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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
NASA NTRSDate not supplied

Enabling Biological Discovery Through Biospecimen Sharing: The Nasa Biological Institutional Scientific Collection

Understanding biological impacts from spaceflight hazards and the subsequent development of countermeasures are a high priority to enable humanity to venture back to the Moon, and then to Mars and beyond. Experiments have been conducted with model organisms flown to space and analogous investigations terrestrially, to identify biological mechanistic impacts from spaceflight hazards and to develop mitigation countermeasures, thus contributing towards basic and applied science goals. However, sending organisms into space is a costly endeavor. To maximize scientific return, all biospecimens not required by spaceflight-relevant Principal Investigators are harvested, preserved, and archived in the NASA Biological Institutional Scientific Collection (NBISC). Biospecimens are collected and preserved according to well-established standard operating procedures to maintain scientific quality and are available on-request by the international scientific community. NBISC currently stores over 32,000 biospecimens from Shuttle, International Space Station, and ground-based space analog investigations. Tissue sharing has resulted in at least 33 publications since 2011 and 51 requests since 2016. Many requests for NBISC biospecimens come from first-time investigators who subsequently submit grants as their point-of-entry into the field of spaceflight biology and health. The NBISC biorepository is part of the NASA ‘Open Science for Life in Space’ collaborative group of projects, which includes NASA Genelab, the Space Biology Program’s Biospecimen Sharing Program, Physical Sciences Informatics, and the Ames Life Sciences Data Archive. NBISC biospecimens have been awarded to NASA Genelab, who then generated various open access science ‘omics datasets through the GeneLab Sample Processing laboratory, with resulting data widely used for biological study. Other NBISC biospecimen awards have led to studies on fecal microbiome analysis, DNA damage analysis using single-cell DNA sequencing, enzymatic-pathway identification involved in spaceflight muscle atrophy, and characterization of ocular morphological changes. Of note, NBISC is expanded to include a new Space Microbial Culture Collection (SMCC) for the collection, identification, documentation, long-term preservation, and distribution of space-related microbial isolates.

Biospecimens↗
NASA NTRSDate not supplied

Metadata Entry Optimization for NASA's Biological Institutional Scientific Collection (NBISC)

The NASA Biological Institutional Sample Collection (NBISC) at NASA’s Ames Research Center is a critical resource housing non-human samples collected from spaceflight missions and ground analog studies, primarily consisting of specimens from rats, mice, and select microbes. The primary objective of NBISC is to systematically receive, document, preserve, and facilitate access to these samples for the global scientific community. NBISC promotes international collaboration and maximizes the return on investment for precious tissues from spaceflight and analog experiments. Researchers can request physical samples through an online request form and subsequent written proposal review process. This study addresses two core research objectives: streamlining the NBISC sample lifecycle processes and strategizing for managing an influx of 50,000 tissue samples from a series of cosmic radiation analog experiments carried out at the NASA Space Radiation Laboratory (NSRL) by Drs. Eleanor Chang (Lawrence Berkeley Laboratory) and Polly Blakely (SRI). The Chang/Blakely studies investigated Harderian gland (HG) tumorigenesis in mice exposed to low dose and LET radiation comprising 8 different exposure protocols in over 4000 mice. NBISC sample metadata is stored in a Laboratory Information Management System (SLIMS). To streamline sample data entry, we customize python scripts using information extracted from the individual experimental protocols. The scripts automate entry into multiple SLIMS data fields including protocol name, unique sample barcode, tissue and sub-tissue information, freezer location, sample preservation method, etc. The semi-automated procedure significantly decreases the time spent on data entry by several orders of magnitude. Automation and data organization are essential, as they free up time for curation and promotion of the collection which, in turn, increase the accessibility of samples to the broader research community. NBISC benefits from streamlined data ingestion, and the methodologies developed here are applicable to other projects which use SLIMS including the NASA Biospecimen Sharing Program and GeneLab. As of Fall 2023, plans include transferring sample data from SLIMS to public facing repositories (OSDR and NLSP), expanding the reach of the Chang/Blakely sample collection. The Human Research Program Space Radiation Element plans to transfer non-human tissues from many more investigations to NBISC in the coming year.

Sample Repository↗
NASA NTRSDate not supplied

Metadata Entry Optimization For NASA's Biological Institutional Scientific Collection (NBISC)

The NASA Biological Institutional Sample Collection (NBISC) at NASA’s Ames Research Center is a critical resource housing non-human samples collected from spaceflight missions and ground analog studies, primarily consisting of specimens from rats, mice, and select microbes. The primary objective of NBISC is to systematically receive, document, preserve, and facilitate access to these samples for the global scientific community. NBISC promotes international collaboration and maximizes the return on investment for precious tissues from spaceflight and analog experiments. Researchers can request physical samples through an online request form and subsequent written proposal review process. This study addresses two core research objectives: streamlining the NBISC sample lifecycle processes and strategizing for managing an influx of 50,000 tissue samples from a series of cosmic radiation analog experiments carried out at the NASA Space Radiation Laboratory (NSRL) by Drs. Eleanor Chang (Lawrence Berkeley Laboratory) and Polly Blakely (SRI). The Chang/Blakely studies investigated Harderian gland (HG) tumorigenesis in mice exposed to low dose and LET radiation comprising 8 different exposure protocols in over 4000 mice. NBISC sample metadata is stored in a Laboratory Information Management System (SLIMS). To streamline sample data entry, we customize python scripts using information extracted from the individual experimental protocols. The scripts automate entry into multiple SLIMS data fields including protocol name, unique sample barcode, tissue and sub-tissue information, freezer location, sample preservation method, etc. The semi-automated procedure significantly decreases the time spent on data entry by several orders of magnitude. Automation and data organization are essential, as they free up time for curation and promotion of the collection which, in turn, increase the accessibility of samples to the broader research community. NBISC benefits from streamlined data ingestion, and the methodologies developed here are applicable to other projects which use SLIMS including the NASA Biospecimen Sharing Program and GeneLab. As of Fall 2023, plans include transferring sample data from SLIMS to public facing repositories (OSDR and NLSP), expanding the reach of the Chang/Blakely sample collection. The Human Research Program Space Radiation Element plans to transfer non-human tissues from many more investigations to NBISC in the coming year.

Biospecimen↗
NASA NTRSDate not supplied

Real Time Nitrogen Monitoring and Quality Control System for NASA Astromaterials Collection

The Nitrogen system is a vital utility supporting the curation office within NASA's Astromaterials Re-search and Exploration Science (ARES) Division at the Johnson Space center (JSC). Since the Apollo samples were returned in 1969. It has played an essential role in preserving NASA’s astromaterial collections (now nine collections) by maintaining contamination-free, controlled environments required for long term curation and advanced scientific research. To meet the stringent purity requirements for contamination control, high purity modified Grade C Liquid Nitrogen (LN2) is delivered weekly by an industrial gas vendor to a 15,000-gallon tank located outside at NASA JSC near the ARES facility. This nitrogen is vital for creating an inert atmosphere to store the collection in, ensuring they are continuously shielded from contaminants and alterations through a constant N2purge. For most of the past 65 years deliveries of LN2 have required a CoA (Certificate of Analysis) prior to delivery. If those were not available, then LN2 deliver were sent to third-party laboratories for verification, creating an operational bottleneck and quality gap. To address this challenge and maintain rigorous quality control, NASA JSC Infrastructure and Astromaterials Acquisition & Curation Office initiated the development of an on-site Analytical Gas Sampling (AGS) Laboratory. Designed to streamline quality verification if a CoA unavailable, the AGS lab was constructed by a subcontractor in Newton, NJ. After a successful factory acceptance test conducted by the NASA ARES Infrastructure team, the lab was trans-ported to NASA JSC, where it was anchored and integrated into the site’s nitrogen pressure system using stainless steel, oxygen-cleaned tubing. The ARES nitrogen system was modified to provide parallel flows to the AGS lab for quality control and to the astromaterials collection labs for maintaining an inert environment. The AGS lab features two operational modes: (1)Primary: Gaseous Nitrogen (GN2) Quality Monitoring –The AGS system continuously samples the site’s GN2 supply every 15 minutes to ensure compliance with required purity levels. (2) Secondary: LN2 Quality Verification when a comprehensive CoA is not available, a cryogenic vaporizer converts LN2 to GN2, which is then analyzed for impurities: H₂, Ar, O₂, CO, CO₂, H₂O, and total hydrocarbons (THC). By significantly enhancing on-site analytical capabilities, the AGS lab eliminates reliance on external testing, ensures uninterrupted quality monitoring of the nitrogen pressure system, and reinforces NASA’s commitment to preserving pristine astromaterials under the highest standards of curation and research integrity.

glove box↗
DOE OSTI2021

Performing optimized collective operations in a irregular subcommunicator of compute nodes in a parallel computer

In a parallel computer, performing optimized collective operations in an irregular subcommunicator of compute nodes may be carried out by: identifying, within the irregular subcommunicator, regular neighborhoods of compute nodes; selecting, for each neighborhood from the compute nodes of the neighborhood, a local root node; assigning each local root node to a node of a neighborhood-wide tree topology; mapping, for each neighborhood, the compute nodes of the neighborhood to a local tree topology having, at its root, the local root node of the neighborhood; and performing a one way, rooted collective operation within the subcommunicator including: performing, in one phase, the collective operation within each neighborhood; and performing, in another phase, the collective operation amongst the local root nodes.

Davis, Kristan Suzanne D.↗
DOE OSTI2023

Phonon-induced collective modes in spin-orbit coupled polar metals

We study the interplay between collective electronic and lattice modes in polar metals in an applied magnetic field aligned with the polar axis. Static spin-orbit coupling leads to the appearance of a particle-hole spin-flip continuum that is gapped at low energies in a finite field. We find that a weak spin-orbit assisted coupling between electrons and polar phonons induces the emergence of electronic collective modes. The strength of the applied magnetic field tunes the number of modes and their energies, which can lie both above and below the particle-hole continuum. For a range of field values, we identify Fano-type interference between the electronic continuum and phonons. Here, we show that signatures of these collective modes can be observed in optical spectroscopy experiments, and we provide the corresponding theoretical predictions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Bulk Photovoltaic Effect Driven by Collective Excitations in a Correlated Insulator

We investigate the bulk photovoltaic effect, which rectifies light into electric current, in a collective quantum state with correlation driven electronic ferroelectricity. We show via explicit real-time dynamical calculations that the effect of the applied electric field on the electronic order parameter leads to a strong enhancement of the bulk photovoltaic effect relative to the values obtained in a conventional insulator. The enhancements include both resonant enhancements at sub-band-gap frequencies, arising from excitation of optically active collective modes, and broadband enhancements arising from nonresonant deformations of the electronic order. The deformable electronic order parameter produces an injection current contribution to the bulk photovoltaic effect that is entirely absent in a rigid-band approximation to a time-reversal symmetric material. Furthermore, our findings establish that correlation effects can lead to the bulk photovoltaic effect and demonstrate that the collective behavior of ordered states can yield large nonlinear optical responses.

14 SOLAR ENERGY↗
DOE OSTI2023

Strange hadron collectivity in pPb and PbPb collisions

The collective behavior of K$_{S}^{0}$ and $Λ/ \overline{Λ}$ strange hadrons is studied by measuring the elliptic azimuthal anisotropy ($\mathcal{v}$ 2 ) using the scalar-product and multiparticle correlation methods. Proton-lead (pPb) collisions at a nucleon-nucleon center-of-mass energy $\sqrt{s_{NN}}$ = 8.16 TeV and lead-lead (PbPb) collisions at $\sqrt{s_{NN}}$ = 5.02 TeV collected by the CMS experiment at the LHC are investigated. Nonflow effects in the pPb collisions are studied by using a subevent cumulant analysis and by excluding events where a jet with transverse momentum greater than 20 GeV is present. The strange hadron $\mathcal{v}$ 2 values extracted in pPb collisions via the four- and six-particle correlation method are found to be nearly identical, suggesting the collective behavior. Comparisons of the pPb and PbPb results for both strange hadrons and charged particles illustrate how event-by-event flow fluctuations depend on the system size.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Quasi-optical beam tracing module development for millimeter-wave high-wavenumber collective scattering on the NSTX-U and EAST tokamaks

A Python3-based beam tracing code utilizing Quasi-Optics has been developed to track both incident and receiving beams in high-k collective millimeter wave scattering systems within magnetic fusion plasmas. In contrast to existing ray tracing codes that solely consider refraction, this beam tracing code incorporates diffraction phenomena, providing a more comprehensive calculation. Here, this enhanced capability allows for a more accurate calculation of the scattering volume and spatial resolution in high-k collective scattering systems, crucial for evaluating system performance and facilitating data analysis. Unlike Geometrical Optics, Quasi-Optics employs the complex eikonal method, representing a Gaussian beam as a collection of coupled rays to accurately preserve diffraction characteristics. The developed code is intended for application in NSTX-Upgrade and EAST high-k beam tracing analyses, targeting frequencies of 693 GHz and 270 GHz, respectively. The high-k system's primary objective is the observation of electron-scale instabilities. Employing a symplectic integrator, the code ensures numerical accuracy, assessed through the conservation of the Hamiltonian. With its precision and efficiency, the code facilitates rapid inter-shot analyses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

The nanoscale distribution of copper and its influence on charge collection in CdTe solar cells

For decades, Cu has been the primary dopant in CdTe photovoltaic absorbers. Typically, Cu acceptor concentrations in these devices are on the order of 1 1014 cm-3, which has made it notoriously difficult to directly correlate nanoscale Cu distributions to the local charge transport properties of these devices. To measure and correlate these properties, measurement techniques require high sensitivity to elemental concentration, large penetration depth, and operando compatibility. Techniques such as secondary-ion mass spectroscopy and X-ray energy dispersive spectroscopy are widely adopted to measure Cu concentrations, but they are limited by penetration depth, sensitivity, or spatial resolution. Additionally, they lack the operando capabilities required to correlate one-to-one Cu concentrations to electrical performance. In this work, correlative X-ray microscopy is used to investigate the spatial distribution of Cu and its impact on charge collection through the depth and breadth of CdTe photovoltaic devices. Plan-view, nanoscale X-ray fluorescence maps clearly demonstrate the spatial segregation of copper around regions thought to be CdTe grain boundaries. Complementary cross-section imaging unveils the transition of the maximum charge-collection efficiency from the ZnTe-CdTe interface to the CdS-CdTe interface as a function of Cu incorporation. The copper concentration through the depth of the CdTe layer is characterized by slow and fast diffusion components, and cross-section charge-transport modeling shows that the experimentally obtained charge collection can be explained by the modeled acceptor distribution through the depth of the CdTe layer.

14 SOLAR ENERGY↗
DOE OSTI2020

Charge collection study with the ATLAS ITk prototype silicon strip sensors ATLAS17LS

The inner tracker of the ATLAS detector is scheduled to be replaced by a completely new silicon-based inner tracker (ITk) for the Phase-II of the CERN LHC (HL-LHC). The silicon strip detector covers the volume 40 < R < 100 cm in the radial and | z | < 300 cm in the longitudinal directions. The silicon sensors for the detector will be fabricated using the n + -on-p 6-inch wafer technology, for a total of 22,000 wafers. Here, intensive studies were carried out on the final prototype sensors ATLAS17LS fabricated by Hamamatsu Photonics (HPK). The charge collection properties were examined using penetrating 90 Sr β -rays and the ALIBAVA fast readout system for the miniature sensors of 1 cm × 1 cm in area. The samples were irradiated by protons in the 27 MeV Birmingham Cyclotron, the 70 MeV CYRIC at Tohoku University, and the 24 GeV CERN-PS, and by neutrons at Ljubljana TRIGA reactor for fluence values up to 2 × 10 15 n eq /cm 2 . The change in the charge collection with fluence was found to be similar to the previous prototype ATLAS12, and acceptable for the ITk. Sensors with two active thicknesses, 300 μ m (standard) and 240 μ m (thin), were compared and the difference in the charge collection was observed to be small for bias voltages up to 500 V. Some samples were also irradiated with gamma radiation up to 2 MGy, and the full depletion voltage was found to decrease with the dose. This was caused by the Compton electrons due to the 60 Co gamma radiation. To summarize, the design of the ATLAS17LS and technology for its fabrication have been verified for implementation in the ITk. We are in the stage of sensor pre-production with the first sensors already delivered in January of 2020.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Azobenzene-based sinusoidal surface topography drives focal adhesion confinement and guides collective migration of epithelial cells

Surface topography is a key parameter in regulating the morphology and behavior of single cells. At multicellular level, coordinated cell displacements drive many biological events such as embryonic morphogenesis. However, the effect of surface topography on collective migration of epithelium has not been studied in detail. Mastering the connection between surface features and collective cellular behaviour is highly important for novel approaches in tissue engineering and repair. Herein, we used photopatterned microtopographies on azobenzene-containing materials and showed that smooth topographical cues with proper period and orientation can efficiently orchestrate cell alignment in growing epithelium. Furthermore, the experimental system allowed us to investigate how the orientation of the topographical features can alter the speed of wound closure in vitro. Our findings indicate that the extracellular microenvironment topography coordinates their focal adhesion distribution and alignment. These topographic cues are able to guide the collective migration of multicellular systems, even when cell–cell junctions are disrupted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Unexpected Rise in Nuclear Collectivity from Short-Range Physics

We discover a surprising relation between the collective motion of nucleons within atomic nuclei, traditionally understood to be driven by long-range correlations, and short-range nucleon-nucleon interactions. Specifically, we find that quadrupole collectivity in low-lying states of 6 Li and 12 C, calculated with state-of-the-art ab initio techniques, is significantly influenced by two opposing 𝑆-wave contact couplings that subtly alter the surface oscillations of one largely deformed nuclear shape, without changing that shape’s overall contribution within the nucleus. The results offer new insights into the nature of emergent nuclear collectivity and its link to the underlying nucleon-nucleon interaction at short distances.

Ab initio calculations↗
DOE OSTI2021

Lattice collective modes from a continuum model of magic-angle twisted bilayer graphene

Here, we show that the insulating states of magic-angle twisted bilayer graphene support a series of collective modes corresponding to local particle-hole excitations on triangular lattice sites. Our theory is based on a continuum model of the magic angle flat bands. When the system is insulating at moiré band filling ν = -3, our calculations show that the ground state supports seven low-energy modes that lie well below the charge gap throughout the moiré Brillouin zone, one of which couples strongly to THz photons. The low-energy collective modes are faithfully described by a model with a local SU(8) degree of freedom in each moiré unit cell that we identify as the direct product of spin, valley, and an orbital pseudospin. Apart from spin and valley-wave modes, the collective mode spectrum includes a low-energy intraflavor exciton mode associated with transitions between flat valence and conduction band orbitals.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Nanosecond isomers and the evolution of collectivity in stable, even- A Hg isotopes

Isomeric states and associated collective structures have been studied up to high spin in 198,200,202 Hg using multinucleon transfer reactions and the Gammasphere array. A coupled rotational band, with possible four-quasiparticle character, is established in 198 Hg. Sequences built on two-quasiparticle, positive- and negative-parity levels are assigned to 202 Hg. New isomers in 202 Hg with I π = (7 – ) and (9 – ), and T 1/2 = 10.4(4) ns and 1.4(3) ns, respectively, have been identified. A half-life of 1.0(3) ns is established for the I π = 12 + state in 200 Hg. B(E2) values deduced from isomeric transitions in Hg isotopes indicate that, while collectivity near the ground state gradually diminishes from N = 112 to N = 124, it is found to increase for the 12 + and 9 – states up to N = 118, followed by a reduction for higher neutron numbers. Calculations using the ultimate cranker code provide insight into the variation of deformation with spin and allow for an understanding of observed band crossings. As a result, the evolution of collectivity with spin, and along the isotopic chain, is described.

190 ≤ A ≤ 219↗
DOE OSTI2022

Investigation of octupole collectivity near the A = 72 shape-transitional point

Enhanced octupole collectivity is expected in the neutron-deficient Ge, Se and Kr isotopes with neutron number N ≈ 40 and has indeed been observed for 70,72 Ge. Shape coexistence and configuration mixing are, however, a notorious challenge for theoretical models trying to reliably predict octupole collectivity in this mass region, which is known to feature rapid shape changes with changing nucleon number and spin of the system. To further investigate the microscopic configurations causing the prolate-oblate-triaxial shape transition at A ≈ 72 and their influence on octupole collectivity, the rare isotopes 72 Se and 74,76 Kr were studied via inelastic proton scattering in inverse kinematics. While significantly enhanced octupole strength of ≈32 Weisskopf units (W.u.) was observed for 72 Se, only strengths of ≈15 W.u. were observed for 74,76 Kr. In combination with existing data, the new data clearly question a simple origin of enhanced octupole strengths around N = 40. Furthermore, the present work establishes two regions of distinct octupole strengths with a sudden strength increase around the A = 72 shape transitional point.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Fourier coefficients of noninterdependent collective motions in heavy-ion collisions

Here, we present a scenario in heavy-ion collisions where different modes of collective motions are noninterdependent, driven by factorized actions in the created nuclear medium. Such physics mechanisms could each dominate at a distinct evolution stage, or coexist simultaneously. If the probability of particle emission is modulated by each nondependent collective motion with a single-harmonic Fourier expansion, the particle azimuthal distribution should be the product of all these expansions. Consequently, nonleading cross terms between collectivity modes appear, and their contributions to experimental observables could be significant. In particular, we argue that the chiral magnetic effect (CME) and elliptic flow can develop separately, with their convolution affecting the observable that is sensitive to the shear-induced CME. We will use the event-by-event anomalous-viscous fluid dynamics model to illustrate the effects of this scenario. Besides giving insights into searches for the CME, we also propose feasible experimental tests based on conventional flow harmonics, and demonstrate the emergence of nonleading cross terms with a multiphase transport model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Improving MPI Collective I/O for High Volume Non-Contiguous Requests With Intra-Node Aggregation

Two-phase I/O is a well-known strategy for implementing collective MPI-IO functions. It redistributes I/O requests among the calling processes into a form that minimizes the file access costs. As modern parallel computers continue to grow into the exascale era, the communication cost of such request redistribution can quickly overwhelm collective I/O performance. In this study, this effect has been observed from parallel jobs that run on multiple compute nodes with a high count of MPI processes on each node. Furthermore, to reduce the communication cost, we present a new design for collective I/O by adding an extra communication layer that performs request aggregation among processes within the same compute nodes. This approach can significantly reduce inter-node communication contention when redistributing the I/O requests. We evaluate the performance and compare it with the original two-phase I/O on Cray XC40 parallel computers (Theta and Cori) with Intel KNL and Haswell processors. Using I/O patterns from two large-scale production applications and an I/O benchmark, we show our proposed method effectively reduces the communication cost and hence maintains the scalability for a large number of processes.

97 MATHEMATICS AND COMPUTING↗