Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Closure”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble

T-box riboswitches are multi-domain noncoding RNAs that surveil individual amino acid availabilities in most Gram-positive bacteria. T-boxes directly bind specific tRNAs, query their aminoacylation status to detect starvation, and feedback control the transcription or translation of downstream amino-acid metabolic genes. Most T-boxes rapidly recruit their cognate tRNA ligands through an intricate three-way stem I-stem II-tRNA interaction, whose establishment is not understood. Using single-molecule FRET, SAXS, and time-resolved fluorescence, we find that the free T-box RNA assumes a broad distribution of open, semi-open, and closed conformations that only slowly interconvert. tRNA directly binds all three conformers with distinct kinetics, triggers nearly instantaneous collapses of the open conformations, and returns the T-box RNA to their pre-binding conformations upon dissociation. This scissors-like dynamic behavior is enabled by a hinge-like pseudoknot domain which poises the T-box for rapid tRNA-induced domain closure. This study reveals tRNA-chaperoned folding of flexible, multi-domain mRNAs through a Venus flytrap-like mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Increasing atmospheric dryness reduces boreal forest tree growth

Rising atmospheric vapour pressure deficit (VPD) associated with climate change affects boreal forest growth via stomatal closure and soil dryness. However, the relationship between VPD and forest growth depends on the climatic context. Here we assess Canadian boreal forest responses to VPD changes from 1951-2018 using a well-replicated tree-growth increment network with approximately 5,000 species-site combinations. Of the 3,559 successful growth models, we observed a relationship between growth and concurrent summer VPD in one-third of the species-site combinations, and between growth and prior summer VPD in almost half of those combinations. The relationship between previous year VPD and current year growth was almost exclusively negative, while current year VPD also tended to reduce growth. Tree species, age, annual temperature, and soil moisture primarily determined tree VPD responses. Younger trees and species like white spruce and Douglas fir exhibited higher VPD sensitivity, as did areas with high annual temperature and low soil moisture. Since 1951, summer VPD increases in Canada have paralleled tree growth decreases, particularly in spruce species. Accelerating atmospheric dryness in the decades ahead will impair carbon storage and societal-economic services.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Pressure-tuned quantum criticality in the large-D antiferromagnet DTN

Strongly correlated spin systems can be driven to quantum critical points via various routes. In particular, gapped quantum antiferromagnets can undergo phase transitions into a magnetically ordered state with applied pressure or magnetic field, acting as tuning parameters. These transitions are characterized by z = 1 or z = 2 dynamical critical exponents, determined by the linear and quadratic low-energy dispersion of spin excitations, respectively. Employing high-frequency susceptibility and ultrasound techniques, we demonstrate that the tetragonal easy-plane quantum antiferromagnet NiCl 2 · 4SC(NH 2 ) 2 (aka DTN) undergoes a spin-gap closure transition at about 4.2 kbar, resulting in a pressure-induced magnetic ordering. The studies are complemented by high-pressure-electron spin-resonance measurements confirming the proposed scenario. Powder neutron diffraction measurements revealed that no lattice distortion occurs at this pressure and the high spin symmetry is preserved, establishing DTN as a perfect platform to investigate z = 1 quantum critical phenomena. The experimental observations are supported by DMRG calculations, allowing us to quantitatively describe the pressure-driven evolution of critical fields and spin-Hamiltonian parameters in DTN.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Molecular model of TFIIH recruitment to the transcription-coupled repair machinery

Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In our model, CSB, CSA, UVSSA, elongation factor 1 (ELOF1), and specific Pol II and UVSSA-bound ubiquitin moieties come together to provide interaction interfaces needed for TFIIH recruitment. STK19 acts as a linchpin of the assembly, orienting the incoming TFIIH and bridging Pol II to core TCR factors and DNA. Molecular simulations of the TCR-associated CRL4CSA ubiquitin ligase complex unveil the interplay of segmental DDB1 flexibility, continuous Cullin4A flexibility, and the key role of ELOF1 for Pol II ubiquitination that enables TCR. Collectively, these findings elucidate the coordinated assembly of repair proteins in early TCR.

Paul, Tanmoy↗
DOE OSTI2025

Cryo-EM structures of the small-conductance Ca 2+ -activated K Ca 2.2 channel

Small-conductance Ca 2+ -activated K + (K Ca 2.1-K Ca 2.3) channels modulate neuronal and cardiac excitability. We report cryo-electron microscopy structures of the K Ca 2.2 channel in complex with calmodulin and Ca 2+ , alone or bound to two small molecule inhibitors, at 3.18, 3.50, 2.99 and 2.97 angstrom resolution, respectively. Extracellular S3-S4 loops in β-hairpin configuration form an outer canopy over the pore with an aromatic box at the canopy’s center. Each S3-S4 β-hairpin is tethered to the selectivity filter in the neighboring subunit by inter-subunit hydrogen bonds. This hydrogen bond network flips the aromatic residue (Tyr362) in the filter’s GYG signature by 180°, causing the outer selectivity filter to widen and water to enter the filter. Disruption of the tether by a mutation narrows the outer selectivity filter, realigns Tyr362 to the position seen in other K + channels, and significantly increases unitary conductance. UCL1684, a mimetic of the bee venom peptide apamin, sits atop the canopy and occludes the opening in the aromatic box. AP14145, an analogue of a therapeutic for atrial fibrillation, binds in the central cavity below the selectivity filter and induces closure of the inner gate. These structures provide a basis for understanding the small unitary conductance and pharmacology of K Ca 2.x channels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Millimeter-wave dielectric tunability driven by topological polar structure switching in PbTiO 3 /SrTiO 3 superlattices

Dielectric tunability induced by an external electric field in materials underpins radio frequency signal modulation devices such as phase shifters, which are critical components in wireless communication and sensing systems. However, the tunability and integrability of current devices have yet to be enhanced for emerging applications, particularly at millimeter-wave frequencies. Here, we demonstrate that topological polar structures formed in PbTiO 3 /SrTiO 3 superlattices exhibit large tunable in-plane dielectric properties, as determined by their multiscale structural configurations and polarization switching behaviors. Under a moderate field of 30 kV cm −1 , the dipole wave structure maintains a tunability exceeding 15% at 70 GHz and above 8% over the measured range up to 110 GHz, contrasting with the weakly tunable flux closure structure. Based on in situ structural characterizations and molecular dynamics simulations, we delineate the polarization switching processes and elucidate the mechanisms underlying the observed tunable millimeter-wave dielectric responses. Our results provide new insights into the high-frequency dielectric properties of topological polar phases, potentially broadening the versatility of these materials in next-generation integrated electronic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Spontaneous crack healing in calcite reveals the influence of dynamic strain evolution and surface chemistry

The mechanics of fracture healing in calcite remain poorly constrained yet are fundamental to managing fluid transport in geothermal reservoirs and hydrocarbon systems. Here, we apply microfocused synchrotron Laue X-ray diffraction and infrared spectroscopy to investigate subcritical crack healing in a 1 mm-thick calcite crystal subjected to controlled loading in a double-torsion device. Over a 44-hour period following load removal, we map the evolution of residual strain fields surrounding the crack tip and observe a progressive increase in compressive strain perpendicular to the crack plane accompanied by infrared spectroscopic signatures that reveal enhanced accumulation of water at the healed interface. The correlation between strain evolution and surface chemistry suggests that spontaneous crack healing in calcite is driven by dynamic anelastic relaxation coupled with irreversible fluid-mineral interactions. These findings offer insight into time-dependent crack closure processes in carbonates and highlight the role of chemically-mediated plasticity in subsurface fracture evolution.

materials science↗
DOE OSTI2022

Phase-field framework with constraints and its applications to ductile fracture in polycrystals and fatigue

Abstract Modeling of ductile fracture in polycrystalline structures is challenging, since it requires integrated modeling of cracks, crystal plasticity, and grains. Here we extend the typical phase-field framework to the situations with constraints on the order parameters, and formulate two types of phase-field models on ductile fracture. The Type-I model incorporates three sets of order parameters, which describe the distributions of cracks, plastic strain, and grains, respectively. Crystal plasticity is employed within grain interiors accommodated by J 2 plasticity at grain boundaries. The applications of the Type-I model to single crystals and bicrystals demonstrate the influences of grain orientations and grain boundaries on crack growth. In the Type-II model, J 2 plasticity is assumed for the whole system and grain structures are neglected. Taking advantage of the efficiency of the fast Fourier transform, our Type-II model is employed to study low cycle fatigue. Crack closure and striation-like patterning of plastic strain are observed in the simulations. Crack growth rate is analyzed as a function of the J -integral, and the simulated fatigue life as a function of plastic strain agrees with the Coffin–Manson relation without a priori assumption.

36 MATERIALS SCIENCE↗
DOE OSTI2026

High-throughput computation of electric polarization in solids via Berry flux diagonalization

Electric polarization in the absence of an externally applied electric field is a key property of polar materials, but the standard interpolation-based ab initio approach to compute polarization differences within the modern theory of polarization presents challenges for automated high-throughput calculations. Berry flux diagonalization [J. Bonini et al., Phys. Rev. B 102, 045141 (2020)] has been proposed as an efficient and reliable alternative, though it has yet to be widely deployed. Here, we assess Berry flux diagonalization using ab initio calculations of a large set of materials, introducing and validating heuristics that ensure branch alignment with a minimal number of intermediate interpolated structures. Our automated implementation of Berry flux diagonalization succeeds in cases where prior interpolation-based workflows fail due to band-gap closures or branch ambiguities. Benchmarking with ab initio calculations of 176 candidate ferroelectrics, we demonstrate the efficacy of the approach on a broad range of insulating materials and obtain accurate effective polarization values with fewer interpolated structures than prior automated interpolation-based workflows. Our real-space heuristics that can predict gauge stability a priori from ionic displacements enable a general automated framework for reliable polarization calculations and efficient high-throughput screening of chemically and structurally diverse polar insulators. These results establish Berry flux diagonalization as a robust and efficient method to compute the effective polarization of solids and to accelerate the data-driven discovery of functional polar materials.

Poteshman, Abigail N. [University of Chicago, IL (↗
DOE OSTI2021

Forty years of durability assessment of nuclear waste glass by standard methods

Abstract Standard methods to assess the durability of vitrified radioactive waste were first developed in the 1980’s and, over the last 40 years, have evolved to yield a range of responses depending on experimental conditions and glass composition. Mechanistic understanding of glass dissolution has progressed in parallel, enhancing our interpretation of the data acquired. With the implementation of subsurface disposal for vitrified radioactive waste drawing closer, it is timely to review the available standard methodologies and reflect upon their relative advantages, limitations, and how the data obtained can be interpreted to support the post-closure safety case for radioactive waste disposal.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

On-demand nanoengineering of in-plane ferroelectric topologies

Hierarchical assemblies of ferroelectric nanodomains, so-called super-domains, can exhibit exotic morphologies that lead to distinct behaviours. Controlling these super-domains reliably is critical for realizing states with desired functional properties. Here we reveal the super-switching mechanism by using a biased atomic force microscopy tip, that is, the switching of the in-plane super-domains, of a model ferroelectric Pb 0.6 Sr 0.4 TiO 3 . We demonstrate that the writing process is dominated by a super-domain nucleation and stabilization process. A complex scanning-probe trajectory enables on-demand formation of intricate centre-divergent, centre-convergent and flux-closure polar structures. Correlative piezoresponse force microscopy and optical spectroscopy confirm the topological nature and tunability of the emergent structures. The precise and versatile nanolithography in a ferroic material and the stability of the generated structures, also validated by phase-field modelling, suggests potential for reliable multi-state nanodevice architectures and, thereby, an alternative route for the creation of tunable topological structures for applications in neuromorphic circuits.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Transition from sub-Rayleigh anticrack to supershear crack propagation in snow avalanches

Snow slab avalanches, characterized by a distinct, broad fracture line, are released following anticrack propagation in highly porous weak snow layers buried below cohesive slabs. The anticrack mechanism is driven by the volumetric collapse of the weak layer, which leads to the closure of crack faces and to the onset of frictional contact. Here, on the basis of snow fracture experiments, full-scale avalanche measurements and numerical simulations, we report the existence of a transition from sub-Rayleigh anticrack to supershear crack propagation. This transition follows the Burridge–Andrews mechanism, in which a supershear daughter crack nucleates ahead of the main fracture front and eventually propagates faster than the shear wave speed. Furthermore, we show that the supershear propagation regime can exist even if the shear-to-normal stress ratio is lower than the static friction coefficient as a result of the loss of frictional resistance during collapse. This finding shows that snow slab avalanches have fundamental similarities with strike-slip earthquakes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Structural basis of the activation of a metabotropic GABA receptor

Metabotropic γ-aminobutyric acid receptors (GABA B ) are involved in the modulation of synaptic responses in the central nervous system and have been implicated in neuropsychological conditions that range from addiction to psychosis. GABA B belongs to class C of the G-protein-coupled receptors, and its functional entity comprises an obligate heterodimer that is composed of the GB1 and GB2 subunits. Each subunit possesses an extracellular Venus flytrap domain, which is connected to a canonical seven-transmembrane domain. In this paper we present four cryo-electron microscopy structures of the human full-length GB1–GB2 heterodimer: one structure of its inactive apo state, two intermediate agonist-bound forms and an active form in which the heterodimer is bound to an agonist and a positive allosteric modulator. The structures reveal substantial differences, which shed light on the complex motions that underlie the unique activation mechanism of GABA B . Our results show that agonist binding leads to the closure of the Venus flytrap domain of GB1, triggering a series of transitions, first rearranging and bringing the two transmembrane domains into close contact along transmembrane helix 6 and ultimately inducing conformational rearrangements in the GB2 transmembrane domain via a lever-like mechanism to initiate downstream signalling. This active state is stabilized by a positive allosteric modulator binding at the transmembrane dimerization interface.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure of the human dopamine transporter and mechanisms of inhibition

Abstract The neurotransmitter dopamine has central roles in mood, appetite, arousal and movement 1 . Despite its importance in brain physiology and function, and as a target for illicit and therapeutic drugs, the human dopamine transporter (hDAT) and mechanisms by which it is inhibited by small molecules and Zn 2+ are without a high-resolution structural context. Here we determine the structure of hDAT in a tripartite complex with the competitive inhibitor and cocaine analogue, (–)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane 2 (β-CFT), the non-competitive inhibitor MRS7292 3 and Zn 2 + (ref. 4 ). We show how β-CFT occupies the central site, approximately halfway across the membrane, stabilizing the transporter in an outward-open conformation. MRS7292 binds to a structurally uncharacterized allosteric site, adjacent to the extracellular vestibule, sequestered underneath the extracellular loop 4 (EL4) and adjacent to transmembrane helix 1b (TM1b), acting as a wedge, precluding movement of TM1b and closure of the extracellular gate. A Zn 2+ ion further stabilizes the outward-facing conformation by coupling EL4 to EL2, TM7 and TM8, thus providing specific insights into how Zn 2+ restrains the movement of EL4 relative to EL2 and inhibits transport activity.

Science & Technology - Other Topics↗
DOE OSTI2026

Direct observation of the superallowed α-decay of 104 Te

The radioactivity of the α particle is among the most compelling evidence for the existence of cluster structures in atomic nuclei. During the decay process, a pre-existing α particle tunnels through the potential barrier formed by the residual nucleus1,2. The degree of preformation of the α particle, a strongly bound system of two protons and two neutrons, is extracted from the data by dividing the α-decay probability by the barrier penetrability for a given particle energy. The preformation probability changes rapidly near nuclear shell closures, which is direct evidence that clustering is connected to nuclear structure3. Enhanced preformation was observed in the lightest α-particle emitters, spherical tellurium and xenon isotopes decaying to magic isotopes of tin. Here we show the most extreme case of α-particle preformation from the measurement of the decay of tellurium-104 (104Te). With a half-life of , 104Te is the fastest ground-state α-emitting nucleus known so far. The deduced preformation demonstrates that the enhancement is greater for 104Te than for any other nucleus. One nuclear model that can explain our observation postulates that the α particle can exist only in the low-nuclear-matter-density regions on the surface of the nucleus. The uniquely high preformation for 104Te is attributed to its relation to doubly magic tin-100 (100Sn), creating conditions conducive to form an α particle.

Cox, Ian↗
DOE OSTI2020

Azobenzene-based sinusoidal surface topography drives focal adhesion confinement and guides collective migration of epithelial cells

Surface topography is a key parameter in regulating the morphology and behavior of single cells. At multicellular level, coordinated cell displacements drive many biological events such as embryonic morphogenesis. However, the effect of surface topography on collective migration of epithelium has not been studied in detail. Mastering the connection between surface features and collective cellular behaviour is highly important for novel approaches in tissue engineering and repair. Herein, we used photopatterned microtopographies on azobenzene-containing materials and showed that smooth topographical cues with proper period and orientation can efficiently orchestrate cell alignment in growing epithelium. Furthermore, the experimental system allowed us to investigate how the orientation of the topographical features can alter the speed of wound closure in vitro. Our findings indicate that the extracellular microenvironment topography coordinates their focal adhesion distribution and alignment. These topographic cues are able to guide the collective migration of multicellular systems, even when cell–cell junctions are disrupted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds

Abstract Battlefield injury management requires specialized care, and wound infection is a frequent complication. Challenges related to characterizing relevant pathogens further complicates treatment. Applying metagenomics to wounds offers a comprehensive path toward assessing microbial genomic fingerprints and could indicate prognostic variables for future decision support tools. Wound specimens from combat-injured U.S. service members, obtained during surgical debridements before delayed wound closure, were subjected to whole metagenome analysis and targeted enrichment of antimicrobial resistance genes. Results did not indicate a singular, common microbial metagenomic profile for wound failure, instead reflecting a complex microenvironment with varying bioburden diversity across outcomes. Genus-level Pseudomonas detection was associated with wound failure at all surgeries. A logistic regression model was fit to the presence and absence of antimicrobial resistance classes to assess associations with nosocomial pathogens. A. baumannii detection was associated with detection of genomic signatures for resistance to trimethoprim, aminoglycosides, bacitracin, and polymyxin. Machine learning classifiers were applied to identify wound and microbial variables associated with outcome. Feature importance rankings averaged across models indicated the variables with the largest effects on predicting wound outcome, including an increase in P. putida sequence reads. These results describe the microbial genomic determinants in combat wound bioburden and demonstrate metagenomic investigation as a comprehensive tool for providing information toward aiding treatment of combat-related injuries.

59 BASIC BIOLOGICAL SCIENCES↗