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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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Emergent disorder and mechanical memory in periodic metamaterials

Ordered mechanical systems typically have one or only a few stable rest configurations, and hence are not considered useful for encoding memory. Multistable and history-dependent responses usually emerge from quenched disorder, for example in amorphous solids or crumpled sheets. In contrast, due to geometric frustration, periodic magnetic systems can create their own disorder and espouse an extensive manifold of quasi-degenerate configurations. Inspired by the topological structure of frustrated artificial spin ices, we introduce an approach to design ordered, periodic mechanical metamaterials that exhibit an extensive set of spatially disordered states. While our design exploits the correspondence between frustration in magnetism and incompatibility in meta-mechanics, our mechanical systems encompass continuous degrees of freedom, and thus generalize their magnetic counterparts. We show how such systems exhibit non-Abelian and history-dependent responses, as their state can depend on the order in which external manipulations were applied. We demonstrate how this richness of the dynamics enables to recognize, from a static measurement of the final state, the sequence of operations that an extended system underwent. Thus, multistability and potential to perform computation emerge from geometric frustration in ordered mechanical lattices that create their own disorder.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Sustained bacterial N 2 O reduction at acidic pH

Nitrous oxide (N 2 O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N 2 O to dinitrogen (N 2 ) is the major consumption process but microbial N 2 O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N 2 O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N 2 O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N 2 O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N 2 O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N 2 O reduction between pH 4.5 and 6, highlighting microbial N 2 O reduction potential in acidic soils.

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

Evolution of connectivity architecture in the Drosophila mushroom body

Brain evolution has primarily been studied at the macroscopic level by comparing the relative size of homologous brain centers between species. How neuronal circuits change at the cellular level over evolutionary time remains largely unanswered. Here, using a phylogenetically informed framework, we compare the olfactory circuits of three closely related Drosophila species that differ in their chemical ecology: the generalists Drosophila melanogaster and Drosophila simulans and Drosophila sechellia that specializes on ripe noni fruit. We examine a central part of the olfactory circuit that, to our knowledge, has not been investigated in these species—the connections between projection neurons and the Kenyon cells of the mushroom body—and identify species-specific connectivity patterns. We found that neurons encoding food odors connect more frequently with Kenyon cells, giving rise to species-specific biases in connectivity. These species-specific connectivity differences reflect two distinct neuronal phenotypes: in the number of projection neurons or in the number of presynaptic boutons formed by individual projection neurons. Finally, behavioral analyses suggest that such increased connectivity enhances learning performance in an associative task. Our study shows how fine-grained aspects of connectivity architecture in an associative brain center can change during evolution to reflect the chemical ecology of a species.

59 BASIC BIOLOGICAL 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

Diversity of visual inputs to Kenyon cells of the Drosophila mushroom body

The arthropod mushroom body is well-studied as an expansion layer representing olfactory stimuli and linking them to contingent events. However, 8% of mushroom body Kenyon cells in Drosophila melanogaster receive predominantly visual input, and their function remains unclear. Here, we identify inputs to visual Kenyon cells using the FlyWire adult whole-brain connectome. Input repertoires are similar across hemispheres and connectomes with certain inputs highly overrepresented. Many visual neurons presynaptic to Kenyon cells have large receptive fields, while interneuron inputs receive spatially restricted signals that may be tuned to specific visual features. Individual visual Kenyon cells randomly sample sparse inputs from combinations of visual channels, including multiple optic lobe neuropils. These connectivity patterns suggest that visual coding in the mushroom body, like olfactory coding, is sparse, distributed, and combinatorial. However, the specific input repertoire to the smaller population of visual Kenyon cells suggests a constrained encoding of visual stimuli.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Asgard archaea modulate potential methanogenesis substrates in wetland soil

The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Rapid discovery and evolution of nanosensors containing fluorogenic amino acids

Binding-activated optical sensors are powerful tools for imaging, diagnostics, and biomolecular sensing. However, biosensor discovery is slow and requires tedious steps in rational design, screening, and characterization. Here we report on a platform that streamlines biosensor discovery and unlocks directed nanosensor evolution through genetically encodable fluorogenic amino acids (FgAAs). Building on the classical knowledge-based semisynthetic approach, we engineer ~15 kDa nanosensors that recognize specific proteins, peptides, and small molecules with up to 100-fold fluorescence increases and subsecond kinetics, allowing real-time and wash-free target sensing and live-cell bioimaging. An optimized genetic code expansion chemistry with FgAAs further enables rapid (~3 h) ribosomal nanosensor discovery via the cell-free translation of hundreds of candidates in parallel and directed nanosensor evolution with improved variant-specific sensitivities (up to ~250-fold) for SARS-CoV-2 antigens. Altogether, this platform could accelerate the discovery of fluorogenic nanosensors and pave the way to modify proteins with other non-standard functionalities for diverse applications.

Biosensors↗
DOE OSTI2024

Electrically interfaced Brillouin-active waveguide for microwave photonic measurements

New strategies for converting signals between optical and microwave domains could play a pivotal role in advancing both classical and quantum technologies. Traditional approaches to optical-to-microwave transduction typically perturb or destroy the information encoded on intensity of the light field, eliminating the possibility for further processing or distribution of these signals. In this paper, we introduce an optical-to-microwave conversion method that allows for both detection and spectral analysis of microwave photonic signals without degradation of their information content. This functionality is demonstrated using an optomechanical waveguide integrated with a piezoelectric transducer. Efficient electromechanical and optomechanical coupling within this system permits bidirectional optical-to-microwave conversion with a quantum efficiency of up to -54.16 dB. Leveraging the preservation of the optical field envelope in intramodal Brillouin scattering, we demonstrate a multi-channel microwave photonic filter by transmitting an optical signal through a series of electro-optomechanical waveguide segments, each with distinct resonance frequencies. Such electro-optomechanical systems could offer flexible strategies for remote sensing, channelization, and spectrum analysis in microwave photonics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Extracting the femtometer structure of strange baryons using the vacuum polarization effect

Abstract One of the fundamental goals of particle physics is to gain a microscopic understanding of the strong interaction. Electromagnetic form factors quantify the structure of hadrons in terms of charge and magnetization distributions. While the nucleon structure has been investigated extensively, data on hyperons are still scarce. It has recently been demonstrated that electron-positron annihilations into hyperon-antihyperon pairs provide a powerful tool to investigate their inner structure. We present a method useful for hyperon-antihyperon pairs of different types which exploits the cross section enhancement due to the effect of vacuum polarization at theJ/ψresonance. Using the 10 billionJ/ψevents collected with the BESIII detector, this allows a precise determination of the hyperon structure function. The result is essentially a precise snapshot of the$$\bar{\Lambda }{\Sigma }^{0}\,(\Lambda {\bar{\Sigma }}^{0})$$ Λ ¯ Σ 0 ( Λ Σ ¯ 0 ) transition process, encoded in the transition form factor ratio and phase. Their values are measured to beR = 0.860 ± 0.029(stat.) ± 0.015(syst.),$$\Delta {\Phi }_{\bar{\Lambda }{\Sigma }^{0}}=(1.011\pm 0.094({{\rm{stat.}}})\pm 0.010({{\rm{syst.}}}))\,{{\rm{r}}}ad$$ Δ Φ Λ ¯ Σ 0 = ( 1.011 ± 0.094 ( stat. ) ± 0.010 ( syst. ) ) r a d and$$\Delta {\Phi }_{\Lambda {\bar{\Sigma }}^{0}}=(2.128\pm 0.094({{\rm{stat.}}})\pm 0.010({{\rm{syst.}}}))\,{{\rm{r}}}ad$$ Δ Φ Λ Σ ¯ 0 = ( 2.128 ± 0.094 ( stat. ) ± 0.010 ( syst. ) ) r a d . Furthermore, charge-parity (CP) breaking is investigated in this reaction and found to be consistent with CP symmetry.

Science & Technology - Other Topics↗
DOE OSTI2024

Mechanochemically responsive polymer enables shockwave visualization

Abstract Understanding the physical and chemical response of materials to impulsive deformation is crucial for applications ranging from soft robotic locomotion to space exploration to seismology. However, investigating material properties at extreme strain rates remains challenging due to temporal and spatial resolution limitations. Combining high-strain-rate testing with mechanochemistry encodes the molecular-level deformation within the material itself, thus enabling the direct quantification of the material response. Here, we demonstrate a mechanophore-functionalized block copolymer that self-reports energy dissipation mechanisms, such as bond rupture and acoustic wave dissipation, in response to high-strain-rate impacts. A microprojectile accelerated towards the polymer permanently deforms the material at a shallow depth. At intersonic velocities, the polymer reports significant subsurface energy absorption due to shockwave attenuation, a mechanism traditionally considered negligible compared to plasticity and not well explored in polymers. The acoustic wave velocity of the material is directly recovered from the mechanochemically-activated subsurface volume recorded in the material, which is validated by simulations, theory, and acoustic measurements. This integration of mechanochemistry with microballistic testing enables characterization of high-strain-rate mechanical properties and elucidates important insights applicable to nanomaterials, particle-reinforced composites, and biocompatible polymers.

Science & Technology - Other Topics↗
DOE OSTI2024

Learning protocols for the fast and efficient control of active matter

Exact analytic calculation shows that optimal control protocols for passive molecular systems often involve rapid variations and discontinuities. However, similar analytic baselines are not generally available for active-matter systems, because it is more difficult to treat active systems exactly. Here we use machine learning to derive efficient control protocols for active-matter systems, and find that they are characterized by sharp features similar to those seen in passive systems. We show that it is possible to learn protocols that effect fast and efficient state-to-state transformations in simulation models of active particles by encoding the protocol in the form of a neural network. We use evolutionary methods to identify protocols that take active particles from one steady state to another, as quickly as possible or with as little energy expended as possible. Our results show that protocols identified by a flexible neural-network ansatz, which allows the optimization of multiple control parameters and the emergence of sharp features, are more efficient than protocols derived recently by constrained analytical methods. Our learning scheme is straightforward to use in experiment, suggesting a way of designing protocols for the efficient manipulation of active matter in the laboratory.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Complex transcriptional regulations of a hyperparasitic quadripartite system in giant viruses infecting protists

Abstract Hyperparasitism is a common pattern in nature that is not limited to cellular organisms. Giant viruses infecting protists can be hyperparasitized by smaller ones named virophages. In addition, both may carry episomal DNA molecules known as transpovirons in their particles. They all share transcriptional regulatory elements that dictate the expression of their genes within viral factories built by giant viruses in the host cytoplasm. This suggests the existence of interactions between their respective transcriptional networks. Here we investigatedAcanthamoeba castellaniicells infected by a giant virus (megavirus chilensis), and coinfected with a virophage (zamilon vitis) and/or a transpoviron (megavirus vitis transpoviron). Infectious cycles were monitored through time-course RNA sequencing to decipher the transcriptional program of each partner and its impact on the gene expression of the others. We found highly diverse transcriptional responses. While the giant virus drastically reshaped the host cell transcriptome, the transpoviron had no effect on the gene expression of any of the players. In contrast, the virophage strongly modified the giant virus gene expression, albeit transiently, without altering the protein composition of mature viral particles. The virophage also induced the overexpression of transpoviron genes, likely through the indirect upregulation of giant virus-encoded transcription factors. Together, these analyses document the intricated transcriptionally regulated networks taking place in the infected cell.

Science & Technology - Other Topics↗
DOE OSTI2024

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development. We identify the gene desert as a regulatory hub containing more than 15 distinct enhancers recapitulating anatomical subdomains of Shox2 expression. Ablation of the gene desert leads to embryonic lethality due to Shox2 depletion in the cardiac sinus venosus, caused in part by the loss of a specific distal enhancer. The gene desert is also required for stylopod morphogenesis, mediated via distributed proximal limb enhancers. In summary, our study establishes a multi-layered role of the Shox2 gene desert in orchestrating pleiotropic developmental expression through modular arrangement and coordinated dynamics of tissue-specific enhancers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

RNA language models predict mutations that improve RNA function

Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences to experimental and predicted optimal growth temperatures of GTDB reference organisms. Using GARNET, we develop sequence- and structure-aware RNA generative models, with overlapping triplet tokenization providing optimal encoding for a GPT-like model. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identify mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Towards large-scale quantum optimization solvers with few qubits

Quantum computers hold the promise of more efficient combinatorial optimization solvers, which could be game-changing for a broad range of applications. However, a bottleneck for materializing such advantages is that, in order to challenge classical algorithms in practice, mainstream approaches require a number of qubits prohibitively large for near-term hardware. Here we introduce a variational solver for MaxCut problems over $m={{\mathcal{O}}}({n}^{k})$ binary variables using only n qubits, with tunable k > 1. The number of parameters and circuit depth display mild linear and sublinear scalings in m , respectively. Moreover, we analytically prove that the specific qubit-efficient encoding brings in a super-polynomial mitigation of barren plateaus as a built-in feature. Altogether, this leads to high quantum-solver performances. For instance, for m = 7000, numerical simulations produce solutions competitive in quality with state-of-the-art classical solvers. In turn, for m = 2000, experiments with n = 17 trapped-ion qubits feature MaxCut approximation ratios estimated to be beyond the hardness threshold 0.941. Our findings offer an interesting heuristics for quantum-inspired solvers as well as a promising route towards solving commercially-relevant problems on near-term quantum devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Automatic speech recognition predicts contemporaneous earthquake fault displacement

Abstract Significant progress has been made in probing the state of an earthquake fault by applying machine learning to continuous seismic waveforms. The breakthroughs were originally obtained from laboratory shear experiments and numerical simulations of fault shear, then successfully extended to slow-slipping faults. Here we apply the Wav2Vec-2.0 self-supervised framework for automatic speech recognition to continuous seismic signals emanating from a sequence of moderate magnitude earthquakes during the 2018 caldera collapse at the Kīlauea volcano on the island of Hawai’i. We pre-train the Wav2Vec-2.0 model using caldera seismic waveforms and augment the model architecture to predict contemporaneous surface displacement during the caldera collapse sequence, a proxy for fault displacement. We find the model displacement predictions to be excellent. The model is adapted for near-future prediction information and found hints of prediction capability, but the results are not robust. The results demonstrate that earthquake faults emit seismic signatures in a similar manner to laboratory and numerical simulation faults, and artificial intelligence models developed for encoding audio of speech may have important applications in studying active fault zones.

58 GEOSCIENCES↗
DOE OSTI2025

High-fidelity remote entanglement of trapped atoms mediated by time-bin photons

Abstract Photonic interconnects between quantum processing nodes are likely the only way to achieve large-scale quantum computers and networks. The bottleneck in such an architecture is the interface between well-isolated quantum memories and flying photons. We establish high-fidelity entanglement between remotely separated trapped atomic qubit memories, mediated by photonic qubits stored in the timing of their pulses. Such time-bin encoding removes sensitivity to polarization errors, enables long-distance quantum communication, and is extensible to quantum memories with more than two states. Using a measurement-based error detection process and suppressing a fundamental source of error due to atomic recoil, we achieve an entanglement fidelity of 97% and show that fundamental limits due to atomic recoil still allow fidelities in excess of 99.9%.

Science & Technology - Other Topics↗
DOE OSTI2025

A cytosolic glyoxylate shunt complements the canonical photorespiratory pathway in Arabidopsis

Photorespiration functions in part to support photosynthetic performance, especially under stress such as high light, yet the underlying mechanisms are poorly understood. To identify modulators of photorespiration under high light, we have isolated genetic suppressors of the photorespiratory mutant hpr1 (hydroxypyruvate reductase 1) from Arabidopsis. A suppressor that partially rescues hpr1 is mapped to GLYR1, which encodes the cytosolic glyoxylate reductase 1 that converts glyoxylate to glycolate. Independent glyr1 mutants also partially rescue hpr1 and another photorespiratory mutant, catalase 2. Our genetic, transcriptomic and metabolic profiling analyses together reveal a connection between cytosolic glyoxylate and a non-canonical photorespiratory route mediated by HPR2, which we name the photorespiratory glyoxylate shunt. This shunt complements the canonical photorespiratory pathway and is especially critical when high photorespiratory fluxes are required and when the major photorespiratory pathway is deficient. Our findings support the metabolic flexibility of photorespiration and may help to improve crop performance under stress.

Light stress↗