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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 631 records · Page 35
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory

The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus. We investigate the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) together with other seven species within the Lamiaceae (mint) family. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones generated by the Callicarpa americana BGC enzymes, including miltiradiene and the terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Emergent geometry and duality in the carbon nucleus

Abstract The carbon atom provides the backbone for the complex organic chemistry composing the building blocks of life. The physics of the carbon nucleus in its predominant isotope, 12 C, is similarly full of multifaceted complexity. Here we provide a model-independent density map of the geometry of the nuclear states of 12 C using the ab initio framework of nuclear lattice effective field theory. We find that the well-known but enigmatic Hoyle state is composed of a “bent-arm” or obtuse triangular arrangement of alpha clusters. We identify all of the low-lying nuclear states of 12 C as having an intrinsic shape composed of three alpha clusters forming either an equilateral triangle or an obtuse triangle. The states with the equilateral triangle formation also have a dual description in terms of particle-hole excitations in the mean-field picture.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Triepoxide formation by a flavin-dependent monooxygenase in monensin biosynthesis

Monensin A is a prototypical natural polyether polyketide antibiotic. It acts by binding a metal cation and facilitating its transport across the cell membrane. Biosynthesis of monensin A involves construction of a polyene polyketide backbone, subsequent epoxidation of the alkenes, and, lastly, formation of cyclic ethers via epoxide-opening cyclization. MonCI, a flavin-dependent monooxygenase, is thought to transform all three alkenes in the intermediate polyketide premonensin A into epoxides. Our crystallographic study has revealed that MonCI’s exquisite stereocontrol is due to the preorganization of the active site residues which allows only one specific face of the alkene to approach the reactive C(4a)-hydroperoxyflavin moiety. Furthermore, MonCI has an unusually large substrate-binding cavity that can accommodate premonensin A in an extended or folded conformation which allows any of the three alkenes to be placed next to C(4a)-hydroperoxyflavin. Importantly, MonCI, with its ability to perform multiple epoxidations on the same substrate in a stereospecific manner, demonstrates the extraordinary versatility of the flavin-dependent monooxygenase family of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site

The HIV-1 fusion peptide (FP) represents a promising vaccine target, but global FP sequence diversity among circulating strains has limited anti-FP antibodies to ~60% neutralization breadth. Here we evolve the FP-targeting antibody VRC34.01 in vitro to enhance FP-neutralization using site saturation mutagenesis and yeast display. Successive rounds of directed evolution by iterative selection of antibodies for binding to resistant HIV-1 strains establish a variant, VRC34.01_mm28, as a best-in-class antibody with 10-fold enhanced potency compared to the template antibody and ~80% breadth on a cross-clade 208-strain neutralization panel. Structural analyses demonstrate that the improved paratope expands the FP binding groove to accommodate diverse FP sequences of different lengths while also recognizing the HIV-1 Env backbone. These data reveal critical antibody features for enhanced neutralization breadth and potency against the FP site of vulnerability and accelerate clinical development of broad HIV-1 FP-targeting vaccines and therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-EM-based protein structure determination. Converting density maps into 3D atomic structures for proteins lacking accurate homologous or predicted structures as templates remains a significant challenge. Here, we introduce Cryo2Struct, a fully automated de novo cryo-EM structure modeling method. Cryo2Struct utilizes a 3D transformer to identify atoms and amino acid types in cryo-EM density maps, followed by an innovative Hidden Markov Model (HMM) to connect predicted atoms and build protein backbone structures. Cryo2Struct produces substantially more accurate and complete protein structural models than the widely used ab initio method Phenix. Additionally, its performance in building atomic structural models is robust against changes in the resolution of density maps and the size of protein structures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity

Abstract The inherent antigen cross-reactivity of the T cell receptor (TCR) is balanced by high specificity. Surprisingly, TCR specificity often manifests in ways not easily interpreted from static structures. Here we show that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen and its wild-type (WT) counterpart emerges from distinct motions within the HLA-A3 peptide binding groove that vary with the identity of the peptide’s first primary anchor. These motions create a dynamic gate that, in the presence of the WT peptide, impedes a large conformational change required for TCR binding. The neoantigen is insusceptible to this limiting dynamic, and, with the gate open, upon TCR binding the central tryptophan can transit underneath the peptide backbone to the opposing side of the HLA-A3 peptide binding groove. Our findings thus reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I binding grooves, with implications for resolving long-standing and often confounding questions about T cell specificity.

Science & Technology - Other Topics↗
DOE OSTI2025

Structure and mechanism of biosynthesis of Streptococcus mutans cell wall polysaccharide

Streptococcus mutans, the causative agent of human dental caries, expresses a cell wall attached Serotype c-specific Carbohydrate (SCC) that is critical for cell viability. SCC consists of a polyrhamnose backbone of →3)α-Rha(1 → 2)α-Rha(1→ repeats with glucose (Glc) side-chains and glycerol phosphate (GroP) decorations. This study reveals that SCC has one predominant and two more minor Glc modifications. The predominant Glc modification, α-Glc, attached to position 2 of 3-rhamnose, is installed by SccN and SccM glycosyltransferases and is the site of the GroP addition. The minor Glc modifications are β-Glc linked to position 4 of 3-rhamnose installed by SccP and SccQ glycosyltransferases, and α-Glc attached to position 4 of 2-rhamnose installed by SccN working in tandem with an unknown enzyme. Both the major and the minor β-Glc modifications control bacterial morphology, but only the GroP and major Glc modifications are critical for biofilm formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Fused-ring isomerism modulates molecular packing and device performance in non-halogenated organic solar cells

Subtle changes in molecular backbone geometry impact intermolecular interactions and performance of organic solar cells. Here, three isomeric small-molecule acceptors (NaO1, NaO2, and NaO3) are investigated to reveal how different fused-ring configurations control molecular packing, electronic coupling, and film formation. Structural and spectroscopic analyses show that the linearly fused NaO1 forms a compact three-dimensional packing network with large and balanced electronic couplings (>24 meV) across multiple directions, while the more curved analogues exhibit excessive crystallization and phase segregation. In-situ optical measurements demonstrate that NaO1 promotes fast and continuous structural evolution during film formation, resulting in smooth morphology and homogeneous phase distribution. These structural and dynamic advantages facilitate efficient charge generation and transport, accompanied by reduced non-radiative energy loss, ultimately achieving an efficiency of 20.07% for non-halogenated ternary devices. Our findings highlight how fused-ring isomerism decisively governs structure–packing–performance relationships in organic solar cells.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural and biochemical insight into a modular β-1,4-galactan synthase in plants

Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the ..beta..-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, here we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.

09 BIOMASS FUELS↗
DOE OSTI2022

Coarse-grained molecular dynamics integrated with convolutional neural network for comparing shapes of temperature sensitive bottlebrushes

Quantification of shape changes in nature-inspired soft material architectures of stimuli-sensitive polymers is critical for controlling their properties but is challenging due to their softness and flexibility. Here, we have computationally designed uniquely shaped bottlebrushes of a thermosensitive polymer, poly(N-isopropylacrylamide) (PNIPAM), by controlling the length of side chains along the backbone. Coarse-grained molecular dynamics simulations of solvated bottlebrushes were performed below and above the lower critical solution temperature of PNIPAM. Conventional analyses (free volume, asphericity, etc.) show that lengths of side chains and their immediate environments dictate the compactness and bending in these architectures. We further developed 100 unique convolutional neural network models that captured molecular-level features and generated a statistically significant quantification of the similarity between different shapes. Thus, our study provides insights into the shapes of complex architectures as well as a general method to analyze them. The shapes presented here may inspire the synthesis of new bottlebrushes.

36 MATERIALS SCIENCE↗
DOE OSTI2021

SuFExable polymers with helical structures derived from thionyl tetrafluoride

Sulfur(VI) fluoride exchange (SuFEx) is a category of click chemistry that enables covalent linking of modular units through sulfur(VI) connective hubs. The efficiency of SuFEx and the stability of the resulting bonds have led to polymer chemistry applications. Now, we report the SuFEx click chemistry synthesis of several structurally diverse SOF 4 -derived copolymers based on the polymerization of bis(iminosulfur oxydifluorides) and bis(aryl silyl ethers). This polymer class presents two key characteristics. First, the [-N=S(=O)F-O-] polymer backbone linkages are themselves SuFExable and undergo precise SuFEx-based post-modification with phenols or amines to yield branched functional polymers. Second, studies of individual polymer chains of several of these new materials indicate helical polymer structures. The robust nature of SuFEx click chemistry offers the potential for post-polymerization modification, enabling the synthesis of materials with control over composition and conformation.

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

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Shape-persistent ladder molecules exhibit nanogap-independent conductance in single-molecule junctions

Molecular electronic devices require precise control over the flow of current in single molecules. However, the electron transport properties of single molecules critically depend on dynamic molecular conformations in nanoscale junctions. Here, in this work, we report a unique strategy for controlling molecular conductance using shape-persistent molecules. Chemically diverse, charged ladder molecules, synthesized via a one-pot multicomponent ladderization strategy, show a molecular conductance (d[log( G/G 0 )]/d x ≈ -0.1 nm -1 ) that is nearly independent of junction displacement, in stark contrast to the nanogap-dependent conductance (d[log( G/G 0 )]/d x ≈ -7 nm -1 ) observed for non-ladder analogues. Ladder molecules show an unusually narrow distribution of molecular conductance during dynamic junction displacement, which is attributed to the shape-persistent backbone and restricted rotation of terminal anchor groups. These principles are further extended to a butterfly-like molecule, thereby demonstrating the strategy's generality for achieving gap-independent conductance. Overall, our work provides important avenues for controlling molecular conductance using shape-persistent molecules. Achieving robust and controllable conductance in single-molecule junctions is challenging due to the dynamic nature of molecular conformations that fluctuate over operational timescales. A strategy using shape-persistent molecules has now been developed that demonstrates nearly junction-displacement-independent conductance, providing a stable solution for single-molecule electronic properties.

molecular electronics↗
DOE OSTI2025

Polymer connectivity governs electrophotocatalytic activity in the solid state

The reductive functionalization of inert substrates such as chloroarenes is a critical yet challenging transformation relevant to both environmental remediation and organic synthesis. Combining electricity and light is an emerging strategy to access the deeply reducing potentials required for single electron transfer to chloroarenes, yet this approach is limited by poor stability and mechanistic ambiguity. Here, in this work, we demonstrate heterogeneous electrophotocatalysis using redox-active rylene diimide polymers for the reduction of chloroarenes. We find that the electrophotocatalytic activity varies dramatically as a function of the rylene diimide and the redox-inactive polymer backbone. In particular, a flexible, non-conjugated perylenediimide polymer outperforms all other tested electrophotocatalysts. Transient absorption spectroscopy reveals that precomplexation between the doubly reduced perylenediimide and the haloarene substrate is key to productive catalysis. Overall, this work highlights heterogeneous electrophotocatalysis using insoluble redox-active organic materials and provides critical structure–property insights into solid-state electrophotocatalytic activity, informing the development of next-generation materials for sustainable synthesis.

electrocatalysis↗
DOE OSTI2020

Multifaceted drivers for onshore wind energy repowering and their implications for energy transition

Wind energy is anticipated to become a backbone of the future energy system. Ageing wind turbine fleets, increasing land-use constraints and rising relevance of societal factors make the deployment of land-based (onshore) wind energy ever more complicated. Consequently, repowering is expected to become a rapidly growing point of focus for the wind industry. Here we propose a more holistic and socially informed project-level approach to analyse repowering activity that enables a more robust understanding of the process and potentials. We demonstrate that for wind pioneer in Denmark, only 67% of the capacity removed in repowering projects was related to the physical space needed for a new turbine. Other factors that drive repowering include regulation (for example, noise-related, 8–17%), development principles (for example, aesthetics, 7–20%) and political bargaining (4–13%). The recognition of repowering as a negotiated process between host communities and wind developers will probably be critical to unlock the full potential of wind energy in the future.

17 WIND ENERGY↗
DOE OSTI2024

Achieving 19% efficiency in non-fused ring electron acceptor solar cells via solubility control of donor and acceptor crystallization

Non-fused ring electron acceptors (NFREAs) potentially have lower synthetic costs than their fused counterparts. However, the low backbone planarity and the presence of bulky substituents adversely affect the crystallinity of NFREAs, impeding charge transport and the formation of bicontinuous morphology in organic solar cells. Here we show that a binary solvent system can individually control the crystallization and phase separation of the donor polymer (for example, D18) and the NFREA (for example, 2BTh-2F-C 2 ). We select solvents such as chloroform and o -xylene that evaporate at different temperatures and rates and have different solubility for D18. Upon evaporation of chloroform, D18 starts to assemble into fibrils. Then, the evaporation of o-xylene induces the rapid formation of a fibril network that phase segregates 2BTh-2F-C 2 into pure domains and leads to a bicontinuous morphology. In conclusion, the well-defined interpenetrating network morphology affords an efficiency of 19.02% on small-area cells and 17.28% on 1 cm 2 devices.

14 SOLAR ENERGY↗
DOE OSTI2023

High-efficiency stretchable light-emitting polymers from thermally activated delayed fluorescence

Stretchable light-emitting materials are the key components for realizing skin-like displays and optical biostimulation. All the stretchable emitters reported to date, to the best of our knowledge, have been based on electroluminescent polymers that only harness singlet excitons, limiting their theoretical quantum yield to 25%. Here we present a design concept for imparting stretchability onto electroluminescent polymers that can harness all the excitons through thermally activated delayed fluorescence, thereby reaching a near-unity theoretical quantum yield. We show that our design strategy of inserting flexible, linear units into a polymer backbone can substantially increase the mechanical stretchability without affecting the underlying electroluminescent processes. As a result, our synthesized polymer achieves a stretchability of 125%, with an external quantum efficiency of 10%. Additionally, we demonstrate a fully stretchable organic light-emitting diode, confirming that the proposed stretchable thermally activated delayed fluorescence polymers provide a path towards simultaneously achieving desirable electroluminescent and mechanical characteristics, including high efficiency, brightness, switching speed and stretchability as well as low driving voltage.

36 MATERIALS SCIENCE↗