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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome

Cryptochromes are ubiquitous flavin-binding light sensors closely related to DNA-repairing photolyases. The animal-like cryptochrome CraCRY from the green alga Chlamydomonas reinhardtii challenges the paradigm of cryptochromes as pure blue-light receptors by acting as a (6-4) photolyase, using 8-hydroxy-5-deazaflavin (8-HDF) as a light-harvesting antenna with a 17.4 Å distance to flavin and showing spectral sensitivity up to 680 nm. The expanded action spectrum is attributed to the presence of the flavin neutral radical (FADH•) in the dark, despite a rapid FADH• decay observed in vitro in samples exclusively carrying flavin. Herein, the red-light response of CraCRY carrying flavin and 8-HDF was studied, revealing a 3-fold prolongation of the FADH• lifetime in the presence of 8-HDF. Millisecond time-resolved ultraviolet-visible spectroscopy showed the red-light-induced formation and decay of an absorbance band at 458 nm concomitant with flavin reduction. Time-resolved Fourier transform infrared (FTIR) spectroscopy and density functional theory attributed these changes to the deprotonation of 8-HDF, challenging the paradigm of 8-HDF being permanently deprotonated in photolyases. FTIR spectra showed changes in the hydrogen bonding network of asparagine 395, a residue suggested to indirectly control flavin protonation, indicating the involvement of N395 in the stabilization of FADH•. Fluorescence spectroscopy revealed a decrease in the energy transfer efficiency of 8-HDF upon flavin reduction, possibly linked to 8-HDF deprotonation. Finally, the discovery of the interdependence of flavin and 8-HDF beyond energy transfer processes highlights the essential role of the antenna, introducing a new concept enabling CraCRY and possibly other bifunctional cryptochromes to fulfill their dual function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

PHOTOMETRIC REDSHIFTS IN THE HAWAII-HUBBLE DEEP FIELD-NORTH (H-HDF-N)

We derive photometric redshifts (z {sub phot}) for sources in the entire (∼0.4 deg{sup 2}) Hawaii-Hubble Deep Field-North (H-HDF-N) field with the EAzY code, based on point-spread-function-matched photometry of 15 broad bands from the ultraviolet (U band) to mid-infrared (IRAC 4.5 μm). Our catalog consists of a total of 131,678 sources. We evaluate the z {sub phot} quality by comparing z {sub phot} with spectroscopic redshifts (z {sub spec}) when available, and find a value of normalized median absolute deviation σ{sub NMAD} = 0.029 and an outlier fraction of 5.5% (outliers are defined as sources having |z{sub phot} – z{sub spec} |/(1 + z{sub spec} ) > 0.15) for non-X-ray sources. More specifically, we obtain σ{sub NMAD} = 0.024 with 2.7% outliers for sources brighter than R = 23 mag, σ{sub NMAD} = 0.035 with 7.4% outliers for sources fainter than R = 23 mag, σ{sub NMAD} = 0.026 with 3.9% outliers for sources having z < 1, and σ{sub NMAD} = 0.034 with 9.0% outliers for sources having z > 1. Our z {sub phot} quality shows an overall improvement over an earlier z {sub phot} work that focused only on the central H-HDF-N area. We also classify each object as a star or galaxy through template spectral energy distribution fitting and complementary morphological parameterization, resulting in 4959 stars and 126,719 galaxies. Furthermore, we match our catalog with the 2 Ms Chandra Deep Field-North main X-ray catalog. For the 462 matched non-stellar X-ray sources (281 having z {sub spec}), we improve their z {sub phot} quality by adding three additional active galactic nucleus templates, achieving σ{sub NMAD} = 0.035 and an outlier fraction of 12.5%. We make our catalog publicly available presenting both photometry and z {sub phot}, and provide guidance on how to make use of our catalog.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Statistical analysis of the horizontal divergent flow in emerging solar active regions

Solar active regions (ARs) are thought to be formed by magnetic fields from the convection zone. Our flux emergence simulations revealed that a strong horizontal divergent flow (HDF) of unmagnetized plasma appears at the photosphere before the flux begins to emerge. In our earlier study, we analyzed HMI data for a single AR and confirmed presence of this precursor plasma flow in the actual Sun. In this paper, as an extension of our earlier study, we conducted a statistical analysis of the HDFs to further investigate their characteristics and better determine the properties. From SDO/HMI data, we picked up 23 flux emergence events over a period of 14 months, the total flux of which ranges from 10{sup 20} to 10{sup 22} Mx. Out of 23 selected events, 6 clear HDFs were detected by the method we developed in our earlier study, and 7 HDFs detected by visual inspection were added to this statistic analysis. We found that the duration of the HDF is on average 61 minutes and the maximum HDF speed is on average 3.1 km s{sup –1}. We also estimated the rising speed of the subsurface magnetic flux to be 0.6-1.4 km s{sup –1}. These values are highly consistent with our previous one-event analysis as well as our simulation results. The observation results lead us to the conclusion that the HDF is a rather common feature in the earliest phase of AR emergence. Moreover, our HDF analysis has the capability of determining the subsurface properties of emerging fields that cannot be directly measured.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Wettability of graphene-laminated micropillar structures

The wetting control of graphene is of great interest for electronic, mechanical, architectural, and bionic applications. In this study, the wettability of graphene-laminated micropillar structures was manipulated by changing the height of graphene-laminated structures and employing the trichlorosilane (HDF-S)-based self-assembly monolayer. Graphene-laminated micropillar structures with HDF-S exhibited higher hydrophobicity (contact angle of 129.5°) than pristine graphene thin film (78.8°), pristine graphene-laminated micropillar structures (97.5°), and HDF-S self-assembled graphene thin film (98.5°). Wetting states of the graphene-laminated micropillar structure with HDF-S was also examined by using a urea solution, which flowed across the surface without leaving any residues.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Antiaging activity, molecular docking, and prediction of percutaneous absorption parameters of quinoline–hydrazone hybrids

The application of antiaging agents can contribute to the prevention and control of skin photoaging. In the current research, nine quinoline–hydrazone hybrids were synthesized to obtain biologically active compounds as possible antiaging agents. The compounds were tested through a comprehensive in vitro evaluation of antielastase, anticollagenase, and antihyaluronidase activities along with the determination of their potential to quench reactive oxygen species (ROS) by the ORAC method. The selected hybrids were subsequently tested on human dermal fibroblasts (HDF) to reveal possible UVB photoprotective activity. The most potent antiaging protection of all the prepared compounds was shown by the trihydroxylated quinoline–hydrazones 5 and 9, which showed the best collagenase inhibition (IC{sub 50} = 39.4 and 45.6 µM, respectively). Compound 5 also showed activity against elastase and hyaluronidase (IC{sub 50} = 164.2 and 318.8 µM, respectively). The molecular docking results suggest that the difference of inhibition between 5 and 9 is principally attributed to the hydrogen bonds interactions in the residues His218 and His228, and Zn atom in collagenase, Val216 in elastase and Tyr75 in hyaluronidase. In addition, compounds 5 and 9 were able to significantly protect human skin cells from UVB radiation in vitro. These compounds significantly decreased UVB-induced MMP-1 and ROS production and inhibited the suppression of type I procollagen synthesis in cultured HDF. The in silico dermatopharmacokinetic parameters showed promising results. Therefore, our study presented promising results for antiaging drug discovery, focusing on quinoline–hydrazone hybrids as dual inhibitors of skin aging-related enzymes, antioxidants, and inhibitors of the biological effects of UVB irradiation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Wound healing potential of adipose tissue stem cell extract

Adipose tissue stem cells (ATSCs) are considered as a promising source in the field of cell therapy and regenerative medicine. In addition to direct cell replacement using stem cells, intercellular molecule exchange by stem cell secretory factors showed beneficial effects by reducing tissue damage and augmentation of endogenous repair. Delayed cutaneous wound healing is implicated in many conditions such as diabetes, aging, stress and alcohol consumption. However, the effects of cell-free extract of ATSCs (ATSC-Ex) containing secretome on wound healing process have not been investigated. In this study, ATSC-Ex was topically applied on the cutaneous wound and healing speed was examined. As a result, wound closure was much faster in the cell-free extract treated wound than control wound at 4, 6, 8 days after application of ATSC-Ex. Dermal fibroblast proliferation, migration and extracellular matrix (ECM) production are critical aspects of wound healing, and the effects of ATSC-Ex on human dermal fibroblast (HDF) was examined. ATSC-Ex augmented HDF proliferation in a dose-dependent manner and migration ability was enhanced by extract treatment. Representative ECM proteins, collagen type I and matrix metalloproteinase-1, are significantly up-regulated by treatment of ATSC-Ex. Our results suggest that the ATSC-Ex have improving effect of wound healing and can be the potential therapeutic candidate for cutaneous wound healing. - Highlights: • Topical application of ATSC-Ex results in faster wound closure than normal wound in vivo. • ATSC-Ex enhances dermal fibroblast proliferation, migration and extracellular matrix production. • This study suggests that ATSC-Ex is an effective source to augment wound healing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Performance characterization of irregular I/O at the extreme scale

Here, this paper reports our experience with irregular I/O and describes lessons learned when running applications with such I/O on supercomputers at the extreme scale. Specifically, we study how irregularities in I/O patterns (i.e., irregular amount of data written per process at each I/O step) in scientific simulations can cause increasing I/O times and substantial loss in scalability. To this end, we quantify the impact of irregular I/O patterns on the I/O performance of scientific applications at the extreme scale by statistically modeling the irregular I/O behavior of two scientific applications: the Monte Carlo application QMCPack and the adaptive mesh refinement application ENZO. For our testing, we feed our model into I/O kernels of two well-known I/O data models (i.e., ADIOS and HDF) to measure the performance of the two applications’ I/O under different I/O settings. Empirically, we show how the growing data sizes and the irregular I/O patterns in these applications are both relevant factors impacting performance.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Quick n Dirty

QnD is a pure Python package for working with binary files. It has built-in support for HDF5, NetCDF3, and PDB formats. It provides a Pythonic, dict-like interface, and allows easy movement among time-like "records". Both reading and writing are enabled. The HDF and NetCDF capabilities rely on external libraries, while the PDB support is part of QnD itself and entirely in Python. QnD works under Python 2 and 3. For interactive use, much less typing is involved than for some other packages.

MUNRO, DavidH.↗
DOE OSTI2022

Advanced Terrestrial Simulator (ATS) evaluation dataset at 7 catchments across the continental United States

This dataset comprises of the input files and other files required for Advanced Terrestrial Simulator (ATS) simulations at 7 catchments across the continental United States. ATS is an integrated surface-subsurface hydrology model. We include Jupyter notebooks (within scripts folder) for individual catchments showing information (including data sources, river network, soil, geology, landuse types etc.) on preparing the machine readable input files. ATS observation output files are provided in the output folder. Figures and analyses (.xlsx sheets) are also provided. The catchments include, Taylor River Upstream (Colorado); (b) Cossatot River (Arkansas); (c) Panther Creek (Alabama); (d) Little Tennessee River (North Carolina and Georgia); (e) Mayo River (Virginia); (f) Flat Brook (New Jersey); (g) Neversink River headwaters (New York). Readme files are provided inside the directories providing more details. Files types include: .xml, .h5, .xlsx, .png, .ipynb, .py, .nc, .txt. All of the files types can be accessed by open source software, details on software requirements are following: .xml (any text editors including notepad and textedit), .h5 (in python using hdf libraries), .xlsx (WPS Office Spreadsheets, OpenOffice Calc, LibreOffice Calc, Microsoft Office etc.), .png (any image viewer), .ipynb (Jupyter notebook), .py (any text editors including notepad and textedit), .nc (using python or other open source software).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Fiber Optic Distributed Acoustic Sensing in DFPS East Well

Fiber optic files in *.hdf format, acquired in the Devine Fracture Pilot Site East well, using Fotech interrogator. There was no change in channel spacing or acquisition settings during the project. Channel spacing is 0.68 m.

Electrically active proppant,Electromagnetic,Fiber↗
DOE OSTI2024

Delta-Rice: A HDF5 Compression Plugin optimized for Digitized Detector Data

Delta-Rice is an HDF5 (The HDF Group et al., 2020) filter plugin that was developed to compress digitized detector signals recorded by the Nab experiment (Fry et al., 2019), a fundamental neutron physics experiment. This is a two-step process where incoming data is passed through a pre-processing filter and then compressed with Rice coding. A routine for determining the optimal pre-processing filter for a dataset is provided along with an example GPU deployment. When applied to data collected by the Nab data acquisition system, this method produced output files 29% their initial size, and was able to do so with an average read/write throughput in excess of 2 GB/s on a single CPU. Compared to the widely used Gzip compression routine, Delta-Rice reduces the file size by 33% more with over an order of magnitude increase in read/write throughput. Delta-Rice is available on CPU to users through the HDF5 library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Damsel: A Data Model Storage Library for Exascale Science

Computational science applications have been described as having one of seven motifs (the “seven dwarfs”), each having a particular pattern of computation and communication. From a storage and I/O perspective, these applications can also be grouped into a number of data model motifs describing the way data is organized and accessed during simulation, analysis, and visualization. Major storage data models developed in the 1990s, such as Network Common Data Format (netCDF) and Hierarchical Data Format (HDF) projects, created support for more complex data models. Development of both netCDF and HDF5 was influenced by multi-dimensional dataset storage requirements, but their access models and formats were designed with sequential storage in mind (e.g., a POSIX I/O model). Although these and other high-level I/O libraries have had a beneficial impact on large parallel applications, they do not always attain a high percentage of peak I/O performance due to fundamental design limitations, and they do not address the full range of current and future computational science data models. The goal of this project is to enable exascale computational science applications to interact conveniently and efficiently with storage through abstractions that match their data models. The project consists of three major activities: (1) identifying major data model motifs in computational science applications and developing representative benchmarks; (2) developing a data model storage library, called Damsel, that supports these motifs, provides efficient storage data layouts, incorporates optimizations to enable exascale operation, and is tolerant to failures; and (3) productizing Damsel and working with computational scientists to encourage adoption of this library by the scientific community. The product of this project, Damsel library, is openly available for download from http://cucis.ece.northwestern.edu/projects/DAMSEL. Several case studies and application programming interface reference are also available to assist new users to learn to use the library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

VERAIO Software Management Plan

VERAIO is a set of utility codes used to provide a common set of input and outputs to the Virtual Environment for Reactor Applications (VERA). VERA is a collection of several different computer codes that all have a common input and output. This prevents the need to manage input and output from each individual code, allowing for ease of use and reducing errors associated with code operability. The VERAIO utilities include VERAIn, VERAView, and VERARun. Each of these utilities is described below. VERAIn is an input processor that reads an ASCII input file generated by users, parses the file, performs some error checking, and writes an XML file to be read by other VERA codes. The main purpose of VERAIn is to provide a common input to all of the VERA codes so users only need to learn one input. VERAIn is written in Perl and uses YAML configuration files to provide flexibility. VERAView is a graphical user interface (GUI) that reads a VERA HDF output file and allows users to visualize results. VERAView is written in Python. VERARun is a script that drives the VERA execution in a high performance computing (HPC) environment. Work performed at the code level supports the Quality Assurance Program Plan (QAPP) (VERA-QA-001), and VERA Software Quality Assurance Plan (VERA-QA-002).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

VERAIO Software Management Plan

VERAIO is a set of utility codes used to provide a common set of inputs and outputs to the Virtual Environment for Reactor Applications (VERA). VERA is a collection of several different computer codes that all have a common input and output. This prevents the need to manage input and output from each individual code, allowing for ease of use and reducing errors associated with code operability. The VERAIO utilities include VERAIn, VERAView, and VERARun. Each of these utilities is described below. VERAIn is an input processor that reads an ASCII input file generated by users, parses the file, performs some error checking, and writes an XML file to be read by other VERA codes. The main purpose of VERAIn is to provide a common input to all of the VERA codes, so users only need to learn one input. VERAIn is written in Perl and uses YAML configuration files to provide flexibility. VERAView is a graphical user interface (GUI) that reads a VERA hierarchical data format (HDF) output file and allows users to visualize results. VERAView is written in Python. VERARun is a script that drives the VERA execution in a high performance computing (HPC) environment. Work performed at the code level supports the quality assurance program plan (QAPP) (VERA-QA-001) and the VERA Software Quality Assurance Plan (VERA-QA-002).

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Restart File Improvements for MPACT

This report documents the work performed to address several defects and features request related to the restart capability in MPACT. The following defects were fixed as a part of this milestone: • #3616 (Defect) Error in MPACT Restart Files with BPRs, • #3637 (Defect) Restart with Semi-PC Yields Inconsistent Results, • #3652 (Defect) Fix Incorrect Exposure Value on HDF File After Restart, • #3777 (Defect) Fix State Point Number when Using Restart File, • #3986 (Defect) Pin Exposures are Incorrect, • #4106 (Defect) Pin Exposures Equal to Zero After Restart, and • #4288 (Defect) Core Average Exposure Wrong when Reading Restart Files. The new features that were added are: • Axial Re-meshing capability, • Incorporation of MAMBA-1D data necessary to restart coupled MPACT/CTF/MAMBA calculations, and • Addition of state variables to the restart file. Numerous tests were also implemented to verify and protect these features and this report was prepared to document the work performed.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2014

VERAOUT - VERA HDF5 Output Specification (Revision 1)

This document describes the revised specification (Revision 1) for the format of the common VERA Output file (VERAOUT). VERAOUT is a binary HDF5 file that all of the physics codes in VERA-CS produce. Having all physics codes write to a single file simplifies post-processing and data comparison. The edits and format written to the VERAOUT file is described below. This specification covers common scalar and array data typically produced by neutronic and fuel performance codes. This document will be periodically revised to add additional data as more physics codes and/or more data is added to VERA-CS. A version number is written to the HDF file to keep track of different versions of the VERAOUT so that backwards compatibility may be maintained. A sample VERAOUT reader has been written to serve as an example for users wishing to do data postprocessing. Information on this program is included below.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Deep CO(1–0) Observations of z = 1.62 Cluster Galaxies with Substantial Molecular Gas Reservoirs and Normal Star Formation Efficiencies

We present an extremely deep CO(1–0) observation of a confirmed z = 1.62 galaxy cluster. We detect two spectroscopically confirmed cluster members in CO(1–0) with signal-to-noise ratio >5. Both galaxies have log(M{sub ⋆}/M{sub ⊙}) > 11 and are gas rich, with M{sub mol}/(M{sub ⋆}+M{sub mol}) ∼ 0.17–0.45. One of these galaxies lies on the star formation rate (SFR)–M{sub ⋆} sequence, while the other lies an order of magnitude below. We compare the cluster galaxies to other SFR-selected galaxies with CO measurements and find that they have CO luminosities consistent with expectations given their infrared luminosities. We also find that they have gas fractions and star formation efficiencies (SFE) comparable to what is expected from published field galaxy scaling relations. The galaxies are compact in their stellar light distribution, at the extreme end for all high-redshift star-forming galaxies. However, their SFE is consistent with other field galaxies at comparable compactness. This is similar to two other sources selected in a blind CO survey of the HDF-N. Despite living in a highly quenched protocluster core, the molecular gas properties of these two galaxies, one of which may be in the process of quenching, appear entirely consistent with field scaling relations between the molecular gas content, stellar mass, star formation rate, and redshift. We speculate that these cluster galaxies cannot have any further substantive gas accretion if they are to become members of the dominant passive population in z<1 clusters.

79 ASTRONOMY AND ASTROPHYSICS↗