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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structure and antigenicity of the divergent human astrovirus VA1 capsid spike

Human astrovirus (HAstV) is a known cause of viral gastroenteritis in children worldwide, but HAstV can cause also severe and systemic infections in immunocompromised patients. There are three clades of HAstV: classical, MLB, and VA/HMO. While all three clades are found in gastrointestinal samples, HAstV-VA/HMO is the main clade associated with meningitis and encephalitis in immunocompromised patients. To understand how the HAstV-VA/HMO can infect the central nervous system, we investigated its sequence-divergent capsid spike, which functions in cell attachment and may influence viral tropism. Here we report the high-resolution crystal structures of the HAstV-VA1 capsid spike from strains isolated from patients with gastrointestinal and neuronal disease. The HAstV-VA1 spike forms a dimer and shares a core beta-barrel structure with other astrovirus capsid spikes but is otherwise strikingly different, suggesting that HAstV-VA1 may utilize a different cell receptor, and an infection competition assay supports this hypothesis. Furthermore, by mapping the capsid protease cleavage site onto the structure, the maturation and assembly of the HAstV-VA1 capsid is revealed. Finally, comparison of gastrointestinal and neuronal HAstV-VA1 sequences, structures, and antigenicity suggests that neuronal HAstV-VA1 strains may have acquired immune escape mutations. Overall, our studies on the HAstV-VA1 capsid spike lay a foundation to further investigate the biology of HAstV-VA/HMO and to develop vaccines and therapeutics targeting it.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Membrane stiffness and myelin basic protein binding strength as molecular origin of multiple sclerosis

Myelin basic protein (MBP) and its interaction with lipids of the myelin sheath plays an important part in the pathology of multiple sclerosis (MS). Previous studies observed that changes in the myelin lipid composition lead to instabilities and enhanced local curvature of MBP-lipid multilayer structures. We investigated the molecular origin of the instability and found that the diseased lipid membrane has a 25% lower bending rigidity, thus destabilizing smooth >1µm curvature radius structures such as in giant unilamellar vesicles. MBP-mediated assembling of lipid bilayers proceeds in two steps, with a slow second step occurring over many days where native lipid membranes assemble into well-defined multilayer structures, whereas diseased lipid membranes form folded assemblies with high local curvature. For both native and diseased lipid mixtures we find that MBP forms dense liquid phases on top of the lipid membranes mediating attractive membrane interactions. Furthermore, we observe MBP to insert into its bilayer leaflet side in case of the diseased lipid mixture, whereas there is no insertion for the native mixture. Insertion increases the local membrane curvature, and could be caused by a decrease of the sphingomyelin content of the diseased lipid mixture. These findings can help to open a pathway to remyelination strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

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

Solvent independent symmetry-breaking charge separation in terrylenediimide guanine-quadruplex nanoparticles

G-quadruplex assemblies are a promising tool for self-assembling π-stacked chromophore arrays to better understand their photophysics. We have shown that coupling a single guanine moiety to terrylenediimide (TDI) produces a structure (GTDI) that self-assembles in tetrahydrofuran (THF) into a nearly monodisperse guanine-quadruplex structure having 16 π-stacked layers (GTDI 4 ) 16 . The TDI surfaces were determined to have a high degree of cofacial overlap and underwent quantitative symmetry-breaking charge separation (SB-CS) upon photoexcitation. Here, we more deeply examine the relationship between solvent and aggregate formation and develop insights into structure–function relationships over a variety of solvent polarities and hydrogen-bonding capabilities. At high concentrations, GTDI assembles into guanine-quadruplex structures (GTDI 4 ) 16 in THF and toluene, as well as (GTDI 4 ) 9 in pyridine and benzonitrile. Here, transient absorption spectroscopy shows that SB-CS occurs in all solvents, regardless of their static dielectric constants, but the SB-CS yield is determined by structure. Solvent polarity independent SB-CS generation is also observed in GTDI films, where there is a complete absence of solvent.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Intra- and Intermolecular Self-Assembly of a 20-nm-Wide Supramolecular Hexagonal Grid.

For the past three decades, the coordination-driven self-assembly of three-dimensional structures has undergone rapid progress; however, parallel efforts to create large discrete two-dimensional architectures-as opposed to polymers-have met with limited success. The synthesis of metallo-supramolecular systems with well-defined shapes and sizes in the range of 10-100 nm remains challenging. Here we report the construction of a series of giant supramolecular hexagonal grids, with diameters on the order of 20 nm and molecular weights greater than 65 kDa, through a combination of intra- and intermolecular metal-mediated self-assembly steps. The hexagonal intermediates and the resulting self-assembled grid architectures were imaged at submolecular resolution by scanning tunnelling microscopy. Characterization (including by scanning tunnelling spectroscopy) enabled the unambiguous atomic-scale determination of fourteen hexagonal grid isomers.

Zhang, Zhe↗
DOE OSTI2021

Coupling morphological and magnetic anisotropy for assembling tetragonal colloidal crystals

Morphological and magnetic anisotropy can be combined in colloidal assembly to create unconventional secondary structures. We show here that magnetite nanorods interact along a critical angle, depending on their aspect ratios and assemble into body-centered tetragonal colloidal crystals. Under a magnetic field, size-dependent attractive and repulsive domains develop on the ends and center of the nanorods, respectively. Our joint experiment-computational multiscale study demonstrates the presence of a critical angle in the attractive domain, which defines the equilibrium bonding states of interacting rods and leads to the formation of non–close-packed yet hard-contact tetragonal crystals. Small-angle x-ray scattering measurement attributes the perfect tetragonal phase to the slow assembly kinetics. The crystals exhibit brilliant structural colors, which can be actively tuned by changing the magnetic field direction. These highly ordered frameworks and well-defined three-dimensional nanochannels may offer new opportunities for manipulating nanoscale chemical transformation, mass transportation, and wave propagation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Environmental stress mediates groundwater microbial community assembly

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and ‘drift’ related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. As a result, our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Structural characterization of high-protein system through ultra-small and small-angle X-ray scattering

High-protein systems exhibit a hierarchical structure consisting of interconnected multiscale length assemblies. Recent investigations are directed toward identifying these structural units under various processing and environmental conditions to establish structure–function correlations. Ultra-small and small-angle X-ray scattering (USAXS/SAXS) has become a crucial tool for characterizing the structures of proteins and their clusters/aggregates, ranging from nanometers to micrometers, with minimal disruption to their original state. Here, this review first describes the facilities and principles of X-ray scattering, followed by discussions on the analysis of scattering data, including the interpretation of fitting models. It then delves into the main applications of USAXS/SAXS in plant and dairy protein-rich systems. Future strategies to enhance the utilization of scattering techniques for elucidating the structure of high-protein systems are also included.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA

Metazoan microRNAs require specificmaturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). In this paper we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. TwodsRBDs form a molecular ruler tomeasure the stem length between the twodsRNA-ssRNAjunctions. The specific organization of thedsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The cryoelectron microscopy structure of the human CDK-activating kinase

The human CDK-activating kinase (CAK), a complex composed of cyclin-dependent kinase (CDK) 7, cyclin H, and MAT1, is a critical regulator of transcription initiation and the cell cycle. It acts by phosphorylating the C-terminal heptapeptide repeat domain of the RNA polymerase II (Pol II) subunit RPB1, which is an important regulatory event in transcription initiation by Pol II, and it phosphorylates the regulatory T-loop of CDKs that control cell cycle progression. Here, we have determined the three-dimensional (3D) structure of the catalytic module of human CAK, revealing the structural basis of its assembly and providing insight into CDK7 activation in this context. The unique third component of the complex, MAT1, substantially extends the interaction interface between CDK7 and cyclin H, explaining its role as a CAK assembly factor, and it forms interactions with the CDK7 T-loop, which may contribute to enhancing CAK activity. We have also determined the structure of the CAK in complex with the covalently bound inhibitor THZ1 in order to provide insight into the binding of inhibitors at the CDK7 active site and to aid in the rational design of therapeutic compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Stabilizing Liquids Using Interfacial Supramolecular Assemblies

Stabilizing liquids based on supramolecular assembly (non-covalent intermolecular interactions) has attracted significant interest, due to the increasing demand for soft, liquid-based devices where the shape of the liquid is far from the equilibrium spherical shape. The components comprising these interfacial assemblies must have sufficient binding energies to the interface to prevent their ejection from the interface when the assemblies are compressed. In this report we highlight recent advances in structuring liquids based on non-covalent intermolecular interactions. We describe some of the progress made that reveals structure–property relationships. In addition to treating advances, we discuss some of the limitations and provide a perspective on future directions to inspire further studies on structured liquids based on supramolecular assembly.

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

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The influence of molecular design on structure–property relationships of a supramolecular polymer prodrug

Supramolecular self-assemblies of hydrophilic macromolecules functionalized with hydrophobic, structure-directing components have long been used for drug delivery. In these systems, loading of poorly soluble compounds is typically achieved through physical encapsulation during or after formation of the supramolecular assembly, resulting in low encapsulation efficiencies and limited control over release kinetics, which are predominately governed by diffusion and carrier degradation. To overcome these limitations, amphiphilic prodrugs that leverage a hydrophobic drug as both the therapeutic and structure-directing component can be used to create supramolecular materials with higher loading and controlled-release kinetics using biodegradable or enzymatically cleavable linkers. Here, we report the design, synthesis, and characterization of a library of supramolecular polymer prodrugs based on poly(ethylene glycol) (PEG) and the proregenerative drug 1,4-dihydrophenonthrolin-4-one-3-carboxylic acid (DPCA). Structure–property relationships were elucidated through experimental characterization of prodrug behavior in both the wet and dry states using scattering techniques and electron microscopy and corroborated by coarse-grained modeling. Molecular architecture and the hydrophobic-to-hydrophilic ratio of PEG–DPCA conjugates strongly influenced their physical state in water, ranging from fully soluble to supramolecular spherical assemblies and nanofibers. Molecular design and supramolecular structure, in turn, were shown to dramatically alter hydrolytic and enzymatic release and cellular transport of DPCA. In addition to potentially expanding therapeutic options for DPCA through control of supramolecular assemblies, the design principles elaborated here may inform the development of other supramolecular prodrugs based on hydrophobic small-molecule compounds.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Stellarator Simplification using Permanent Magnets (PM4Stell)

This Report describes the design and prototyping of an array of rare-Earth permanent magnets to form a stellarator. This effort was motivated by the hypothesis that the usage of permanent magnets, rather than electromagnetic coils with complex geometry, could reduce the cost of stellarator construction and thereby make increase the feasibility of the stellarator as a technology for a fusion-based power plant. In this project, we have developed novel methods for specifying the positions, shapes, and polarizations of the magnets in the array, and have developed designs for mounting structures and tooling for assembly. We have also performed detailed finite-element modeling to qualify the accuracy of the magnetic field produced by the magnet array as designed, and to confirm that the structure can withstand the forces between the magnets. We have also developed techniques for measuring the magnetic field produced by the array once constructed, as well as for correcting errors in the field arising from misalignments and offsets within the tolerances for mounting and fabrication. Finally, we have constructed a tabletop prototype of a section of the array to qualify the concept for assembling and mounting magnets within the array.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Stellarator Simplification using Permanent Magnets (PM4Stell)

This Report describes the design and prototyping of an array of rare-Earth permanent magnets to form a stellarator. This effort was motivated by the hypothesis that the usage of permanent magnets, rather than electromagnetic coils with complex geometry, could reduce the cost of stellarator construction and thereby make increase the feasibility of the stellarator as a technology for a fusion-based power plant. In this project, we have developed novel methods for specifying the positions, shapes, and polarizations of the magnets in the array, and have developed designs for mounting structures and tooling for assembly. We have also performed detailed finite-element modeling to qualify the accuracy of the magnetic field produced by the magnet array as designed, and to confirm that the structure can withstand the forces between the magnets. We have also developed techniques for measuring the magnetic field produced by the array once constructed, as well as for correcting errors in the field arising from misalignments and offsets within the tolerances for mounting and fabrication. Finally, we have constructed a tabletop prototype of a section of the array to qualify the concept for assembling and mounting magnets within the array.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Probing the Self-Assembly dynamics of cellulose nanocrystals by X-ray photon correlation spectroscopy

Charge-stabilized colloidal cellulose nanocrystals (CNCs) can self-assemble into higher-ordered chiral nematic structures by varying the volume fraction. The assembly process exhibits distinct dynamics during the isotropic to liquid crystal phase transition, which can be elucidated using X-ray photon correlation spectroscopy (XPCS). Anionic CNCs were dispersed in propylene glycol (PG) and water spanning a range of volume fractions, encompassing several phase transitions. Coupled with traditional characterization techniques, XPCS was conducted to monitor the dynamic evolution of the different phases. Additionally, simulated XPCS results were obtained using colloidal rods and compared with the experimental data, offering additional insights into the dynamic behavior of the system. The results indicate that the particle dynamics of CNCs undergo a stepped decay in three stages during the self-assembly process in PG, coinciding with the observed phases. The phase transitions are associated with a total drop of Brownian diffusion rates by four orders of magnitude, a decrease of more than a thousand times slower than expected in an ideal system of repulsive Brownian rods. Given the similarity in the phase behaviors in CNCs dispersed in PG and in water, we hypothesize that these dynamic behaviors can be extrapolated to other polar solvent environments. Importantly, these findings represent the direct measurement of CNC dynamics using XPCS, underscoring the feasibility of directly assessing the dynamic behavior of other rod-like colloidal suspensions.

36 MATERIALS SCIENCE↗
DOE OSTI2023

High efficiency translucent solar module integrated with greenhouse roof structures

A translucent solar module assembly for integration with a greenhouse having a frame with a plurality of roof supports includes a pair of brackets attachable to each of the plurality of roof supports, a bi-facial solar panel attachable to the pair of brackets, and a pair of reflector rails attachable to each of the plurality of roof supports. A dichroic reflector is attachable to the pair of reflector rails.

Pan, Wei↗