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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2022

Whence the Interstellar Magnetic Field Shaping the Heliosphere?

Measurements of starlight polarized by aligned interstellar dust grains are used to probe the relation between the orientation of the ambient interstellar magnetic field (ISMF) and the ISMF traced by the ribbons of energetic neutral atoms discovered by the Interstellar Boundary Explorer spacecraft. We utilize polarization data, many acquired specifically for this study, to trace the configuration of the ISMF within 40 pc. A statistical analysis yields a best-fit ISMF orientation, B magpol , aligned with Galactic coordinates ℓ = 42°, b = 49°. Further analysis shows the ISMF is more orderly for "downfield" stars located over 90° from Bmagpol. The data subset of downfield stars yields an orientation for the nearby ISMF at ecliptic coordinates λ, β ≈ 219° ± 15°, 43° ± 9° (Galactic coordinates l, b ≈ 40°, 56°, ±17°). This best-fit ISMF orientation from polarization data is close to the field direction obtained from ribbon models. This agreement suggests that the ISMF shaping the heliosphere belongs to an extended ordered magnetic field. Extended filamentary structures are found throughout the sky. A previously discovered filament traversing the heliosphere nose region, "Filament A," extends over 300° of the sky, and crosses the upwind direction of interstellar dust flowing into the heliosphere. Filament A overlaps the locations of the Voyager kilohertz emissions, three quasar intraday variables, cosmic microwave background (CMB) components, and the inflow direction of interstellar grains sampled by Ulysses and Galileo. These features are likely located in the upstream outer heliosheath where ISMF drapes over the heliosphere, suggesting Filament A coincides with a dusty magnetized plasma. A filament 55° long is aligned with a possible shock interface between local interstellar clouds. A dark spot in the CMB is seen within 5° of the filament and within 10° of the downfield ISMF direction. Two large magnetic arcs are centered on the directions of the heliotail. The overlap between CMB components and the aligned dust grains forming Filament A indicates the configuration of dust entrained in the ISMF interacting with the heliosphere provides a measurable foreground to the CMB.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Nickel-rich Nickel Manganese Cobalt (NMC622) Cathode Lithiation Mechanism and Extended Cycling Effects Using Operando X-ray Absorption Spectroscopy

Ni-rich NMC materials are a particularly promising class of Li-ion cathodes for various applications. LiNi 0.6 Mn 0.2 Co 0.2 O 2 (NMC622) offers a unique balance of thermal stability and energy density, thus attracting attention for electric vehicle implementation. However, upon extended cycling, capacity fade is prevalent due to structural degradation, which is a major drawback for layered oxide cathodes. Therefore, exploring the underlying phenomena that drive detrimental structural response can lead to future improvements. For the first time, operando X-ray absorption spectroscopy (XAS) was performed on NMC622 pouch cells at three different stages. An extensive description of the first cycle (de)lithiation mechanisms was achieved through X-ray absorption near-edge structure analyses and extended X-ray absorption fine structure modeling. Transition metal specific electrochemical participation and structural variation revealed that much of the delivered capacity and distortion is a result of Ni redox behavior, while the local structure of Co and Mn are impacted due to their interdependencies. Key mechanistic components were identified, as the local structural variation from redox processes and Ni 3+ Jahn–Teller distortion were decoupled. Further, operando XAS was used to investigate the structural response of NMC622 to extended cycling and was supported by X-ray diffraction, X-ray photoelectron spectroscopy, and electrochemical impedance spectroscopy analyses. In this work, reduced capacity was found in the cell after 100 cycles and is attributed to structural degradation and cathode–electrolyte interphase buildup from repeated Li (de)insertion processes, which limit the electrochemical reversibility of Ni and Co through increased polarization. These results expand the understanding of a Ni-rich NMC material under extended cycling, which is vital to the future design of electrode materials.

25 ENERGY STORAGE↗
DOE OSTI2025

Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction

Abstract The Rev response element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 (human immunodeficiency virus type 1) infection. However, the structures and mechanisms underlying this process remain largely unknown. Here, we determined the crystal structure of the HIV-1 RRE stem-loop II (SLII), revealing a unique three-way junction architecture in which the base stem (IIa) bifurcates into the stem-loops (IIb and IIc) to compose Rev binding sites. The crystal structures of various SLII mutants demonstrated that while some mutants retain the same “compact” fold as the wild type, other single-nucleotide mutants induce drastic conformational changes, forming an “extended” SLII structure. Through in vitro Rev binding assays and Rev activity measurements in HIV-1-infected cells using structure-guided SLII mutants designed to favor specific conformers, we showed that while the compact fold represents a functional SLII, the alternative extended conformation inhibits Rev binding and oligomerization and consequently stimulates HIV-1 RNA nuclear export dysfunction. The propensity of SLII to adopt multiple conformations as captured in crystal structures and their influence on Rev oligomerization illuminate emerging perspectives on RRE structural plasticity-based regulation of HIV-1 nuclear export and provide opportunities for developing anti-HIV drugs targeting specific RRE conformations.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Establishing substitution rules of functional groups for high-capacity organic anode materials in Na-ion batteries

Tailoring molecular structures of organic electrode materials (OEMs) can enhance their performance in Na-ion batteries, however, the substitution rules and the consequent effect on the specific capacity and working potential remain elusive. Herein, by examining three sodium carboxylates with selective N substitution or extended conjugation structure, we exploited the correlation between structure and performance to establish substitution rules for high-capacity OEMs. Our results show that substitution position and types of functional groups are essential to create active centers for uptake/removal of Na+ and thermodynamically stabilize organic structures. Furthermore, rational host design and electrolytes modulation were performed to extend the cycle life to 500 cycles. A full cell based on the optimal 2,2’-bipyridine-4,4’-dicarboxylic acid disodium salt anode and the polyaniline cathode is demonstrated to confirm the feasibility of achieving all-organic batteries. Lastly, this work provides a valuable guideline for the design principle of high-capacity and stable OEMs for sustainable energy storage.

25 ENERGY STORAGE↗
DOE OSTI2021

Manipulating meso-scale solvent structure from Pd nanoparticle deposits in deep eutectic solvents

Deep Eutectic Solvents (DESs) are complex solutions that present unique challenges compared to traditional electrolytes. Unlike most electrolytes and ionic liquids, DESs have delicate hydrogen bond networks that are responsible for their highly sensitive compositional dependence on the melting point. Prior work has demonstrated unique nanoscale structure both experimentally and theoretically that brings both challenges and opportunities to their adoption in traditional electrochemical processes. In this study, we use in-situ sample-rotated ultra-small angle X-ray scattering to resolve the near-interface solvent structure after electrodepositing Pd nanoparticles onto a glassy carbon electrode in choline chloride:urea and choline chloride:ethylene glycol DESs. Our results indicate that solvent structure can be observed on the meso-scale in the choline chloride:urea and choline chloride:ethylene glycol systems. Importantly, this extended solvent structure peaks at -0.5 V (vs. Ag/AgCl) and decreases slightly with higher overpotentials during Pd electrodeposition. Experimentally, the nature of this structure is more pronounced in the ethylene glycol system, as evidenced by both the X-ray scattering as well as the electrochemical impedance spectroscopy (EIS). Here, molecular dynamics simulations and dipolar orientation analysis reveal that chloride delocalization near the Pd interface and long-range interactions between the choline and each hydrogen bond donor are very different and qualitatively consistent with the experimental data. These results show how the long-range solvent-deposit interactions can be tuned by changing the hydrogen bond donor in the DES and the applied potential.

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

Kinetically Controlled Linker Binding in Rare Earth-2,5-Dihydroxyterepthalic Acid Metal–Organic Frameworks and Its Predicted Effects on Acid Gas Adsorption

In the pursuit of highly stable and selective metal–organic frameworks (MOFs) for the adsorption of caustic acid gas species, an entire series of rare earth MOFs have been explored. Each of the MOFs in this series (RE-DOBDC; RE = La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu; DOBDC = 2,5-dihydroxyterepthalic acid) was synthesized in the tetragonal space group I4/m. Crystallized MOF samples, specifically Eu-DOBDC, were seen to have a combination of monodentate and bidentate binding when synthesized under typical reaction conditions, resulting in a contortion of the structure. However, extended crystallization times determined that this binding is kinetically controlled and that the monodentate binding option was crystallographically eliminated by extended reaction times at higher temperatures. Furthermore, this series allows for the direct study of the effect of the metal center on the structure of the of the MOF; herein, the lanthanide metal ionic radii contraction across the periodic table results in a reduction of the MOF pore size and lattice parameters. Scanning electron microscopy–energy-dispersive spectroscopy was used to investigate the stages of crystal growth for these RE-DOBDC MOFs. All MOFs, except Er-DOBDC had a minimum of two stages of growth. These analogues were demonstrated by analysis of neutron diffraction (PND) to exhibit a cooperative rotational distortion of the secondary building unit, resulting in two crystallographically distinct linker sublattices. Computational modeling efforts were used to show distinct differences on acid gas (NO 2 and SO 2 ) binding energies for RE-DOBDC MOFs when comparing the monodentate/bidentate combined linker with the bidentate-only linker crystal structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Modular repeat protein sculpting using rigid helical junctions

The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ~10-nm-diameter “L” and “V” shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Shear Pleasure: The Structure, Formation, and Thermodynamics of Crystallographic Shear Phases

A renaissance of interest in crystallographic shear structures and our recent work in this remarkable class of materials inspired this review. We first summarize the geometrical aspects of shear plane formation and possible transformations in ReO 3 , rutile, and perovskite-based structures. Then we provide a mechanistic overview of crystallographic shear formation, plane ordering, and propagation. Next we describe the energetics of planar defect formation and interaction, equilibria between point and extended defect structures, and thermodynamic stability of shear compounds. Finally, we emphasize the remaining challenges and propose future directions in this exciting area.

Materials Science↗
DOE OSTI2020

Refining internal bilayer structure of bicelles resolved by extended-q small angle X-ray scattering

The internal profile across the bilayer reveals important structural information regarding the crystallinity of acyl chains or the positions of encapsulated species. Here, we demonstrate that a simple five-layer-core-shell discoidal model can be employed tobest fit the extended-qsmall angle X-ray scattering (SAXS) data and resolvethe bilayer internal structure (with sub-nanometer resolution) of a nanoscale discoidal system comprised of a mixture of long-and short-chain lipids(known as “bicelles”). In contrast to the traditional core-shell discoidal model, the detailed structure in the hydrophobic core such as the methylene and methyl groups can be distinguished via this model. The refined model is validated by the SAXS data of bicelles whose electron scattering length density of the hydrophobic core is adjusted by the addition of a long-chain lipid with a fluorine-end group.The higher resolution of the bilayer internal structure can be employed to advance our understanding of the interaction and conformation of the membrane and associated molecules, such as membrane-associated proteins and locations of entrapped species in the lipid nanoparticles.

36 MATERIALS SCIENCE↗
DOE OSTI2022

TDCOSMO. VII. Boxyness/discyness in lensing galaxies: Detectability and impact on H 0

In the context of gravitational lensing, the density profile of lensing galaxies is often considered to be perfectly elliptical. Potential angular structures are generally ignored, except to explain flux ratios of point-like sources (i.e. flux ratio anomalies). Surprisingly, the impact of azimuthal structures on extended images of the source has not been characterised, nor has its impact on the H 0 inference. We address this task by creating mock images of a point source embedded in an extended source and lensed by an elliptical galaxy on which multipolar components are added to emulate boxy or discy isodensity contours. Modelling such images with a density profile free of angular structure allows us to explore the detectability of image deformation induced by the multipoles in the residual frame. Multipole deformations are almost always detectable for our highest signal-to-noise ratio (S/N) mock data. However, the detectability depends on the lens ellipticity and Einstein radius, on the S/N of the data, and on the specific lens modelling strategy. Multipoles also introduce small changes to the time-delays. We therefore quantify how undetected multipoles would impact H 0 inference. When no multipoles are detected in the residuals, the impact on H 0 for a given lens is in general less than a few k ms -1 Mpc -1 , but in the worst-case scenario, combining low S/N in the ring and large intrinsic boxyness or discyness, the bias on H0 can reach 10-12 km s -1 Mpc -1 . If we now look at the inference on H 0 from a population of lensing galaxies with a distribution of multipoles representative of what is found in the light profile of elliptical galaxies, we find a systematic bias on H 0 of less than 1%. A comparison of our mock systems to the state-of-the-art time-delay lens sample studied by the H0LiCOW and TDCOSMO collaborations indicates that multipoles are currently unlikely to be a source of substantial systematic bias on the inferred value of H 0 from time-delay lenses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Deciphering the Solvent Effect for the Solvation Structure of Ca 2+ in Polar Molecular Liquids

Although the crystal structures for many inorganic compounds are readily available, researchers are still working hard to understand the relations between the structures and chemical properties of solutions because most of the chemical reactions take place in solutions. A huge amount of effort has been put toward modeling the ion solvation structure from the perspectives of both experiments and theories. In this study, the solvation structures of Ca 2+ ions in aqueous and alcoholic solutions at different concentrations were carefully evaluated by Ca K-edge X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses. Further, density functional theory (DFT) calculations were also performed to correlate the results with the experimental data and then further extended to other similar systems. It was found that the number of coordinating solvent molecules decreases with increasing Ca 2+ concentration and increasing solvent molecule sizes. From the EXAFS data, it was observed that the first solvation shell of Ca 2+ splits into two Ca-O distances in a methanol solution and the counter ion Cl - might also be within the first shell at high concentrations. For the first time, the effects of solvents with different polarities and sizes on the ion solvation environment were systematically evaluated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Shadow of the Future: Developing Trust and Software within the Exascale Computing Project

Collaboration and team science are emerging areas of interest in software production. Historically, multi-institutional research collaborations are difficult to initiate and maintain, negatively impacting communication, negotiation, and dialogue between industry, government, and academic researchers. The Exascale Computing Project (ECP), a massive, multi-team, high-stakes initiative, facilitated broader research collaboration under a shared funding structure and extended timeline to support scientific discovery. Here, we conducted interviews with ECP teams, representing a variety of domain specialties, research institutions, and programming backgrounds. Using thematic analysis, we assessed how ECP’s structure created an environment of increased trust among projects and how software shared between teams facilitated sustained collaboration. We found that the expectation of future collaboration, i.e., the shadow of the future, greatly enhanced trust among teams and the quality of scientific software produced. Based on our findings within ECP projects, we connect to the existing literature on trust in software engineering and share recommendations for sustainable multi-institutional collaboration and shared best software practices.

Exascale computing project↗
DOE OSTI2021

Anomalous X-Ray Scattering and Extended X-Ray Absorption Fine Structure Study of the Local Structure of CrFeCoNiMo x (x = 0.11, 0.18, and 0.23) High-Entropy Alloys

Anomalous x-ray scattering (AXS) and extended x-ray absorption fine structure (EXAFS) were used to determine the local structure of Mo in CrFeCoNiMo x (x = 0.11, 0.18, and 0.23), a high-entropy alloy with a face-centered cubic (FCC) lattice. No superlattice peaks were observed down to the 10 -4 intensity level. This observation along with the nearly constant decrease of the FCC diffraction peaks above the Mo K absorption edge suggests that Mo atoms have no preferred site occupancy in the FCC lattice. Modeling of the EXAFS data suggests a local chemical order in CrFeCoNiMo x , where in Mo-rich samples (e.g., x = 0.23), Mo atoms are preferably surrounded by lighter atoms, such as Cr.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Exploration, Prediction, and Experimental Verification of Structure and Optoelectronic Properties in I 2 -Eu-IV-X 4 (I = Li, Cu, Ag; IV = Si, Ge, Sn; X = S, Se) Chalcogenide Semiconductors

Recently, there has been extensive research into photovoltaic, thermoelectric, and nonlinear optical applications of chalcogenide semiconductors within the large set of defect-resistant I 2 -II-IV-X4 (I = Li, Cu, Ag; II = Ba, Sr, Eu, Pb; IV = Si, Ge, Sn; X = S, Se) compounds. Five Eu-including compounds have previously been reported within this family, but a comparative study of possible structures and electronic properties of all 18 Eu-based combinations is still absent. Herein, we use hybrid density functional theory to study rare-earth-including I 2 -II-IV-X 4 semiconductors with Eu on the II site, in order to further understand this family and test the geometric tolerance factor approach (reported in our previous work) as a tool for predicting potential stable structures. We investigate how the exchange mixing parameter of the HSE06 density functional, α, affects the energetic positions of electronic levels, especially of the localized f-electron orbitals near the band edges of the extended semiconductor structures, using literature photoemission and band gap data of EuS for comparison. Lowest-energy quaternary structure candidates, energy band structures, and densities of states are computationally predicted for all 18 materials. Based on its predicted photovoltaics-relevant band gap, the previously unknown compound Cu 2 EuSnSe 4 was selected and synthesized. Furthermore, the experimental structure, lattice parameters, and band gap of Cu 2 EuSnSe 4 are consistent with the computational predictions, confirming a 1.55 eV band gap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Experimental characterization of turbulence properties in negative triangularity DIII-D plasmas

Negative Triangularity (NT) plasmas have demonstrated robustly ELM-free high-performance operation and provide a unique testbed to study how plasma shaping affects turbulent transport. The Beam Emission Spectroscopy (BES) diagnostic provides localized 2D measurements of low-k ($k_{\theta} \rho_s < 1$) density fluctuations. In a sweep of upper triangularity at fixed power, H-mode access is suppressed and an NT-edge is observed. The turbulence amplitude ($\tilde{n}/n$) is shown to decrease by $\sim50\%$ for $\rho<0.9$ in the NT-edge phase as compared to the H-mode phase. Additionally, low-velocity edge modes below 70 kHz are suppressed by triangularity and the dominant mode propagating in the electron diamagnetic direction is seen to broaden in wavenumber space in the NT-edge phase. In a strong NT plasma ($\delta_{avg}\sim-0.5$), low amplitude modes ($\tilde{n}/n <0.5\%$) propagating in the ion-diamagnetic direction with radially-poloidally symmetric eddy structure are identified for $\rho \sim 0.65-0.83$ consistent with Ion Temperature Gradient (ITG) turbulence. Modes consistent with Trapped Electron Mode (TEM) turbulence are observed propagating in the electron-diamagnetic direction for $\rho\gtrsim0.83$ with poloidally extended eddy structure and reduced amplitudes observed at the separatrix. The turbulence properties presented in this paper help validate our understanding of NT turbulence and help explain the improved confinement and unique edge features of NT plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Chemistry and Interfacial Structure Promoting Quasi-van der Waals Epitaxial Growth of WS 2 Nanosheets on Sapphire for Prospective Application in Field-Effect Transistors

How do chemical and structural modifications to the supporting crystal surface affect the subsequent van der Waals (vdW) or quasi(Q)-vdW epitaxial growth of 2D nanocrystals? Developing an atomic-scale picture of such an interfacial system is crucial for understanding its impact on the physical and chemical properties of the supported 2D materials. The elucidation of the interfacial structure and chemistry needed to promote the Q-vdW epitaxial growth of 2D tungsten disulfide (WS 2 ) nanocrystals contributes to the growth mechanism understanding, thus pushing forward the integration of such atomically thin semiconductors toward real field-effect transistor applications. In addition to an atomic-force microscopy top view, we showcase a combination of X-ray techniques for a top-to-bottom investigation of the complexities of the buried interface structures. Furthermore, this approach uses X-ray photoelectron spectroscopy, X-ray standing wave excited X-ray fluorescence, and crystal truncation rod scattering to produce a highly resolved chemical-state-specific 3D atomic map for the extended interface structure of WS 2 /α-Al 2 O 3 (001). Employing these detailed analysis methods, along with density functional theory to further refine the picoscale structure, we demonstrate how two different types of interface engineering during the pregrowth stage lead to significant differences in the chemical and structural modifications to the terminal surface of c-face sapphire, which in turn leads to substantial differences in the submonolayer growth of supported WS 2 2D nanocrystals in terms of lateral domain sizes, epitaxial registry, vdW gaps, and stability.

36 MATERIALS SCIENCE↗