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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 1,585 records · Page 88
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Regioselective surface encoding of nanoparticles for programmable self-assembly

Surface encoding of colloidal nanoparticles with DNA is fundamental for fields where recognition interaction is required, particularly controllable material self-assembly. However, regioselective surface encoding of nanoparticles is still challenging because of the difficulty associated with breaking the identical chemical environment on nanoparticle surfaces. Here we demonstrate the selective blocking of nanoparticle surfaces with a diblock copolymer (polystyrene-b-polyacrylic acid). By tuning the interfacial free energies of a ternary system involving the nanoparticles, solvent and copolymer, controllable accessibilities to the nanoparticles’ surfaces are obtained. Through the modification of the polymer-free surface region with single-stranded DNA, regioselective and programmable surface encoding is realized. The resultant interparticle binding potential is selective and directional, allowing for an increased degree of complexity of potential self-assemblies. As a result, the versatility of this regioselective surface encoding strategy is demonstrated on various nanoparticles of isotropic or anisotropic shape and a total of 24 distinct complex nanoassemblies are fabricated.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

Inverse chirality-induced spin selectivity effect in chiral assemblies of π -conjugated polymers

Coupling of spin and charge currents to structural chirality in non-magnetic materials, known as chirality-induced spin selectivity, is promising for application in spintronic devices at room temperature. Although the chirality-induced spin selectivity effect has been identified in various chiral materials, its Onsager reciprocal process, the inverse chirality-induced spin selectivity effect, remains unexplored. Here we report the observation of the inverse chirality-induced spin selectivity effect in chiral assemblies of π-conjugated polymers. Using spin-pumping techniques, the inverse chirality-induced spin selectivity effect enables quantification of the magnitude of the longitudinal spin-to-charge conversion driven by chirality-induced spin selectivity in different chiral polymers. By widely tuning conductivities and supramolecular chiral structures via a printing method, we found a very long spin relaxation time of up to several nanoseconds parallel to the chiral axis. Furthermore, our demonstration of the inverse chirality-induced spin selectivity effect suggests possibilities for elucidating the puzzling interplay between spin and chirality, and opens a route for spintronic applications using printable chiral assemblies.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant–microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. In this paper, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. Finally, this discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

De novo design of pH-responsive self-assembling helical protein filaments

Abstract Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge

Abstract Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.

Science & Technology - Other Topics↗
DOE OSTI2017

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids

Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

A neutron tomography study: probing the spontaneous crystallization of randomly packed granular assemblies

We study the spontaneous crystallization of an assembly of highly monodisperse steel spheres under shaking, as it evolves from localized icosahedral ordering towards a packing reaching crystalline ordering. Towards this end, real space neutron tomography measurements on the granular assembly are carried out, as it is systematically subjected to a variation of frequency and amplitude. As expected, we see a presence of localized icosahedral ordering in the disordered initial state (packing fraction ≈ 0.62). As the frequency is increased for both the shaking amplitudes (0.2 and 0.6 mm) studied here, there is a rise in packing fraction, accompanied by an evolution to crystallinity. The extent of crystallinity is found to depend on both the amplitude and frequency of shaking. We find that the icosahedral ordering remains localized and its extent does not grow significantly, while the crystalline ordering grows rapidly as an ordering transition point is approached. In the ordered state, crystalline clusters of both face centered cubic (FCC) and hexagonal close packed (HCP) types are identified, the latter of which grows from stacking faults. Our study shows that an earlier domination of FCC gives way to HCP ordering at higher shaking frequencies, suggesting that despite their coexistence, there is a subtle dynamical competition at play. This competition depends on both shaking amplitude and frequency, as our results as well as those of earlier theoretical simulations demonstrate. It is likely that this involves the very small free energy difference between the two structures.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Top-down fabrication of high-uniformity nanodiamonds by self-assembled block copolymer masks

Abstract Nanodiamonds hosting colour centres are a promising material platform for various quantum technologies. The fabrication of non-aggregated and uniformly-sized nanodiamonds with systematic integration of single quantum emitters has so far been lacking. Here, we present a top-down fabrication method to produce 30.0 ± 5.4 nm uniformly-sized single-crystal nanodiamonds by block copolymer self-assembled nanomask patterning together with directional and isotropic reactive ion etching. We show detected emission from bright single nitrogen vacancy centres hosted in the fabricated nanodiamonds. The lithographically precise patterning of large areas of diamond by self-assembled masks and their release into uniformly sized nanodiamonds open up new possibilities for quantum information processing and sensing.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein

Oligomerization of Pr55 Gag is a critical step of the late stage of the HIV life cycle. It has been known that the binding of IP6, an abundant endogenous cyclitol molecule at the MA domain, has been linked to the oligomerization of Pr55 Gag . However, the exact binding site of IP6 on MA remains unknown and the structural details of this interaction are missing. Here, we present three high-resolution crystal structures of the MA domain in complex with IP6 molecules to reveal its binding mode. Additionally, extensive Differential Scanning Fluorimetry analysis combined with cryo- and ambient-temperature X-ray crystallography and GNM-based transfer entropy calculations identify the key residues that participate in IP6 binding. Our data provide novel insights about the multilayered HIV-1 virion assembly process that involves the interplay of IP6 with PIP2, a phosphoinositide essential for the binding of Pr55 Gag to membrane. IP6 and PIP2 have neighboring alternate binding sites within the same highly basic region (residues 18–33). This indicates that IP6 and PIP2 bindings are not mutually exclusive and may play a key role in coordinating virion particles’ membrane localization. Based on our three different IP6-MA complex crystal structures, we propose a new model that involves IP6 coordination of the oligomerization of outer MA and inner CA domain’s 2D layers during assembly and budding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Hydrodynamic trapping for rapid assembly and in situ electrical characterization of droplet interface bilayer arrays

The droplet interface bilayer (DIB) is a modular technique for assembling planar lipid membranes between water droplets in oil. The DIB method thus provides a unique capability for developing digital, droplet-based membrane platforms for rapid membrane characterization, drug screening and ion channel recordings. This paper demonstrates a new, low-volume microfluidic system that automates droplet generation, sorting, and sequential trapping in designated locations to enable the rapid assembly of arrays of DIBs. The channel layout of the device is guided by an equivalent circuit model, which predicts that a serial arrangement of hydrodynamic DIB traps enables sequential droplet placement and minimizes the hydrodynamic pressure developed across filled traps to prevent squeeze-through of trapped droplets. Furthermore, the incorporation of thin-film electrodes fabricated via evaporation metal deposition onto the glass substrate beneath the channels allows for the first time in situ, simultaneous electrical interrogation of multiple DIBs within a sealed device. Combining electrical measurements with imaging enables measurements of membrane capacitance and resistance and bilayer area, and our data show that DIBs formed in different trap locations within the device exhibit similar sizes and transport properties. Simultaneous, single channel recordings of ion channel gating in multiple membranes are obtained when alamethicin peptides are incorporated into the captured droplets, qualifying the thin-film electrodes as a means for measuring stimuli-responsive functions of membrane-bound biomolecules. Furthermore, this novel microfluidic-electrophysiology platform provides a reproducible, high throughput method for performing electrical measurements to study transmembrane proteins and biomembranes in low-volume, droplet-based membranes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Automated glycan assembly of galactosylated xyloglucan oligosaccharides and their recognition by plant cell wall glycan-directed antibodies

We report the automated glycan assembly of oligosaccharides related to the plant cell wall hemicellulosic polysaccharide xyloglucan. The synthesis of galactosylated xyloglucan oligosaccharides was enabled by introducing p-methoxybenzyl (PMB) as a temporary protecting group for automated glycan assembly. The generated oligosaccharides were printed as microarrays, and the binding of a collection of xyloglucan-directed monoclonal antibodies (mAbs) to the oligosaccharides was assessed. We also demonstrated that the printed glycans can be further enzymatically modified while appended to the microarray surface by Arabidopsis thaliana xyloglucan xylosyltransferase 2 (AtXXT2).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Plasmonic circular dichroism of vesicle-like nanostructures by the template-less self-assembly of achiral Janus nanoparticles

Chiral nanostructures have been attracting extensive interest in recent years primarily because of the unique materials properties that can be exploited for diverse applications. In this study, gold Janus nanoparticles, with hexanethiolates and 3-mercapto-1,2-propanediol segregated on the two hemispheres of the metal cores (dia. 2.7 ± 0.4 nm), self-assembled into vesicle-like, hollow nanostructures in both water or organic media, and exhibited apparent plasmonic circular dichroism (PCD) absorption in the visible range. This was in contrast to individual Janus nanoparticles, bulk-exchange nanoparticles where the two ligands were homogeneously mixed on the nanoparticle surface, or nanoparticles capped with only one kind of the ligands. The PCD signals were found to become intensified with increasing coverage of the 3-mercapto-1,2-propanediol ligands on the nanoparticle surface. This was accounted for by the dipolar property of the structurally asymmetrical Janus nanoparticles, and theoretical simulations based on first principles calculations showed that when the nanoparticle dipoles self-assembled onto the surface of a hollow sphere, a vortex was formed which gave rise to the unique chiral characteristics. The resulting chiral nanoparticle vesicles could be exploited for the separation of optical enantiomers, as manifested in the selective identification and separation of D-alanine from the L-isomer

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Investigations into the assembly behaviour of a ‘rigidified’ p -carboxylatocalix[4]arene

The p-carboxylatocalix[4]arenes have been shown to be versatile supramolecular building blocks capable of forming a range of bi-layers, capsules and nanoscale tubules in the solid state. In this work, we report the synthesis of a new ‘rigidified’ analogue, as well as investigations into its self-assembly and related coordination chemistry. These behaviours are reminiscent of other p-carboxylatocalix[4]arenes despite the presence of rigidifying groups at the lower-rim, suggesting that this building block may be further exploited in the assembly of a range of new metal–organic cages and coordination polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Solvent-free and rapid synthesis of mesoporous Pt–iron oxide catalysts via mechanochemical assembly

Mesoporous Fe x O y and Pt@Fe x O y have proven promising performance in catalysis. Yet, current methods usually use wet chemistry, which poses several drawbacks. Here, we introduce a simple process of mechanochemical assembly between an iron salt and a triblock copolymer in the solid state that can not only directly form abundant mesopores into Fe x O y , but also enable a high dispersion of Pt species at the nm or sub-nm scale. In this regard, mesoporous FexOy and Pt@Fe x O y catalysts with high surface areas (up to 149 m 2 g -1 ) and narrow pore size distributions (~5 nm) can be obtained in a solvent-free and rapid (0.5 h) way. The kinetic energy and frictional heating of ball milling are expected to promote the interaction and diffusion between iron precursors and surfactants, while the solvent-free feature confines their assembly to the mesophase of the P123 copolymer. Moreover, these Pt@Fe x O y catalysts provide good activity in the total oxidation of propylene and CO.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Heliconical-layered nanocylinders (HLNCs) – hierarchical self-assembly in a unique B4 phase liquid crystal morphology

A unique morphology for bent-core liquid crystals forming the B4 phase has been found for a class of tris-biphenyl bent-core liquid crystal molecules with a single chiral side chain in the longer para-side of the molecule. Unlike the parent molecules with two chiral side chains or a chiral side chain in the shorter meta-side, which form helical nano- or microfilament B4 phases, the two derivatives described here form heliconical-layered nanocylinders composed of up to 10 coaxial heliconical layers, which can split or merge, braid, and self-assemble into a variety of modes including feather- or herringbone-type structures, concentric rings, or hollow nest-like superstructures. Finally, these multi-level hierarchical self-assembled structures, rivaling muscle fibers, display blue structural color and show immense structural and morphological complexity.

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

A versatile strategy for controlled assembly of plasmonic metal/semiconductor hemispherical nano-heterostructure arrays

Recent advances in manipulating plasmonic properties of metal/semiconductor heterostructures have opened up new avenues for basic research and applications. Herein, we present a versatile strategy for the assembly of arrays of plasmonic metal/semiconductor hemispherical nano-heterostructures (MSHNs) with control over spacing and size of the metal/semiconductor heterostructure array, which can facilitate a wide range of scientific studies and applications. The strategy combines nanosphere lithography for generating the metal core array with solution-based chemical methods for the semiconductor shell that are widely available and kinetically controllable. Periodic arrays of Au/Cu 2 O and Ag/Cu 2 O heterostructures are synthesized to demonstrate the approach and highlight the versatility and importance of the tunability of plasmonic properties. The morphology, structure, optical properties, and elemental compositions of the heterostructures were analyzed. Finally, this strategy can be important for understanding and manipulating fundamental nanoscale solid-state physical and chemical properties, as well as assembling heterostructures with desirable structure and functionality for applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Temperature-mediated molecular ladder self-assembly employing Diels–Alder cycloaddition

Dynamic covalent self-assembly processes often exhibit poor capacities for error-correction owing to the relatively low connectivity rearrangement rates of dynamic covalent interactions and the common use of reaction conditions where the equilibrium state remains fixed. Here, we report a dynamic covalent self-assembly technique employing temperature, a conventional, externally-applied stimulus, to mediate the hybridization of peptoid oligomers bearing maleimide- and furan-based pendant groups to afford molecular ladders incorporating Diels–Alder adduct-based rungs. By raising or lowing the reaction temperature, this system enables the equilibrium state to be readily varied without altering reagent concentrations. Both triethylamine and the Lewis acidic scandium triflate were examined as candidate reaction catalysts; however, only scandium triflate increased the rate of single strand conversion. Additionally, as the Diels–Alder cycloaddition reaction does not liberate a small molecule, a registry-dependent mass change was effected by employing a base-catalyzed thiol-Michael addition reaction between any un-reacted maleimide pendant groups and a low molecular weight thiol to enable the number of Diels–Alder adduct rungs to be readily determined by mass spectrometry. Finally, by employing a slow temperature ramp from high to low temperature, approximating the thermal cycle employed for nucleic acid hybridization, sequence-selective hybridization between model, tetra-functional precursor strands was demonstrated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗