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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

CFD Analysis of Upper Plenum Flow for a Sodium-Cooled Small Modular Reactor

Upper plenum flow behavior is important for many operational and safety issues in sodium fast reactors. The Prototype Gen-IV Sodium Fast Reactor (PGSFR), a pool-type, 150 MWe output power design, was used as a reference case for a detailed characterization of upper plenum flow for normal operating conditions. Computational Fluid Dynamics (CFD) simulation was utilized with detailed geometric modeling of major structures. Core outlet conditions based on prior system-level calculations were mapped to approximate the outlet temperatures and flow rates for each core assembly. Core outlet flow was found to largely bypass the Upper Internal Structures (UIS). Flow curves over the shield and circulates within the pool before exiting the plenum. Cross-flows and temperatures were evaluated near the core outlet, leading to a proposed height for the core outlet thermocouples to ensure accurate assembly-specific temperature readings. A passive scalar was used to evaluate fluid residence time from core outlet to IHX inlet, which can be used to assess the applicability of various methods for monitoring fuel failure. Additionally, the gas entrainment likelihood was assessed based on the CFD simulation results. Based on the evaluation of velocity gradients and turbulent kinetic energies and the available gas entrainment criteria in the literature, it was concluded that significant gas entrainment is unlikely for the current PGSFR design.

computational fluid dynamics↗
DOE OSTI2017

A new electron-ion coincidence 3D momentum-imaging method and its application in probing strong field dynamics of 2-phenylethyl-N, N-dimethylamine

In this paper, we report the development of a new three-dimensional (3D) momentum-imaging setup based on conventional velocity map imaging to achieve the coincidence measurement of photoelectrons and photo-ions. This setup uses only one imaging detector (microchannel plates (MCP)/phosphor screen) but the voltages on electrodes are pulsed to push both electrons and ions toward the same detector. The ion-electron coincidence is achieved using two cameras to capture images of ions and electrons separately. The time-of-flight of ions and electrons are read out from MCP using a digitizer. We demonstrate this new system by studying the dissociative single and double ionization of PENNA (2-phenylethyl-N,N-dimethylamine). Finally, we further show that the camera-based 3D imaging system can operate at 10 kHz repetition rate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

GADRAS Batch Inject Tool User Guide

Gamma Detector Response and Analysis Software (GADRAS) is used by the radiation detection and emergency response community to perform modeling and spectral analysis for gamma detector systems. Built into GADRAS is the ability to define a detector, geometry, background characteristics and source composition to generate synthetic spectra for drills and exercises (injects). Consequence Management is currently in development of a sample result data simulator tool in which a deposition model is probed for source conditions at moments in time and locations in space. These values are used to generate realistic sample results for use in drills and exercises. In addition to sample results, there is a need to simulate the actual spectra that would be observed in the field by downlooking HPGe instruments given a deposition activity. This way, the FRMAC Gamma Spectroscopist can practice their process of generating quantified results from spectra on realistic data as well. Recognizing the decades of work done in GADRAS to accurately generate synthetic spectra, this team decided to build a link between the new simulator and GADRAS to generate these spectra quickly and easily. The simulator tool will generate a file that specifies the name of the spectra, its location, date/time of measurement, duration of measurement, height off the ground, and the deposition activity and age for every radionuclide in the simulation. Then, a new tool within the Inject Tab of GADRAS was developed to read in this file given a detector selection and generate In-Situ spectra for each row in the file in any file format the user chooses. This way, simulation cell staff can take these files and then upload them to the appropriate data system (RAMS or RadResponder) for use during drills and exercises. An advanced feature of this tool allows for generating any spectra given an appropriate model and mapping of source to model layer in the batch inject tool. This way, spectra from field sample counts, mobile laboratories, or even fixed laboratories can be generated in bulk given an estimate of the radioactivity concentration or total radioactivity in an import file. This expands the capabilities of this tool a great deal and will make it a more useful tool for CM and others to help estimate detector response for nearly any situation. This user guide will explain the steps needed to perform a batch inject file generation.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2017

Photon counting phosphorescence lifetime imaging with TimepixCam

TimepixCam is a novel fast optical imager based on an optimized silicon pixel sensor with a thin entrance window, and read out by a Timepix ASIC. The 256 x 256 pixel sensor has a time resolution of 15 ns at a sustained frame rate of 10 Hz. We used this sensor in combination with an image intensifier for wide-field time-correlated single photon counting (TCSPC) imaging. We have characterised the photon detection capabilities of this detector system, and employed it on a wide-field epifluorescence microscope to map phosphorescence decays of various iridium complexes with lifetimes of about 1 μs in 200 μm diameter polystyrene beads.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Collective memory transfer devices and methods for multiple-core processors

This disclosure provides systems, methods, and apparatus for collective memory transfers. A control unit may be configured to coordinate a transfer of data between a memory and processor cores. For a read data transfer operation, the control unit may receive a trigger packet identifying a read data transfer operation and identifying a first plurality of data lines based on data values included in the trigger packet. The control unit may read the first plurality of data lines from the memory sequentially and send a second plurality of data lines to the processor cores. For a write data transfer operation, the control unit may send a request for at least one data line to a plurality of processor cores, may receive and reorder the requested data lines, and may write the data lines to a memory. The control unit may determine a mapping between processor cores and the memory.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum , at ~3 Å resolution is described using a combination of homology modeling with MODELLER , molecular-replacement phasing with Phaser , deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot . This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies

The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Comparative analysis of nonlinear dimensionality reduction techniques for breast MRI segmentation

Purpose: Visualization of anatomical structures using radiological imaging methods is an important tool in medicine to differentiate normal from pathological tissue and can generate large amounts of data for a radiologist to read. Integrating these large data sets is difficult and time-consuming. A new approach uses both supervised and unsupervised advanced machine learning techniques to visualize and segment radiological data. This study describes the application of a novel hybrid scheme, based on combining wavelet transform and nonlinear dimensionality reduction (NLDR) methods, to breast magnetic resonance imaging (MRI) data using three well-established NLDR techniques, namely, ISOMAP, local linear embedding (LLE), and diffusion maps (DfM), to perform a comparative performance analysis. Methods: Twenty-five breast lesion subjects were scanned using a 3T scanner. MRI sequences used were T1-weighted, T2-weighted, diffusion-weighted imaging (DWI), and dynamic contrast-enhanced (DCE) imaging. The hybrid scheme consisted of two steps: preprocessing and postprocessing of the data. The preprocessing step was applied for B{sub 1} inhomogeneity correction, image registration, and wavelet-based image compression to match and denoise the data. In the postprocessing step, MRI parameters were considered data dimensions and the NLDR-based hybrid approach was applied to integrate the MRI parameters into a single image, termed the embedded image. This was achieved by mapping all pixel intensities from the higher dimension to a lower dimensional (embedded) space. For validation, the authors compared the hybrid NLDR with linear methods of principal component analysis (PCA) and multidimensional scaling (MDS) using synthetic data. For the clinical application, the authors used breast MRI data, comparison was performed using the postcontrast DCE MRI image and evaluating the congruence of the segmented lesions. Results: The NLDR-based hybrid approach was able to define and segment both synthetic and clinical data. In the synthetic data, the authors demonstrated the performance of the NLDR method compared with conventional linear DR methods. The NLDR approach enabled successful segmentation of the structures, whereas, in most cases, PCA and MDS failed. The NLDR approach was able to segment different breast tissue types with a high accuracy and the embedded image of the breast MRI data demonstrated fuzzy boundaries between the different types of breast tissue, i.e., fatty, glandular, and tissue with lesions (>86%). Conclusions: The proposed hybrid NLDR methods were able to segment clinical breast data with a high accuracy and construct an embedded image that visualized the contribution of different radiological parameters.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Mapping DNA polymerase errors by single-molecule sequencing

Genomic integrity is compromised by DNA polymerase replication errors, which occur in a sequence-dependent manner across the genome. Accurate and complete quantification of a DNA polymerase's error spectrum is challenging because errors are rare and difficult to detect. We report a high-throughput sequencing assay to map in vitro DNA replication errors at the single-molecule level. Unlike previous methods, our assay is able to rapidly detect a large number of polymerase errors at base resolution over any template substrate without quantification bias. To overcome the high error rate of high-throughput sequencing, our assay uses a barcoding strategy in which each replication product is tagged with a unique nucleotide sequence before amplification. Here, this allows multiple sequencing reads of the same product to be compared so that sequencing errors can be found and removed. We demonstrate the ability of our assay to characterize the average error rate, error hotspots and lesion bypass fidelity of several DNA polymerases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

A comprehensive investigation of the accuracy and reproducibility of a multitarget single isocenter VMAT radiosurgery technique

Purpose: Recent trends in stereotactic radiosurgery use multifocal volumetric modulated arc therapy (VMAT) plans to simultaneously treat several distinct targets. Conventional verification often involves low resolution measurements in a single plane, a cylinder, or intersecting planes of diodes or ion chambers. This work presents an investigation into the consistency and reproducibility of this new treatment technique using a comprehensive commissioned high-resolution 3D dosimetry system (PRESAGE{sup ®}/Optical-CT).Methods: A complex VMAT plan consisting of a single isocenter but five separate targets was created in Eclipse for a head phantom containing a cylindrical PRESAGE{sup ®} dosimetry insert of 11 cm diameter and height. The plan contained five VMAT arcs delivering target doses from 12 to 20 Gy. The treatment was delivered to four dosimeters positioned in the head phantom and repeated four times, yielding four separate 3D dosimetry verifications. Each delivery was completely independent and was given after image guided radiation therapy (IGRT) positioning using Brainlab ExacTrac and cone beam computed tomography. A final delivery was given to a modified insert containing a pin-point ion chamber enabling calibration of PRESAGE{sup ®} 3D data to dose. Dosimetric data were read out in an optical-CT scanner. Consistency and reproducibility of the treatment technique (including IGRT setup) was investigated by comparing the dose distributions in the four inserts, and with the predicted treatment planning system distribution.Results: Dose distributions from the four dosimeters were registered and analyzed to determine the mean and standard deviation at all points throughout the dosimeters. A dose standard deviation of <3% was found from dosimeter to dosimeter. Global 3D gamma maps show that the predicted and measured dose matched well [3D gamma passing rate was 98.0% (3%, 2 mm)].Conclusions: The deliveries of the irradiation were found to be consistent and matched the treatment plan, demonstrating high accuracy and reproducibility of both the treatment machine and the IGRT procedure. The complexity of the treatment (multiple arcs) and dosimetry (multiple strong gradients) pose a substantial challenge for comprehensive verification. 3D dosimetry can be uniquely effective in this scenario.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2021

Downscaled precipitation and mean air temperature datasets; East-Taylor subbasin; 2008-2019; daily temporal resolution; 400 m spatial resolution

This dataset provides gridded meteorological forcing data (specifically, daily precipitation and daily mean air temperature). The dataset has been generated by downscaling the Parameter-elevation Regressions on Independent Slopes Model (PRISM) dataset from a spatial resolution of 800 m to 400 m. The time period is 2008-2019, and the mapped area is East Taylor subbasin in Upper Colorado. The data are in the form of NetCDF files, arranged by year. Compared to the PRISM dataset, the dates of the downscaled dataset are shifted backwards by one (e.g., downscaled data for May 25 corresponds to PRISM data for May 26). This temporal shifting makes the meteorological forcing correspond more closely to the prescribed date. The NetCDF format is a standard raster format that can be read using any Geographic Information System (GIS) software; plenty of modules exist in popular scripting languages (such as Python, R and Matlab) that can also be used to read NetCDF files.East_Taylor_Tavg_PRISM400 corresponds to mean air temperature.East_Taylor_Precip_PRISM400.zip corresponds to precipitation.The proprietary PRISM data (800 m resolution) were purchased with funding from the Watershed Function Scientific Focus Area supported by U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under award no. DE-AC02-05CH11231.Dataset update on March 9, 2022:Uploaded new data files that are identical to the earlier files but are now in the NetCDF format, arranged by year. Earlier, the files were in the GeoTiff format, arranged by date.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

59 BASIC BIOLOGICAL SCIENCES↗
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↗
NASA NTRS1982

Familiarization with LANDSAT imagery

Learning objectives of the activities provided include: (1) reading the annotation of a LANDSAT image; (2) becoming acquainted with the characteristics of 1:1,000,000 scale transparencies and prints of MSS images; (3) noting the general information visible in LANDSAT photo products; (4) observing changes of appearance of any ground feature or class in the black and white images made from the four MSS bands and the characteristic color of each class in color composites; (5) determining the degree to which a LANDSAT image meets map accuracy standards and can be fitted to map projections; (6) assessing the effects of LANDSAT enlargements and scale changes and of the limitations of satellite resolution relative to aerial photos; (7) observing the influence of time of acquisition (season) on a scene; (8) getting a feel for image quality as dependent on processing and photoreproduction; (9) appreciating the characteristics of the RBV and thermal band imagery obtained from LANDSAT-3; and (10) becoming familiar with certain attributes of adjacent LANDSAT images which permit them to be joined in mosaics and to be viewed in stereo.

Source record↗
NASA NTRS2013

Master Console, SMC

The Master Console oversees the function of Computer Systems in Firing room 1 (FR1). Master Console Operators, MCOs' for short, are our customer. I was integrated into the System Monitoring and Control (SMC) software team that is under the guidance of David Slaiman, who is the product group lead. I have been brought up to speed with System Monitoring and Control. The initial time spent reading SMC software design description and understanding how it works. The current Firing Room 1 Console Display is a floor layout giving the MCO two essential pieces of information which are Health and Status. When an issue arises, the MCO has to look on the display to find which console is affected and then the MCO must use the Reference designator from the display to manually search for the Portal Workstation (PWS) installed in the console using the hardware map; which is a long process to lookup a PWS if an issue is present. My project is to make the FR1 Console Display easier for the MCO's to pinpoint PWS's without having to lookup additional resources in the process. My project also includes updating Firing Room 1 Console Display to include the F1R Non-Redundant Set. The display does not have good use of space and functionality. PWS numbers were not present in the previous design and are the critical component in efficient understanding and administration of the consoles. Part of the process includes getting feedback from the customer, instead of just emailing them with a question, we made a proposal with changes so they could respond and give us their input; which proved to be an effective method for engaging them. In order to do this I had to use the Display Editor (DE) tool developed by NASA, Paint.Net and Visio. The process I have been using has been Visio to alter the floor layout of Firing Room and take advantage of the white areas, and then I take the altered floor plan into Paint.Net. Once in Paint.Net I put the new floor plan as a background to the standard console display. Paint.Net also serves as a tool to create the new service state bars for the new background; finally I used the DE to assemble everything and setup the right CUI's for each PWS.

MCO↗
DOE OSTI2014

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data

We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS1982

User's manual for THPLOT, A FORTRAN 77 Computer program for time history plotting

A general purpose FORTRAN 77 computer program (THPLOT) for plotting time histories using Calcomp pen plotters is described. The program is designed to read a time history data file and to generate time history plots for selected time intervals and/or selected data channels. The capabilities of the program are described. The card input required to define the plotting operation is described and examples of card input and the resulting plotted output are given. The examples are followed by a description of the printed output, including both normal output and error messages. Lastly, implementation of the program is described. A complete listing of the program with reference maps produced by the CDC FTN 5.0 compiler is included.

Murray, J. E.↗
NASA NTRS1997

(abstract) Realization of a Faster, Cheaper, Better Mission and Its New Paradigm Star Tracker, the Advanced Stellar Compass

The first Danish satellite, rsted, will be launched in August of 1997. The scientific objective of sted is to perform a precision mapping of the Earth's magnetic field. Attitude data for the payload and the satellite are provided by the Advanced Stellar Compass (ASC) star tracker. The ASC consists of a CCD star camera and a capable microprocessor which operates by comparing the star image frames taken by the camera to its internal star catalogs.

ASC Advanced Stellar Compass Denmark CCD star cata↗