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All sources NASA NTRS DOE OSTI

DOE OSTI2021

Anaerobic Microbial Metabolism of Dichloroacetate

Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising “Candidatus Dichloromethanomonas elyunquensis” strain RM utilizes DCA as an energy source, and the transient formation of formate, H 2 , and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated “Candidatus Dichloromethanomonas elyunquensis” strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg -1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1990

Foundation design for a radio telescope on the moon

A foundation design for a 122 m diameter dish-type radio telescope on the moon is presented. The 1.2 m wide and 43 m diameter circular strip footing was analyzed for settlement due to compaction during installation and also for total and differential settlement under in-service laods. An axisymmetrical finite element code of the uppdated Lagrangian formulation was used. Interface slip elements were also used. The nonlinear hyperbolic stress-strain model parameters for the regolith were derived from load-deflection characteristics of astronauts' bootprints and the Rover tracks.

Chua, Koon Meng↗

NASA NTRS2024

Investigation into the Origin of the RF Phase Noise for the LISA Laser Transmitter

The Laser Interferometer Space Antenna (LISA) mission is a collaborative consortium led by the European Space Agency (ESA)in cooperation with the National Aeronautics and Space Administration (NASA). LISA’s goal is to capture gravitational wave events, such as spacetime distortions caused by massive orbiting bodies. Multiple low noise, single frequency master oscillator power amplifier (MOPA) lasers with a polarization-maintaining Yb-fiber amplifier will serve as the light sources for the LISA observatory. The NASA Goddard Space Flight Center (GSFC)is currently developing the laser transmitters for this project. The LISA lasers will carry radio frequency (RF)sidebands for exchanging reference RF clock information between spacecrafts. Excess phase noise, especially carrier-sideband differential phase noise added to the modulation side band by the phase modulator and the fiber amplifier, becomes a concern. In the gravitational wave frequency ranges, leading sources of this RF “differential” phase noise can be both intrinsic and extrinsic. Examples of intrinsic sources include thermal load on the active fiber, thermo-mechanical induced birefringence, and nonlinearities in the various passive and active fibers. Extrinsic sources can include external temperature fluctuations and infrasonic mechanical strain or vibrations. These noise spectra usually include both white and pink (1/f) thermal noise contributions. This work investigates the physical origins and impact of these sources of RF phase noise, and their characteristic spectra and management will be discussed.

Laser Interferometer Space Antenna↗

DOE OSTI2021

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗

DOE OSTI2021

Transcriptional and translational landscape of Candida auris in response to caspofungin

Candida auris has emerged as a serious worldwide threat by causing opportunistic infections that are frequently resistant to one or more conventional antifungal medications resulting in high mortality rates. Against this backdrop, health warnings around the world have focused efforts on understanding C. auris fungal biology and effective prevention and treatment approaches to combat this fungus. To date, there is little information about the differentially expressed genes when this fungus is treated with conventional antifungals, and caspofungin is a standard echinocandin deployed in the therapy against C. auris. In this work, we treated two distinct strains of C. auris for 24h with caspofungin, and the cellular responses were evaluated at the morphological, translational and transcriptional levels. We first observed that the echinocandin caused morphological alterations, aggregation of yeast cells, and modifications in the cell wall composition of C. auris. Transcriptomic analysis revealed an upregulation of genes related to the synthesis of the cell wall, ribosome, and cell cycle after exposure to caspofungin. Supporting these findings, the integrated proteomic analysis showed that caspofungin-treated cells were enriched in ribosome-related proteins and cell wall, especially mannoproteins. Altogether, these results provide further insights into the biology of C. auris and expands our understanding regarding the antifungal activity of caspofungin and reveal cellular targets, as the mannose metabolism, that can be further explored for the development of novel antifungals.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1989

On damping mechanisms in beams

A partial differential equation model of a cantilevered beam with a tip mass at its free end is used to study damping in a composite. Four separate damping mechanisms consisting of air damping, strain rate damping, spatial hysteresis and time hysteresis are considered experimentally. Dynamic tests were performed to produce time histories. The time history data is then used along with an approximate model to form a sequence of least squares problems. The solution of the least squares problem yields the estimated damping coefficients. The resulting experimentally determined analytical model is compared with the time histories via numerical simulation of the dynamic response. The procedure suggested here is compared with a standard modal damping ratio model commonly used in experimental modal analysis.

Banks, H. T.↗

NASA NTRS1991

On damping mechanisms in beams

Banks, H. T.↗

NASA NTRS2005

Unraveling the Material Processing Conditions for Optimizing FSW Process

In friction stir welding (FSW), a rotating threaded pin tool is inserted into a weld seam and literally stirs the edges of the seam together. This environmentally friendly, solid-state technique has been successfully used in the joining of materials that are difficult to fusion weld. To determine optimal processing parameters for producing a defect free weld a better understanding of the resulting metal deformation flow path and velocity is required. In this study the metal flow fields are marked by the use of thin (0.001? tungsten) wires embedded in the weld seam at various locations. X-ray radiographs record the position and segmentation of the wire and are used to elucidate the flow field. Microstructures observed in a FSW cross-section in an aluminum alloy are related to their respective strain-strain rate-temperature histories along their respective flow trajectories. Two kinds of trajectories, each subjecting the weld metal to a distinct thermomechanical process and imparting a distinct microstructure, can be differentiated within the weld structure.

Schneider, Judy↗

NASA NTRS2005

Quantifying the Material Processing Conditions for an Optimized FSW Process

In friction stir welding (FSW), a rotating threaded pin tool is inserted into a weld seam and literally stirs the edgs of the seam together. This environmentally friendly, solid-state technique has been successfully used in the joining of materials that are difficult to fusion weld. To determine optimal processing parameters for producing a defect free weld, a better understanding of the resulting metal deformation flow path and velocity is required. In this study the metal flow fields are marked by the use of thin (0.001 in. tungsten) wires embedded in the weld seam at various locations. X-ray radiographs record the position and segmentation of the wire and are used to elucidate the flow field. Microstructures observed in a FSW cross-section in an aluminum alloy are related to their respective strain-strain rate-temperature histones along their respective flow trajectories. Two kinds of trajectories, each subjecting the weld metal to a distinct thermomechanical process and imparting a distinct microstructure, can be differentiated within the weld structure.

Schneider, Judy↗

NASA NTRS1989

Tailorable infrared sensing device with strain layer superlattice structure

An infrared photodetector is formed of a heavily doped p-type Ge(x)Si(1-x)/Si superlattice in which x is pre-established during manufacture in the range 0 to 100 percent. A custom tailored photodetector that can differentiate among close wavelengths in the range of 2.7 to 50 microns is fabricated by appropriate selection of the alloy constituency value, x, to establish a specific wavelength at which photodetection cut-off will occur.

Cheng, Li-Jen↗

DOE OSTI2021

A stochastic solver based on the residence time algorithm for crystal plasticity models

Abstract The deformation of crystalline materials by dislocation motion takes place in discrete amounts determined by the Burgers vector. Dislocations may move individually or in bundles, potentially giving rise to intermittent slip. This confers plastic deformation with a certain degree of variability that can be interpreted as being caused by stochastic fluctuations in dislocation behavior. However, crystal plasticity (CP) models are almost always formulated in a continuum sense, assuming that fluctuations average out over large material volumes and/or cancel out due to multi-slip contributions. Nevertheless, plastic fluctuations are known to be important in confined volumes at or below the micron scale, at high temperatures, and under low strain rate/stress deformation conditions. Here, we develop a stochastic solver for CP models based on the residence-time algorithm that naturally captures plastic fluctuations by sampling among the set of active slip systems in the crystal. The method solves the evolution equations of explicit CP formulations, which are recast as stochastic ordinary differential equations and integrated discretely in time. The stochastic CP model is numerically stable by design and naturally breaks the symmetry of plastic slip by sampling among the active plastic shear rates with the correct probability. This can lead to phenomena such as intermittent slip or plastic localization without adding external symmetry-breaking operations to the model. The method is applied to body-centered cubic tungsten single crystals under a variety of temperatures, loading orientations, and imposed strain rates.

42 ENGINEERING↗

DOE OSTI2020

Thermophysical properties of high-density, sintered monoliths of yttrium dihydride in the range 373–773 K

Yttrium dihydride is a promising nuclear reactor moderator for high-temperature, thermal micro-reactors due to its ability to retain hydrogen to high temperatures while having a relatively low impact on neutron economy. However, it is difficult to fabricate yttrium dihydride in high-density, near net-shape monoliths for moderator applications due to challenges associated with the hydrogen absorption process. Here, high-density monoliths of yttrium dihydride were prepared by powder metallurgical methods. The lattice strain and thermal expansion coefficient were measured using neutron diffraction of powders of directly-hydrided yttrium, while the molar heat capacity and thermal diffusivity of sintered yttrium dihydride were measured using differential scanning calorimetry (DSC) and laser flash analysis (LFA), respectively. The molar heat capacity of yttrium dihydride was also calculated using density functional theory (DFT) for comparison. These parameters were used to then calculate the thermal conductivity and resistivity of yttrium dihydride as a function of temperature. The thermophysical properties of materials produced by both methods were observed to be consistent with the values from literature for yttrium dihydride. Due to the novelty of producing yttrium dihydride by powder metallurgical methods, this result indicated that the sintered monoliths were of high quality and that powder metallurgy is a viable method for large-scale production of yttrium dihydride monoliths for nuclear reactor moderator applications.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Structural stability of mechanically alloyed amorphous (FeCoNi) 70 Ti 10 B 20 under high-temperature and high-pressure

Nanostructured (FeCoNi) 70 Ti 10 B 20 (at%) alloy was synthesized by mechanical alloying from elemental powder mixture of Fe, Co, Ni, Ti and B using ball milling. The effect of ball milling time on the evolution of structure and morphology was investigated by X-ray diffraction, scanning and transmission electron microscopy and differential thermal analysis. It was observed that the formation of solid solution of (FeCoNi) 70 Ti 10 B 20 started from the very onset of the milling process. Crystallite size and lattice strains seemed to be leveled off after 20 h of milling with no further major changes. The milling process for longer periods introduced severe plastic deformations causing formation of amorphous phase of (FeCoNi) 70 Ti 10 B 20 . The amorphous alloy composition was confirmed by energy dispersive X-ray spectroscopy analysis that showed an excellent homogeneity of the alloying elements. The phase stability of the mechanically alloyed amorphous sample was further verified by employing high-temperature and high-pressure studies. The alloy samples heat-treated at 700 °C revealed crystallization of the amorphous phase. However, synchrotron-based high-pressure ambient temperature X-ray diffraction studies confirmed that the amorphous phase of the alloy remained stable up to the pressure of 30 GPa. Here, the 50 h milled sample after being annealed at 350 °C showed improvement in the soft magnetic properties of the alloy, which was due to the probable elimination of the residual stress in the amorphous phase of the alloy powders.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts

The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (~210 kb) than BI-Viruses and BII-V1. BII-Vs share ~90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Unveiling nano-scale crystal deformation using coherent X-ray dynamical diffraction

Visualization of internal deformation fields in crystalline materials helps bridge the gap between theoretical models and practical applications. Applying Bragg coherent diffraction imaging under X-ray dynamical diffraction conditions provides a promising approach to the longstanding challenge of investigating the deformation fields in micron-sized crystals. Here, we present an automatic differentiation-based reconstruction method that integrates dynamical scattering theory to accurately reconstruct deformation fields in large crystals. Using this forward model, our simulated and experimental results demonstrate that three-dimensional local strain information inside a large crystal can be accurately reconstructed under coherent X-ray dynamical diffraction conditions with Bragg coherent X-ray diffraction imaging. These findings open an avenue for extending the investigation of local deformation fields to microscale crystals while maintaining nanoscale resolution, leveraging the enhanced coherence and brightness of advanced X-ray sources.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

In vitro antibiotic susceptibility testing often fails to accurately predict in vivo drug efficacies, in part due to differences in the molecular composition between standardized bacteriologic media and physiological environments within the body. Here, we investigate the interrelationship between antibiotic susceptibility and medium composition in Escherichia coli K-12 MG1655 as contextualized through machine learning of transcriptomics data. Application of independent component analysis, a signal separation algorithm, shows that complex phenotypic changes induced by environmental conditions or antibiotic treatment are directly traced to the action of a few key transcriptional regulators, including RpoS, Fur, and Fnr. Integrating machine learning results with biochemical knowledge of transcription factor activation reveals medium-dependent shifts in respiration and iron availability that drive differential antibiotic susceptibility. By extension, the data generation and data analytics workflow used here can interrogate the regulatory state of a pathogen under any measured condition and can be applied to any strain or organism for which sufficient transcriptomics data are available.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

Study of recrystallization and devitrification of lunar glass

The technique of differential thermal analysis (DTA) was applied to the study of the Apollo 17 orange soil (74220,63) and the Apollo 16 glass coated anorthite (64455,21). These glasses show accentuated exotherms of strain relief in the annealing range which is indicative of rapid cooling. These are amenable to interpretation by comparison to the known history of synthetic glasses. Synthetic glasses were prepared whose similarity in behavior between the lunar glasses and their synthetic analogs is striking. Approximate rates of cooling of the lunar glasses were determined from comparative DTA of lunar and synthetic glasses and from the determination of the relation of strain relief in the annealing range to quench rate. At higher temperatures the glasses show exotherms of crystallization. The crystallization products associated with the exothermic reactions have been identified by X-ray diffraction and the surface morphologies developed by strain relief and crystallization have been characterized with scanning electron microscopy.

Ulrich, D. R.↗

NASA NTRS2002

Finite-Strain Fractional-Order Viscoelastic (FOV) Material Models and Numerical Methods for Solving Them

Fraction-order viscoelastic (FOV) material models have been proposed and studied in 1D since the 1930's, and were extended into three dimensions in the 1970's under the assumption of infinitesimal straining. It was not until 1997 that Drozdov introduced the first finite-strain FOV constitutive equations. In our presentation, we shall continue in this tradition by extending the standard, FOV, fluid and solid, material models introduced in 1971 by Caputo and Mainardi into 3D constitutive formula applicable for finite-strain analyses. To achieve this, we generalize both the convected and co-rotational derivatives of tensor fields to fractional order. This is accomplished by defining them first as body tensor fields and then mapping them into space as objective Cartesian tensor fields. Constitutive equations are constructed using both variants for fractional rate, and their responses are contrasted in simple shear. After five years of research and development, we now possess a basic suite of numerical tools necessary to study finite-strain FOV constitutive equations and their iterative refinement into a mature collection of material models. Numerical methods still need to be developed for efficiently solving fraction al-order integrals, derivatives, and differential equations in a finite element setting where such constitutive formulae would need to be solved at each Gauss point in each element of a finite model, which can number into the millions in today's analysis.

Freed, Alan D.↗