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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Cryo-EM structure of a methanogen nitrogenase-PII protein supercomplex

Abstract Nitrogenases are metalloenzymes that catalyze the reduction of atmospheric dinitrogen to ammonia, sustaining the global nitrogen cycle. While bacterial nitrogenase has been extensively characterized, the architecture and regulation of archaeal nitrogenases remain unknown despite longstanding evidence of nitrogen fixation in methanogens. Here we report a 3.1 Å cryo-electron microscopy structure of a native nitrogenase–PII protein supercomplex from Methanosarcina acetivorans. The structure reveals an unprecedented assembly of three NifDK heterotetramers bridged by six NifI1,2 heterotrimeric PII complexes, which sterically block NifH association and lock the enzyme in an inactive state. The NifI complexes display asymmetric binding of ADP and 2-oxoglutarate, coupling nitrogenase inhibition directly to cellular energy and nitrogen status. Addition of 2-oxoglutarate and ATP releases the NifI complexes, stimulating a threefold increase in NifDK activity in vitro. This higher-order architecture uncovers a previously unrecognized regulatory strategy in methanogens, in which PII proteins drive nitrogenase oligomerization to control activity. The discovery that nitrogenase activity may be modulated through direct assembly into higher-order structures opens new avenues for exploring nitrogenase evolution, regulation, and biotechnological applications. One sentence summary Discovery of a nitrogenase-PII protein supercomplex in methanogens, uncovering a metabolite-gated assembly mechanism for nitrogenase inhibition.

Nitrogenase, Electron Transfer, Methanogen↗
DOE OSTI2020

Heat-driven acoustic phonons in lamellar nanoplatelet assemblies

Colloidal CdSe nanoplatelets, with the electronic structure of quantum wells, self-assemble into lamellar stacks due to large co-facial van der Waals attractions. These lamellar stacks are shown to display coherent acoustic phonons that are detected from oscillatory changes in the absorption spectrum observed in infrared pump, electronic probe measurements. Rather than direct electronic excitation of the nanocrystals using a femtosecond laser, impulsive transfer of heat from the organic ligand shell, excited at C–H stretching vibrational resonances, to the inorganic core of individual nanoplatelets occurs on a time-scale of <100 ps. This heat transfer drives in-phase longitudinal acoustic phonons of the nanoplatelet lamellae, which are accompanied by subtle deformations along the nanoplatelet short axes. The frequencies of the oscillations vary from 0.7 to 2 GHz (3–8 μeV and 0.5–1 ns oscillation period) depending on the thickness of the nanoplatelets—but not their lateral areas—and the temperature of the sample. Temperaturedependence of the acoustic phonon frequency conveys a substantial stiffening of the organic ligand bonds between nanoplatelets with reduced temperature. Overall, these results demonstrate a potential for acoustic modulation of the excitonic structure of nanocrystal assemblies in self-assembled anisotropic semiconductor systems at temperatures at or above 300 K.

36 MATERIALS SCIENCE↗
DOE OSTI2020

SAS PDF: pair distribution function analysis of nanoparticle assemblies from small-angle scattering data

SASPDF, a method for characterizing the structure of nanoparticle assemblies (NPAs), is presented. The method is an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime. The PDFgetS3 software package for computing the PDF from SAS data is also presented. An application of the SASPDF method to characterize structures of representative NPA samples with different levels of structural order is then demonstrated. The SASPDF method quantitatively yields information such as structure, disorder and crystallite sizes of ordered NPA samples. The method was also used to successfully model the data from a disordered NPA sample. The SASPDF method offers the possibility of more quantitative characterizations of NPA structures for a wide class of samples.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Relaxation and Aging of Nanosphere Assemblies at a Water–Oil Interface

The relaxation and aging of an assembly of spherical nanoparticles (NPs) at a water-oil interface are characterized in situ by grazing incidence X-ray photon correlation spectroscopy. The dynamics of the interfacial assembly is measured while the interface saturates with NPs. Weak attractions between NPs lead to gel-like structures in the assembly, where the in-plane ordering is inhibited by the broad size distribution of the NPs. Structural rearrangements on the length scale of the NP-NP center-to-center distances proceed by intermittent fluctuations instead of continuous cooperative motions. Here, the coexistence of rapid and slow NP populations is confirmed, as commonly observed in soft glass-forming materials. Dynamics are increasingly slowed as the NPs initially segregate to the locally clustered interface. The structural relaxation of the NPs in these localized clusters is 5 orders of magnitude slower than that of free particles in the bulk. When the interface is nearly saturated, the time for relaxation increases suddenly due to the onset of local jamming, and the dynamics slow exponentially afterward until the system reaches collective jamming by cooperative rearrangements. This investigation provides insights into structural relaxations near the glass transition and the evolution of the structure and dynamics of the assemblies as they transition from an isotropic liquid to a dense disordered film.

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

Optical super-resolution microscopy in polymer science

The advent of optical super-resolution microscopy (OSRM) over two decades ago has transformed light-mediated interrogation of systems down to the nanoscale. This innovative set of approaches to optics breaks the so-called diffraction limit of light (~200 nm), allowing for the first time to use optics in the far field to visualize behavior on nanoscopic length scales. While these visualization tools have rapidly found widespread use in biology and related fields, their implementation in materials and, more specifically, in polymer science has been far slower. To overcome possible barriers and highlight possible future directions, we present in this paper an introduction to OSRM for polymer scientists, beginning with an overview of relevant techniques and existing optical probes. We then show and examine the first examples of OSRM adaptation across major areas of polymer science, including: polymerization and structural characterization, self-assembly and solution behavior, bulk structure and behavior, crystallization, gel structure and behavior, phase transitions, and biofunctionality. We hope and anticipate that the discussions provided in this review will draw the attention of the polymer community to the capacities of these hitherto underexplored optical visualization techniques to further transform polymer science.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Study of self-assembly behavior and ionic conductivity of conjugated liquid crystals with T-shaped facial-polyphilic structure

The unique self-assembly of liquid crystals (LCs), combined with their potential application as organic semiconductors, has become a focus of recent research. Here, a joint experimental and computational study of the self-assembly and ionic conduction was carried out on a series of T-shaped conjugated LCs consisting of three incompatible components. By extending the EOn side-chain length, several experimental evaluations confirmed a decrease of the order-disorder transition temperature, while coarse-grained simulations revealed a structural evolution from a smectic phase to a columnar phase. Ionic conductivity of these molecules was achieved by adding Li salt, leading to a maximum conductivity of 1.1 × 10 −3 siemens per centimeter observed at 120°C. All-atom simulations were performed to examine the Li-ion solvation environment and to evaluate the intrachain and interchain Li-ion hopping mechanisms. The molecule with a long EOn side chain was found to generate a densely distributed network of Li-ion solvation sites, which can facilitate effective interchain hopping to promote ion transport.

Liu, Ziwei [Cornell Univ., Ithaca, NY (United Stat↗
DOE OSTI2025

Directed self-assembly of chiral liquid crystals into biomimetic bouligand structures in thin film

The Bouligand structure, renowned for its helicoidal arrangement and enhanced mechanical properties, has attracted significant research interest for its ability to impart enhanced strength to intrinsically soft materials. Biomimetic approaches have centered on fibrous structures in bulk materials, but translating this architecture into thin-film regime for miniaturized-wearable devices with programmable functions remains challenging. Here, we direct the self-assembly of cholesteric liquid crystals (CLCs) into hierarchical helical structures using chemically patterned surfaces. Alternating surface anchoring regions align uniform lying-down helices at the nanoscale, guiding a secondary microscale helical structure exhibiting both left- and right-handed twists. This mimetic Bouligand structure in CLCs enables optical modulation under applied field and strain with enhanced mechanical response. Simulations reveal the structural evolution from initial Bouligand configuration in LC layers to alternating twist helices. This research provides a basis for designing and manufacturing miniaturized or wearable devices with nanometer-scale precision in regulating electro-optical and mechanical properties. Bouligand structures, which offer strength in natural materials, are of interest but difficult to obtain. Here, the authors report the development of such structures by directed self-assembly of cholesteric single crystals into hierarchical helical structures, with the secondary structure having right and left-handed twists.

Bouligand structure↗
DOE OSTI2026

Supramolecular Assembly of Multielement Ribbon-like Structures Derived from Halide Perovskites

Halide perovskites are crucial materials with broad applications owing to their exceptional optoelectronic properties. Vacancy-ordered double perovskites, featuring highly tunable transition metal sites, enable controllable optoelectronic properties through multielement compositional design. Here, in this study, we introduced 18-crown-6 into the vacancy-ordered double perovskites system and developed two-dimensional ribbon-like single crystals (18C6@K) 2 {PtSnTeIrRe} 1 Cl 6 via an antisolvent supramolecular assembly method, demonstrating morphology modulation through multielement composition design. The crystals crystallize in the centrosymmetric space group $P\bar{1}$. The dumbbell-shaped structural units (crown ether@A)2MX6 pack along a and b axes to form a 2-dimensional (2D) monolayer, and these monolayers further stack along the c axis to generate the ribbon-like single crystals. Energy-dispersive X-ray spectroscopy (EDX) qualitatively confirmed the uniform distribution of the five transition metals throughout the crystal, while inductively coupled plasma atomic emission spectroscopy (ICP–AES) quantitatively verified their atomic ratios. We further investigated the origin of the morphology, distinct from the previously reported cube-like single crystals with the $R\bar{3}$ space group. When acetonitrile was used as the solvent, three-dimensional crystals with $R\bar{3}$ symmetry were obtained, whereas dimethylformamide (DMF) was essential for forming two-dimensional ribbon-like single crystals. The essential role of DMF could be ascribed to its capability to maintain a higher concentration of the building blocks. Moreover, Ir 4+ and Pt 4+ cations also played critical roles in inducing the two-dimensional ribbon-like morphology. The three-element (18C6@K) 2 {PtSnTe}1Cl 6 single crystals exhibited bright yellow emission under 375 nm laser excitation, demonstrating the tunability of optoelectronic properties of this class of material.

Zhu, Heqing [University of California, Berkeley, C↗
DOE OSTI2023

Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions

Understanding the structural diversity of honeybee-infecting viruses is critical to maintain pollinator health and manage the spread of diseases in ecology and agriculture. We determine cryo-EM structures of $T$ = 4 and $T$ = 3 capsids of virus-like particles (VLPs) of Lake Sinai virus (LSV) 2 and delta-N48 LSV1, belonging to tetraviruses, at resolutions of 2.3–2.6 Å in various pH environments. Structural analysis shows that the LSV2 capsid protein (CP) structural features, particularly the protruding domain and C-arm, differ from those of other tetraviruses. The anchor loop on the central β-barrel domain interacts with the neighboring subunit to stabilize homo-trimeric capsomeres during assembly. Delta-N48 LSV1 CP interacts with ssRNA via the rigid helix α1’, α1’–α1 loop, β-barrel domain, and C-arm. Cryo-EM reconstructions, combined with X-ray crystallographic and small-angle scattering analyses, indicate that pH affects capsid conformations by regulating reversible dynamic particle motions and sizes of LSV2 VLPs. C-arms exist in all LSV2 and delta-N48 LSV1 VLPs across varied pH conditions, indicating that autoproteolysis cleavage is not required for LSV maturation. The observed linear domino-scaffold structures of various lengths, made up of trapezoid-shape capsomeres, provide a basis for icosahedral $T$ = 4 and $T$ = 3 architecture assemblies. These findings advance understanding of honeybee-infecting viruses that can cause Colony Collapse Disorder.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Novel self-assembled two-dimensional layered oxide structure incorporated with Au nanoinclusions towards multifunctionalities

Two-dimensional (2D) layered oxides have recently attracted wide attention owing to the strong coupling among charges, spins, lattice, and strain, which allows great flexibility and opportunities in structure designs as well as multifunctionality exploration. In parallel, plasmonic hybrid nanostructures exhibit exotic localized surface plasmon resonance (LSPR) providing a broad range of applications in nanophotonic devices and sensors. A hybrid material platform combining the unique multifunctional 2D layered oxides and plasmonic nanostructures brings optical tuning into the new level. Here, a novel self-assembled Bi 2 MoO 6 (BMO) 2D layered oxide incorporated with plasmonic Au nanoinclusions has been demonstrated via one-step pulsed laser deposition (PLD) technique. Comprehensive microstructural characterizations, including scanning transmission electron microscopy (STEM), differential phase contrast imaging (DPC), and STEM tomography, have demonstrated the high epitaxial quality and particle-in-matrix morphology of the BMO-Au nanocomposite film. DPC-STEM imaging clarifies the magnetic domain structures of BMO matrix. Three different BMO structures including layered supercell (LSC) and superlattices have been revealed which is attributed to the variable strain states throughout the BMO-Au film. Owing to the combination of plasmonic Au and layered structure of BMO, the nanocomposite film exhibits a typical LSPR in visible wavelength region and strong anisotropy in terms of its optical and ferromagnetic properties. This study opens a new avenue for developing novel 2D layered complex oxides incorporated with plasmonic metal or semiconductor phases showing great potential for applications in multifunctional nanoelectronics devices.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Self-Assembly of Metallo-Supramolecules under Kinetic or Thermodynamic Control: Characterization of Positional Isomers Using Scanning Tunneling Spectroscopy

Coordination-driven self-assembly has been extensively employed to construct a variety of discrete structures as a bottom-up strategy. However, mechanistic understanding regarding whether self-assembly is under kinetic or thermodynamic control is less explored. To date, such mechanistic investigation has been limited to distinct, assembled structures. It still remains a formidable challenge to study the kinetic and thermodynamic behavior of self-assembly systems with multiple assembled isomers due to the lack of characterization methods. Herein, we use a stepwise strategy which combined self-recognition and self-assembly processes to construct giant metallo-supramolecules with 8 positional isomers in solution. With the help of ultrahigh-vacuum, low-temperature scanning tunneling microscopy and scanning tunneling spectroscopy, we were able to unambiguously differentiate 14 isomers on the substrate which correspond to 8 isomers in solution. Through measurement of 162 structures, the experimental probability of each isomer was obtained and compared with the theoretical probability. Finally, such a comparison along with density functional theory (DFT) calculation suggested that although both kinetic and thermodynamic control existed in this self-assembly, the increased experimental probabilities of isomers compared to theoretical probabilities should be attributed to thermodynamic control.

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

The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for intermodular communication in assembly-line polyketide biosynthesis

Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. Here, to investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain–domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Inferring assembly-curving trends of bacterial micro-compartment shell hexamers from crystal structure arrangements

Bacterial microcompartments (BMC) are complex macromolecular assemblies that participate in varied chemical processes in about one fourth of bacterial species. BMC-encapsulated enzymatic activities are segregated from other cell contents by means of semipermeable shells, justifying why BMC are viewed as prototype nano-reactors for biotechnological applications. Herein, we undertook a comparative study of bending propensities of BMC hexamers (BMC-H), the most abundant shell constituents. Published data show that some BMC-H, like β -carboxysomal CcmK, tend to assemble flat whereas other BMC-H often build curved objects. Inspection of available crystal structures presenting BMC-H in tiled arrangements permitted us to identify two major assembly modes with a striking connection with experimental trends. All-atom molecular dynamics (MD) supported that BMC-H bending is triggered robustly only from the arrangement adopted in crystals by BMC-H that experimentally form curved objects, leading to very similar arrangements to those found in structures of recomposed BMC shells. Simulations on triplets of planar-behaving hexamers, which were previously reconfigured to comply with such organization, confirmed that bending propensity is mostly defined by the precise lateral positioning of hexamers, rather than by BMC-H identity. Finally, an interfacial lysine was pinpointed as the most decisive residue in controlling PduA spontaneous curvature. Globally, results presented herein should contribute to improve our understanding of the variable mechanisms of biogenesis characterized for BMC, and of possible strategies to regulate BMC size and shape.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Preserving Structurally Labile Peptide Nanosheets After Molecular Functionalization of the Self-Assembling Peptides

A significant challenge in creating supramolecular materials is that conjugating molecular functionalities to building blocks often results in dissociation or undesired morphological transformation of their assemblies. Here we present a facile strategy to preserve structurally labile peptide assemblies after molecular modification of the self-assembling peptides. Sheet-forming peptides are designed to afford a staggered alignment with the segments bearing chemical modification sites protruding from the sheet surfaces. The staggered assembly allows for simultaneous separation of attached molecules from each other and from the underlying assembly motifs. Strikingly, using PEGs as the external molecules, PEG 400 - and PEG 700 -peptide conjugates directly self-associate into nanosheets with the PEG chains localized on the sheet surfaces. In contrast, the sheet formation based on in-register lateral packing of peptides does not recur upon the peptide PEGylation. This strategy allows for fabrication of densely modified assemblies with a variety of molecules, as demonstrated using biotin (hydrophobic molecule), c(RGDfK) (cyclic pentapeptide), and nucleic acid aptamer (negatively charged ssDNA). The staggered co-assembly also enables extended tunability of the amount/density of surface molecules, as exemplified by screening ligand-appended assemblies for cell targeting. In conclusion, this study paves the way for functionalization of historically challenging fragile assemblies while maintaining their overall morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Surfactant-like peptide gels are based on cross-β amyloid fibrils

Surfactant-like peptides, in which hydrophilic and hydrophobic residues are encoded within different domains in the peptide sequence, undergo facile self-assembly in aqueous solution to form supramolecular hydrogels. These peptides have been explored extensively as substrates for the creation of functional materials since a wide variety of amphipathic sequences can be prepared from commonly available amino acid precursors. The self-assembly behavior of surfactant-like peptides has been compared to that observed for small molecule amphiphiles in which nanoscale phase separation of the hydrophobic domains drives the self-assembly of supramolecular structures. Here, we investigate the relationship between sequence and supramolecular structure for a pair of bola-amphiphilic peptides, Ac-KLIIIK-NH 2 (L2) and Ac-KIIILK-NH 2 (L5). Despite similar length, composition, and polar sequence pattern, L2 and L5 form morphologically distinct assemblies, nanosheets and nanotubes, respectively. Cryo-EM helical reconstruction was employed to determine the structure of the L5 nanotube at near-atomic resolution. Rather than displaying self-assembly behavior analogous to conventional amphiphiles, the packing arrangement of peptides in the L5 nanotube displayed steric zipper interfaces that resembled those observed in the structures of β-amyloid fibrils. Like amyloids, the supramolecular structures of the L2 and L5 assemblies were sensitive to conservative amino acid substitutions within an otherwise identical amphipathic sequence pattern. This study highlights the need to better understand the relationship between sequence and supramolecular structure to facilitate the development of functional peptide-based materials for biomaterials applications.

Das, Abhinaba [Emory University, Atlanta, GA (Unit↗