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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 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Mesoscale Simulation of Proton Transport in Proton Exchange Membranes

Previous efforts to model proton transport through fuel cell membranes have largely focused on disparate length scales: molecular dynamics at the atomistic level and fuel cell stack engineering approaches at the macroscale. A new multiscale approach to bridge these extremes is proposed in this work which combines concepts from coarse-grained (CG) modeling with smoothed particle hydrodynamics (SPH) to capture the qualitative morphology and transport behavior of a proton exchange membrane at the length scale of tens of nanometers. This method allows for connection to atomistic simulations via the inclusion of transport coefficients from molecular dynamics and coarse-grained forces derived for the polymer backbone, side chain, proton, and water interactions. Information pertaining to macroscopic conductivity is obtained by volume averaging based on the flux and chemical potential fields within the membrane. Proton transport is effectively coarse-grained via introduction of a composition variable associated with each interacting site which carries the field information. By combining this technique with local electrostatics and coordinate dependent diffusion constants, the effects of double layer formation within the water pores and the influence of proximity to sulfonate groups on transport is recovered. The combined CG-SPH method is validated and subsequently applied to an equilibrated hydrated Nafion structure with a box length of 40 nm. The resulting conductivities calculated for the material agree very well with trends from experiment and provide insight into the complex interplay of morphology, proton distribution, and diffusion coefficients at a length scale that can be expanded beyond feasible atomistic molecular dynamics simulations to capture the effects of mesoscopic morphology on proton conduction.

Jorn, Ryan↗
DOE OSTI2015

CD14 and IL18 gene polymorphisms associated with colorectal cancer subsite risks among atomic bomb survivors

Colorectal cancer (CRC) is a common malignancy worldwide, and chronic inflammation is a risk factor for CRC. In this study, we carried out a cohort study among the Japanese atomic bomb (A-bomb) survivor population to investigate any association between immune- and inflammation-related gene polymorphisms and CRC. We examined the effects of six single-nucleotide polymorphisms of CD14 and IL18 on relative risks (RRs) of CRC. Results showed that RRs of CRC, overall and by anatomic subsite, significantly increased with increasing radiation dose. The CD14–911A/A genotype showed statistically significant higher risks for all CRC and distal CRC compared with the other two genotypes. In addition, the IL18–137 G/G genotype showed statistically significant higher risks for proximal colon cancer compared with the other two genotypes. In phenotype–genotype analyses, the CD14–911A/A genotype presented significantly higher levels of membrane and soluble CD14 compared with the other two genotypes, and the IL18–137 G/G genotype tended to be lower levels of plasma interleukin (IL)-18 compared with the other two genotypes. These results suggest the potential involvement of a CD14-mediated inflammatory response in the development of distal CRC and an IL18-mediated inflammatory response in the development of proximal colon cancer among A-bomb survivors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus

Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, here we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by 15 N 2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni–Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N 2 that is important for this beetle to subsist on woody biomass.

Ceja-Navarro, Javier A.↗
DOE OSTI2011

The Crystal Structure of GXGD Membrane Protease FlaK

The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. In conclusion, N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Interfacial control of oxygen vacancy doping and electrical conduction in thin film oxide heterostructures

Oxygen vacancies in proximity to surfaces and heterointerfaces in oxide thin film heterostructures have major effects on properties, resulting, for example, in emergent conduction behaviour, large changes in metal-insulator transition temperatures or enhanced catalytic activity. Here we report the discovery of a means of reversibly controlling the oxygen vacancy concentration and distribution in oxide heterostructures consisting of electronically conducting In2O3 films grown on ionically conducting Y2O3-stabilized ZrO2 substrates. Oxygen ion redistribution across the heterointerface is induced using an applied electric field oriented in the plane of the interface, resulting in controlled oxygen vacancy (and hence electron) doping of the film and possible orders-of-magnitude enhancement of the film's electrical conduction. The reversible modified behaviour is dependent on interface properties and is attained without cation doping or changes in the gas environment.

Veal, Boyd W.↗
DOE OSTI2017

Drebrin-mediated microtubule–actomyosin coupling steers cerebellar granule neuron nucleokinesis and migration pathway selection

Neuronal migration from a germinal zone to a final laminar position is essential for the morphogenesis of neuronal circuits. While it is hypothesized that microtubule–actomyosin crosstalk is required for a neuron’s ‘two-stroke’ nucleokinesis cycle, the molecular mechanisms controlling such crosstalk are not defined. By using the drebrin microtubule–actin crosslinking protein as an entry point into the cerebellar granule neuron system in combination with super-resolution microscopy, we investigate how these cytoskeletal systems interface during migration. Lattice light-sheet and structured illumination microscopy reveal a proximal leading process nanoscale architecture wherein f-actin and drebrin intervene between microtubules and the plasma membrane. Functional perturbations of drebrin demonstrate that proximal leading process microtubule–actomyosin coupling steers the direction of centrosome and somal migration, as well as the switch from tangential to radial migration. Finally, the Siah2 E3 ubiquitin ligase antagonizes drebrin function, suggesting a model for control of the microtubule–actomyosin interfaces during neuronal differentiation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Stripe-like nanoscale structural phase separation in superconducting BaPb 1-x Bi x O 3

The phase diagram of BaPb 1-x Bi x O 3 exhibits a superconducting dome in the proximity of a charge density wave phase. For the superconducting compositions, the material coexists as two structural polymorphs. Here we show, via high-resolution transmission electron microscopy, that the structural dimorphism is accommodated in the form of partially disordered nanoscale stripes. Identification of the morphology of the nanoscale structural phase separation enables determination of the associated length scales, which we compare with the Ginzburg–Landau coherence length. We find that the maximum T c occurs when the superconducting coherence length matches the width of the partially disordered stripes, implying a connection between the structural phase separation and the shape of the superconducting dome.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Tunnelling spectroscopy of Andreev states in graphene

A normal conductor placed in good contact with a superconductor can inherit its remarkable electronic properties. This proximity effect microscopically originates from the formation in the conductor of entangled electron–hole states, called Andreev states. Spectroscopic studies of Andreev states have been performed in just a handful of systems. The unique geometry, electronic structure and high mobility of graphene make it a novel platform for studying Andreev physics in two dimensions. In this paper, we use a full van der Waals heterostructure to perform tunnelling spectroscopy measurements of the proximity effect in superconductor–graphene–superconductor junctions. The measured energy spectra, which depend on the phase difference between the superconductors, reveal the presence of a continuum of Andreev bound states. Moreover, our device heterostructure geometry and materials enable us to measure the Andreev spectrum as a function of the graphene Fermi energy, showing a transition between different mesoscopic regimes. Furthermore, by experimentally introducing a novel concept, the supercurrent spectral density, we determine the supercurrent–phase relation in a tunnelling experiment, thus establishing the connection between Andreev physics at finite energy and the Josephson effect. Finally, this work opens up new avenues for probing exotic topological phases of matter in hybrid superconducting Dirac materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate

Abstract Photosynthetic microalgae are responsible for 50% of the global atmospheric CO2 fixation into organic matter and hold potential as a renewable bioenergy source. Their metabolic interactions with the surrounding microbial community (the algal microbiome) play critical roles in carbon cycling, but due to methodological limitations, it has been challenging to examine how community development is influenced by spatial proximity to their algal host. Here we introduce a copolymer-based porous microplate to co-culture algae and bacteria, where metabolites are constantly exchanged between the microorganisms while maintaining physical separation. In the microplate, we found that the diatom Phaeodactylum tricornutum accumulated to cell abundances ~20 fold higher than under normal batch conditions due to constant replenishment of nutrients through the porous structure. We also demonstrate that algal-associated bacteria, both single isolates and complex communities, responded to inorganic nutrients away from their host as well as organic nutrients originating from the algae in a spatially predictable manner. These experimental findings coupled with a mathematical model suggest that host proximity and algal culture growth phase impact bacterial community development in a taxon-specific manner through organic and inorganic nutrient availability. Our novel system presents a useful tool to investigate universal metabolic interactions between microbes in aquatic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Scale-invariant magnetic textures in the strongly correlated oxide NdNiO 3

Strongly correlated quantum solids are characterized by an inherently granular electronic fabric, with spatial patterns that can span multiple length scales in proximity to a critical point. Here, we use a resonant magnetic X-ray scattering nanoprobe with sub-100 nm spatial resolution to directly visualize the texture of antiferromagnetic domains in NdNiO 3 . Surprisingly, our measurements reveal a highly textured magnetic fabric, which we show to be robust and nonvolatile even after thermal erasure across its ordering temperature. The scale-free distribution of antiferromagnetic domains and its non-integral dimensionality point to a hitherto-unobserved magnetic fractal geometry in this system. These scale-invariant textures directly reflect the continuous nature of the magnetic transition and the proximity of this system to a critical point. The present study not only exposes the near-critical behavior in rare earth nickelates but also underscores the potential for X-ray scattering nanoprobes to image the multiscale signatures of criticality near a critical point.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Momentum-independent magnetic excitation continuum in the honeycomb iridate H 3 LiIr 2 O 6

Understanding the interplay between the inherent disorder and the correlated fluctuating-spin ground state is a key element in the search for quantum spin liquids. H 3 LiIr 2 O 6 is considered to be a spin liquid that is proximate to the Kitaev-limit quantum spin liquid. Its ground state shows no magnetic order or spin freezing as expected for the spin liquid state. However, hydrogen zero-point motion and stacking faults are known to be present. The resulting bond disorder has been invoked to explain the existence of unexpected low-energy spin excitations, although data interpretation remains challenging. Here, we use resonant X-ray spectroscopies to map the collective excitations in H 3 LiIr 2 O 6 and characterize its magnetic state. In the low-temperature correlated state, we reveal a broad bandwidth of magnetic excitations. The central energy and the high-energy tail of the continuum are consistent with expectations for dominant ferromagnetic Kitaev interactions between dynamically fluctuating spins. Furthermore, the absence of a momentum dependence to these excitations are consistent with disorder-induced broken translational invariance. Our low-energy data and the energy and width of the crystal field excitations support an interpretation of H 3 LiIr 2 O 6 as a disordered topological spin liquid in close proximity to bond-disordered versions of the Kitaev quantum spin liquid.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Multipolar condensates and multipolar Josephson effects

When single-particle dynamics are suppressed in certain strongly correlated systems, dipoles arise as elementary carriers of quantum kinetics. These dipoles can further condense, providing physicists with a rich realm to study fracton phases of matter. Whereas recent theoretical discoveries have shown that an unconventional lattice model may host a dipole condensate as the ground state, we show that dipole condensates prevail in bosonic systems due to a self-proximity effect. Our findings allow experimentalists to manipulate the phase of a dipole condensate and deliver dipolar Josephson effects, where supercurrents of dipoles arise in the absence of particle flows. The self-proximity effects can also be utilized to produce a generic multipolar condensate. The kinetics of the n -th order multipoles unavoidably creates a condensate of the ( n + 1)-th order multipoles, forming a hierarchy of multipolar condensates that will offer physicists a whole new class of macroscopic quantum phenomena.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

An integrated atom array-nanophotonic chip platform with background-free imaging

Arrays of neutral atoms trapped in optical tweezers have emerged as a leading platform for quantum information processing and quantum simulation due to their scalability, reconfigurable connectivity, and high-fidelity operations. Individual atoms are promising candidates for quantum networking due to their capability to emit indistinguishable photons that are entangled with their internal atomic states. Integrating atom arrays with photonic interfaces would enable distributed architectures in which nodes hosting many processing qubits could be efficiently linked together via the distribution of remote entanglement. However, many atom array techniques cease to work in close proximity to photonic interfaces, with atom detection via standard fluorescence imaging presenting a major challenge due to scattering from nearby photonic devices. Here, we demonstrate an architecture that combines atom arrays with up to 64 optical tweezers and a millimeter-scale photonic chip hosting more than 100 nanophotonic cavities. We achieve high-fidelity ( ~ 99.2%), background-free imaging in close proximity to nanofabricated cavities using a multichromatic excitation and detection scheme. The atoms can be imaged while trapped a few hundred nanometers above the dielectric surface, which we verify using Stark shift measurements of the modified trapping potential. Finally, we rearrange atoms into defect-free arrays and load them simultaneously onto the same or multiple devices.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Near-Field Corrosion Interactions between Glass and Corrosion Resistant Alloys

This study explores the corrosion interactions between model nuclear waste glass materials and corrosion resistant alloys, under conditions that simulate the near field of a nuclear waste repository. The interactions between the corrosion of stainless steel (SS) 316, alloy G30, or alloy 625, and international simple glass or soda-lime silica glass are systematically studied. The dissimilar materials were exposed in close proximity to each other in different electrolytes at 90 oC. After exposure, the glass surface exposed near metals showed different regimes of corrosion, with distinct surface morphologies and chemistries that were likely affected by the local environment created by the localized corrosion of metals. Surface and solution analyses showed that the corrosion rate of glass was enhanced by the presence of metals. Infrared spectroscopy data suggested the local build-up of stresses in the contact area of glass, which may lead to the mechanical instability of the glass alteration layer. On the other hand, the effect of glass on metal corrosion is strongly dependent on the leaching solution. In electrolytes containing abundant aggressive anions such as Cl-, glass seems to suppress the localized corrosion of SS by the precipitation of a Si-rich surface film that protects the SS substrate from solutions. However, in less aggressive electrolytes, the corrosion rate of SS was increased by the presence of glass corrosion products. Overall, our study showed that the hidden and localized damage on glass in contact with metals may enhance the release of incorporated radionuclides compared to typical uniform glass corrosion. Therefore, more attention should be paid to the corrosion interactions between metals and glass under repository conditions.

Guo, Xiaolei↗
DOE OSTI2020

Coulomb blockade effects in a topological insulator grown on a high- T c cuprate superconductor

The evidence for proximity-induced superconductivity in heterostructures of topological insulators and high- T c cuprates has been intensely debated. We use molecular-beam epitaxy to grow thin films of topological insulator Bi 2 Te 3 on a cuprate Bi 2 Sr 2 CaCu 2 O 8+x , and study the surface of Bi 2 Te 3 using low-temperature scanning tunneling microscopy and spectroscopy. In few unit-cell thick Bi 2 Te 3 films, we find a V-shaped gap-like feature at the Fermi energy in d I /d V spectra. By reducing the coverage of Bi 2 Te 3 films to create nanoscale islands, we discover that this spectral feature dramatically evolves into a much larger hard gap, which can be understood as a Coulomb blockade gap. This conclusion is supported by the evolution of d I /d V spectra with the lateral size of Bi 2 Te 3 islands, as well as by topographic measurements that show an additional barrier separating Bi 2 Te 3 and Bi 2 Sr 2 CaCu 2 O 8+x . We conclude that the prominent gap-like feature in d I /d V spectra in Bi 2 Te 3 films is not a proximity-induced superconducting gap. Instead, it can be explained by Coulomb blockade effects, which take into account additional resistive and capacitive coupling at the interface. Our experiments provide a fresh insight into the tunneling measurements of complex heterostructures with buried interfaces.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗