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At least 397 records · Page 22

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DOE OSTI2020

Vibronic mixing enables ultrafast energy flow in light-harvesting complex II

Since the discovery of quantum beats in the two-dimensional electronic spectra of photosynthetic pigment-protein complexes over a decade ago, the origin and mechanistic function of these beats in photosynthetic light-harvesting has been extensively debated. The current consensus is that these long-lived oscillatory features likely result from electronic-vibrational mixing, however, it remains uncertain if such mixing significantly influences energy transport. Here, we examine the interplay between the electronic and nuclear degrees of freedom (DoF) during the excitation energy transfer (EET) dynamics of light-harvesting complex II (LHCII) with two-dimensional electronic-vibrational spectroscopy. Particularly, we show the involvement of the nuclear DoF during EET through the participation of higher-lying vibronic chlorophyll states and assign observed oscillatory features to specific EET pathways, demonstrating a significant step in mapping evolution from energy to physical space. These frequencies correspond to known vibrational modes of chlorophyll, suggesting that electronic-vibrational mixing facilitates rapid EET over moderately size energy gaps.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Perovskite neural trees

Trees are used by animals, humans and machines to classify information and make decisions. Natural tree structures displayed by synapses of the brain involves potentiation and depression capable of branching and is essential for survival and learning. Demonstration of such features in synthetic matter is challenging due to the need to host a complex energy landscape capable of learning, memory and electrical interrogation. We report experimental realization of tree-like conductance states at room temperature in strongly correlated perovskite nickelates by modulating proton distribution under high speed electric pulses. This demonstration represents physical realization of ultrametric trees, a concept from number theory applied to the study of spin glasses in physics that inspired early neural network theory dating almost forty years ago. We apply the tree-like memory features in spiking neural networks to demonstrate high fidelity object recognition, and in future can open new directions for neuromorphic computing and artificial intelligence.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

Abstract Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum , ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

End of Green Sahara amplified mid- to late Holocene megadroughts in mainland Southeast Asia

Between 5 and 4 thousand years ago, crippling megadroughts led to the disruption of ancient civilizations across parts of Africa and Asia, yet the extent of these climate extremes in mainland Southeast Asia (MSEA) has never been defined. This is despite archeological evidence showing a shift in human settlement patterns across the region during this period. We report evidence from stalagmite climate records indicating a major decrease of monsoon rainfall in MSEA during the mid- to late Holocene, coincident with African monsoon failure during the end of the Green Sahara. Through a set of modeling experiments, we show that reduced vegetation and increased dust loads during the Green Sahara termination shifted the Walker circulation eastward and cooled the Indian Ocean, causing a reduction in monsoon rainfall in MSEA. Our results indicate that vegetation-dust climate feedbacks from Sahara drying may have been the catalyst for societal shifts in MSEA via ocean-atmospheric teleconnections.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease

Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since their discovery nearly 30 years ago despite the potential for developing vaccines that target these enzymes to block infection. Here we show through a series of cryo-electron microscopy single particle reconstructions how the Streptococcus pneumoniae IgA1 protease facilitates IgA1 substrate recognition and how this can be inhibited. Specifically, the Streptococcus pneumoniae IgA1 protease subscribes to an active-site-gated mechanism where a domain undergoes a 10.0 Å movement to facilitate cleavage. Monoclonal antibody binding inhibits this conformational change, providing a direct means to block infection at the host interface. These structural studies explain decades of biological and biochemical studies and provides a general strategy to block Streptococcus pneumoniae IgA1 protease activity to potentially prevent infection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Multiple fermion scattering in the weakly coupled spin-chain compound YbAlO 3

The Heisenberg antiferromagnetic spin-1/2 chain, originally introduced almost a century ago, is one of the best studied models in quantum mechanics due to its exact solution, but nevertheless it continues to present new discoveries. Its low-energy physics is described by the Tomonaga-Luttinger liquid of spinless fermions, similar to the conduction electrons in one-dimensional metals. In this work we investigate the Heisenberg spin-chain compound YbAlO3 and show that the weak interchain coupling causes Umklapp scattering between the left- and right-moving fermions and stabilizes an incommensurate spin-density wave order at q = 2k F under finite magnetic fields. These Umklapp processes open a route to multiple coherent scattering of fermions, which results in the formation of satellites at integer multiples of the incommensurate fundamental wavevector Q = nq. Our work provides surprising and profound insight into bandstructure control for emergent fermions in quantum materials, and shows how neutron diffraction can be applied to investigate the phenomenon of coherent multiple scattering in metals through the proxy of quantum magnetic systems.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Timing of iceberg scours and massive ice-rafting events in the subtropical North Atlantic

Abstract High resolution seafloor mapping shows extraordinary evidence that massive (>300 m thick) icebergs once drifted >5,000 km south along the eastern United States, with >700 iceberg scours now identified south of Cape Hatteras. Here we report on sediment cores collected from several buried scours that show multiple plow marks align with Heinrich Event 3 (H3), ~31,000 years ago. Numerical glacial iceberg simulations indicate that the transport of icebergs to these sites occurs during massive, but short-lived, periods of elevated meltwater discharge. Transport of icebergs to the subtropics, away from deep water formation sites, may explain why H3 was associated with only a modest increase in ice-rafting across the subpolar North Atlantic, and implies a complex relationship between freshwater forcing and climate change. Stratigraphy from subbottom data across the scour marks shows there are additional features that are both older and younger, and may align with other periods of elevated meltwater discharge.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A structured RNA motif locks Argonaute2:miR-122 onto the 5’ end of the HCV genome

microRNAs (miRNAs) form regulatory networks in metazoans. Viruses engage miRNA networks in numerous ways, with Flaviviridae members exploiting direct interactions of their RNA genomes with host miRNAs. For hepatitis C virus (HCV), binding of liver-abundant miR-122 stabilizes the viral RNA and regulates viral translation. Here, we investigate the structural basis for these activities, taking into consideration that miRNAs function in complex with Argonaute (Ago) proteins. The crystal structure of the Ago2:miR-122:HCV complex reveals a structured RNA motif that traps Ago2 on the viral RNA, masking its 5’ end from enzymatic attack. The trapped Ago2 can recruit host factor PCBP2, implicated in viral translation, while binding of a second Ago2:miR-122 competes with PCBP2, creating a potential molecular switch for translational control. Combined results reveal a viral RNA structure that modulates Ago2:miR-122 dynamics and repurposes host proteins to generate a functional analog of the mRNA cap-binding complex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction

Abstract Plasmids are used extensively in basic and applied biology. However, design and construction of plasmids, specifically the ones carrying complex genetic information, remains one of the most time-consuming, labor-intensive, and rate-limiting steps in performing sophisticated biological experiments. Here, we report the development of a versatile, robust, automated end-to-end platform named PlasmidMaker that allows error-free construction of plasmids with virtually any sequences in a high throughput manner. This platform consists of a most versatile DNA assembly method using Pyrococcus furiosus Argonaute ( Pf Ago)-based artificial restriction enzymes, a user-friendly frontend for plasmid design, and a backend that streamlines the workflow and integration with a robotic system. As a proof of concept, we used this platform to generate 101 plasmids from six different species ranging from 5 to 18 kb in size from up to 11 DNA fragments. PlasmidMaker should greatly expand the potential of synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Evidence of high-temperature exciton condensation in a two-dimensional semimetal

Electrons and holes can spontaneously form excitons and condense in a semimetal or semiconductor, as predicted decades ago. This type of Bose condensation can happen at much higher temperatures in comparison with dilute atomic gases. Two-dimensional (2D) materials with reduced Coulomb screening around the Fermi level are promising for realizing such a system. Here we report a change in the band structure accompanied by a phase transition at about 180 K in single-layer ZrTe 2 based on angle-resolved photoemission spectroscopy (ARPES) measurements. Below the transition temperature, gap opening and development of an ultra-flat band top around the zone center are observed. This gap and the phase transition are rapidly suppressed with extra carrier densities introduced by adding more layers or dopants on the surface. The results suggest the formation of an excitonic insulating ground state in single-layer ZrTe 2 , and the findings are rationalized by first-principles calculations and a self-consistent mean-field theory. Our study provides evidence for exciton condensation in a 2D semimetal and demonstrates strong dimensionality effects on the formation of intrinsic bound electron–hole pairs in solids.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Actinide inverse trans influence versus cooperative pushing from below and multi-center bonding

Actinide-ligand bonds with high multiplicities remain poorly understood. Decades ago, an effect known as 6p pushing from below (PFB) was proposed to enhance actinide covalency. A related effect—also poorly understood—is inverse trans influence (ITI). The present computational study of actinide-ligand covalent interactions with high bond multiplicities quantifies the energetic contributions from PFB and identifies a hitherto overlooked fourth bonding interaction for 2nd-row ligands in the studied organometallic systems. The latter are best described by a terminal O/N ligand exhibiting quadruple bonding interactions with the actinide. The 4th interaction may be characterized as a multi-center or charge-shift bond involving the trans ligand. It is shown in this work that the 4th bonding interaction is a manifestation of ITI, assisted by PFB, and provides a long-sought missing piece in the understanding of actinide chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Elliptic anisotropy measurement of the f 0 (980) hadron in proton-lead collisions and evidence for its quark-antiquark composition

Despite the f 0 (980) hadron having been discovered half a century ago, the question about its quark content has not been settled: it might be an ordinary quark-antiquark ($q\bar{q}$) meson, a tetraquark ($q\bar{q}$$q\bar{q}$) exotic state, a kaon-antikaon ($K\bar{K}$) molecule, or a quark-antiquark-gluon ($q\bar{q}$g) hybrid. This paper reports strong evidence that the f 0 (980) state is an ordinary $q\bar{q}$ meson, inferred from the scaling of elliptic anisotropies (v 2 ) with the number of constituent quarks (n q ), as empirically established using conventional hadrons in relativistic heavy ion collisions. The f 0 (980) state is reconstructed via its dominant decay channel f 0 (980) → π + π − , in proton-lead collisions recorded by the CMS experiment at the LHC, and its v 2 is measured as a function of transverse momentum (p T ). It is found that the n q = 2 ($q\bar{q}$ state) hypothesis is favored over n q = 4 ($q\bar{q}$$q\bar{q}$ or $K\bar{K}$ states) by 7.7, 6.3, or 3.1 standard deviations in the p T < 10, 8, or 6 GeV/c ranges, respectively, and over n q = 3 ($q\bar{q}$g hybrid state) by 3.5 standard deviations in the p T < 8 GeV/c range. This result represents the first determination of the quark content of the f 0 (980) state, made possible by using a novel approach, and paves the way for similar studies of other exotic hadron candidates.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Improving the fast-charging capability of NbWO-based Li-ion batteries

The discovery of Nb-W-O materials years ago marks the milestone of charging a lithium-ion battery in minutes. Nevertheless, for many applications, charging lithium-ion battery within one minute is urgently demanded, the bottleneck of which largely lies in the lack of fundamental understanding of Li + storage mechanisms in these materials. Herein, by visualizing Li + intercalated into representative Nb 16 W 5 O 55 , we find that the fast-charging nature of such material originates from an interesting rate-dependent lattice relaxation process associated with the Jahn-Teller effect. Furthermore, in situ electron microscopy further reveals a directional, [010]-preferred Li + transport mechanism in Nb 16 W 5 O 55 crystals being the “bottleneck” toward fast charging that deprives the entry of any desolvated Li + through the prevailing non-(010) surfaces. Hence, we propose a machine learning-assisted interface engineering strategy to swiftly collect desolvated Li + and relocate them to (010) surfaces for their fast intercalation. As a result, a capacity of ≈ 116 mAh g −1 (68.5% of the theoretical capacity) at 80 C (45 s) is achieved when coupled with a Li negative electrode.

batteries↗

DOE OSTI2025

Divergent evolution of slip banding in CrCoNi alloys

Abstract Metallic materials under high stress often exhibit deformation localization, manifesting as slip banding. Over seven decades ago, Frank and Read introduced the well-known model of dislocation multiplication at a source, explaining slip band formation. Here, we reveal two distinct types of slip bands (confined and extended) in compressed CrCoNi alloys through multi-scale testing and modeling from microscopic to atomic scales. The confined slip band, characterized by a thin glide zone, arises from the conventional process of repetitive full dislocation emissions at Frank–Read source. Contrary to the classical model, the extended band stems from slip-induced deactivation of dislocation sources, followed by consequent generation of new sources on adjacent planes, leading to rapid band thickening. Our findings provide insights into atomic-scale collective dislocation motion and microscopic deformation instability in advanced structural materials.

Science & Technology - Other Topics↗

DOE OSTI2025

Observation of interface piezoelectricity in superconducting devices on silicon

The development of superconducting quantum processors relies on understanding and mitigating decoherence in superconducting qubits. Piezoelectric coupling contributes to decoherence by mediating energy exchange between microwave photons and acoustic phonons. Although bulk centrosymmetric materials like silicon and sapphire are non-piezoelectric and commonly used as qubit substrates, the lack of centrosymmetry at interfaces may induce piezoelectric losses. This effect was predicted decades ago but never experimentally observed in superconducting devices. Here, we report interface piezoelectricity at aluminum-silicon junctions and demonstrate it as a significant loss channel in superconducting devices. Using aluminum interdigital transducers on silicon, we observe piezoelectric transduction from room to millikelvin temperatures, with an effective electromechanical coupling factor K 2 ≈ (3 ± 0.4) × 10−5%, comparable to weakly piezoelectric substrates. Modeling shows this mechanism limits qubit quality factors to Q ~ 10 4 − 10 8 , depending on surface participation and mode matching. These findings reveal interface piezoelectricity as a major dissipation channel and highlight the need for heterostructure and phononic engineering in next-generation superconducting qubits.

Zhou, Haoxin [University of California, Berkeley, ↗

DOE OSTI2022

The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence

To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Dynamic genome evolution in a model fern

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Predicting stress response and improved protein overproduction in Bacillus subtilis

Abstract Bacillus subtilis is a well-characterized microorganism and a model for the study of Gram-positive bacteria. The bacterium can produce proteins at high densities and yields, which has made it valuable for industrial bioproduction. Like other cell factories, metabolic modeling of B. subtilis has discovered ways to optimize its metabolism toward various applications. The first genome-scale metabolic model (M-model) of B. subtilis was published more than a decade ago and has been applied extensively to understand metabolism, to predict growth phenotypes, and served as a template to reconstruct models for other Gram-positive bacteria. However, M-models are ill-suited to simulate the production and secretion of proteins as well as their proteomic response to stress. Thus, a new generation of metabolic models, known as metabolism and gene expression models (ME-models), has been initiated. Here, we describe the reconstruction and validation of a ME model of B. subtilis , i JT964-ME. This model achieved higher performance scores on the prediction of gene essentiality as compared to the M-model. We successfully validated the model by integrating physiological and omics data associated with gene expression responses to ethanol and salt stress. The model further identified the mechanism by which tryptophan synthesis is upregulated under ethanol stress. Further, we employed i JT964-ME to predict amylase production rates under two different growth conditions. We analyzed these flux distributions and identified key metabolic pathways that permitted the increase in amylase production. Models like i JT964-ME enable the study of proteomic response to stress and the illustrate the potential for optimizing protein production in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗