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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 1,477 records · Page 82
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles

Cell-free protein synthesis is an important tool for studying gene expression and harnessing it for applications. In cells, gene expression is regulated in part by the spatial organization of transcription and translation. Unfortunately, current cell-free approaches are unable to control the organization of molecular components needed for gene expression, which limits the ability to probe and utilize its effects. In this work, we show, using complementary computational and experimental approaches, that macromolecular crowding can be used to control the spatial organization and translational efficiency of gene expression in cell-sized vesicles. Computer simulations and imaging experiments reveal that, as crowding is increased, DNA plasmids become localized at the inner surface of vesicles. Ribosomes, in contrast, remain uniformly distributed, demonstrating that crowding can be used to differentially organize components of gene expression. We further carried out cell-free protein synthesis reactions in cell-sized vesicles and quantified mRNA and protein abundance. At sufficiently high levels of crowding, we observed localization of mRNA near vesicle surfaces, a decrease in translational efficiency and protein abundance, and anomalous scaling of protein abundance as a function of vesicle size. These results are consistent with high levels of crowding causing altered spatial organization and slower diffusion. Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression in cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Laser Spectroscopic and Theoretical Studies of Encapsulation Complexes of Calix[4]arene

The complexes between the host calix[4]arene (C4A) and various guest molecules such as NH3, N2, CH4, and C2H2 have been investigated via experimental and theoretical methods. The S1-S0 electronic spectra of these guest-host complexes are observed by mass-selected resonant two-photon ionization (R2PI) and laser induced fluorescence (LIF) spectroscopy. The infrared (IR) spectra of the complexes formed in molecular beams are obtained by IR-UV double resonance (IR-UV DR) and IR photodissociation (IRPD) spectroscopy. The supramolecular structures of the complexes are investigated by electronic structure methods (density functional and second order perturbation theory). The current results for the various molecular guests are put in perspective with the previously reported ones for the C4A-Rare Gas (Rg) (Phys. Chem. Chem. Phys. 2007, 126, 141101) and C4A-H2O complexes (J. Phys. Chem. A, 2010, 114, 2967). The electronic spectra of the complexes of C4A with N2, CH4 and C2H2 exhibit red-shifts of similar magnitudes with the ones observed for the C4A-Rg complexes, whereas the complexes of C4A with H2O and NH3 show much larger red-shifts. Most of the IR-UV DR spectra of the complexes, except for C4A-C2H2, show a broad hydrogen bonded OH stretching band with a peak at ~3160 cm-1. The analysis of the experimental results, in agreement with the ones resulted from the electronic structure calculations, suggest that C4A preferentially forms endo-complexes with all the guest species reported in this study. We discuss the similarities and differences of the structures, binding energies and the nature of the interaction between the C4A host and the various guest species. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy

08 HYDROGEN↗
DOE OSTI2017

Tunable orbital angular momentum in high-harmonic generation

Optical vortices are currently one of the most intensively studied topics in optics. These light beams, which carry orbital angular momentum (OAM), have been successfully utilized in the visible and infrared in a wide variety of applications. Moving to shorter wavelengths may open up completely new research directions in the areas of optical physics and material characterization. Here, we report on the generation of extreme-ultraviolet optical vortices with femtosecond duration carrying a controllable amount of OAM. From a basic physics viewpoint, our results help to resolve key questions such as the conservation of angular momentum in highly nonlinear light–matter interactions, and the disentanglement and independent control of the intrinsic and extrinsic components of the photon’s angular momentum at short-wavelengths. Finally, the methods developed here will allow testing some of the recently proposed concepts such as OAM-induced dichroism, magnetic switching in organic molecules and violation of dipolar selection rules in atoms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Research Update: Electrical monitoring of cysts using organic electrochemical transistors

Organotypic three-dimensional (3D) cell culture models have the potential to act as surrogate tissues in vitro, both for basic research and for drug discovery/toxicology. 3D cultures maintain not only 3D architecture but also cell-cell and cell extracellular matrix interactions, particularly when grown in cysts or spheroids. Characterization of cell cultures grown in 3D formats, however, provides a significant challenge for cell biologists due to the incompatibility of these structures with commonly found optical or electronic monitoring systems. Electronic impedance spectroscopy is a cell culture monitoring technique with great potential; however, it has not been possible to integrate 3D cultures with commercially available systems to date. Cyst-like 3D cultures are particularly challenging due to their small size and difficulty in manipulation. Herein, we demonstrate isolation of cyst-like 3D cultures by capillarity and subsequent integration with the organic electrochemical transistor for monitoring the integrity of these structures. We show not only that this versatile device can be adapted to the cyst format for measuring resistance and, therefore, the quality of the cysts, but also can be used for quantitative monitoring of the effect of toxic compounds on cells in a 3D format. The ability to quantitatively predict effects of drugs on 3D cultures in vitro has large future potential for the fields of drug discovery and toxicology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Tracking metal ions through a Cu/Ag efflux pump assigns the functional roles of the periplasmic proteins

Copper is an essential nutrient for all aerobic organisms but is toxic in excess. At the host–pathogen interface, macrophages respond to bacterial infection by copper-dependent killing mechanisms, whereas the invading bacteria are thought to counter with an up-regulation of copper transporters and efflux pumps. The tripartite efflux pump CusCBA and its metallochaperone CusF are vital to the detoxification of copper and silver ions in the periplasm of Escherichia coli . However, the mechanism of efflux by this complex, which requires the activation of the inner membrane pump CusA, is poorly understood. In this paper, we use selenomethionine (SeM) active site labels in a series of biological X-ray absorption studies at the selenium, copper, and silver edges to establish a “switch” role for the membrane fusion protein CusB. We determine that metal-bound CusB is required for activation of cuprous ion transfer from CusF directly to a site in the CusA antiporter, showing for the first time (to our knowledge) the in vitro activation of the Cus efflux pump. This metal-binding site of CusA is unlike that observed in the crystal structures of the CusA protein and is composed of one oxygen and two sulfur ligands. Finally, our results suggest that metal transfer occurs between CusF and apo-CusB, and that, when metal-loaded, CusB plays a role in the regulation of metal ion transfer from CusF to CusA in the periplasm.

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

Excluded-volume model for quarkyonic matter: Three-flavor baryon-quark mixture

The single-flavor excluded-volume model based on the effective size of baryons reproduces the hard-soft density evolution of the equation of state (EoS) required by the recent studies of GW170817. This phenomenological model basically realizes the concept of quarkyonic matter which is introduced from large-$N_c$ gauge theory for dense matter. Further, enhanced nucleon interactions and dynamically generated quark degrees of freedom can reproduce the hard-soft evolution of the EoS. In this paper, we extend the excluded-volume model to a three-flavor system by considering electromagnetic charge and possible weak equilibrium in order to obtain a proper description for the hard-soft behavior of the EoS inferred from the gravitational waves observations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Multi-objective optimization of root phenotypes for nutrient capture using evolutionary algorithms

Root phenotypes are avenues to the development of crop cultivars with improved nutrient capture, which is an important goal for global agriculture. The fitness landscape of root phenotypes is highly complex and multidimensional. It is difficult to predict which combinations of traits (phene states) will create the best performing integrated phenotypes in various environments. Brute force methods to map the fitness landscape by simulating millions of phenotypes in multiple environments are computationally challenging. Evolutionary optimization algorithms may provide more efficient avenues to explore high dimensional domains such as the root phenotypic space. We coupled the three-dimensional functional–structural plant model, SimRoot, to the Borg Multi-Objective Evolutionary Algorithm (MOEA) and the evolutionary search over several generations facilitated the identification of optimal root phenotypes balancing trade-offs across nutrient uptake, biomass accumulation, and root carbon costs in environments varying in nutrient availability. Our results show that several combinations of root phenes generate optimal integrated phenotypes where performance in one objective comes at the cost of reduced performance in one or more of the remaining objectives, and such combinations differed for mobile and non-mobile nutrients and for maize (a monocot) and bean (a dicot). Functional–structural plant models can be used with multi-objective optimization to identify optimal root phenotypes under various environments, including future climate scenarios, which will be useful in developing the more resilient, efficient crops urgently needed in global agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Symbiont-Mediated Protection of Acromyrmex Leaf-Cutter Ants from the Entomopathogenic Fungus Metarhizium anisopliae

Many fungus-growing ants engage in a defensive symbiosis with antibiotic-producing ectosymbiotic bacteria in the genus Pseudonocardia, which help protect the ants’ fungal mutualist from a specialized mycoparasite, Escovopsis. Here, using germfree ant rearing and experimental pathogen infection treatments, we evaluate if Acromyrmex ants derive higher immunity to the entomopathogenic fungus Metarhizium anisopliae from their Pseudonocardia symbionts. We further examine the ecological dynamics and defensive capacities of Pseudonocardia against M. anisopliae across seven different Acromyrmex species by controlling Pseudonocardia acquisition using ant-nonnative Pseudonocardia switches, in vitro challenges, and in situ mass spectrometry imaging (MSI). We show that Pseudonocardia protects the ants against M. anisopliae across different Acromyrmex species and appears to afford higher protection than metapleural gland (MG) secretions. Although Acromyrmex echinatior ants with nonnative Pseudonocardia symbionts receive protection from M. anisopliae regardless of the strain acquired compared with Pseudonocardia-free conditions, we find significant variation in the degree of protection conferred by different Pseudonocardia strains. Additionally, when ants were reared in Pseudonocardia-free conditions, some species exhibit more susceptibility to M. anisopliae than others, indicating that some ant species depend more on defensive symbionts than others. In vitro challenge experiments indicate that Pseudonocardia reduces Metarhizium conidiospore germination area. Our chemometric analysis using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) reveals that Pseudonocardia-carrying ants produce more chemical signals than Pseudonocardia-free treatments, indicating that Pseudonocardia produces bioactive metabolites on the Acromyrmex cuticle. Our results indicate that Pseudonocardia can serve as a dual-purpose defensive symbiont, conferring increased immunity for both the obligate fungal mutualist and the ants themselves.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence

The carbohydrate-rich coating of human tissues and cells provide a first point of contact for colonizing and invading bacteria. Commensurate with N-glycosylation being an abundant form of protein glycosylation that has critical functional roles in the host, some host-adapted bacteria possess the machinery to process N-linked glycans. The human pathogen Streptococcus pneumoniae depolymerizes complex N-glycans with enzymes that sequentially trim a complex N-glycan down to the Man 3 GlcNAc 2 core prior to the release of the glycan from the protein by endo-β-N-acetylglucosaminidase (EndoD), which cleaves between the two GlcNAc residues. Here we examine the capacity of S. pneumoniae to process high-mannose N-glycans and transport the products. Through biochemical and structural analyses we demonstrate that S. pneumoniae also possesses an α-(1,2)-mannosidase (SpGH92). This enzyme has the ability to trim the terminal α-(1,2)-linked mannose residues of high-mannose N-glycans to generate Man 5 GlcNAc 2 . Through this activity SpGH92 is able to produce a substrate for EndoD, which is not active on high-mannose glycans with α-(1,2)-linked mannose residues. Binding studies and X-ray crystallography show that NgtS, the solute binding protein of an ABC transporter (ABC NG ), is able to bind Man 5 GlcNAc, a product of EndoD activity, with high affinity. Finally, we evaluated the contribution of EndoD and ABC NG to growth of S. pneumoniae on a model N-glycosylated glycoprotein, and the contribution of these enzymes and SpGH92 to virulence in a mouse model. We found that both EndoD and ABC NG contribute to growth of S. pneumoniae, but that only SpGH92 and EndoD contribute to virulence. Therefore, N-glycan processing, but not transport of the released glycan, is required for full virulence in S. pneumoniae. To conclude, we synthesize our findings into a model of N-glycan processing by S. pneumoniae in which both complex and high-mannose N-glycans are targeted, and in which the two arms of this degradation pathway converge at ABC NG .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Evaluation of Simulated Marine Aerosol Production Using the WaveWatchIII Prognostic Wave Model Coupled to the Community Atmosphere Model within the Community Earth System Model

Primary marine aerosol (PMA) is emitted into the atmosphere via breaking wind waves on the ocean surface. Most parameterizations of PMA emissions use 10-meter wind speed as a proxy for wave action. This investigation coupled the 3 rd generation prognostic WAVEWATCH-III wind-wave model within a coupled Earth system model (ESM) to drive PMA production using wave energy dissipation rate – analogous to whitecapping – in place of 10-meter wind speed. The wind speed parameterization did not capture basin-scale variability in relations between wind and wave fields. Overall, the wave parameterization did not improve comparison between simulated versus measured AOD or Na + , thus highlighting large remaining uncertainties in model physics. Results confirm the efficacy of prognostic wind-wave models for air-sea exchange studies coupled with laboratory- and field-based characterizations of the primary physical drivers of PMA production. No discernible correlations were evident between simulated PMA fields and observed chlorophyll or sea surface temperature.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Seasonal controls on dynamic hyporheic zone redox biogeochemistry

Hyporheic zones (where surface water and groundwater mix in streambeds) play a critical role in the movement of chemicals within watersheds, particularly in upland headwater streams. Seasonal hydrology controls the expansion and contraction of hyporheic zones, with greater downwelling oxic river water influence during periods of peak river discharge (linked to snowmelt), and greater influence of upwelling anoxic groundwater during periods of low- and base-flow. Through this work, we aimed to quantify upwelling and downwelling fluxes across seasons and assess the impact of these dynamics on microbial community assembly and geochemical gradients at East River, Colorado. Further, we performed high spatial resolution sampling to capture heterogeneous mixing patterns around a characteristic meander on the river and developed reactive transport models to explain seasonal patterns of manganese (Mn) cycling in riverbed sediments. We were able to measure a dominant period of downwelling river water associated with high river discharge in Spring 2017 that led to the mixing of microbial communities across a 60-cm depth profile through the riverbed at three locations around the meander, and higher rates of aerobic respiration via delivery of dissolved oxygen (O2) and dissolved organic carbon (DOC). Conversely, we demonstrated that depth-resolved microbial communities became more distinct and stratified across a depth gradient during periods of low- and base-flow when upwelling groundwater exerted more influence in the riverbed. We also observed an increase in Mn concentrations within deeper streambed sediments during the baseflow season. Reactive transport models were developed to understand seasonal changes in Mn cycling in the streambed because Mn oxides influence the mobility of other metals in streams. In field observations and models, dissolved Mn is flushed from the streambed during spring snowmelt. A shift to upwelling conditions over the subsequent baseflow period allows for groundwater rich in dissolved Mn to mix with oxygenated river water in the shallow subsurface, resulting in net accumulation of Mn-oxides until the bed freezes in winter. We also developed models for hydrograph scenarios with snowmelt events of various size and timing. Our scenarios suggest that in years with less snowpack and a longer baseflow season, Mn oxidation will be favored in the upper riverbed sediments over more of the year, which may increase the sorption capacity of the streambed for other metals. Finally, we assessed fine-scale geochemical and hydrologic heterogeneity in the meandering riverbed by sampling pore water at 20 cm depth across more than 100 locations in August 2018. Sample locations span distinct zones of up-welling groundwater that contrast against dominant down-welling conditions. Clear differences in carbon quality and concentrations of redox sensitive solutes were detected between these zones, highlighting the importance of understanding heterogeneity at small scales across streambeds. Geochemical differences were associated with differences in microbial assemblage, but microbial diversity was generally uniform and high across all locations at the same depth, regardless of the extent of groundwater influence.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Development of X-Ray FEL Oscillators with Higher Out-Coupling Efficiency

This program focused on the development of high-outcoupling efficiency resonators for x-ray free-electron laser oscillators (XFELOs). The goal was to produce a viable design for an XFELO that can be implemented on the LCLS-II which is the x-ray FEL facility under construction at the Stanford Linear Accelerator Center (SLAC). The program designed at regenerative amplifier (RAFEL) design that employs a high-gain undulator with a low-Q resonator with the goal of producing a scientific design for the RAFEL as well as a software suite that can be used to design XFELOs. The Phase I program considered a resonator consisting of six diamond Bragg reflectors/mirrors with two focusing lenses. This resonator was used in conjunction with the electron beam produced by the LCLS-II and the HXR undulator to design a RAFEL producing 3.05 keV photons in the fundamental resonance and 9.15 keV photons in the 3rd harmonic. The research program included the extension of the Optics Propagation Code (OPC) to describe Bragg reflection from diamond crystal mirrors and went on to use OPC, in conjunction with the MINERVA simulation code to treat the undulator interaction, to simulate the RAFEL. Simulations were conducted in both the steady-state and time-dependent regimes to determine the basic performance characteristics of the RAFEL.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

High Momentum Transfer Nucleon Elastic Electromagnetic Form Factor Measurements Using Super BigBite Spectrometer at Jefferson Lab

The nucleons - protons and neutrons - are the basic building blocks of atomic nuclei. We now know that the nucleon consists of fundamental particles called quarks and gluons. The quarks interact with each other by exchanging gluons via the strong interaction. Understanding the quark-gluon structure of the nucleon, especially the confinement of quarks within the nucleon in its ground state, remains one of the main unsolved puzzles of particle physics. The nucleon electromagnetic form factors are directly related to the internal structure of the nucleon. A new generation of high precision experiments, GEp-V, GEn-II, GEn-RP, and GMn, measuring the ground state nucleon space-like electro-magnetic form factor at high momentum transfer is underway at Jefferson Lab experimental Hall-A as part of the Super Bigbite Spectrometer (SBS) program. This series of experiments will provide a new level of understanding of the nucleon structure. These experiments are highly demanding due to the extremely fast drop off of the elastic cross section with the increasing four-momentum transfer squared(Q2). This thesis provides an overview of the SBS physics program and reports on the extensive R&D program carried out to achieve the high rate running conditions essential for carrying out the SBS experiments. SBS will provide an intermediate solid angle of approximately 35 msr, which is significantly larger than the solid angle of other dipole based spectrometers at Jefferson lab. Of course, there are much larger acceptance spectrometers at Jefferson Lab, CLAS12 for example. What is special about SBS is that it provides a sizable acceptance while operating at the highest possible luminosity at Jefferson Lab. With this combination of medium acceptance and the highest available luminosity, SBS provides an unparalleled opportunity to explore the nucleon in its ground state with unprecedented resolution. The relatively large acceptance of SBS is achieved by using a large gap dipole magnet and placing it close to the target. An unavoidable consequence of this is that the SBS GEM trackers and other detectors have a clear line-of-sight view of the target and a portion of the beam-line. As a result, the background hit rate in the SBS front GEM trackers is expected to be up to 500 kHz/cm2, over the entire active area of 6000 cm2. To the best of our knowledge, this extremely high rate over such a large area is unprecedented in any particle tracking system used anywhere in the world before. Correctly reconstructing the particle tracks of interest in this very high background environment is achieved by using especially adapted high rate techniques at every step of the tracking process: optimizing the GEM module and tracker design at the hardware level, using high bandwidth electronics and real time Field Programmable Gate Array (FPGA) based background suppression techniques at the Data Acquisition (DAQ) level, and developing highly specialized tracking algorithms to pick out the signal hits from among the vast amount of background hits. In order to ensure a smooth start and running of the SBS experiments, it is extremely crucial that these techniques are developed, implemented, and tested under realistic conditions well before the actual start of the SBS experimental program. A detailed Geant4 simulation of the experiment was combined with a digitization package to generate the detector level pseudodata similar to what is expected in the actual experiments. The digitization procedures were calibrated against actual GEM data from cosmic-ray runs, X-ray tests, beam test runs in experimental Hall-A, and the PRad experiment in Hall B. Then, optimized tracking algorithms were developed and implemented in an analysis program used to analyze these pseudo-data and to extract expected high-level parameters. These extracted quantities were then compared with the input parameters from the simulation to verify and determine the performance characteristics for the SBS tracker. From this work, a final tracking efficiency of 69% at 25% occupancy was achieved, with the required reconstruction accuracy, for the GMn experiment, the first experiment in the SBS program, with background level at 100 kHz/cm2. These demonstrated parameters are adequate for the successful running of not only the GMn experiment but as well as for GEn-RP and GEn-II experiments, the second and third experiments in the program. This work builds the solid ground to further improve the tracking performance for these experiments and achieve similar conditions for the running of the GEp-V experiment, the most demanding experiment in the SBS program, with an expected background level at 500 kHz/cm2.

Di, Danning↗
DOE OSTI2016

Two poplar-associated bacterial isolates induce additive favorable responses in a constructed plant-microbiome system

Here, the biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. In this work we study the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Inoculation individually with either bacterial isolate increased root growth relative to uninoculated controls. Root area, photosynthetic efficiency, gene expression and metabolite expression data in individual and dual inoculated treatments indicate that the effects of these bacteria are unique and additive, suggesting that the function of a microbiome community may be predicted from the additive functions of the individual members.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1981

Solar observations

High energy processes that take place in the Sun's atmosphere and the relationship of these phenomena to the basic problems of solar activity are discussed. Gamma ray emission exhibits characteristics of the conditions in regions where accelerated high energy particles interact. A number of gamma ray production mechanisms are considered. These include: the Compton effect, magnetobremsstrahlung, pi meson production by proton-proton interaction or by proton-antiproton annihilation, fission and neutral of charged particle radiative capture on inelastic scatter.

Source record↗
NASA NTRS1983

Wall-temperature effects on the aerodynamics of a hydrogen-fueled transport concept in Mach 8 blowdown and shock tunnels

Results are presented from two separate tests on the same blended wing-body hydrogen fueled transport model at a Mach number of about 8 and a range of Reynolds numbers (based on theoretical body length) of 0.597 x 10 to the 6th power to about 156.22 x 10 to the 6th power. Tests were made in conventional hypersonic blowdown tunnel and a hypersonic shock tunnel at angles of attack of -2 deg to about 8 deg, with an extensive study made at a constant angle of attack of 3 deg. The model boundary-layer flow varied from laminar at the lower Reynolds numbers to predominantly turbulent at the higher Reynolds numbers. Model wall temperatures and stream static temperatures varied widely between the two tests, particularly at the lower Reynolds numbers. These temperature differences resulted in marked variations of the axial-force coefficients between the two tests, due in part to the effects of induced pressure and viscous interaction variations. The normal-force coefficient was essentially independent of Reynolds number. Analysis of results utilized current theoretical computer programs and basic boundary-layer theory.

Penland, J. A.↗
NASA NTRS1984

Analysis of some acoustics-jet flow interaction problems

Analytical problems in the interactions between the mean-shear flows and the acoustic field in the planar and circular jets are examined. These problems are basic in understanding the effects of coherent large structure on the generation and complications of sound in a sub-sonic jet. Three problems were investigated: (1) spatial (vs. temporal) normal mode analysis in a planar jets; (2) a slightly divergent, planar jet; and (3) acoustic waves in an axisymmetrical jet.

Chow, P. L.↗