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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Host-specific and tissue-dependent orchestration of microbiome community structure in traditional rice paddy ecosystems

Abstract Background and aim Rice and duckweed are two monocotyledonous plants that naturally coexist in paddy fields. While the presence of duckweed in paddy fields significantly improves rice productivity, the interplay between soil microbes and the two plant hosts in this agroecosystem remains unexplored. Methods We compared the bacterial community structure between duckweed, rice and soil from multiple rice paddies. We also isolated bacteria from these communities and characterized their modes of bacterial colonization and plant growth-promotion using model plants. Results Our data indicate that host-specific and tissue-dependent factors reproducibly orchestrate the bacterial community structure associated with their plant hosts. This is corroborated by results from culture-dependent approaches in which the dominant genus Pantoea isolated from rice aerial tissues can strongly attach and colonize gnotobiotic duckweed in spite of the low representation of this bacterial genus in the natural duckweed microbiome. Our study identified a core of 254 bacterial taxa that are consistently found in all rice and duckweed tissue samples from rice paddy fields. Furthermore, characterizing auxin-producing bacteria isolates from both plant species identified potential plant growth-promoting bacteria that may improve growth for both duckweed and rice in paddy fields. Conclusions Results from this work provide evidence for the importance of the host tissue and species context in determining plant colonization by microbes in the paddy field system. The resources generated in this study could facilitate the agronomic deployment of microbes for more sustainable rice production.

Agriculture↗
DOE OSTI2019

Reconstitution of the heliobacterial photochemical reaction center and cytochrome c 553 into a proteoliposome system

The heliobacterial reaction center (HbRC) is the simplest understood photochemical reaction center, in terms of its polypeptide composition. In the heliobacterial cells, its electron donor is a cytochrome (cyt) c 553 attached to the membrane via a covalent linkage with a diacylglycerol. We have reconstituted purified HbRC into liposomes mimicking the phospholipid composition of heliobacterial membranes. We also incorporated a lipid with a headgroup containing Ni(II):nitrilotriacetate (NTA) to provide a binding site for the soluble version of the heliobacterial cyt c 553 in which the N-terminal membrane attachment site is replaced by a hexahistidine tag. The HbRC was inserted into the liposomes with the donor side preferentially exposed to the exterior; this bias increased to nearly 100% with higher concentrations (≥ 10 mol%) of the Ni(II)-NTA lipid in the membrane, and is most likely due to the net negative charge of the surface of the membrane. The HbRC in proteoliposomes without the Ni(II)-NTA lipid exhibited normal charge separation and subsequent charge recombination of the P + 800 F - X state in 15 ms; however, the oxidized primary donor (P + 800 ) was not significantly reduced by added H 6 -cyt c 553 . In contrast, with proteoliposomes containing the Ni(II)-NTA lipid, addition of H 6 -cyt c 553 resulted in a new kinetic component resulting from fast reduction (2–5 ms) of P + 800 by H 6 -cyt c 553 . The contribution of this kinetic component varied with the concentration of added H 6 -cyt c 553 and could represent 80% or more of the total P + 800 decay. As a result, the HbRC and its interaction with its native electron donor have been reconstituted into an artificial membrane system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Inkjet printing of epitaxially connected nanocrystal superlattices

Access to a blossoming library of colloidal nanomaterials provides building blocks for complex assembled materials. The journey to bring these prospects to fruition stands to benefit from the application of advanced processing methods. Epitaxially connected nanocrystal (or quantum dot) superlattices present a captivating model system for mesocrystals with intriguing emergent properties. The conventional processing approach to creating these materials involves assembling and attaching the constituent nanocrystals at the interface between two immiscible fluids. Processing small liquid volumes of the colloidal nanocrystal solution involves several complexities arising from the concurrent spreading, evaporation, assembly, and attachment. The ability of inkjet printers to deliver small (typically picoliter) liquid volumes with precise positioning is attractive to advance fundamental insights into the processing science, and thereby potentially enable new routes to incorporate the epitaxially connected superlattices into technology platforms. In this study, we identified the processing window of opportunity, including nanocrystal ink formulation and printing approach to enable delivery of colloidal nanocrystals from an inkjet nozzle onto the surface of a sessile droplet of the immiscible subphase. We demonstrate how inkjet printing can be scaled-down to enable the fabrication of epitaxially connected superlattices on patterned sub-millimeter droplets. Furthermore, we anticipate that insights from this work will spur on future advances to enable more mechanistic insights into the assembly processes and new avenues to create high-fidelity superlattices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2026

Impedance Based Fixture Neutralization (FINE) Method to Replicate Field Environments in Laboratory Settings

Test article vibration test responses will vary from one test laboratory to another due to differences in shaker and fixture dynamic characteristics. This is also seen between the field and laboratory due to the differing dynamic characteristics between field assembly loading and boundary conditions compared to the laboratory configuration. This work introduces a technique called Impedance Fixture Neutralization which customizes input forces to cause consistent responses for the Device Under Test across different vibration testing conditions. The customized force neutralizes the dynamic variations between configurations for the Device Under Test. The device responses can be replicated in several situations: when using a different fixture with the same attachment points, when the test article mounting location on the fixture changes, when the force location changes, or any combination of these situations. Impedance Fixture Neutralization uses the uncoupled dynamic characteristics of the test article and excitation fixtures to customize the input thereby causing the same test article responses between two mounting configurations (either field to laboratory or two different laboratory configurations). The application of the technique is shown using an analytical model of a two-beam system and analytically using experimental FRFs from plate and frame component hardware characterization tests. In both cases a device under test is attached to two test fixtures wherein the dynamic differences in the configurations are neutralized.

Laboratory↗
DOE OSTI2023

Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor

Histamine dehydrogenase from the gram-negative bacterium Rhizobium sp. 4-9 (HaDHR) is a member of a small family of dehydrogenases containing a covalently attached FMN, and the only member so far identified to date that does not exhibit substrate inhibition. Here, in this study, we present the 2.1 Å resolution crystal structure of HaDHR. This new structure allowed for the identification of the internal electron transfer pathway to abiological ferrocene-based mediators. Alanine 437 was identified as the exit point of electrons from the Fe 4 S 4 cluster. The enzyme was modified with a Ser436Cys mutation to facilitate covalent attachment of a ferrocene moiety. When modified with Fc-maleimide, this new construct demonstrated direct electron transfer from the enzyme to a gold electrode in a histamine concentration-dependent manner without the need for any additional electron mediators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Portable interactive visualization of large-scale simulations in geotechnical engineering using Unity3D

Development in large-scale geotechnical engineering simulation places tremendous demand for efficient visualization of such simulation data. This study presents a lightweight software tool, i.e. Geotechnical Interactive Visualization (GIV), as a solution to this challenge, which achieves efficient interactive visualization of large-scale simulations data in geotechnical engineering. Visualization data flow and algorithms specifically optimized for common geotechnical engineering applications are implemented in GIV. GIV can visualize geotechnical structure models with time-varying attributes attached to mesh with fixed topology, and also models with time-varying mesh topologies but no attributes attached, the two most common visualization tasks in geotechnical engineering. Furthermore, challenges for large-scale simulation data visualization, including parallel simulation data redundancy, massive data size, dynamic user interaction, and portability are overcome via specifically designed algorithms for simulation data preprocessing and optimized visualization modules using the powerful 3D rendering and interactive game engine Unity3D. Comparison of GIV with several widely used visualization tools for the visualization of large-scale idealized datasets and realistic geotechnical simulations highlights the visualization efficiency, smooth interactivity, and lightweight features of GIV.

42 ENGINEERING↗
DOE OSTI2022

Quantifying biofilm propagation on chemically modified surfaces

Conditions affecting biofilm formation differ among bacterial species and this presents a challenge to studying biofilms in the lab. This work leverages functionalized silanes to control surface chemistry in the study of early biofilm propagation, quantified with a semi-automated image processing algorithm. These methods support the study of Pantoea sp. YR343, a gram-negative bacterium isolated from the poplar rhizosphere. We found that Pantoea sp. YR343 does not readily attach to hydrophilic surfaces but will form biofilms with a “honeycomb” morphology on hydrophobic surfaces. Our image processing algorithm described here quantified the evolution of the honeycomb morphology over time, and found the propagation to display a logarithmic behavior. This methodology was repeated with a flagella-deficient fliR mutant of Pantoea sp. YR343 which resulted in reduced surface attachment. Quantifiable differences between Pantoea WT and ΔfliR biofilm morphologies were captured by the image processing algorithm, further demonstrating the insight gained from these methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Dielectrophoresis assisted rapid, selective and single cell detection of antibiotic resistant bacteria with G-FETs

Time-consuming, expensive and low sensitivity diagnostic methods used for monitoring bacterial infections lead to unnecessary or delays in prescription of the right antibiotic treatment. Determining an optimal clinical treatment requires rapid detection and identification of pathogenic bacteria and their sensitivity to specific antimicrobials. However, diagnostic devices that meet all of these criteria have proven elusive thus far. Graphene field effect transistors (G-FET) are a promising solution, since they are highly sensitive to chemical/biological modification, can have fast detection times and can be placed on different substrates. Here, by integrating specific peptide probes over G-FETs, we present a proof-of-concept study for species and strain specific label-free detection of clinical strains of pathogenic bacteria with high specificity and sensitivity. We found that pyrene-conjugated peptides immobilized on G-FETs were capable of detecting pathogenic Staphylococcus aureus at the single-cell level and discriminate against other gram-positive and gram-negative bacterial pathogens. A similar device was able to discriminate between antibiotic resistant and sensitive strains of Acinetobacter baumannii , suggesting that these devices can also be used for detecting antibiotic resistive pathogens. Furthermore, a new means of enhancing attachment, electric-field assisted binding, reduced the detection limit to 104 cells/ml and the detection time to below 5 minutes. Here, the combination of single step attachment, inexpensive production, rapid, selective and sensitive detection suggest G-FETs plus pyrene-conjugated peptides are a new platform for solving major challenges faced in point of care diagnostics to fight infectious diseases and antimicrobial resistance.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Most of the rhamnogalacturonan-I from cultured Arabidopsis cell walls is covalently linked to arabinogalactan-protein

To characterize a purified rhamnogalacturonan-I (RG-I) containing both RG-I and arabinogalactan-protein (AGP) types of glycosyl residues, an AGP-specific β-1,3-galactanase that can cleave the AG backbone and release the AG sidechain was applied to this material. Carbohydrate analysis and NMR spectroscopy verified that the galactanase-released carbohydrate consists of RG-I covalently attached to the AG sidechain, proving a covalent linkage between RG-I and AGP. Size exclusion chromatography-multiangle light scattering-refractive index detection revealed that the galactanase-released RG-I has an average molecular weight of 41.6 kDa, which, together with the percentage of pectic sugars suggests an RG-I-AGP comprising one AGP covalently linked to two RG-I glycans. Carbohydrate analysis and NMR results of the RG-I-AGP, the galactanase-released glycans, and the RG lyase-released glycans demonstrated that the attached RG-I glycans are decorated with α-1,5-arabinan, β-1,4-galactan, xylose, and 4-O-Me-xylose sidechains. Furthermore, our measurement suggests that the covalently linked RG-I-AGP is the major component of the traditionally prepared RG-I.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

FtsZ-mediated fission of a cuboid bacterial symbiont

Less than a handful of cuboid and squared cells have been described in nature, which makes them a rarity. Here, we show how Candidatus Thiosymbion cuboideus, a cube-like gammaproteobacterium, reproduces on the surface of marine free-living nematodes. Immunostaining of symbiont cells with an anti-fimbriae antibody revealed that they are host-polarized, as these appendages exclusively localized at the host-proximal (animal-attached) pole. Moreover, by applying a fluorescently labeled metabolic probe to track new cell wall insertion in vivo, we observed that the host-attached pole started septation before the distal one. Similarly, Ca. T. cuboideus cells immunostained with an anti-FtsZ antibody revealed a proximal-to-distal localization pattern of this tubulin homolog. Although FtsZ has been shown to arrange into squares in synthetically remodeled cuboid cells, here we show that FtsZ may also mediate the division of naturally occurring ones. This implies that, even in natural settings, membrane roundness is not required for FtsZ function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Effects of particle shape and surface roughness on van der Waals interactions and coupling to dynamics in nanocrystals

The van der Waals interaction between colloids and nanoparticles is one of the key components to understanding particle aggregation, attachment, and assembly. While the ubiquity of anisotropic particle shapes and surface roughness is well-recognized in nanocrystalline materials, the effect of both on van der Waals forces and torques has not been adequately investigated. Here, in this study, we develop a numerical scheme and determine the van der Waals forces and torques between cubic particles with multiple configurations and relative orientations. Our results show that the van der Waals torque due to anisotropic particle shapes is appreciable at nearly all configurations and mutual angles, outcompeting Brownian motion for various materials systems and conditions. The effect of surface roughness increases this shape effect, resulting in stronger van der Waals interactions ascribed to protrusions in the rough surfaces. Moreover, a scaling analysis indicates that the surface roughness alters the separation dependence of the van der Waals force and, more importantly, significantly influences the dynamics of two approaching particles. Our results clearly demonstrate that surface roughness and anisotropic shape play a crucial role in the energetics and kinetics of various particle-scale and emergent phenomena, such as crystal growth by oriented attachment, nanomaterials synthesis and assembly, mud flow rheology, as well as the deposition of natural nanocrystals within the subsurface.

Arbitrary configurations↗
DOE OSTI2023

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene (“BMIE”), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu ++ and Zn ++ in bidentate (N 2 ) and tridentate (N 2 S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn ++ , Cu ++ , and Co ++ . EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu ++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H 2 O/HO – , tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn ++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. Finally, these features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

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

Cluster dynamics simulation of xenon diffusion during irradiation in UO 2

Diffusion of fission gas in UO 2 nuclear fuel impacts several important performance metrics, such as fission gas release, swelling, and thermal conductivity. Current empirical models of fission gas release have significant uncertainty, some of which derives from the bulk diffusion rate and its dependence on, for example, fuel chemistry and irradiation. In this work, we have applied the previously-developed Free Energy Cluster Dynamics (FECD) methodology in the code Centipede to calculate xenon cluster concentrations in UO 2 under intrinsic (high temperature) and irradiation-enhanced (intermediate temperature) conditions in order to develop a model of the xenon diffusion coefficient based on the atomic scale mechanisms responsible for transport. While the diffusion mechanism for xenon in UO 2 is adequately described by the Xe + U 2 O vacancy cluster for intrinsic conditions, a similar process is not capable of capturing measured in-pile fission gas diffusivity at intermediate temperatures. Therefore, a different diffusion mechanism must dominate under this regime. Using calculated atomistic data, we have shown that irradiation-enhanced diffusion at intermediate temperatures occurs via the larger Xe + U 4 O y vacancy clusters, which have lower migration barriers and increase in concentration by several orders of magnitude compared to intrinsic conditions. This mechanism is enabled by the increased uranium vacancy concentration under irradiation due to Frenkel pair production. In addition, the fast migration of uranium interstitials with two attached oxygen interstitials lowers the total uranium interstitial concentration through reactions with sinks. This allows the extended defects, such as Xe + U 4 O y vacancy clusters, to maintain high concentrations by limiting annihilation with attached vacancies. Furthermore, predictions using the Xe + U 4 O y diffusion mechanism are in good agreement with experiment, albeit with some differences in the Arrhenius slope, which we believe may be related to either experimental or model parameter uncertainty. Lastly, an analytical expression suitable for application in fuel performance simulations was derived to capture the predictions of the Centipede simulations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Ir(III)-Naphthoquinone complex as a platform for photocatalytic activity

Inspired by the primary events that take place in Photosystem II (PSII), we designed and synthesized a heteroleptic Ir(III) complex featuring an attached naphthoquinone (NQ) as an electron transfer (ET) auxiliary reminiscent of the plastoquinone electron acceptor in PSII. In this design, NQ is covalently attached to the 2,2'-bipyridyl (bpy) ligand of [Ir(dF(CF 3 )ppy) 2 (bpy)][PF 6 ], (dF(CF 3 )ppy = 2-(2,4-difluorophenyl)-5-(trifluoromethyl)pyridine). Following excitation of the photocatalyst ([Ir(dF(CF 3 )ppy) 2 (bpy-NQ)][PF 6 ]), reduced NQ (NQ •– ) was observed in transient absorption spectroscopy. Here, this novel catalyst has potential applications in oxidative and reductive photocatalytic processes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Hybrid manufacturing of Invar mold for carbon fiber layup using structured light scanning

This paper describes coordinate system definition and transfer for five-axis machining of additively-manufactured preforms. In this method, a set of fiducials are attached to the temporarily attached to the part, and their location relative to the preform geometry is calibrated using a structured light scanner. Those fiducials can then be measured in the machine tool to determine the location and orientation of the part. The method is demonstrated by finish-machining a carbon fiber layup mold from an additively manufactured Invar preform. In addition to showing the coordinate transfer methods necessary to machine the part, several key challenges with machining additively-manufactured preforms are discussed and potential solutions are proposed. Unfortunately, the final part was ultimately unusable due to porosity inside the part left from the additive process. Future work will remanufacture this part while taking steps to avoid porosity and other challenges encountered.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Effects of laminin-111 peptide coatings on rat neural stem/progenitor cell culture

Neurons require adhesive scaffolds for their growth and differentiation. Laminins are a major cell adhesive component of basement membranes and have various biological activities in the peripheral and central nervous systems. Here, we evaluated the biological activities of 5 peptides derived from laminin-111 as a scaffold for mouse neuroblastoma Neuro2a cells and rat neural stem/progenitor cells (NPCs). The 5 peptides showed Neuro2a cell attachment activity similar to that of poly-d-lysine. However, when NPCs were cultured on the peptides, 2 syndecan-binding peptides, AG73 (RKRLQVQLSIRT, mouse laminin α1 chain 2719-2730) and C16 (KAFDITYVRLKF, laminin γ1 chain 139–150), demonstrated significantly higher cell attachment and neurite extension activities than other peptides including integrin-binding ones. Long-term cell culture experiments showed that both AG73 and C16 supported the growth of neurons and astrocytes that had differentiated from NPCs. Furthermore, C16 markedly promoted the expression of neuronal markers such as synaptosomal-associated protein-25 and syntaxin 1A. These results indicate that AG73 and C16 are useful for NPC cultures and that C16 can be applied to specialized research on synapses in differentiated neurons. These peptides have the potential for use as valuable biomaterials for NPC research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Shaker-structure interaction modeling and analysis for nonlinear force appropriation testing

Nonlinear force appropriation is an extension of its linear counterpart where sinusoidal excitation is applied to a structure with a modal shaker and phase quadrature is achieved between the excitation and response. While a standard practice in modal testing, modal shaker excitation has the potential to alter the dynamics of the structure under test. Previous studies have been conducted to address several concerns, but this work specifically focuses on a shaker-structure interaction phenomenon which arises during the force appropriation testing of a nonlinear structure. Under pure-tone sinusoidal forcing, a nonlinear structure may respond not only at the fundamental harmonic but also potentially at sub- or superharmonics, or it can even produce aperiodic and chaotic motion in certain cases. Shaker-structure interaction occurs when the response physically pushes back against the shaker attachment, producing non-fundamental harmonic content in the force measured by the load cell, even for pure tone voltage input to the shaker. This work develops a model to replicate these physics and investigates their influence on the response of a nonlinear normal mode of the structure. Experimental evidence is first provided that demonstrates the generation of harmonic content in the measured load cell force during a force appropriation test. This interaction is replicated by developing an electromechanical model of a modal shaker attached to a nonlinear, three-mass dynamical system. Several simulated experiments are conducted both with and without the shaker model in order to identify which effects are specifically due to the presence of the shaker. Finally, the results of these simulations are then compared to the undamped nonlinear normal modes of the structure under test to evaluate the influence of shaker-structure interaction on the identified system’s dynamics.

42 ENGINEERING↗
DOE OSTI2020

The mean logarithm emerges with self-similar energy balance.

The attached eddy hypothesis of Townsend (The Structure of Turbulent Shear Flow, 1956, Cambridge University Press) states that the logarithmic mean velocity admits self-similar energy-containing eddies which scale with the distance from the wall. Over the past decade, there has been a significant amount of evidence supporting the hypothesis, placing it to be the central platform for the statistical description of the general organisation of coherent structures in wall-bounded turbulent shear flows. Nevertheless, the most fundamental question, namely why the hypothesis has to be true, has remained unanswered over many decades. Under the assumption that the integral length scale is proportional to the distance from the wall y , in the present study we analytically demonstrate that the mean velocity is a logarithmic function of y if and only if the energy balance at the integral length scale is self-similar with respect to y , providing a theoretical basis for the attached eddy hypothesis. The analysis is subsequently verified with the data from a direct numerical simulation of incompressible channel flow at the friction Reynolds number Reτ≃5200 (Lee & Moser, J. Fluid Mech., vol. 774, 2015, pp. 395–415).

42 ENGINEERING↗