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At least 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Analysis of the molecular determinants for furin cleavage of the spike protein S1/S2 site in defined strains of the prototype coronavirus murine hepatitis virus (MHV)

We analyzed the spike protein S1/S2 cleavage of selected strains of a prototype coronavirus, mouse hepatitis virus (MHV) by the cellular protease furin, in order to understand the structural requirements underlying the sequence selectivity of the scissile segment. The probability of cleavage of selected MHV strains was first evaluated from furin cleavage scores predicted by the ProP computer software, and then cleavage was measured experimentally with a fluorogenic peptide cleavage assay consisting of S1/S2 peptide mimics and purified furin. We found that in vitro cleavability varied across MHV strains in line with predicted results—but with the notable exception of MHV-A59, which was not cleaved despite a high score predicted for its sequence. Using the known X-Ray structure of furin in complex with a substrate-like inhibitor as an initial structural reference, we carried out molecular dynamics (MD) simulations to learn the modes of binding of the peptides in the furin active site, and the suitability of the complex for initiation of the enzymatic cleavage. We identified the 3D structural requirements of the furin active site configuration that enable bound peptides to undergo cleavage, and the way in which the various strains tested experimentally are fulfilling these requirements. We find that despite some flexibility in the organization of the peptide bound to the active site of the enzyme, the presence of a histidine at P2 of MHV-A59 fails to properly orient the sidechain of His194 of the furin catalytic triad and therefore produces a distortion that renders the peptide/complex structural configuration in the active site incompatible with requirements for cleavage initiation. The Ser/Thr in P1 of MHV-2 and MHV-S has a similar effect of distorting the conformation of the furin active site residues produced by the elimination of the canonical salt-bridge formed by arginine in P1 position. This work informs a study of coronavirus infection and pathogenesis with respect to the function of the viral spike protein, and suggests an important process of viral adaptation and evolution within the spike S1/S2 structural loop.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

In Situ Liquid Secondary Ion Mass Spectrometry: A Surprisingly Soft Ionization Process for Investigation of Halide Ion Hydration

The understanding of ion solvation phenomenon is of significance due to their influences on many important chemical, biological and environmental processes. Mass spectrometry (MS) based methods have been used to investigate this topic with molecular insights. As ion-solvent interactions are weak, ionization processes should be as soft as possible in order to retain solvation structures. An in situ liquid secondary ion MS (SIMS) approach developed in our group has been recently utilized in investigations of Li ion solvation in non-aqueous solution and detected a series of solvated Li ions. As traditionally SIMS has long been recognized as a hard ionization process with strong damage occurring at the sputtering interface, it is very interesting to study further how soft in situ liquid SIMS can be. In this work, we used halide ion hydration as an example to compare the ionization performance of in situ liquid SIMS approach with regular electrospray ionization MS (ESI-MS). Results show that although ESI has been recognized as a soft ionization method, nearly no solvated halide ions were detected by ESI-MS analysis, which acquired only strong signals of salt ion clusters. In contrast, in liquid SIMS spectra, a series of obvious hydrated halide ion compositions could be observed. We further evaluated the hydration numbers of halide ions and revealed the effects of the ion size, charge density and polarizability on the hydration phenomenon. Our findings demonstrated that the in situ liquid SIMS approach is surprisingly soft, and expected to have very broad applications on investigation of various ion-solvent interactions and many other interesting chemical processes (e.g., the initial nucleation of nanoparticle formation) in liquid environment.

Zhang, Yanyan↗
DOE OSTI2025

First-Principles Statistical Mechanics Study of Magnetic Fluctuations and Order–Disorder in the Spinel LiNi 0.5 Mn 1.5 O 4 Cathode

While significant magnetic interactions exist in lithium transition metal oxides, commonly used as Li-ion cathodes, the interplay between magnetic couplings, disorder, and redox processes remains poorly understood. In this work, we focus on the high-voltage spinel LiNi 0.5 Mn 1.5 O 4 (LNMO) cathode as a model system on which to apply a computational framework that uses first principles-based statistical mechanics methods to predict the finite temperature magnetic properties of materials and provide insights into the complex interplay between magnetic and chemical degrees of freedom. Density functional theory calculations on multiple distinct Ni–Mn orderings within the LNMO system, including the ordered ground-state structure (space group P4332), reveal a preference for a ferrimagnetic arrangement of the Ni and Mn sublattices due to strong antiferromagnetic superexchange interactions between neighboring Mn 4+ and Ni 2+ ions and ferromagnetic Mn–Mn and Ni–Ni couplings, as revealed by magnetic cluster expansions. These results are consistent with qualitative predictions using the Goodenough-Kanamori-Anderson rules. Simulations of the finite temperature magnetic properties of LNMO are conducted using Metropolis Monte Carlo. We find that a “semiclassical” Monte Carlo sampling method based on the Heisenberg Hamiltonian accurately predicts experimental magnetic transition temperatures observed in magnetometry measurements. This study highlights the importance of a robust computational toolkit that accurately captures the complex chemomagnetic interactions and predicts finite temperature magnetic behavior to help analyze experimental magnetic and magnetic resonance spectroscopy data acquired ex situ and operando.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Two-Dimensional CsAg 5 Te 3– x S x Semiconductors: Multi-anion Chalcogenides with Dynamic Disorder and Ultralow Thermal Conductivity

Metal chalcogenides underpin a wide variety of energyrelated applications and are ideal systems for probing lattice dynamics and fundamental transport phenomena. Here we describe the synthesis and transport properties of CsAg 5 TeS 2 and its solid solution CsAg 5 Te 3-x S x (x = 1-2), new semiconductors with tunable band gaps ranging from 0.17 to 0.30 eV. CsAg 5 TeS 2 has a fully ordered two-dimensional structure that includes a group of Ag atoms in a heteroleptic tetrahedral coordination geometry (AgTe 2 S 2 ). Single-crystal X-ray diffraction indicates that the compounds crystallize in the tetragonal space group P 4/ mmm , while pair distribution function (PDF) analysis reveals off-centering at the heteroleptic Ag sites, signifying the lower-symmetry I4/ mcm space group. The underlying disorder as a phonon-blocking mechanism that helps facilitate an ultralow lattice thermal conductivity below 0.40 Wm -1 • K -1 at , ~ 300 K , highlighting the importance of local disorder in thermal transport. In conclusion, density functional theory provides additional insight into the electronic and thermal properties of the materials, which are good candidates for p-type thermoelectrics.

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

Molecular Mechanisms of Sorbed Ion Effects during Boehmite Particle Aggregation

Classical theories of particle aggregation, such as Derjaguin–Landau–Verwey–Overbeek (DLVO), do not explain recent observations of ion-specific effects or the complex concentration dependence for aggregation. Thus, here, we probe the molecular mechanisms by which selected alkali nitrate ions (Na + , K + , and NO 3 –) influence aggregation of the mineral boehmite (γ-AlOOH) nanoparticles. Nanoparticle aggregation was analyzed using classical molecular dynamics (CMD) simulations coupled with the metadynamics rare event approach for stoichiometric surface terminations of two boehmite crystal faces. Calculated free energy landscapes reveal how electrolyte ions alter aggregation on different crystal faces relative to pure water. Consistent with experimental observations, we find that adding an electrolyte significantly reduces the energy barrier for particle aggregation (~3–4×). However, in this work, we show this is due to the ions disrupting interstitial water networks, and that aggregation between stoichiometric (010) basal–basal surfaces is more favorable than between (001) edge–edge surfaces (~5–6×) due to the higher interfacial water densities on edge surfaces. The interfacial distances in the interlayer between aggregated particles with electrolytes (~5–10 Å) are larger than those in pure water (a few Ångströms). Together, aggregation/disaggregation in salt solutions is predicted to be more reversible due to these lower energy barriers, but there is uncertainty on the magnitudes of the energies that lead to aggregation at the molecular scale. By analyzing the peak water densities of the first monolayer of interstitial water as a proxy for solvent ordering, we find that the extent of solvent ordering likely determines the structures of aggregated states as well as the energy barriers to move between them. Further, the results suggest a path for developing a molecular-level basis to predict the synergies between ions and crystal faces that facilitate aggregation under given solution conditions. Such fundamental understanding could be applied extensively to the aggregation and precipitation utilization in the biological, pharmaceutical, materials design, environmental remediation, and geological regimes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Ultranarrow TaS 2 Nanoribbons

Imposing additional confinement in two-dimensional (2D) materials can yield further control over the associated electronic, optical, and topological properties. However, synthesis of ultra-narrow nanoribbons (NRs) remains a challenge, particularly for the transition metal dichalcogenides (TMDs), and synthesizing TMD NRs narrower than 50 nm has remained elusive. In this paper, we report the vapor-phase synthesis of ultra-narrow TaS 2 NRs. The NRs are grown within the hollow cavity of carbon nanotubes, thereby limiting their lateral dimensions and layer number, while simultaneously stabilizing them against the environment. The NRs reach the monolayer (ML) limit and exhibit widths as low as 2.5 nm. Atomic-resolution scanning transmission electron microscopy (STEM) reveals the detailed atomic structure of the ultra-narrow NRs and we observe a hitherto unseen atomic structure supermodulation phenomenon of ordered defect arrays within the NRs. First-principles calculations based on density functional theory (DFT) show the presence of flat bands, as well as edge- and boundary-localized states, and help identify the atomic configuration of the supermodulation. Nanotube-templated synthesis represents a unique, transferable, and broadly deployable route toward ultra-narrow TMD NR growth.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2019

Layer-Dependent Electronic Structure of Atomically Resolved Two-Dimensional Gallium Selenide Telluride

Alloying two-dimensional (2D) semiconductors provides a powerful method to tune their physical properties, especially those relevant to optoelectronic applications. However, as the crystal structure becomes more complex, it becomes increasingly difficult to accurately correlate response characteristics to detailed atomic structure. We investigate, via annular dark-field scanning transmission electron microscopy, electron energy loss spectroscopy, and second harmonic generation, the layered III-VI alloy GaSe 0.5 Te 0.5 as a function of layer number. The local atomic structure and stacking sequence for different layers is explicitly determined. We complement the measurements with first-principles calculations of the total energy and electronic band structure of GaSe 0.5 Te 0.5 for different crystal structures and layer number. The electronic band gap as well as the π and π + σ plasmons are found to be sensitive to layer number.

2D semiconductor alloys↗
DOE OSTI2022

Smooth Modified Surfaces of Silicon for the Study of Ionic Liquid Interfaces by Neutron Reflectometry

Silicon surfaces with termination of hydrogen (H–Si), quartz, native silicon (native-Si), and chemically deposited (Au–Si) cd and sputtered gold (Au–Si) s were fabricated with roughness less than 6 Å to study the solid–liquid interface of the ionic liquid (IL) methyltrioctylammonium bis(trifluoromethylsulfonyl)imide, [N 1888 ][TFSI], by neutron reflectometry (NR). The modifications made to the silicon surface were to obtain a native positive or negative charge similar to a charged surface in electrochemical systems. The differences in scattering length density (SLD) based on mass density and composition of IL were examined. Perpendicular to the substrate surface, a distinct transition between the first ion layer and the bulk liquid is resolved out of the reflectivity data for the gold surfaces and in particular the chemically deposited Au–Si. Other interfaces are best described by a diffuse transition between regions of different SLDs. The diffuse transitions between SLDs observed here suggest that the interfacial structure of IL, while ordered, is best described by a continuous variation in composition as opposed to distinct layers of ions.

25 ENERGY STORAGE↗
DOE OSTI2019

Modular Pd/Zeolite Composites Demonstrating the Key Role of Support Hydrophobic/Hydrophilic Character in Methane Catalytic Combustion

Complete catalytic oxidation of methane in the presence of steam at low temperatures (T < 400 °C) is a crucial reaction for emission control, yet it presents profound challenges. The activation of the strong C–H bond of methane at low temperature is difficult, and the water present in any realistic application poisons the active surface and promotes sintering of Pd particles during the reaction. Finding materials that can deliver high reaction rates while being more resistant to the presence of water is imperative for advancing several technological applications of natural gas-based systems. However, methods to fairly compare the activity of Pd catalysts (the most active metal for methane combustion) are needed in order to perform useful structure–property relationship studies. Here in this paper, we report a method to study how zeolite hydrophobicity affects the activity of Pd nanoparticles in the reaction, which led to a significant improvement in the water resistance. Mesoporous zeolites were synthesized starting from commercially available microporous zeolites. In this way, a variety of hierarchically porous zeolites, with different hydrophobic/hydrophilic character, were prepared. Preformed colloidal Pd nanoparticles could be deposited within mesostructured zeolites. This approach enabled the systematic study of key parameters such as zeolite framework, Al content, and the Pd loading while maintaining the same Pd particle size and structure for all the samples. Detailed catalytic studies revealed an optimum hydrophobic/hydrophilic character, and a promising steam-resistant catalyst, namely, 3.2 nm Pd particles supported on mesoporous zeolite beta or USY with a Si/Al ratio of 40, emerged from this multiparametric study with a T 50 of 355 °C and T 90 of 375 °C (where T 50 and T 90 are temperature values at which the samples reach 50% and 90% methane conversion, respectively) in steam-containing reaction conditions. Finally, we verified that the designed catalysts were stable by in-depth postcatalysis characterization and operando diffuse-reflectance infrared Fourier-transform spectroscopy (DRIFTS) analyses confirming that water adsorbs less strongly on the active PdO surface due to interaction with the zeolite acid sites. This method can be of general use to study how zeolite supports affect the reactivity of supported metals in several catalytic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Cascade of transitions in twisted and non-twisted graphene layers within the van Hove scenario

Abstract Motivated by measurements of compressibility and STM spectra in twisted bilayer graphene, we analyze the pattern of symmetry breaking for itinerant fermions near a van Hove singularity. Making use of an approximate SU(4) symmetry of the Landau functional, we show that the structure of the spin/isospin order parameter changes with increasing filling via a cascade of transitions. We compute the feedback from different spin/isospin orders on fermions and argue that each order splits the initially 4-fold degenerate van Hove peak in a particular fashion, consistent with the STM data and compressibility measurements, providing a unified interpretation of the cascade of transitions in twisted bilayer graphene. Our results follow from a generic analysis of an SU(4)-symmetric Landau functional and are valid beyond a specific underlying fermionic model. We argue that an analogous van Hove scenario explains the cascade of phase transitions in non-twisted Bernal bilayer and rhombohedral trilayer graphene.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Spiral spin cluster in the hyperkagome antiferromagnet Mn 3 RhSi

Local spin correlation orders emerge in a paramagnetic state, with notable examples such as the partial order, cooperative paramagnetism, and soliton spin liquid. The noncentrosymmetric intermetallic antiferromagnet Mn 3 RhSi also exhibits the local spin correlation order in the paramagnetic state as magnetic short-range order in a wide temperature range. Here, we show that the local spin correlation order has a spiral structure by neutron scattering measurement of a Mn 3 RhSi single crystal. The possible origins of the magnetic cluster formation are discussed in terms of the Lifshitz invariant and the Griffiths phase, and compared with the room-temperature skyrmion phase of Co 7 Zn 7 Mn 6 and non-Fermi liquid behavior of β-Mn.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Synthesis and optical properties of ordered-vacancy perovskite cesium bismuth halide nanocrystals

Perovskite-phase cesium bismuth halide (Cs 3 Bi 2 X 9 ; X= Cl, Br, I) nanocrystals were synthesized using a hot-injection approach. These nanocrystals adopted ordered-vacancy perovskite crystal structures and demonstrated composition-tunable optical properties. Growth occurred by initial formation of Bi 0 seeds, and morphology was controlled by precursor and seed concentration. The Cs 3 Bi 2 I 9 nanocrystals demonstrated excellent stability under ambient conditions for several months. Contrary to previous reports, we find that photoluminescence originates from the precursor material as opposed to the perovskite nanocrystals.

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

Local structure effects of carbon-doping on the phase change material Ge 2 Sb 2 Te 5

Ge 2 Sb 2 Te 5 is used in phase change memory, a nonvolatile memory technology, due to its phase change properties. The primary advantage of phase change memory over the state-of-the-art (flash memory) is its simple and small device geometry, which allows for denser nodes and lower power consumption. In phase change memory, resistive heating induces fast switching between the high resistance amorphous and low resistance crystalline phases, corresponding to storage of low and high digital states, respectively. However, the instability of the amorphous phase of Ge 2 Sb 2 Te 5 presents issues with processing and long-term data storage; such issues can be resolved by C doping, which stabilizes the amorphous phase and raises the crystallization temperature. To better understand the local structural effects of C doping on Ge 2 Sb 2 Te 5 , in situ Ge K-edge X-ray absorption spectroscopy measurements were taken during heating of films with various C doping concentrations. Here, the range of structural transformation temperatures derived from X-ray absorption near-edge structure analysis across the C doping series proved narrower than crystallization temperatures reported in similar in situ X-ray diffraction experiments, which may reflect changes in local structure that precede long-range ordering during crystallization. In addition, rigorous extended X-ray absorption fine structure fitting across and between temperature series revealed effects of C doping on the rigidity of Ge–Te bonds at low (2 at% and 4 at%) C concentrations.

Langhout, John D.↗
DOE OSTI2025

Material extrusion additive manufacturing of wood pulp-reinforced epoxy composites

Direct ink writing (DIW) is an extrusion-based form of 3D-printing that has gained popularity over the last decade. DIW uses thixotropic fluid extrusion to form a particular shape. In order to form stable structures, the rheology of the paste is important to allow for extrusion from the syringe, stability of the growing print, and prevention of unwanted seeping flow during jog moves. In this work, we use wood pulp as a bio-based filler that can provide shear thinning properties to the ink, which produces a stable ink for DIW processing. Additionally, the filler imparts improved mechanical and thermal performance compared to neat resin. The wood pulp provided the shear thinning behavior necessary for DIW printing, and pulp loadings greater than 6 wt%, provided sufficient yield stress so that the composite could self-support during printing. Nanoclay was utilized to further improve ink rheology and appearance to enable larger scale printing. Overall, this work showed successful DIW of an epoxy resin with a sustainable filler improving its stiffness and thermal properties and provides an avenue for further development of bio-based inks for DIW towards various applications.

Lamm, Meghan E. [Oak Ridge National Laboratory (OR↗
DOE OSTI2017

MnNiO 3 revisited with modern theoretical and experimental methods

MnNiO 3 is a strongly correlated transition metal oxide that has recently been investigated theoretically for its potential application as an oxygen-evolution photocatalyst. However, there is no experimental report on critical quantities such as the band gap or bulk modulus. Recent theoretical predictions with standard functionals such as LDA+U and HSE show large discrepancies in the band gaps (about 1.23 eV), depending on the nature of the functional used. Hence there is clearly a need for an accurate quantitative prediction of the band gap to gauge its utility as a photocatalyst. In this work, we present a diffusion quantum Monte Carlo study of the bulk properties of MnNiO 3 and revisit the synthesis and experimental properties of the compound. We predict quasiparticle band gaps of 2.0(5) eV and 3.8(6) eV for the majority and minority spin channels, respectively, and an equilibrium volume of 92.8 Å 3 , which compares well to the experimental value of 94.4 Å 3 . A bulk modulus of 217 GPa is predicted for MnNiO 3 . As a result, we rationalize the difficulty for the formation of ordered ilmenite-type structure with specific sites for Ni and Mn to be potentially due to the formation of antisite defects that form during synthesis, which ultimately affects the physical properties of MnNiO 3 .

36 MATERIALS SCIENCE↗
DOE OSTI2018

AGES: Automated Gas Environment System for in situ neutron powder diffraction

High fluxes available at modern neutron and synchrotron sources have opened up a wide variety of in situ and operando studies of real processes using scattering techniques. This has allowed the user community to follow chemistry in the beam, which often requires high temperatures, gas flow, etc. In this paper, we describe an integrated gas handling system for the general-purpose powder diffraction beamline Powgen at the Spallation Neutron Source. The Automated Gas Environment System (AGES) allows control of both gas flow and temperature (room temperature to 850 °C), while measuring the partial pressure of oxygen and following the effluent gas by mass spectrometry, concurrent with neutron powder diffraction, in order to follow the structural evolution of materials under these conditions. The versatility of AGES is illustrated by two examples of experiments conducted with the system. In solid oxide fuel cell electrode materials, oxygen transport pathways in double perovskites PrBaCo 2 O 5+δ and NdBaCo 2 O 5+δ were elucidated by neutron diffraction measurements under atmosphere with oxygen partial pressures (pO 2 ) of 10 –1 to 10 –4 (achieved using mixtures of nitrogen and oxygen) and temperatures from 575 to 850 °C. In another example, the potential oxygen storage material La 1–x Sr x FeO 3 was measured under alternating flows of 15% CH 4 in N 2 and air (20% O 2 in N 2 ) at temperatures from 135 to 835 °C. As a result, from the oxygen stoichiometry, the optimal composition for oxygen storage was determined.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Predictability as a probe of manifest and latent physics: The case of atomic scale structural, chemical, and polarization behaviors in multiferroic Sm-doped BiFeO 3

The predictability of a certain effect or phenomenon is often equated with the knowledge of relevant physical laws, typically understood as a functional or numerically derived relationship between the observations and known states of the system. Correspondingly, observations inconsistent with prior knowledge can be used to derive new knowledge on the nature of the system or indicate the presence of yet unknown mechanisms. In this work, we explore the applicability of Gaussian processes (GP) to establish predictability and uncertainty of local behaviors from multimodal observations, providing an alternative to this classical paradigm. Using atomic resolution scanning transmission electron microscopy (STEM) of multiferroic Sm-doped BiFeO 3 across a broad composition range, we directly visualize the atomic structure and structural, physical, and chemical order parameter fields for the material. GP regression is used to establish the predictability of the local polarization field from different groups of parameters, including the adjacent polarization values and several combinations of physical and chemical descriptors, including lattice parameters, column intensities, etc. We observe that certain elements of microstructure, including charged and uncharged domain walls and interfaces with the substrate, are best predicted with specific combinations of descriptors, and this predictability and associated uncertainties are consistent across the composition series. The associated generative physical mechanisms are discussed. It is also found that certain parameter combinations tend to predict the orthorhombic phase in the cases where rhombohedral phase is observed, suggesting a potential role of clamping and confinement phenomena in phase equilibrium in Sm-BiFeO 3 system close to morphotropic phase boundary. We argue that predictability and uncertainty in observational data offer a new pathway to probe the physics of condensed matter systems from multimodal local observations.

74 ATOMIC AND MOLECULAR PHYSICS↗