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At least 253 records · Page 14

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DOE OSTI2021

A DNA packaging motor inchworms along one strand allowing it to adapt to alternative double-helical structures

Abstract Ring ATPases that translocate disordered polymers possess lock-washer architectures that they impose on their substrates during transport via a hand-over-hand mechanism. Here, we investigate the operation of ring motors that transport ordered, helical substrates, such as the bacteriophage ϕ29 dsDNA packaging motor. This pentameric motor alternates between an ATP loading dwell and a hydrolysis burst wherein it packages one turn of DNA in four steps. When challenged with DNA-RNA hybrids and dsRNA, the motor matches its burst to the shorter helical pitches, keeping three power strokes invariant while shortening the fourth. Intermittently, the motor loses grip on the RNA-containing substrates, indicating that it makes optimal load-bearing contacts with dsDNA. To rationalize these observations, we propose a helical inchworm translocation mechanism in which, during each cycle, the motor increasingly adopts a lock-washer structure during the ATP loading dwell and successively regains its planar form with each power stroke during the burst.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Active conformation of the p97-p47 unfoldase complex

The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a “hand-over-hand” mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A 2D chiral microcavity based on apparent circular dichroism

Abstract Engineering asymmetric transmission between left-handed and right-handed circularly polarized light in planar Fabry–Pérot (FP) microcavities would enable a variety of chiral light-matter phenomena, with applications in spintronics, polaritonics, and chiral lasing. Such symmetry breaking, however, generally requires Faraday rotators or nanofabricated polarization-preserving mirrors. We present a simple solution requiring no nanofabrication to induce asymmetric transmission in FP microcavities, preserving low mode volumes by embedding organic thin films exhibiting apparent circular dichroism (ACD); an optical phenomenon based on 2D chirality. Importantly, ACD interactions are opposite for counter-propagating light. Consequently, we demonstrated asymmetric transmission of cavity modes over an order of magnitude larger than that of the isolated thin film. Through circular dichroism spectroscopy, Mueller matrix ellipsometry, and simulation using theoretical scattering matrix methods, we characterize the spatial, spectral, and angular chiroptical responses of this 2D chiral microcavity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Spin switchable optical phenomena in Rashba band structures through intersystem crossing in momentum space in solution-processing 2D-superlattice perovskite film

Spin-switchable phenomena are a critical element for the development of spintronic and chiroptic devices. Herein we combine a 2D-superlattice perovskite (4,4-DFPD2PbI4) film with a ferromagnetic cobalt (Co) layer to form a multiferroic perovskite/Co interface, and demonstrate spin-switchable circularly polarized luminescence (CPL) between right-handed σ+ and left-handed σ− polarizations. When the ferromagnetic spins of Co at the Co/perovskite interface are altered between positive and negative magnetic field directions, the CPL from the 2D-superlattice perovskite switches from σ+ to σ− polarization. The magnetic field effects present a unique method to confirm that CPL is generated by the circular-orbital momentum of light-emitting excitons within Rashba band structures, eliminating artifacts involving structural birefringence. Our polarized neutron reflectometry measurements confirm a super long-range spin-orbit interaction occurring in the 2D-superlattice perovskite films. The temperature dependence of spin-switchable phenomenon indicates an extraordinarily long orbital polarization lifetime, reaching microseconds at room temperature and milliseconds at 5 K.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Directed self-assembly of chiral liquid crystals into biomimetic bouligand structures in thin film

The Bouligand structure, renowned for its helicoidal arrangement and enhanced mechanical properties, has attracted significant research interest for its ability to impart enhanced strength to intrinsically soft materials. Biomimetic approaches have centered on fibrous structures in bulk materials, but translating this architecture into thin-film regime for miniaturized-wearable devices with programmable functions remains challenging. Here, we direct the self-assembly of cholesteric liquid crystals (CLCs) into hierarchical helical structures using chemically patterned surfaces. Alternating surface anchoring regions align uniform lying-down helices at the nanoscale, guiding a secondary microscale helical structure exhibiting both left- and right-handed twists. This mimetic Bouligand structure in CLCs enables optical modulation under applied field and strain with enhanced mechanical response. Simulations reveal the structural evolution from initial Bouligand configuration in LC layers to alternating twist helices. This research provides a basis for designing and manufacturing miniaturized or wearable devices with nanometer-scale precision in regulating electro-optical and mechanical properties. Bouligand structures, which offer strength in natural materials, are of interest but difficult to obtain. Here, the authors report the development of such structures by directed self-assembly of cholesteric single crystals into hierarchical helical structures, with the secondary structure having right and left-handed twists.

Bouligand structure↗

DOE OSTI2020

Near-Field Corrosion Interactions between Glass and Corrosion Resistant Alloys

This study explores the corrosion interactions between model nuclear waste glass materials and corrosion resistant alloys, under conditions that simulate the near field of a nuclear waste repository. The interactions between the corrosion of stainless steel (SS) 316, alloy G30, or alloy 625, and international simple glass or soda-lime silica glass are systematically studied. The dissimilar materials were exposed in close proximity to each other in different electrolytes at 90 oC. After exposure, the glass surface exposed near metals showed different regimes of corrosion, with distinct surface morphologies and chemistries that were likely affected by the local environment created by the localized corrosion of metals. Surface and solution analyses showed that the corrosion rate of glass was enhanced by the presence of metals. Infrared spectroscopy data suggested the local build-up of stresses in the contact area of glass, which may lead to the mechanical instability of the glass alteration layer. On the other hand, the effect of glass on metal corrosion is strongly dependent on the leaching solution. In electrolytes containing abundant aggressive anions such as Cl-, glass seems to suppress the localized corrosion of SS by the precipitation of a Si-rich surface film that protects the SS substrate from solutions. However, in less aggressive electrolytes, the corrosion rate of SS was increased by the presence of glass corrosion products. Overall, our study showed that the hidden and localized damage on glass in contact with metals may enhance the release of incorporated radionuclides compared to typical uniform glass corrosion. Therefore, more attention should be paid to the corrosion interactions between metals and glass under repository conditions.

Guo, Xiaolei↗

DOE OSTI2021

Single crystals of mechanically entwined helical covalent polymers

Double helical conformation of polymer chains is widely observed in biomacromolecules and plays an essential role in exerting their biological functions, such as molecular recognition and information storage. It has remained challenging, however, to prepare synthetic helical polymers, and those that exist have mainly been limited to single-stranded polymers or short oligomeric double helices. In this work, we report the synthesis of covalent helical polymers, with a high molecular weight, from the achiral monomer hexahydroxytriphenylene through to spiroborate formation. Polymerization and crystallization occurred simultaneously under solvothermal conditions to form single crystals of the resulting helical covalent polymers. Characterization by single-crystal X-ray diffraction showed that each crystal consisted of pairs of mechanically entwined polymers. No strong non-covalent interactions were observed between the two helical polymers that formed a pair; instead, each strand interacted with neighbouring pairs through hydrogen bonding. Each individual crystal was made up of helical polymers of the same handedness, but the crystallization process produced a racemic conglomerate, with equal amounts of right-handed and left-handed crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Arbuscular mycorrhizal fungi equalize differences in plant fitness and facilitate plant species coexistence through niche differentiation

Mycorrhizal fungi are essential to the establishment of the vast majority of plant species but are often conceptualized with contradictory roles in plant community assembly. On the one hand, host-specific mycorrhizal fungi may allow a plant to be competitively dominant by enhancing growth. On the other hand, host-specific mycorrhizal fungi with different functional capabilities may increase nutrient niche partitioning, allowing plant species to coexist. Here, to resolve the balance of these two contradictory forces, we used a controlled greenhouse study to manipulate the presence of two main types of mycorrhizal fungus, ectomycorrhizal fungi and arbuscular mycorrhizal fungi, and used a range of conspecific and heterospecific competitor densities to investigate the role of mycorrhizal fungi in plant competition and coexistence. We find that the presence of arbuscular mycorrhizal fungi equalizes fitness differences between plants and stabilizes competition to create conditions for host species coexistence. Furthermore, our results show how below-ground mutualisms can shift outcomes of plant competition and that a holistic view of plant communities that incorporates their mycorrhizal partners is important in predicting plant community dynamics.

09 BIOMASS FUELS↗

DOE OSTI2023

Mass measurements show slowdown of rapid proton capture process at waiting-point nucleus 64Ge

Abstract X-ray bursts are among the brightest stellar objects frequently observed in the sky by space-based telescopes. A type-I X-ray burst is understood as a violent thermonuclear explosion on the surface of a neutron star, accreting matter from a companion star in a binary system. The bursts are powered by a nuclear reaction sequence known as the rapid proton capture process (rp process), which involves hundreds of exotic neutron-deficient nuclides. At so-called waiting-point nuclides, the process stalls until a slower β + decay enables a bypass. One of the handful of rp process waiting-point nuclides is 64 Ge, which plays a decisive role in matter flow and therefore the produced X-ray flux. Here we report precision measurements of the masses of 63 Ge, 64,65 As and 66,67 Se—the relevant nuclear masses around the waiting-point 64 Ge—and use them as inputs for X-ray burst model calculations. We obtain the X-ray burst light curve to constrain the neutron-star compactness, and suggest that the distance to the X-ray burster GS 1826–24 needs to be increased by about 6.5% to match astronomical observations. The nucleosynthesis results affect the thermal structure of accreting neutron stars, which will subsequently modify the calculations of associated observables.

Physics↗

DOE OSTI2025

How short peptides disassemble tau fibrils in Alzheimer’s disease

Reducing fibrous aggregates of the protein tau is a possible strategy for halting the progression of Alzheimer’s disease (AD). Previously, we found that in vitro, the d-enantiomeric peptide (D-peptide) D-TLKIVWC disassembles ultra-stable tau fibrils extracted from the autopsied brains of individuals with AD (hereafter, these tau fibrils are referred to as AD-tau) into benign segments, with no energy source other than ambient thermal agitation. To consider D-peptide-mediated disassembly as a potential route to therapeutics for AD, it is essential to understand the mechanism and energy source of the disassembly action. Here, in this work, we show that the assembly of D-peptides into amyloid-like (‘mock-amyloid’) fibrils is essential for AD-tau disassembly. These mock-amyloid fibrils have a right-handed twist but are constrained to adopt a left-handed twist when templated in complex with AD-tau. The release of strain that accompanies the conversion of left-twisted to right-twisted, relaxed mock-amyloid produces a torque that is sufficient to break the local hydrogen bonding between tau molecules, and leads to the fragmentation of AD-tau. This strain-relief mechanism seems to operate in other examples of amyloid fibril disassembly, and could inform the development of first-in-class therapeutics for amyloid diseases.

Alzheimer's disease↗

DOE OSTI2022

Carbon dioxide-enhanced metal release from kerogen

Heavy metals released from kerogen to produced water during oil/gas extraction have caused major environmental concerns. To curtail water usage and production in an operation and to use the same process for carbon sequestration, supercritical CO 2 (scCO 2 ) has been suggested as a fracking fluid or an oil/gas recovery agent. It has been shown previously that injection of scCO 2 into a reservoir may cause several chemical and physical changes to the reservoir properties including pore surface wettability, gas sorption capacity, and transport properties. Using molecular dynamics simulations, we here demonstrate that injection of scCO 2 might lead to desorption of physically adsorbed metals from kerogen structures. This process on one hand may impact the quality of produced water. On the other hand, it may enhance metal recovery if this process is used for in-situ extraction of critical metals from shale or other organic carbon-rich formations such as coal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Relative importance of nonlinear electron-phonon coupling and vertex corrections in the Holstein model

Determining the range of validity of Migdal’s approximation for electron-phonon (e-ph) coupled systems is a long-standing problem. Many attempts to answer this question employ the Holstein Hamiltonian, where the electron density couples linearly to local lattice displacements. When these displacements are large, however, nonlinear corrections to the interaction must also be included, which can significantly alter the physical picture obtained from this model. Using determinant quantum Monte Carlo and the self-consistent Migdal approximation, we compared superconducting and charge-density-wave correlations in the Holstein model with and without second-order nonlinear interactions. We find a disagreement between the two cases, even for relatively small values of the e-ph coupling strength, and, importantly, that this can occur in the same parameter regions where Migdal’s approximation holds. Our results demonstrate that questions regarding the validity of Migdal’s approximation go hand in hand with questions of the validity of a linear e-ph interaction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2026

Curvilinear magnetic effects in helicoid nanotubes

We report the fabrication and characterization of ferromagnetic helicoid nanotubes with a tunable surface curvature and chirality. Through combining focused electron beam induced deposition and magnetron sputtering we realize these complex curvilinear magnetic architectures. Electron holography reveals two distinct states: a single domain remanent state, with a magnetic chirality governed by the geometric chirality, and a vortex-anti-vortex domain wall, preferentially forming at areas of lower curvature. Micromagnetic simulations reveal how the geometry, specifically pitch and local surface curvature, affects the stability and formation of magnetic domain walls. Furthermore, we show that the interplay between magnetic and geometric chirality has a strong impact on domain wall motion, whereby a right-handed geometric chirality leads to faster domain wall motion and a left-handed geometry hinders domain wall transport. The results shown here highlight the potential of 3D magnetic architectures in spintronic devices and offer insights into how geometry and curvature affect the magnetization, the distribution of magnetic solitons and the motion of domain walls.

3D Nanomagnetism↗

DOE OSTI2019

Unravelling donor–acceptor film morphology formation for environmentally-friendly OPV ink formulations

The challenge of coating organic photovoltaics (OPV) from green solvents is to achieve the required nanostructured interpenetrating network of donor and acceptor domains based on a rational choice of solvent approach as opposed to the usual trial-and-error methods. We demonstrate here that we can achieve a bicontinuous interpenetrating network with nanoscale phase separation for the chosen donor–acceptor material system poly[2,3-bis-(3-octyloxyphenyl)quinoxaline-5,8-diyl-alt-thiophene-2,5-diyl]:phenyl-C 61 butyric acid methyl ester (TQ1:PC 61 BM) when processing from green solvent ink formulations. This structure is achieved by first calculating the Hansen solubility parameters (HSP) of the donor and acceptor materials, followed by careful choice of solvents with selective relative solubilities for the two materials based on the desired order of precipitation necessary for forming a nanostructured interdigitated network morphology. We found that the relative distances in Hansen space (R a ) between TQ1 and the primary solvent, on the one hand, and PC 61 BM and the primary solvent, on the other hand, could be correlated to the donor–acceptor morphology for the formulations based on the solvents d-limonene, anisole, and 2-methyl anisole, as well as the halogenated reference solvent o-dichlorobenzene. This nanostructured blend film morphology was characterised with scanning transmission X-ray microscopy (STXM) and transmission electron microscopy (TEM), and the film surface composition was analysed by near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Hansen solubility theory, based on solution thermodynamics, has been used and we propose an HSP-based method that is a general platform for the rational design of ink formulations for solution-based organic electronics, in particular facilitating the green solvent transition of organic photovoltaics. Our results show that the bulk heterojunction morphology for a donor–acceptor system processed from customised solvent mixtures can be predicted by the HSP-based method with good reliability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A Hybrid Pathway to Biojet Fuel via 2,3-Butanediol

Production of biomass-derived sustainable alternative jet fuels (SAJF) has been considered as an important approach to decarbonize the aviation industry but still possesses various challenges in technology advancement, particularly in achieving high carbon efficiency. Here we report a hybrid pathway to SAJF from 2,3-butanediol (2,3-BDO), integrating biologically converting biomass to 2,3-BDO with catalytically upgrading of 2,3-BDO to jet-range hydrocarbons. This pathway is demonstrated to have a high carbon recovery to liquid hydrocarbons from corn stover (25–28%) (74–82% of the theoretical maximum efficiency). The catalytic conversion steps involve 2,3-BDO to C3+ olefins, oligomerization, and hydrogenation where the first two steps are the focus of this study. Under optimum reaction conditions (523 K, 115 kPa, 1.0 h-1 weight hourly space velocity), 2,3-BDO conversion and C3+ olefin selectivity are >97% and 94–98% during 40 h time on stream, respectively. To demonstrate the adaptability of this technology with bio-derived 2,3-BDO, we also investigated the impact of water and other organic coproducts (acetoin and acetic acid) inherited from the fermentation broth on the catalyst performance and product selectivities. We have shown that the catalyst can handle a significant amount of water in the liquid feed (40 wt% water/60 wt% 2,3-BDO) and maintain catalyst stability for ~40 h. Acetoin can be converted to similar C3+ olefins as 2,3-BDO with complete conversion of acetoin. Co-feeding 10 wt% acetoin with 2,3-BDO is found to have no impact on 2,3-BDO conversion, C3+ olefin selectivity, and catalyst stability. The utilization of organic coproduct like acetoin can help to improve overall carbon conversion efficiency when using real biomass-derived 2,3-BDO. On the other hand, the presence of 10 wt% acetic acid is shown to drastically inhibit methyl ethyl ketone (MEK) hydrogenation and butene oligomerization as revealed by the increased MEK and butene selectivities, implying the importance of separating organic acids when feeding bio-derived 2,3-BDO. The formed C3–C6 olefins from 2,3-BDO are further oligomerized over Amberlyst-36 catalyst to longer-chain hydrocarbons with >70 wt% jet-range hydrocarbons including predominantly iso-olefins/iso-paraffins. The overall carbon efficiency for the jet-range hydrocarbons is 19–22%, exceeding most of the reported biojet pathways, which makes it a promising approach for SAJF production.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2025

Computer-aided design of stability enhanced nicotinamide cofactor biomimetics for cell-free biocatalysis

Cell-free biocatalysis (CFB) is an efficient and environmentally friendly method to synthesize molecules such as pharmaceuticals, biochemicals, and biofuels through the in vitro use of enzyme cascades. These enzymes often require redox cofactors to drive chemical reactions. Natural redox cofactors (NAD(P)H) are expensive to isolate, motivating synthetic nicotinamide cofactor biomimetics (NCBs) as a cost-effective solution. A select handful of NCBs have been identified as potential NAD(P)H alternatives with comparable or improved redox capabilities, however, they display a tendency to degrade in common buffers. In this study, a library of 132 NCB candidates is systematically generated, over 85% of which have not been characterized in the literature, to expand the diversity of currently explored NCBs. The decomposition mechanism of NCBs in phosphate is evaluated using density functional theory (DFT), revealing protonation at the nicotinamide C5 position as a reporter of cofactor stability. Based on this result, we trained a linear regression model on DFT calculated descriptors to predict NCB stability in phosphate buffer, achieving mean absolute error (MAE) and root mean squared error (RMSE) values within computational accuracy. Analysis of key atomic descriptors and qualitative trends in our dataset informed the design of novel NCB candidates we propose with optimized stability. This work enables researchers to predict the relative stability of NCBs before synthesis, thereby streamlining the process to make CFB more affordable and viable at industry scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Correlation between the gas-phase metallicity and ionization parameter in extragalactic H II regions

The variations of the metallicity and ionization parameter in H II regions are usually thought to be the dominant factors that produce the variations we see in the observed emission line spectra. There is an increasing amount of evidence that these two quantities are physically correlated, although the exact form of this correlation is debatable in the literature. Simulated emission line spectra from photoionized clouds provide important clues about the physical conditions of H II regions and are frequently used for deriving metallicities and ionization parameters. Through a systematic investigation on the assumptions and methodology used in applying photoionization models, we find that the derived correlation has a strong dependence on the choice of model parameters. On the one hand, models that give consistent predictions over multiple emission-line ratios yield a positive correlation between the metallicity and ionization parameter for the general population of H II regions or star-forming galaxies. On the other hand, models that are inconsistent with the data locus in high-dimensional line ratio space yield discrepant correlations when different subsets of line ratios are used in the derivation. The correlation between the metallicity and ionization parameter has a secondary dependence on the surface density of the star formation rate (SFR), with the higher SFR regions showing a higher ionization parameter but weaker correlations. The existence of the positive correlation contradicts the analytical wind-driven bubble model for H II regions. We explore assumptions in both dynamical models and photoionization models, and conclude that there is a potential bias associated with the geometry. However, this is still insufficient to explain the correlation. Mechanisms that suppress the dynamical influence of stellar winds in realistic H II regions might be the key to solving this puzzle, though more sophisticated combinations of dynamical models and photoionization models to test are required.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Plume dynamics and gas-phase molecular formation in transient laser-produced uranium plasmas

The dynamics of expansion, thermodynamics, and chemical reactions in laser-produced plasmas is of general interest for all laser ablation applications. This study investigates the complex morphology and behavior of reactive species in nanosecond laser-produced uranium plasmas. Comparing plasma morphology in various inert and reactive ambient gases provides information about the role of gas-phase chemistry in plume hydrodynamics. Background gases including nitrogen and argon foster collisional interactions leading to more significant plume confinement and the increase in persistence of uranium species. On the other hand, environments containing reactive gases such as oxygen promote chemical reactions between the plasma and ambient species. By comparing the expansion dynamics of uranium plumes in nitrogen, air, and argon, we discover that chemical reactions modify the hydrodynamics of the plume at later times of its evolution in the air background. Furthermore, we observe that varying the concentration of oxygen in the fill gas promotes different reaction pathways that lead to the formation of uranium oxides. The reaction pathways from atoms to diatomic to polyatomic molecules strongly vary with ambient oxygen concentration. Lower oxygen concentrations enhance the formation of uranium monoxide from atomic uranium, whereas higher oxygen concentrations tend to depopulate both atomic uranium and uranium monoxide concentrations through the formation of more complex uranium oxides.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗