilient power grid that can quickly recover from weather-related damage. At the distribution level, power restoration is a complex, multi-stage process involving multiple response entities. Providing utility stakeholders, government regulators, and the public with information about outage duration and estimated time to restoration is crucial. The research employs a multi-agent simulation approach, which allows for the simulation of decision-making behaviors among different entities and the incorporation of various uncertainties. Specifically, the study uses the open-source simulation package Mesa-Geo in conjunction with the Python language and constructs a road network using the open-source network extension pgRouting for routing queries. The research design includes several experiments focused on Florida as a case study, comparing repair crew sizes, power outage numbers, and road damage scenarios. The findings could offer valuable managerial guidance on resource allocation in the restoration process.

Chen, Yang↗
DOE OSTI2023

Desiccation induces varied responses within a soil bacterial genus

Abstract Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation‐induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128‐day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium . We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage‐resistant bacterium, Deinococcus radiodurans . However, within the genus, there were also 10‐fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up‐regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up‐regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB , the chaperone groEL , and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.

59 BASIC BIOLOGICAL SCIENCES↗