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Results for “structure assembly”

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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Engineering hybrid textile braids for tendon and ligament repair application

Abstract Challenges involving tendon and ligament repair have motivated the investigation of new strategies to improve clinical outcomes. These have been mainly based on polymer constructs, which may be non‐biodegradable or biodegradable. The former typically fails due to lack of device integration and the latter demands a complex balance between biodegradability and tissue ingrowth, often failing due to insufficient mechanical properties. This work presents the development of hybrid braids based on polyethylene terephthalate (PET) and polylactic acid (PLA) yarns. A textile technique was used to fabricate braids based on 16 multifilament yarns of varying PLA/PET composition. The composition was varied to maximize biodegradability while ensuring mechanical performance. The braids' morphology, physical and mechanical properties were characterized. As production parameters and architecture were maintained, the braids exhibited similar porosity and wicking ability. The breaking force and stiffness decreased significantly as the number of PLA yarns increased, although strain levels remained constant. Braids containing 10 and 12 PET yarns (out of the total 16 yarns) demonstrated good creep and force‐relaxation behavior, as well as resistance to cyclic loading. These compositions were selected for future work, to be assembled into more elaborate structures to mimic the fibrous organization and tensile properties of different tendons/ligaments.

Peixoto, Tânia↗
DOE OSTI2023

Assessing mechanisms for microbial taxa and community dynamics using process models

Disentangling the assembly mechanisms controlling community composition, structure, distribution, functions, and dynamics is a central issue in ecology. Although various approaches have been proposed to examine community assembly mechanisms, quantitative characterization is challenging, particularly in microbial ecology. Here, we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations. Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes, we tested the applicability of three ecological models: the consumer–resource model, the neutral model, and the combined model. Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions. The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated. In contrast, the neutral model showed the best performance for rare taxa. Our analysis further indicated that immigration rates decreased with taxa abundance and competitions between taxa were strongly correlated with phylogeny, but within a certain phylogenetic distance only. The determinism underlying taxa and community dynamics were quantitatively assessed, showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning. Given its mechanistic basis, the framework developed here is expected to be potentially applicable beyond microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Toward controlled functional sequencing and hierarchical structuring in imidazolium ionenes

This focused mini-review highlights recent advances related to the design and applications of imidazolium ionenes and forward-looking perspectives. Creative strategies which employ established synthetic approaches and utilize the modularity of the imidazole moiety unlock great potential for tailoring both functional and structural features arising from precise spacing of ionic groups within the polymer backbone. Here, as imidazolium ionenes draw more interest, increased sophistication of chemical modifications and material processing is occurring, with a corresponding shift toward more demanding applications. Synthetic routes for placement and sequencing of ionic content are discussed, in addition to recent approaches to control structure and self-assembly or tune behaviors of imidazolium ionenes and composites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A view of the pan‐genome of domesticated Cowpea ( Vigna unguiculata [L.] Walp.)

Abstract Cowpea, Vigna unguiculata L . Walp., is a diploid warm‐season legume of critical importance as both food and fodder in sub‐Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K‐499‐35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A feasible order-arbitrarily-tunable optical differentiator

We propose a feasible temporal filtering (or spectrum weighting) system to implement optical differentiation with arbitrarily-tunable order. Differentiation order is tuned by programming the temporal weighting mask (TWM) as power function of different exponents, not limited by the structure of the system. Assembly of the system is feasible, since the active parts are implemented by electro-optic elements and some key elements are reused between sub-systems involved in the scheme. Tuning of the system is simple, since electronically pre-stored TWMs are easy to switch among each other. The order-tunable functionality is verified by numerically testing the differentiation cases of normalized input pulse duration ranging from 0.1 to 0.4, and of differentiation order tuned from 1 to 10. Good accuracy is achieved, and measured by root mean square error lower than 0.1. Feasibilities of the system are also verified in terms of accuracy maintaining and distortion avoiding. Compared with existing methods, apart from the arbitrary order-tunable capacity and good accuracy, our proposed optical differentiator also possesses properties of good compactness and constant complexity. The proposed differentiator has unique applications on multi-peak waveform generation for optical communications and photonics-aided Radars with enhanced agility and feasibility.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Solvent Processing and Ionic Liquid-Enabled Long-Range Vertical Ordering in Block Copolymer Films with Enhanced Film Stability

Rapid and reliable processing methods for forming ordered block copolymer (BCP) materials with low defect density in a thin film geometry are required for many nanotechnology applications. Vertically aligned BCP structures, in particular, have applications ranging from nanolithography for electronics and photonics to nanoporous membranes for water remediation and novel batteries for flexible electronics. However, the attainment of nearly complete vertical orientational order of the BCP ordered phase remains challenging. Solvent-based techniques, such as direct immersion annealing (DIA) and solvent vapor annealing (SVA), have immense potential for these applications of BCP films, as it allows for tuning of their thermodynamic, structural, and chain mobility driven kinetic properties. We first demonstrate that DIA, using a judicious choice of binary solvent mixtures along with a relatively hydrophobic ionic liquid (IL), induces the rapid vertical ordering in polystyrene-b-polymethylmethacrylate (PS-PMMA) block copolymer in lamellar films. The IL establishes synergy to the binary solvent mixture of toluene and heptane to 1 create a near-neutral solvent environment for attaining the vertical microstructure of the BCP. Next, we show that IL can suppress the de-wetting of the PS-PMMA films to achieve long-range order using SVA in cylindrical films for long annealing times. Both vertical and horizontal morphology is attained in these films by selecting different solvent environments. Furthermore, attaining enhanced vertical and horizontal BCP structure with long-range defect-free order by tuning solvent quality and using additives like IL can render them useful for many nanotech applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Interfacial Fabrication of Supramolecular Polymer Networks Using Mussel-Inspired Catechol–Iron Complexes

The liquid–liquid interface provides a promising platform to construct supramolecular polymers and materials with advanced functions. However, supramolecular polymerization at the interface usually requires monomers with different or even orthogonal solubilities, which significantly limit the number of usable monomers. Here, in this work, we report a new strategy to construct supramolecular polymer networks at the oil–water interface using a water-soluble catechol–iron complex and an oil-soluble diend-functionalized polymer. Owing to the dynamic catechol–iron coordination bond and imine bond, the resulting supramolecular polymer networks demonstrate excellent dynamic features and responsiveness to different stimuli including the pH, redox, competing ligands, and temperature. With a supramolecular polymer network serving as a building block, emulsions and 2D films can be generated that have potential applications in encapsulation, release, and molecular separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Broadband Plasmonic Photocurrent Enhancement from Photosystem I Assembled with Tailored Arrays of Au and Ag Nanodisks

Plasmonic interactions between metal nanostructures and fluorophores have been increasingly employed to alter photoexcitation pathways in multichromophore photosynthetic proteins like photosystem I (PSI). Our recent experimental studies demonstrated a sixfold plasmon-enhanced photocurrent from PSI assembled on Fischer patterns of Ag nanopyramids. However, lack of control over the specific resonance modes limited the magnitude and selectivity of the plasmonic enhancement. To this end, the present study investigates the excitation wavelength-dependent plasmon-enhanced photocurrents from PSI immobilized around highly ordered Au (AuND) and Ag (AgND) nanodisks with dipolar plasmon resonances that are tuned to ~680 and 560 nm, respectively. Specifically, we report plasmon-induced photocurrent enhancements of ~6.8 and 17.5 for excitation wavelengths of ~680 and 565 nm, respectively, as compared to PSI assembled on planar ITO substrates. We also report the action spectra for photocurrent enhancements recorded over wavelengths of 395–810 nm with nine discrete LED light sources. The results indicate the following: (1) concurrence between the photocurrent-enhancement spectra from PSI assemblies and the plasmonic resonances for the respective nanopatterned substrates, and (2) broadband photocurrent enhancements due to plasmon-coupled photoactivation in the otherwise blind chlorophyll regions of the native PSI absorption spectra. Lastly, these intriguing findings pave the path for rational assembly of future biohybrid structures composed of natural light-harvesting antennae and plasmonic metal nanostructures.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Three-Dimensional Patterning of Nanoparticles by Molecular Stamping

Directing the formation of nanoscale architectures from nanoparticles is one of the key challenges in designing nanomaterials with prescribed functions. Atomic systems, given their ability to form molecules and crystals via directional chemical bonds, provide an inspiration for establishing approaches where nanoparticles with designed anisotropic binding modalities can be assembled into nanoscale architectures. However, fabricating such nanoparticles has been challenging due to their small dimensions and limited ways for site-specific control of their surface. To this end, we present a Molecular Stamping (MOST) approach to pattern DNA-coated nanoparticles with molecules at the predefined positions on a nanoparticle surface. This patterning is realized by use of a rigid and coordinative DNA frame as a molecular stamping apparatus (MOST App). The MOST App transfers multiple types of molecular “inks”, DNA sequences, onto nanoparticle surface and fixes these molecular inks into place to form a designed pattern. After a nanoparticle release from MOST App, it possesses single-molecule patches that can provide anisotropic bonds with distinctive affinities. We further use these stamped nanoparticles to assemble prescribed clusters, whose structure is determined by the locations of patches. Using electron microscopy and tomographic methods, we investigate the efficiency of cluster formation and the resulting spatial arrangements of nanoparticles. The presented approach provides a single-molecule and spatiallydetermined control over nanoparticle functionalization for creating nanoparticles with designed placement of different molecules and for realizing a rational fabrication of nanomaterial architectures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Structural Characterization of the Platinum Nanoparticle Hydrogen-Evolving Catalyst Assembled on Photosystem I by Light-Driven Chemistry

Directed assembly of abiotic catalysts onto biological redox protein frameworks is of interest as an approach for the synthesis of biohybrid catalysts that combine features of both synthetic and biological materials. In this report, we provide a multiscale characterization of the platinum nanoparticle (NP) hydrogen-evolving catalysts that are assembled by light-driven reductive precipitation of platinum from an aqueous salt solution onto the photosystem I protein (PSI), isolated from cyanobacteria as trimeric PSI. The resulting PSI-NP assemblies were analyzed using a combination of X-ray energy-dispersive spectroscopy (XEDS), high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM), small-angle X-ray scattering (SAXS), and high-energy X-ray scattering with atomic pair distribution function (PDF) analyses. The results show that the PSI-supported NPs are approximately 1.8 nm diameter disk-shaped particles that assemble at discrete sites with 145 Å separation. This separation is too large to be consistent with NP nucleation and growth at a site adjacent to the F B cofactor site. Instead, we suggest a mechanism for NP growth at hydrophobic sites on the PSI stromal surface. The NPs photoreductively assembled on the PSI stromal surface are found to be analogous to the nanostructures produced by successive cycles of atomic layer deposition (ALD) of platinum onto 40 nm porous anodic alumina oxide supports, although the mechanisms for nucleation appear to differ. In conclusion, this work establishes a foundation for the investigation of the reductive assembly of abiotic metal catalysts at sites connected to photochemically reducing equivalent production in PSI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Nicotinamide-Loaded Peptoid Nanotubes for Energy Regeneration in Acute Brain Injury

Acute brain injuries such as perinatal asphyxia, stroke, and traumatic brain injury result in ischemia, oxidative stress, excitotoxicity, and inflammation, leading to a depletion of ATP. Nicotinamide adenine dinucleotide (NAD+) is crucial for ATP regeneration and DNA repair during postinjury recovery. However, the therapeutic benefits of NAD+ and its precursors, such as nicotinamide (NAM), are limited by challenges in achieving effective cell-specific intracellular delivery. In this study, we use a nanopeptoid delivery strategy to replenish the cellular redox state and increase energy production in the acutely injured brain. By self-assembling peptoids into tubular structures, we created biocompatible NAM-conjugated peptoid nanotubes (NAM-PNTs) that vary in tubular length. NAM-PNTs demonstrated significant therapeutic benefits by enhancing cell viability and replenishing intracellular ATP levels within 24 h of treatment in oxygen–glucose-deprived (OGD) BV-2 cells. In organotypic brain slices, NAM-PNT treatment promoted glial proliferation, reduced proinflammatory cytokines, and increased anti-inflammatory cytokines after OGD, an ex vivo model of hypoxia-ischemia. The effect of NAM-PNTs is associated with their uptake into microglia via fluid-phase phagocytosis and caveolae-mediated endocytosis. A single systemic dose of NAM-PNTs localized in microglia in the injured hemisphere and reduced brain tissue loss and improved neuropathology after hypoxia-ischemia in term-equivalent rats. These findings highlight the therapeutic potential of NAM-PNTs for cell-specific targeted delivery and energy restoration in the acutely injured neonatal brain. In the neonatal brain injury field, this work demonstrates the development of an innovative nanoparticle platform from first-principles design and synthesis to in vitro screening and then demonstration of efficacy in vivo .

ATP↗
DOE OSTI2024

Supramolecular Motion Enables Chondrogenic Bioactivity of a Cyclic Peptide Mimetic of Transforming Growth Factor-β1

Transforming growth factor (TGF)-β1 is a multifunctional protein that is essential in many cellular processes that include fibrosis, inflammation, chondrogenesis, and cartilage repair. In particular, cartilage repair is important to avoid physical disability since this tissue does not have the inherent capacity to regenerate beyond full development. We report here on supramolecular coassemblies of two peptide amphiphile molecules, one containing a TGF-β1 mimetic peptide, and another which is one of two constitutional isomers lacking bioactivity. Using human articular chondrocytes, we investigated the bioactivity of the supramolecular copolymers of each isomer displaying either the previously reported linear form of the mimetic peptide or a novel cyclic analogue. Based on fluorescence depolarization and 1 H NMR spin–lattice relaxation times, we found that coassemblies containing the cyclic compound and the most dynamic isomer exhibited the highest intracellular TGF-β1 signaling and gene expression of cartilage extracellular matrix components. Here, we conclude that control of supramolecular motion is emerging as an important factor in the binding of synthetic molecules to receptors that can be tuned through chemical structure.

Antigens↗
DOE OSTI2022

Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery

Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV’s complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein’s post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Reweighting configurations generated by transferable, machine learned models for protein sidechain backmapping

Multiscale modeling requires the linking of models at different levels of detail, with the goal of gaining accelerations from lower fidelity models while recovering fine details from higher resolution models. Communication across resolutions is particularly important in modeling soft matter, where tight couplings exist between molecular-level details and mesoscale structures. While multiscale modeling of biomolecules has become a critical component in exploring their structure and self-assembly, backmapping from coarse-grained to fine-grained, or atomistic, representations presents a challenge, despite recent advances through machine learning. A major hurdle, especially for strategies utilizing machine learning, is that backmappings can only approximately recover the atomistic ensemble of interest. We demonstrate conditions for which backmapped configurations may be reweighted to exactly recover the desired atomistic ensemble. By training separate decoding models for each sidechain type, we develop an algorithm based on normalizing flows and geometric algebra attention to autoregressively propose backmapped configurations for any protein sequence. Critical for reweighting with modern protein force fields, our trained models include all hydrogen atoms in the backmapping and make probabilities associated with atomistic configurations directly accessible. We also demonstrate, however, that reweighting is extremely challenging despite state-of-the-art performance on recently developed metrics and generation of configurations with low energies in atomistic protein force fields. Through detailed analysis of configurational weights, we show that machine-learned backmappings must not only generate configurations with reasonable energies, but also correctly assign relative probabilities under the generative model. These are broadly important considerations in generative modeling of atomistic molecular configurations.

Monroe, Jacob I. [Univ. of Arkansas, Fayetteville,↗
DOE OSTI2022

SCONCE : a cosmic web finder for spherical and conic geometries

The latticework structure known as the cosmic web provides a valuable insight into the assembly history of large-scale structures. Despite the variety of methods to identify the cosmic web structures, they mostly rely on the assumption that galaxies are embedded in a Euclidean geometric space. Here, we present a novel cosmic web identifier called SCONCE (Spherical and CONic Cosmic wEb finder) that inherently considers the 2D (RA, DEC) spherical or the 3D (RA, DEC, z) conic geometry. The proposed algorithms in sconce generalize the well-known subspace constrained mean shift (SCMS) method and primarily address the predominant filament detection problem. They are intrinsic to the spherical/conic geometry and invariant to data rotations. We further test the efficacy of our method with an artificial cross-shaped filament example and apply it to the SDSS galaxy catalogue, revealing that the 2D spherical version of our algorithms is robust even in regions of high declination. Finally, using N-body simulations from Illustris, we show that the 3D conic version of our algorithms is more robust in detecting filaments than the standard SCMS method under the redshift distortions caused by the peculiar velocities of haloes. Our cosmic web finder is packaged in python as SCONCE-SCMS and has been made publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation

The class IB phosphoinositide 3-kinase (PI3K), PI3Kγ, is a master regulator of immune cell function and a promising drug target for both cancer and inflammatory diseases. Critical to PI3Kγ function is the association of the p110γ catalytic subunit to either a p101 or p84 regulatory subunit, which mediates activation by G protein–coupled receptors. Here, we report the cryo–electron microscopy structure of a heterodimeric PI3Kγ complex, p110γ-p101. This structure reveals a unique assembly of catalytic and regulatory subunits that is distinct from other class I PI3K complexes. p101 mediates activation through its Gβγ-binding domain, recruiting the heterodimer to the membrane and allowing for engagement of a secondary Gβγ-binding site in p110γ. Mutations at the p110γ-p101 and p110γ–adaptor binding domain interfaces enhanced Gβγ activation. A nanobody that specifically binds to the p101-Gβγ interface blocks activation, providing a novel tool to study and target p110γ-p101–specific signaling events in vivo.

59 BASIC BIOLOGICAL SCIENCES↗