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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform

Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

MolDiscovery: learning mass spectrometry fragmentation of small molecules

Identification of small molecules is a critical task in various areas of life science. Recent advances in mass spectrometry have enabled the collection of tandem mass spectra of small molecules from hundreds of thousands of environments. To identify which molecules are present in a sample, one can search mass spectra collected from the sample against millions of molecular structures in small molecule databases. The existing approaches are based on chemistry domain knowledge, and they fail to explain many of the peaks in mass spectra of small molecules. Here, we present molDiscovery, a mass spectral database search method that improves both efficiency and accuracy of small molecule identification by learning a probabilistic model to match small molecules with their mass spectra. A search of over 8 million spectra from the Global Natural Product Social molecular networking infrastructure shows that molDiscovery correctly identify six times more unique small molecules than previous methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Shatter Thresholds and Fragment Size Distributions of Deuterium–Neon Mixture Cryogenic Pellets for Tokamak Thermal Mitigation

Reliable mitigation is necessary to eliminate the detrimental effects of a disruption event in large high-current tokamaks such as ITER. To avoid serious damage to plasma-facing components during the thermal quench phase of a disruption, material is injected to radiate the plasma energy over the inner surface of the machine. The most promising method of material injection is a process known as shattered pellet injection (SPI). SPI utilizes cryogenic cooling to desublimate gas into the barrel of a pipe gun to form a solid pellet. High-pressure gas or a mechanical punch is used to dislodge the pellet and accelerate it into a bent tube to intentionally fracture it. Pellets made of a mixture of deuterium and neon are likely candidates for thermal mitigation. The survivability of these pellets throughout their flight path, before striking the shatter tube, is essential for reliable SPI operation. Experiments were conducted to determine intact speed limits for various mixtures. In this paper, we outline the details of brittle fracture theory and compare a theory-based model to experimental results from various mixtures of deuterium and neon pellets.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Quantifying uncertainties on fission fragment mass yields with mixture density networks

Probabilistic machine learning techniques can learn both complex relations between input features and output quantities of interest as well as take into account stochasticity or uncertainty within a data set. In this initial work, we explore the use of one such probabilistic network, the mixture density network (MDN), to reproduce fission yields and their uncertainties. In this paper, we study mass yields for the spontaneous fission of 252 Cf, exploring the number of training samples needed for converged predictions, how different levels of uncertainty propagate from the training set to the MDN predictions, and how well physical constraints of the yields—such as normalization and symmetry—are upheld by the algorithm. Finally, we test the ability of the MDN to interpolate between and extrapolate beyond samples in the training set using energy-dependent mass yields for the neutron-induced fission on 235 U. The MDN provides a reliable way to include and predict uncertainties and is a promising path forward for supplementing sparse sets of nuclear data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

The role of magnetic fields in the stability and fragmentation of filamentary molecular clouds: two case studies at OMC-3 and OMC-4

We present the stability analysis of two regions, OMC-3 and OMC-4, in the massive and long molecular cloud complex of Orion A. We obtained 214 $\mu$m HAWC + /SOFIA polarization data, and we make use of archival data for the column density and C 18 O (1–0) emission line. We find clear depolarization in both observed regions and that the polarization fraction is anticorrelated with the column density and the polarization-angle dispersion function. We find that the filamentary cloud and dense clumps in OMC-3 are magnetically supercritical and strongly subvirial. This region should be in the gravitational collapse phase and is consistent with many young stellar objects (YSOs) forming in the region. Our histogram of relative orientation (HRO) analysis shows that the magnetic field is dynamically sub-dominant in the dense gas structures of OMC-3. We present the first polarization map of OMC-4. We find that the observed region is generally magnetically subcritical except for an elongated dense core, which could be a result of projection effect of a filamentary structure aligned close to the line of sight. The relative large velocity dispersion and the unusual positive shape parameters at high column densities in the HROs analysis suggest that our viewing angle may be close to axes of filamentary substructures in OMC-4. The dominating strong magnetic field in OMC-4 is unfavourable for star formation and is consistent with much fewer YSOs than in OMC-3.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography

Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)] 2 . The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.

59 BASIC BIOLOGICAL SCIENCES↗