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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 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Pitfalls in the n -mode representation of vibrational potentials

Simulations of anharmonic vibrational motion rely on computationally expedient representations of the governing potential energy surface. The n-mode representation (n-MR)—effectively a many-body expansion in the space of molecular vibrations—is a general and efficient approach that is often used for this purpose in vibrational self-consistent field (VSCF) calculations and correlated analogues thereof. In the present analysis, a lack of convergence in many VSCF calculations is shown to originate from negative and unbound potentials at truncated orders of the n-MR expansion. For cases of strong anharmonic coupling between modes, the n-MR can both dip below the true global minimum of the potential surface and lead to effective single-mode potentials in VSCF that do not correspond to bound vibrational problems, even for bound total potentials. The present analysis serves mainly as a pathology report of this issue. Furthermore, this insight into the origin of VSCF non-convergence provides a simple, albeit ad hoc, route to correct the problem by “painting in” the full representation of groups of modes that exhibit these negative potentials at little additional computational cost. Somewhat surprisingly, this approach also reasonably approximates the results of the next-higher n-MR order and identifies groups of modes with particularly strong coupling. The method is shown to identify and correct problematic triples of modes—and restore SCF convergence—in two-mode representations of challenging test systems, including the water dimer and trimer, as well as protonated tropine.

Chemistry↗
DOE OSTI2020

Visualization of the HIV-1 Env glycan shield across scales

The dense array of N-linked glycans on the HIV-1 envelope glycoprotein (Env), known as the “glycan shield,” is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure–function analysis. Here, we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of interglycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same cell line used for vaccine production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner, we found that highly connected glycan clusters are resistant to digestion and help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structure of RADX and mechanism for regulation of RAD51 nucleofilaments

Replication fork reversal is a fundamental process required for resolution of encounters with DNA damage. A key step in the stabilization and eventual resolution of reversed forks is formation of RAD51 nucleoprotein filaments on exposed single strand DNA (ssDNA). To avoid genome instability, RAD51 filaments are tightly controlled by a variety of positive and negative regulators. RADX (RPA-related RAD51-antagonist on the X chromosome) is a recently discovered negative regulator that binds tightly to ssDNA, directly interacts with RAD51, and regulates replication fork reversal and stabilization in a context-dependent manner. Here, we present a structure-based investigation of RADX’s mechanism of action. Mass photometry experiments showed that RADX forms multiple oligomeric states in a concentration-dependent manner, with a predominance of trimers in the presence of ssDNA. The structure of RADX, which has no structurally characterized orthologs, was determined ab initio by cryo-electron microscopy (cryo-EM) from maps in the 2 to 4 Å range. The structure reveals the molecular basis for RADX oligomerization and the coupled multi-valent binding of ssDNA binding. The interaction of RADX with RAD51 filaments was imaged by negative stain EM, which showed a RADX oligomer at the end of filaments. Based on these results, we propose a model in which RADX functions by capping and restricting the end of RAD51 filaments.

Science & Technology - Other Topics↗
DOE OSTI2024

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO 2 in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate (HCO$^–_3$), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic β-carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO$^–_3$ relative to CO 2 . To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO 2 -concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO 2 assimilation in a crowded model carboxysome. Despite a relatively high CO 2 permeability of approximately 10 -2 cm/s across the carboxysome shell, the shell proteins reflect enough CO 2 back toward rubisco that 2,650 CO 2 molecules can be fixed by rubisco for every 1 CO 2 molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants

Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.

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

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

Abstract CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Antitoxin control of optimal transcriptional repression in the atypical HigB–HigA toxin–antitoxin system from Proteus vulgaris

Abstract Bacterial toxin–antitoxin (TA) pairs transcriptionally autoregulate their expression via a repression/derepression mechanism in response to changing environmental conditions. The structural diversity of TA systems influences the mechanisms of transcriptional regulation. Here, we define the molecular mechanism for the plasmid-encoded HigB–HigA TA pair originally identified in a post-operative infection with antibiotic-resistant Proteus vulgaris. We determine DNA binding and promoter activity by the HigB–HigA complex supported by structural biology and molecular dynamics simulations of an elusive DNA operator–TA repressor complex. To define the optimal oligomeric TA repressor–DNA operator complex required for derepression, we engineered a dedicated trimeric HigB–HigA2 complex that represses transcription more than 26-fold as compared to the tetrameric HigB2–HigA2. These results expand the known diversity of how the HigB–HigA TA family is autoregulated.

Biochemistry & Molecular Biology↗
DOE OSTI2026

CP26 is not involved in qE- or qZ-type non-photochemical quenching in Arabidopsis

CP26 is a monomeric minor light-harvesting complex of Photosystem II (LHCII) protein located at the interface between LHCII trimers and the PSII core in thylakoid membranes. Previous studies have proposed that CP26 plays a role in non-photochemical quenching (NPQ) in addition to light harvesting. Here, we utilized biophysical and pharmacological approaches to investigate this role using single- and higher-order Arabidopsis (Arabidopsis thaliana) cp26 mutants, examining its relationship to known NPQ regulators (Photosystem II subunit S, PsbS, violaxanthin de-epoxidase, and the pH gradient across the thylakoid membrane). cp26 mutants showed significantly reduced maximum PSII quantum efficiencies (F v /F m ) in darkness, indicating a constitutively quenched state, further confirmed by fluorescence lifetime measurements. Destabilized PSII-LHCII supercomplexes observed in native gel electrophoresis and tighter PSII supercomplex packing were potential causes, with no other antenna proteins capable of rescuing this phenotype. In addition, the cp26 mutants exhibited altered NPQ capacity—modest in single mutants but substantial in double mutants—independent of PsbS and violaxanthin de-epoxidase. Together, these results show that CP26 is not involved in qE or qZ but may primarily play an indirect role in apparent NPQ responses via PSII-LHCII supercomplex organization.

Walter, Julia [University of Cambridge (United Kin↗
DOE OSTI2026

The small protein SbtC is a functional component of the CO 2 concentrating mechanism in Synechocystis sp. PCC 6803

Oxygenic phototrophs fix CO 2 via the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which shows relatively low CO 2 affinity and specificity. To circumvent low and fluctuating CO 2 concentrations in aquatic systems, cyanobacteria and algae have evolved sophisticated inorganic carbon (Ci) concentrating mechanisms (CCMs). Bicarbonate transporters such as SbtA play a crucial role in the cyanobacterial CCM and hence display multiple layers of tight regulation. Control of sbtA gene expression and corresponding transporter activity involves the PII-like protein SbtB, whose gene is frequently co-transcribed with sbtA. A previously non-annotated gene located upstream of the sbtAB operon in the model Synechocystis sp. PCC 6803 encodes the small protein SbtC, composed of 80 amino acids. Presence of SbtC was confirmed by immunoblotting of the sbtC-coding sequence fused to a Flag-tag. Similar to sbtAB , transcription of the sbtC locus is induced by low CO 2 availability; however, it is controlled independently. Mutation of the sbtC locus in a wild-type background produced only a mild phenotype, even under low CO 2 , but impaired diurnal growth resembled that of the mutant ΔsbtB . Biochemical analysis indicated a trimeric SbtABC complex in the membrane. Bicarbonate leakage from cells was strongly elevated when either sbtB or sbtC was deleted from recombinant Synechocystis strains harboring only SbtA as single Ci uptake system. Here, our results provide evidence that SbtC contributes to the formation of the SbtAB complex, thereby regulating bicarbonate exchange at the cytoplasmic membrane. Well-conserved SbtC-like proteins encoded in the neighborhood of sbtAB exist in many cyanobacterial genomes, pointing toward an important role in the cyanobacterial CCM.

Walke, Peter [Univ. of Rostock (Germany)] (ORCID:0↗
DOE OSTI2025

Short-range magnetic order and planar anisotropy in the topological ferrimagnet Mn 3 ⁢Si 2 ⁢Te 6

Mn 3 ⁢Si 2 ⁢Te 6 is a ferrimagnetic topological nodal-line semiconductor that exhibits unconventional colossal magnetoresistance behavior, with short-range spin fluctuations being potentially intimately linked to the emergent properties. Here we determine the short-range magnetic order and anisotropy through total neutron scattering and polarized neutron powder diffraction measurements on polycrystalline Mn 3 ⁢Si 2⁢ Te 6 . Strong in-plane anisotropy is quantified on the Mn ions through extraction of the local site susceptibility tensor. Here, the real-space local spin structure is determined through the application of magnetic pair distribution function analysis covering a wide temperature range. Short-range order over a locally frustrated trimer of three nearest neighbors is found to exist well above the long-range ferrimagnetic transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Topological protection of coherence in disordered open quantum systems

Here, we consider topological protection mechanisms in dissipative quantum systems in the presence of quenched disorder, with the intent to prolong the coherence time of a fiducial qubit. The qubit is part of a network of other qubits and dissipative cavities whose coupling parameters are tunable, such that topological edge states can be stabilized. The evolution of the fiducial qubit is entirely determined by a non-Hermitian Hamiltonian which thus emerges from a bona fide physical process. Even in the presence of disorder, a winding number W can be defined and evaluated in real space, as long as certain symmetries are preserved. Hence we can construct the topological phase diagrams of noisy open quantum models, such as the non-Hermitian disordered Su-Schrieffer-Heeger dimer model and a trimer model that includes longer-range couplings. For finite-size systems we find that there are precisely W modes localized at one end of the chain. In such topological phases the qubit's coherence lifetime is exponentially large in the system size. In the presence of competing disorder parameters, interesting reentrance phenomena of topologically nontrivial sectors are observed. This means that in certain parameter regions, increasing disorder drastically increases the coherence time of the fiducial qubit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Bayesian inference for plasmonic nanometrology

Here, we introduce a Bayesian method for the characterization of plasmonic nanoparticles, which is applicable to both near- and far-field problems. Designed to combine data generated from any photon-plasmon interaction experiment with physically motivated theoretical models, our approach leverages state-of-the-art Markov chain Monte Carlo sampling techniques and returns parameter estimates on nanometric scales. Simulated spectral data sets, describing resonant scattering of photons from ellipsoidal and toroidal nanoparticles, are explored as concrete examples of our approach, with the resulting Bayesian estimates showing excellent agreement with the ground truth, even under conditions of high statistical noise. By incorporating Bayes factors into the method as well, we reveal how model selection can determine which one of competing geometric shapes better explains the observed data. Our comprehensive nanometrology procedure can be tailored to a variety of light-particle interaction models, and its reliance on Bayesian inference furnishes automatic uncertainty quantification. In addition to applicability to a host of plasmonic configurations such as nanoparticle dimers, trimers, and array studies, it is proposed that the presented analysis can be extended to the quantum regime, where nonclassical photon statistics may provide additional insight for inference of scatterer properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Ultrafast spin-nematic and ferroelectric phase transitions induced by femtosecond light pulses

We report, optically induced phase transitions of the manganite Pr 1/3 Ca 2/3 MnO 3 have been simulated by using a model Hamiltonian that captures the dynamics of strongly correlated charge, orbital, lattice, and spin degrees of freedom. Its parameters have been extracted from first-principles calculations. Beyond a critical intensity of a femtosecond light pulse, the material undergoes an ultrafast and nonthermal magnetic phase transition from a noncollinear to collinear antiferromagnetic phase. The light-pulse excites selectively either a spin-nematic or a ferroelectric phase, depending on the light polarization. The behavior can be traced to an optically induced ferromagnetic coupling between Mn trimers, i.e., polarons which are delocalized over three Mn sites. The polarization guides the polymerization of the polaronic crystal into distinct patterns of ferromagnetic chains determining the target phase.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Magnetic structure and multiferroicity of Sc-substituted hexagonal YbFeO 3

The hexagonal rare-earth ferrite RFeO 3 family represents a unique class of multiferroics exhibiting weak ferromagnetism, and a strong coupling between magnetism and structural trimerization is predicted. However, the hexagonal structure for RFeO 3 remains metastable in conventional conditions. We have succeeded in stabilizing the hexagonal structure of polycrystalline YbFeO 3 by partial Sc substitution of Yb. Using bulk magnetometry and neutron diffraction, we find that Yb 0.42 Sc 0.58 FeO 3 orders into a canted antiferromagnetic state with the Néel temperature T N ~ 165K, below which the Fe 3+ moments form the triangular configuration in the ab plane and their in-plane projections are parallel to the [100] axis, consistent with magnetic space group P6 3 c'm'. It is determined that the spin canting is aligned along the c axis, giving rise to the weak ferromagnetism. Furthermore, the Fe 3+ moments reorient toward a new direction below reorientation temperature T R ~ 40K, satisfying magnetic subgroup P6 3 , while the Yb 3+ moments order independently and ferrimagnetically along the c axis at the characteristic temperature T Yb ~ 15K. Interestingly, reproducible modulation of electric polarization induced by magnetic field at low temperature is achieved, suggesting that the delicate structural distortion associated with two-up/one-down buckling of the Yb/Sc planes and tilting of the FeO 5 bipyramids may mediate the coupling between ferroelectric and magnetic orders under magnetic field. Furthermore, the present work represents substantial progress to search for high-temperature multiferroics in hexagonal ferrites and related materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Structural and magnetic transitions in the planar antiferromagnet Ba 4 Ir 3 O 10

We report the structural and magnetic ground state properties of the monoclinic compound barium iridium oxide Ba 4 Ir 3 O 10 using a combination of resonant x-ray scattering, magnetometry, and thermodynamic techniques. Magnetic susceptibility exhibits a pronounced antiferromagnetic transition at T N ≈ 25 K, a weaker anomaly at T S ≈ 142 K, and strong magnetic anisotropy at all temperatures. Resonant elastic x-ray scattering experiments reveal a second order structural phase transition at T S and a magnetic transition at T N . Both structural and magnetic superlattice peaks are observed at L = half integer values. The magnetization anomaly at T S implies the presence of magnetoelastic coupling, which conceivably facilitates the symmetry lowering. Mean field critical scattering is observed above T S . The magnetic structure of the antiferromagnetic ground state is discussed based on the measured magnetic superlattice peak intensity. Furthermore, our study not only presents essential information for understanding the intertwined structural and magnetic properties in Ba 4 Ir 3 O 10 but also highlights the necessary ingredients for exploring novel ground states with octahedra trimers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Crystal structures and formation mechanisms of boron-rich tungsten borides

Boron-rich tungsten borides tend to adopt mechanically unfavorable layered structures but experimentally exhibit excellent mechanical properties rivalling traditional superhard solids. Unravelling the contraindicated structure-property relationship, however, has been impeded by their structural ambiguities because of the difficulty in probing boron and atomic deficiency of these borides. Here, we study crystal structures of boron-rich tungsten borides WB 3+x and WB 2+x by neutron diffraction based on high-quality samples prepared by a high-pressure method, leading to definitive structural resolutions for both borides with unique compositions of WB 5.14 and WB 2.34 . Combined with theoretical calculations, their structural stability is revealed to be closely related to atomic deficiency, which is governed by the valence-band filling with an optimal valence-electron concentration of ~10 per cell. The presence of interstitial boron trimers at the vacant W : 2b sites in WB 5.14 alters the crystal symmetry, making the Wyckoff 2d site more favorably occupied by W, rather than the 2c site, as previously misassigned. Here, the staggered planar boron layers and wrinkled boron bonding in WB 2.34 are identified to be crucial for stabilizing its structure. These findings unveil the longstanding structural mysteries of boron-rich tungsten borides and offer powerful insights for rational design of borides by defect chemistry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Multiple ferroic orders and toroidal magnetoelectricity in the chiral magnet BaCoSiO 4

Discovering ferroic phase transitions and their consequential physical properties is at the core of condensed matter science due to rich physics and tremendous technological promises. BaCoSiO 4 , a chiral antiferromagnet, belongs to the tetrahedron-based chiral system, and exhibits diverse ferroic orders with coexisting chirality, polarity, trimerization, ferrorotational distortions, and magnetism. However, their mutual couplings remain to be explored. Here in this work, we used a comprehensive combination of several experimental tools—in situ x-ray, transmission electron microscopy, magnetization, and magnetoelectric measurements of single-crystalline BaCoSiO 4 —to investigate hierarchical phase transitions, their microscopic domain structures, and the resulting magnetoelectricity. We found that two different structural chiralities develop through distinct processes: global homochirality and local heterochirality induced by the ferrorotational distortions on top of existing polarization. In addition, magnetic chirality, with the simultaneous presence of net magnetic moment and magnetic toroidal moment, develops below 3.2 K due to the global chirality, which leads to magnetic field tunable toroidal magnetoelectricity. Thus, BaCoSiO 4 exhibits uniquely all four types of ferroic orders and provides an avenue to explore, for example, tunable or dynamic coupling of multiple ferroic degrees of freedom.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Thermal hysteretic behavior and negative magnetoresistance in the charge density wave material EuTe 4

EuTe 4 is a van der Waals material exhibiting a charge density wave (CDW) with a large thermal hysteresis in the resistivity and CDW gap. In this paper, we systematically study the electronic structure and transport properties of EuTe 4 using high-resolution angle-resolved photoemission spectroscopy (ARPES), magnetoresistance (MR) measurements, and scanning tunneling microscopy (STM). Here, we observe a CDW gap of ~ 200meV at low temperatures that persists up to 400 K, suggesting that the CDW transition occurs at a much higher temperature. The ARPES intensity near the Fermi level shows large thermal hysteretic behavior, consistent with the resistivity measurement. The hysteresis in the resistivity measurement does not change under a magnetic field up to 7 T, excluding the thermal magnetic hysteretic effect. Instead, the surface topography measured with STM shows surface domains with different CDW trimerization directions, which may be important for the thermal hysteretic behavior. Interestingly, we reveal a large negative MR at low temperatures that can be associated with the canting of magnetically ordered Eu spins. Our results shed light on the understanding of magnetic, transport, and electronic properties of EuTe 4 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗