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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 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
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 OSTI2022

Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein–DNA Nanostructures

We present here the combination of experimental and computational modeling tools for the design and characterization of protein–DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein–DNA linker identity and length; (2) optimizing the design of protein–DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein–DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable in-silico validation of nanostructured systems before their experimental realization. Finally, these tools will facilitate the design of complex hybrid protein–DNA nanostructures that seamlessly integrate the two different biomolecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Size and Structural Control of Mechanoluminescent ZnS:Mn 2+ Nanocrystals for Optogenetic Neuromodulation

Mechanoluminescent materials hold immense potential for various transformative applications, from medical imaging and diagnostics to health monitoring and wearable displays. Conventionally produced as bulk powders or microparticles, they face significant size limitations for advanced applications, particularly in biological systems and microscale devices. Here, this work presents an approach to ZnS:Mn 2+ nanocrystal synthesis that involves self-assembly and subsequent calcination. In addition to effective size control within the nanoscale, this approach promotes the formation of abundant stacking faults, significantly enhancing piezoelectric and mechanoluminescent properties by increasing trap density and reducing trap depth. Unlike mechanoluminescent materials produced using conventional methods, these nanocrystals demonstrate strong mechanoluminescence without requiring UV pre-excitation, and the light emission persists even after mechanical stress is removed. These advantageous properties make them promising candidates for optogenetic neuromodulation, as they can effectively trigger electrical signals in neurons upon ultrasound stimulation both with and without UV pre-excitation. The persistent mechanoluminescence prolongs the duration of neuronal electrical activity, providing an extended temporal window for neuromodulation compared to conventional mechanoluminescent materials. This study provides a scalable method for producing efficient mechanoluminescent nanoparticles and reveals the crucial role of particle size and defect structures in determining their mechanoluminescent behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Understanding the Re-entrant Phase Transition in a Non-magnetic Scheelite

We report the stereochemical activity of lone pair electrons plays a central role in determining the structural and electronic properties of both chemically simple materials such as H 2 O, as well as more complex condensed phases such as photocatalysts or thermoelectrics. TlReO 4 is a rare example of a non-magnetic material exhibiting a re-entrant phase transition and emphanitic behavior in the long-range structure. Here, we describe the role of the Tl + 6s 2 lone pair electrons in these unusual phase transitions and illustrate its tunability by chemical doping, which has broad implications for functional materials containing lone pair bearing cations. First-principles density functional calculations clearly show the contribution of the Tl + 6s 2 in the valence band region. Local structure analysis, via neutron total scattering, revealed that changes in the long-range structure of TlReO 4 occur due to changes in the correlation length of the Tl + lone pairs. This has a significant effect on the anion interactions, with long-range ordered lone pairs creating a more densely packed structure. This resulted in a trade-off between anionic repulsions and lone pair correlations that lead to symmetry lowering upon heating in the long-range structure, whereby lattice expansion was necessary for the Tl + lone pairs to become highly correlated. Similarly, introducing lattice expansion through chemical pressure allowed long-range lone pair correlations to occur over a wider temperature range, demonstrating a method for tuning the energy landscape of lone pair containing functional materials.

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

Achieving Ultra-High Selectivity to Hydrogen Production from Formic Acid on Pd–Ag Alloys

Palladium-silver based alloy catalysts have a great potential for CO-free hydrogen production from formic acid for fuel cell applications. However, the structural factors affecting the selectivity of formic acid decomposition is still debated. Herein, the decomposition pathways of formic acid on Pd-Ag alloys with different atomic configurations have been investigated to identify the alloy structures yielding high H 2 selectively. Several Pd x Ag 1-x surface alloys with various compositions were generated on a Pd(111) single crystal; their atomic distribution and electronic structure were determined by a combination of infrared reflection absorption spectroscopy (IRAS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). It was established that the Ag atoms with Pd neighbors are electronically altered, and the degree of alteration correlates with the number of nearest Pd. Temperature programmed reaction spectroscopy (TPRS) and DFT demonstrated that the electronically altered Ag domains create a new reaction pathway that selectively dehydrogenates formic acid. In contrast, Pd monomers surrounded by Ag are demonstrated to have a similar reactivity compared to pristine Pd(111), yielding CO and H 2 O in addition to the dehydrogenation products. Furthermore, they bind to the produced CO weaker than pristine Pd, demonstrating an enhancement in resistance to CO poisoning. This work therefore shows that surface Ag domains modified by interaction with subsurface Pd are the key active sites for selective decomposition of formic acid, while surface Pd atoms are detrimental for selectivity. Hence the decomposition pathways can be tailored for CO-free H 2 production on Pd-Ag alloy systems.

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

Critical Role of Framework Flexibility and Disorder in Driving High Ionic Conductivity in LiNbOCl 4

Understanding Li-ion transport is key for the rational design of superionic solid electrolytes with exceptional ionic conductivities. LiNbOCl 4 is reported to be one of the most highly conducting materials in the recently realized new class of soft oxyhalide solid electrolytes, exhibiting an ionic conductivity of ~11 mS·cm -1 . Here, we apply X-ray/neutron diffraction and pair distribution function analysis - coupled with density functional theory/ab-initio molecular dynamics - to determine a structural model that provides a rationale for the high conductivity that we observe experimentally in this nanocrystalline solid. We show that it arises from unusually high framework flexibility at room temperature. This owes to isolated 1-D [NbOCl 4 ] - anionic chains which exhibit energetically favorable orientational disorder that is - in turn - correlated to multiple, disordered and equi-energetic Li + sites in the lattice. As the Li-ions sample the 3-D energy landscape with a fast predicted diffusion coefficient of 5.1 x 10 -7 cm 2 /s at room temperature (σ i calc = 17.4 mS·cm -1 ), the inorganic polymer chains can reorient or vice versa. The activation energy barrier for Li migration through the frustrated energy landscape is especially reduced by the elastic nature of the NbO 2 Cl 4 octahedra evident from very widely dispersed Cl-Nb-Cl bond angles in AIMD snapshots at 300 K. The phonon spectra are predominantly influenced by Cl vibrations in the low energy range, and there is strong overlap between the framework (Cl, Nb) and Li partial pDOS in the region between 1.2 - 4.0 THz. The framework flexibility is also reflected in a relatively low bulk modulus of 22 GPa. In conclusion, our findings pave the way for investigation of future “flex-ion” inorganic solids and open up a new direction for the design of high conductivity, soft solid electrolytes for all-solid-state batteries.

AIMD↗
DOE OSTI2026

Bridge Connectivity Dictates Spin Interactions and Triplet Pair Dynamics in Intramolecular Singlet Fission

Electron spin plays a critical role in determining the structure, dynamics, and reactivities of molecular excited states, including multiexciton processes such as singlet fission. These systems exhibit triplet pair states whose excited state dynamics can be widely tuned through molecular engineering. For example, the electronic coupling between covalently linked chromophores can be readily modulated using chemical bridges to control proximity, quantum interference, or resonance effects. However, less is known about how spin coupling interactions are impacted by chromophore architecture, and how this influences triplet pair recombination dynamics. Here, in this study, we investigate the role of bridge connectivity and chromophore identity in modulating interchromophore exchange and dipolar coupling interactions for a series of pentacene and tetracene dimers bridged by alternant hydrocarbons (phenylene, naphthalene, anthracene). Using both time-resolved electron paramagnetic resonance and transient absorption spectroscopy, we find that the boundedness and recombination pathways of the triplet pair spins are highly sensitive to molecular architecture and chromophore-specific magnetic dipolar interactions. Notably, nominally ferromagnetic and antiferromagnetic eigenstates result in distinct spin state orderings, consistent with predictions from quantum interference-based graphical models. These findings establish new design principles for tuning spin dynamics in iSF materials, with implications for photonic and quantum information applications.

He, Guiying [City Univ. of New York (CUNY), NY (Un↗
DOE OSTI2020

Using Ambient Noise Seismic Interferometry and Local and Teleseismic Earthquakes to Determine Crustal Thickness and Moho Structure of the Northwestern Gulf of Mexico Margin

Abstract The northwestern part of the Gulf of Mexico has undergone two episodes of continental rifting and collision and produced structural artifacts that are now buried under many kilometers of sediments, complicating investigations of the region. The deep sedimentary package precludes outcrops and points to a need for the application of seismic techniques, but low rates of seismicity in the region and sparse seismic monitoring limit the utility of traditional seismic methods. We therefore use diverse data to perform two‐dimensional seismic tomography across the dry land portion of the margin. Data are gleaned from teleseismic and regional earthquakes, postcritical SsPmp arrivals, and direct P wave energy identified with seismic interferometry that were recorded by a broadband, three‐component array and partially overlapping short‐period, vertical‐component array. The Pn and postcritical SsPmp phase help constrain the Moho discontinuity, which a previous receiver function study suggested was absent beneath the seaward portion of this transect. A high‐velocity body is observed in the crust at the same location as the Houston Magnetic Anomaly, possibly marking rocks from the Alleghenian continental assembly. The crust thins from NW to SE, indicating that extension occurred mostly to the south of the Ouachita orogeny. Our model indicates that the margin's sediment package reaches a maximum thickness of ~15 km at the coast and becomes unresolvably thin near the Llano Uplift.

58 GEOSCIENCES↗
DOE OSTI2020

DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines

Ebola virus (EBOV) glycoprotein (GP) can be recognized by neutralizing antibodies (NAbs) and is the main target for vaccine design. Here, we first investigate the contribution of the stalk and heptad repeat 1-C (HR1 C ) regions to GP metastability. Specific stalk and HR1 C modifications in a mucin-deleted form (GPΔmuc) increase trimer yield, whereas alterations of HR1 C exert a more complex effect on thermostability. Crystal structures are determined to validate two rationally designed GPΔmuc trimers in their unliganded state. We then display a modified GPΔmuc trimer on reengineered protein nanoparticles that encapsulate a layer of locking domains (LD) and a cluster of helper T-cell epitopes. In mice and rabbits, GP trimers and nanoparticles elicit cross-ebolavirus NAbs, as well as non-NAbs that enhance pseudovirus infection. Repertoire sequencing reveals quantitative profiles of vaccine-induced B-cell responses. This study demonstrates a promising vaccine strategy for filoviruses, such as EBOV, based on GP stabilization and nanoparticle display.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A unique class of Zn 2+ -binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile

Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn 2+ -binding motif that influences β-lactam binding and protein stability. The Zn 2+ -binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn 2+ might function as a redox sensor to regulate cell wall synthesis for survival in adverse or anaerobic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural characterization of a soil viral auxiliary metabolic gene product – a functional chitosanase

Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin – a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Molecular asymmetry of a photosynthetic supercomplex from green sulfur bacteria

The photochemical reaction center (RC) features a dimeric architecture for charge separation across the membrane. In green sulfur bacteria (GSB), the trimeric Fenna-Matthews-Olson (FMO) complex mediates the transfer of light energy from the chlorosome antenna complex to the RC. Here we determine the structure of the photosynthetic supercomplex from the GSB Chlorobaculum tepidum using single-particle cryogenic electron microscopy (cryo-EM) and identify the cytochrome c subunit (PscC), two accessory protein subunits (PscE and PscF), a second FMO trimeric complex, and a linker pigment between FMO and the RC core. The protein subunits that are assembled with the symmetric RC core generate an asymmetric photosynthetic supercomplex. One linker bacteriochlorophyll (BChl) is located in one of the two FMO-PscA interfaces, leading to differential efficiencies of the two energy transfer branches. The two FMO trimeric complexes establish two different binding interfaces with the RC cytoplasmic surface, driven by the associated accessory subunits. This structure of the GSB photosynthetic supercomplex provides mechanistic insight into the light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex from the primitive homodimeric RC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel

Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP 3 and Ca 2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP 3 R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP 3 , Ca 2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP 3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP 3 R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Emergence of lignin-carbohydrate interactions during plant stem maturation visualized by solid-state NMR

Lignification waterproofs and strengthens secondary plant cell walls but increases the energy cost of sugar release for biofuels. The physical association between lignin and the carbohydrate scaffold that accommodates lignin polymerization, along with the distinct roles of lignin units and carbohydrate partners during lignification, remain unclear. Here, we map lignin-carbohydrate spatial proximity by solid-state NMR in 13 C-labeled Arabidopsis inflorescence stems during secondary cell wall formation. Analyses include wild-type plants and mutants that selectively or globally disrupt lignin biosynthesis. Mature walls in basal regions show enrichment of S-lignin and dense carbohydrate-lignin packing. Acetylated xylan predominantly associates with S-lignin, while methylated pectin unexpectedly interacts with G-lignin during early-stage lignification. The importance of S-lignin in stabilizing the carbohydrate-lignin interface is highlighted by weak lignin-carbohydrate contacts and compromised mechanical properties in the low-S fah1 mutant, whereas the ref3 mutant, despite reduced lignin content, remains unaffected due to a high S/G ratio. Thus, molecular mixing patterns, rather than lignin content, critically determine the structure and properties of lignocellulosic materials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Can ferric-oxyl excited states explain elongated iron-oxygen bonds in heme peroxidase catalytic intermediates?

The use of X-ray structures to determine and interpret the ferryl iron-oxygen bond order in molecular oxygen-activating heme enzymes has, in the past, been controversial. This has mainly stemmed from the susceptibility of ferryl species to X-ray-induced electronic state changes. In this work we establishe using time-resolved serial femtosecond X-ray crystallography (tr-SFX) on a dye-decolourising peroxidase that the ferryl intermediate species (Compounds I and II) captured following in situ mixing of microcrystals with H 2 O 2 have single, rather than the double bond character expected. X-ray emission validated tr-SFX data with quantum refinement, time-dependent-DFT calculations and QM/MM geometry optimizations together support the concept that the single iron-oxygen bond character is not an indication of ferryl reduction or a protonated form (Fe IV -OH) but is instead attributed to the existence of accessible excited states possessing ferric-oxyl (Fe III –O •– ) character. Such states offer insight into the nature of ferryl heme.

Williams, Lewis J. [University of Essex, Colcheste↗
DOE OSTI2020

From magnetic order to quantum disorder in the Zn-barlowite series of S = 1/2 kagomé antiferromagnets

We report a comprehensive muon spectroscopy study of the Zn-barlowite series of $S=\frac{1}{2}$ kagomé antiferromagnets, Zn x Cu 4-x (OH) 6 FBr, for x= 0.00 to 0.99(1). By combining muon spin relaxation and rotation measurements with state-of-the-art density-functional theory muon-site calculations, we observe the formation of both μ–F and μ–OH complexes in Zn-barlowite. From these stopping sites, implanted muon spins reveal the suppression of long-range magnetic order into a possible quantum spin liquid state upon the increasing concentration of Zn-substitution. In the parent compound (x = 0), static long-range magnetic order below T N = 5 K manifests itself in the form of spontaneous oscillations in the time-dependent muon asymmetry signal consistent with the dipolar fields expected from the calculated muon stopping sites and the previously determined magnetic structure of barlowite. Meanwhile, in the x = 1.0 end-member of the series—in which antiferromagnetic kagomé layers of Cu 2+ $S=\frac{1}{2}$ moments are decoupled by diamagnetic Zn 2+ ions—we observe that dynamic magnetic moment fluctuations persist down to at least 50 mK, indicative of a quantum disordered ground state. We demonstrate that this crossover from a static to dynamic magnetic ground state occurs for compositions of Zn-barlowite with x > 0.5, which bears resemblance to the dynamical behaviour of the widely studied Zn-paratacamite series that contains the quantum spin liquid candidate herbertsmithite.

36 MATERIALS SCIENCE↗