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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Tatooine's future: the eccentric response of Kepler's circumbinary planets to common-envelope evolution of their host stars

Inspired by the recent Kepler discoveries of circumbinary planets orbiting nine close binary stars, we explore the fate of the former as the latter evolve off the main sequence. We combine binary star evolution models with dynamical simulations to study the orbital evolution of these planets as their hosts undergo common-envelope (CE) stages, losing in the process a tremendous amount of mass on dynamical timescales. Five of the systems experience at least one Roche-lobe overflow and CE stage (Kepler-1647 experiences three), and the binary stars either shrink to very short orbits or coalesce; two systems trigger a double-degenerate supernova explosion. Kepler’s circumbinary planets predominantly remain gravitationally bound at the end of the CE phase, migrate to larger orbits, and may gain significant eccentricity; their orbital expansion can be more than an order of magnitude and can occur over the course of a single planetary orbit. The orbits these planets can reach are qualitatively consistent with those of the currently known post-CE, eclipse-time variations circumbinary candidates. Our results also show that circumbinary planets can experience both modes of orbital expansion (adiabatic and nonadiabatic) if their host binaries undergo more than one CE stage; multiplanet circumbinary systems like Kepler-47 can experience both modes during the same CE stage. Additionally, unlike Mercury orbiting the Sun, a circumbinary planet with the same semimajor axis can survive the CE evolution of a close binary star with a total mass of 1 M{sub ⊙}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Experimental single-strain mobilomics reveals events that shape pathogen emergence

Virulence and resistance genes carried on mobile DNAs such as genomic islands (GIs) and plasmids promote bacterial pathogen emergence. An early step in the mobilization of GIs is their excision, which produces both a circular form of the GI and a deletion site in the chromosome; circular forms have also been described for some bacterial insertion sequences (ISs). We demonstrate that the recombinant sequence produced at the junction of such circles, and their corresponding deletion sites, can be detected sensitively in high throughput sequencing data, using new computational methods that enable empirical discovery of new mobile DNAs. Applied to the rich mobilome of a single strain (Kpn2146) of the emerging multidrug-resistant pathogen Klebsiella pneumoniae, our approach detected circular junctions for six GIs and seven IS types (several of the latter not previously known to circularize). Our methods further revealed differential biology of multiple mobile DNAs, imprecision of integrases and transposases, and differential activity among identical IS copies for IS26, ISKpn18 and ISKpn21. Exonuclease was used to enrich for circular dsDNA molecules, and internal calibration with the native Kpn2146 plasmids showed that not all molecules bearing GI and IS circular junctions were circular dsDNAs. Transposition events were also detected, revealing replicon preference (ISKpn18 preferring a conjugative IncA/C2 plasmid), local action (IS26), regional preferences, selection (against capsule synthesis), and left-right IS end swapping. Efficient discovery and global characterization of numerous mobile elements per experiment will allow detailed accounting of bacterial evolution, explaining the new gene combinations that arise in emerging pathogens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Impact of recent ENDF nuclear data update, high initial enrichment and high burnup fuel on critical experiments applicability determination via the integral index c k for burnup credit validation

In 2012, NUREG/CR-7109 reported on the validation of burnup credit calculations involving major and minor actinides and major fission products which was investigated for pressurized and boiling water reactor (PWR and BWR) fuel enrichments up to 5 wt% 235 U and assembly-average burnups up to 60 GWd/MTU. Recently, there has been interest in increasing the maximum enrichment used in PWR fuel as high as 8 wt% 235 U and correspondingly increasing the maximum assembly-average burnups to approximately 75 GWd/MTU. These proposed increases in enrichment and burnup necessitate reinvestigation of the validation basis for k eff calculations for this expanded application space. Additionally, the 2012 study was performed by using the Evaluated Nuclear Data File (ENDF)/B-VII.0 nuclear data with the SCALE 6 covariance library, and the effects of using the newly released ENDF/B-VII.1 and ENDF/B-VIII.0 nuclear data and covariance libraries should be evaluated. In this work, published in NUREG/CR-7309 in 2025, the validation assessment was performed consistently with NUREG/CR-7109: modeling irradiated fuel assemblies in the Generic Burnup Credit (GBC)-32 cask defined in NUREG/CR-6747. The TSUNAMI-3D sequence was used to generate sensitivity data for the application model, and the data were compared with sensitivity data from select benchmark models. The integral parameter c k is the metric of similarity used in this study and is consistent with NUREG/CR-7109, where a c k value in excess of 0.8 indicates sufficient similarity for use in validation. A new set of benchmark experiments with sensitivity data has been assembled for this effort. The number of experiments with available sensitivity data is now 2,104, compared to 474 in NUREG/CR-7109. This increase was facilitated by the efforts of the Nuclear Energy Agency to generate sensitivity data for a majority of the experiments in the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook to supplement the data available in the Oak Ridge National Laboratory (ORNL) Verified, Archived Library of Inputs and Data (VALID). The complete set of benchmarks considered here includes experiments for low-enriched uranium (LEU), intermediate enriched uranium (IEU), and a mixture of uranium and plutonium (MIX) from the ICSBEP Handbook and VALID, as well as ORNL models of the Haut Taux de Combustion (HTC) experiments and other potentially relevant models not included in VALID. The updated similarity study shows that none of the extended burnup and higher enrichment combinations considered show a significant decrease in the number of potentially applicable experiments, meaning sufficient critical experiments exist for the validation of BUC criticality safety calculations, with initial enrichments up to 8 wt% 235 U and burnups up to 80 GWd/MTU. Additionally, both the ENDF/B-VII.1 and ENDF/B-VIII.0 nuclear data libraries can be used for validation since the number of critical experiments applicable for validation increases for most cases with the most recent nuclear data compared to the previous one. As in previous BUC validation studies, the French HTC experiments are the most similar in a majority of the application cases studied, especially from representative discharge burnups ranging from 40 to 80 GWd/MTU. In conclusion, these results match the conclusions presented in NUREG/CR-7109 regarding validation of the primary actinides in BUC analyses.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

An optimized ChIP-Seq framework for profiling histone modifications in Chromochloris zofingiensis

The eukaryotic green alga Chromochloris zofingiensis is a reference organism for studying carbon partitioning and a promising candidate for the production of biofuel precursors. Recent transcriptome profiling transformed our understanding of its biology and generally algal biology, but epigenetic regulation remains understudied and represents a fundamental gap in our understanding of algal gene expression. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a powerful tool for the discovery of such mechanisms, by identifying genome-wide histone modification patterns and transcription factor-binding sites alike. Here, we established a ChIP-Seq framework for Chr. zofingiensis yielding over 20 million high-quality reads per sample. The most critical steps in a ChIP experiment were optimized, including DNA shearing to obtain an average DNA fragment size of 250 bp and assessment of the recommended formaldehyde concentration for optimal DNA-protein cross-linking. We used this ChIP-Seq framework to generate a genome-wide map of the H3K4me3 distribution pattern and to integrate these data with matching RNA-Seq data. In line with observations from other organisms, H3K4me3 marks predominantly transcription start sites of genes. Our H3K4me3 ChIP-Seq data will pave the way for improved genome structural annotation in the emerging reference alga Chr. zofingiensis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A Case Study in the Application of TSUNAMI-3D - Part 2, Continuous Energy

The use of the sensitivity and uncertainty tool suite within SCALE, which is known as the TSUNAMI suite, has grown following its initial introduction more than a decade ago. Proper use of this tool provides a more complete understanding of system responses to perturbations, especially in the area of nuclear cross section uncertainties. Recent advances within TSUNAMI have added generalized perturbation theory to the k{sub eff} sensitivity capability that was included in TSUNAMI originally. The sensitivities can also be used to quantify the similarity of two systems. As an example, calculated sensitivities can be combined with cross section uncertainties to determine the similarity index ck. The generation of sensitivity data is encouraged in the review process for new critical experiment requests sponsored by the US Department of Energy (DOE) Nuclear Criticality Safety Program (NCSP) to demonstrate that the proposed experiment will satisfy the identified data need. Many analysts participate in this process, but many have not received proper training in the use of the TSUNAMI tools. The adjoint perturbation theory used to calculate sensitivities is not typically included in nuclear engineering curricula, leaving inexperienced engineers particularly at risk for incorrect use of the tools. The first step in the use of the TSUNAMI tools is the generation of a sensitivity data file (SDF), which contains all of the energy-dependent sensitivity data generated for a model. Most often, the SDF is generated from a three-dimensional (3D) model using either the KENO V.a or KENO-VI code within the TSUNAMI-3D sequence. The sensitivity data generated in TSUNAMI-3D must be accurate for correct quantification of system similarity or any other use of the sensitivity data. The sensitivities calculated by TSUNAMI can be affected by many of the input parameters, cross section processing models, and geometry modeling techniques used within the TSUNAMI-3D input. Fortunately, the total sensitivity of the most important nuclides can be confirmed simply by using direct perturbation (DP) calculations. Confirmation of the total sensitivity of these important nuclides provides confidence that the flux and importance function calculated within the TSUNAMI sequence will yield accurate sensitivities for all nuclides, reactions, and energies of interest. This process is essentially identical for multigroup (MG) and continuous-energy (CE) methods introduced in SCALE 6.2. This paper discusses the use of direct perturbation calculations and provides a case study in the use of DP calculations to confirm accurate sensitivities generated by the CE CLUTCH methods in TSUNAMI-3D for a particular benchmark experiment. A companion paper provides a similar case study applying the MG TSUNAMI capability to the same critical experiment. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Preliminary Analysis of Source Physics Experiment Explosion-Triggered Microseismicity Using the Back-Projection Method

A series of four chemical explosions were detonated in a deep borehole within the Yucca Flat Dry Alluvium Geology (DAG) at the Nevada National Security Site between 2018 and 2019. The two larger chemical explosions of 50 tons (DAG-2) and 10 tons (DAG-4) TNT equivalent yield triggered energetic aftershock sequences numbering 1392 and 347 microearthquakes, respectively, within the first 10 days. No significant aftershock activity was observed for the two smaller 1-ton explosions (DAG-1 and DAG-3). Here, we used a back-projection method based on travel-time migration and stacking of signal-to-noise ratio traces to detect, associate and locate aftershocks from a subset of 22-geophones within a larger 2 urn:x-wiley:21699313:media:jgrb54910:jgrb54910-math-0001 2 km seismic array surrounding the borehole. The aftershocks located within 300 m of the borehole and the depths were above the working points of 300 and 50 m depths of DAG-2 and DAG-4, respectively, ruling out triggering slip on geologic faults or disturbances beneath neighboring collapse craters. DAG-2 and DAG-4 aftershocks decayed at similar rates, with power-law exponents of p = 1.48 and p = 1.49, respectively. These decay rates are comparable to aftershocks sequences triggered by earthquakes and historical nuclear explosions at Yucca Flat. A smooth power-law aftershock decay within the first 10 days suggests a triggering mechanism from explosion generated stress relaxation due to the diffusion of high gas pressures in the cavity and radial fractures. A more random and episodic aftershock rate would be expected due to cavity collapse or falling rubble in chimney formation.

58 GEOSCIENCES↗
DOE OSTI2022

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Inter-slice bidirectional registration-based segmentation of the prostate gland in MR and CT image sequences

Purpose: Accurate segmentation and volume estimation of the prostate gland in magnetic resonance (MR) and computed tomography (CT) images are necessary steps in diagnosis, treatment, and monitoring of prostate cancer. This paper presents an algorithm for the prostate gland volume estimation based on the semiautomated segmentation of individual slices in T2-weighted MR and CT image sequences. Methods: The proposedInter-Slice Bidirectional Registration-based Segmentation (iBRS) algorithm relies on interslice image registration of volume data to segment the prostate gland without the use of an anatomical atlas. It requires the user to mark only three slices in a given volume dataset, i.e., the first, middle, and last slices. Next, the proposed algorithm uses a registration algorithm to autosegment the remaining slices. We conducted comprehensive experiments to measure the performance of the proposed algorithm using three registration methods (i.e., rigid, affine, and nonrigid techniques). Results: The results with the proposed technique were compared with manual marking using prostate MR and CT images from 117 patients. Manual marking was performed by an expert user for all 117 patients. The median accuracies for individual slices measured using the Dice similarity coefficient (DSC) were 92% and 91% for MR and CT images, respectively. The iBRS algorithm was also evaluated regarding user variability, which confirmed that the algorithm was robust to interuser variability when marking the prostate gland. Conclusions: The proposed algorithm exploits the interslice data redundancy of the images in a volume dataset of MR and CT images and eliminates the need for an atlas, minimizing the computational cost while producing highly accurate results which are robust to interuser variability.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Structure and Interactions of the CS Domain of Human H/ACA RNP Assembly Protein Shq1

Shq1 is an essential protein involved in the early steps of biogenesis and assembly of H/ACA ribonucleoprotein particles (RNPs). Shq1 binds to dyskerin (Cbf5 in yeast) at an early step of H/ACA RNP assembly and is subsequently displaced by the H/ACA RNA. Shq1 contains an N-terminal CS and a C-terminal Shq1-specific domain (SSD). Dyskerin harbors many mutations associated with dyskeratosis congenita. Structures of yeast Shq1 SSD bound to Cbf5 revealed that only a subset of these mutations is in the SSD binding site, implicating another subset in the putative CS binding site. Here in this paper, we present the crystal structure of human Shq1 CS (hCS) and the nuclear magnetic resonance (NMR) and crystal structures of hCS containing a serine substitution for proline 22 that is associated with some prostate cancers. The structure of hCS is similar to yeast Shq1 CS domain (yCS) and consists of two β-sheets that form an immunoglobulin-like β-sandwich fold. The N-terminal affinity tag sequence AHHHHHH associates with a neighboring protein in the crystal lattice to form an extra β-strand. Deletion of this tag was required to get spectra suitable for NMR structure determination, while the tag was required for crystallization. NMR chemical shift perturbation (CSP) experiments with peptides derived from putative CS binding sites on dyskerin and Cbf5 revealed a conserved surface on CS important for Cbf5/dyskerin binding. A HADDOCK (high-ambiguity-driven protein-protein docking) model of a Shq1-Cbf5 complex that defines the position of CS domain in the pre-H/ACA RNP was calculated using the CSP data.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass

Abstract A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum ( Paspalum vaginatum ) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession of P. vaginatum . Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.

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

Massive compression for high data rate macromolecular crystallography (HDRMX): impact on diffraction data and subsequent structural analysis

New higher-count-rate, integrating, large-area X-ray detectors with framing rates as high as 17400 images per second are beginning to be available. These will soon be used for specialized macromolecular crystallography experiments but will require optimal lossy compression algorithms to enable systems to keep up with data throughput. Some information may be lost. Can we minimize this loss with acceptable impact on structural information? To explore this question, we have considered several approaches: summing short sequences of images, binning to create the effect of larger pixels, use of JPEG-2000 lossy wavelet-based compression, and use of Hcompress, which is a Haar-wavelet-based lossy compression borrowed from astronomy. We also explore the effect of the combination of summing, binning, and Hcompress or JPEG-2000. In each of these last two methods one can specify approximately how much one wants the result to be compressed from the starting file size. These provide particularly effective lossy compressions that retain essential information for structure solution from Bragg reflections.

47 OTHER INSTRUMENTATION↗
DOE OSTI2015

Dismantling of primary shielding with prototype machines in a compact sodium cooled reactor - 15463

The Compact Sodium Cooled Reactor Facility Karlsruhe (KNK), a prototype reactor to demonstrate the Fast Breeder Reactor Technology in Germany, was in operation from 1971 to 1991. The dismantling activities started in 1991. The project aim is the green field in 2020. Most of the reactor internals as well as the primary and secondary cooling loops have already been dismantled. The contaminated sodium inventory has already been disposed of completely. Only the highly activated reactor vessel shielding structures remain. Due to their high dose rates, these structures must be dismantled remotely. For the removal of the primary shielding of the reactor vessel, 12 stacked cast iron blocks with a total mass of 90 Mg and individual masses of up to 15.5 Mg, a remote-controlled multifunctional dismantling device (HWZ) was designed, manufactured and tested in a mock-up. Since it is not possible to remove the segments in one piece for offsite treatment, a special prototype band-saw (BWZ) had to be developed for sawing the segments both horizontally and vertically into smaller pieces. The resulting sub-segments are transferred directly into repository containers. After the successful approval of the test sequences by the authorities and intensive training of the operational staff, both prototype machines were installed inside the reactor building containment for final assembly. The dismantling started in 2013. The present paper covers the successful dismantling of the primary shielding as well as the experiences gained through the development, use and improvement of these prototype machines. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

Sequence Ion Structures and Dissociation Chemistry of Deprotonated Sucrose Anions

We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B{sub 1}-Y{sub 1} and C{sub 1}-Z{sub 1} reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B{sub 1} and C{sub 1} product anions. For the C{sub 1} anions, barriers to interconversion of the pyranose [α-glucose-H]{sup −}, C{sub 1} anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol{sup −1}) consistent with the observation of a band assigned to a carbonyl stretch at ~ 1680–1720 cm{sup −1}. For the B{sub 1} anions, our transition structure calculations predict the presence of both deprotonated 1,6-anhydroglucose and carbon 2-ketone ((4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one) anion structures, with the latter predominating. This hypothesis is supported by our spectroscopic data which show diagnostic bands at 1600, 1674, and 1699 cm{sup −1} (deprotonated carbon 2-ketone structures), and at ~ 1541 cm{sup −1} (both types of structure) and RRKM rate calculations. The deprotonated carbon 2-ketone structures are also the lowest energy product B{sub 1} anions. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Optimal control of the signal-to-noise ratio per unit time of a spin 1/2 particle: The crusher gradient and the radiation damping cases

We show to which extent the signal to noise ratio per unit time of a spin 1/2 particle can be maximized. We consider a cyclic repetition of experiments made of a measurement followed by a radio-frequency magnetic field excitation of the system, in the case of unbounded amplitude. In the periodic regime, the objective of the control problem is to design the initial state of the system and the pulse sequence which leads to the best signal to noise performance. We focus on two specific issues relevant in nuclear magnetic resonance, the crusher gradient and the radiation damping cases. Optimal control techniques are used to solve this non-standard control problem. We discuss the optimality of the Ernst angle solution, which is commonly applied in spectroscopic and medical imaging applications. In the radiation damping situation, we show that in some cases, the optimal solution differs from the Ernst one.

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

Evolution of intermittent filaments in the scrape-off layer of NSTX

Filamentary structures naturally arise from background turbulence in the scrape-off layer (SOL) of plasmas, leading to significant particle and heat transport that can degrade overall plasma confinement. This enhanced transport can contribute to unacceptably high heat loads on plasma-facing components. As such, understanding the physics of SOL plasma filaments is critical for predicting and mitigating their effects in future fusion devices. On the National Spherical Torus Experiment (NSTX), plasma filaments—commonly referred to as “blobs”—were investigated using the gas-puff imaging (GPI) diagnostic in the edge and SOL regions. The analysis involved identifying, segmenting, and tracking the characteristic contours of the blobs in each frame of the GPI video sequences. Their evolution was characterized through shape descriptors, velocity, and angular velocity derived from their contour coordinates. The results indicate that as the blob area increases, their shapes become more concave and less circular, suggesting reduced structural stability in larger blobs. This result aligns with previous theoretical results where it was shown that larger blobs are more susceptible to instabilities [Krasheninnikov et al., J. Plasma Phys. 74, 679–717 (2008) and D'Ippolito et al., Phys. Plasmas 18, 060501 (2011)]. A positive correlation was observed between radial velocity and radial position, suggesting radially outward acceleration of the filaments, potentially driven by decreasing viscous drag toward the far SOL. Interestingly, blobs in background SOL turbulence exhibited minimal spinning in contrast to filaments originating from edge localized modes, which show substantial rotation during their paths [Lampert et al., Phys. Plasmas 29, 102502 (2022)]. Statistical analysis of the solidity and total curvature shape descriptors, along with their temporal evolution, revealed relatively broad, near-Gaussian distributions. This suggests that blob morphology is strongly influenced by stochastic turbulent processes in the surrounding plasma environment. Blob parameters were also compared with bulk plasma and radial profile measurements. Notable trends were found between blob rotation and poloidal velocity with collisionality and line-integrated density. These findings contribute to a deeper understanding of blob dynamics and provide valuable insights for refining SOL turbulence models.

Covariance and correlation↗
DOE OSTI2022

Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli

Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in Escherichia coli. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in E. coli and other bacteria. Three replication restart pathways have been identified in E. coli: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon-insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the priB replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel priB interactions were discovered. Targeted genetic and imaging-based experiments with priB and its genetic partners revealed significant double-strand DNA break accumulation in strains with mutations in dam, rep, rdgC, lexA, or polA. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of rdgC or lexA mutations in ΔpriB cells. Taken together, our results highlight roles for several genes in double-strand DNA break homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in E. coli.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MILK : a Python scripting interface to MAUD for automation of Rietveld analysis

Modern diffraction experiments ( e.g. in situ parametric studies) present scientists with many diffraction patterns to analyze. Interactive analyses via graphical user interfaces tend to slow down obtaining quantitative results such as lattice parameters and phase fractions. Furthermore, Rietveld refinement strategies ( i.e. the parameter turn-on-off sequences) tend to be instrument specific or even specific to a given dataset, such that selection of strategies can become a bottleneck for efficient data analysis. Managing multi-histogram datasets such as from multi-bank neutron diffractometers or caked 2D synchrotron data presents additional challenges due to the large number of histogram-specific parameters. To overcome these challenges in the Rietveld software Material Analysis Using Diffraction ( MAUD ), the MAUD Interface Language Kit ( MILK ) is developed along with an updated text batch interface for MAUD . The open-source software MILK is computer-platform independent and is packaged as a Python library that interfaces with MAUD . Using MILK , model selection ( e.g. various texture or peak-broadening models), Rietveld parameter manipulation and distributed parallel batch computing can be performed through a high-level Python interface. A high-level interface enables analysis workflows to be easily programmed, shared and applied to large datasets, and external tools to be integrated with MAUD . Through modification to the MAUD batch interface, plot and data exports have been improved. The resulting hierarchical folders from Rietveld refinements with MILK are compatible with Cinema: Debye–Scherrer , a tool for visualizing and inspecting the results of multi-parameter analyses of large quantities of diffraction data. In this manuscript, the combined Python scripting and visualization capability of MILK is demonstrated with a quantitative texture and phase analysis of data collected at the HIPPO neutron diffractometer.

97 MATHEMATICS AND COMPUTING↗