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Results for “intrinsic disorder”

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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Nanoscale electrostatic control in ultraclean van der Waals heterostructures by local anodic oxidation of graphite gates

In an all-van der Waals heterostructure, the active layer, gate dielectrics and gate electrodes are assembled from two-dimensional crystals that have a low density of atomic defects. This design allows two-dimensional electron systems with very low disorder to be created, particularly in heterostructures where the active layer also has intrinsically low disorder, such as crystalline graphene layers or metal dichalcogenide heterobilayers. A key missing ingredient has been nanoscale electrostatic control, with existing methods for fabricated local gates typically introducing unwanted contamination. Here we describe a resist-free local anodic oxidation process for patterning sub-100 nm features in graphite gates, and their subsequent integration into an all-van der Waals heterostructure. We define a quantum point contact in the fractional quantum Hall regime as a benchmark device and observe signatures of chiral Luttinger liquid behaviour, indicating an absence of extrinsic scattering centres in the vicinity of the point contact. In the integer quantum Hall regime, we demonstrate in situ control of the edge confinement potential, a key requirement for the precision control of chiral edge states. In conclusion, this technique may enable the fabrication of devices capable of single anyon control and coherent edge-state interferometry in the fractional quantum Hall regime.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Visualization of Multifractal Superconductivity in a Two-Dimensional Transition Metal Dichalcogenide in the Weak-Disorder Regime

Eigenstate multifractality is a distinctive feature of noninteracting disordered metals close to a metal–insulator transition, whose properties are expected to extend to superconductivity. While multifractality in three dimensions (3D) only develops near the critical point for specific strong-disorder strengths, multifractality in 2D systems is expected to be observable even for weak disorder. Here we provide evidence for multifractal features in the superconducting state of an intrinsic, weakly disordered single-layer NbSe 2 by means of low-temperature scanning tunneling microscopy/spectroscopy. The superconducting gap, characterized by its width, depth, and coherence peaks’ amplitude, shows a characteristic spatial modulation coincident with the periodicity of the quasiparticle interference pattern. The strong spatial inhomogeneity of the superconducting gap width, proportional to the local order parameter in the weak-disorder regime, follows a log-normal statistical distribution as well as a power-law decay of the two-point correlation function, in agreement with our theoretical model. Furthermore, the experimental singularity spectrum f(α) shows anomalous scaling behavior typical from 2D weakly disordered systems.

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

Extended experimental inferential structure determination method in determining the structural ensembles of disordered protein states

Proteins with intrinsic or unfolded state disorder comprise a new frontier in structural biology, requiring the characterization of diverse and dynamic structural ensembles. Here we introduce a comprehensive Bayesian framework, the Extended Experimental Inferential Structure Determination (X-EISD) method, which calculates the maximum log-likelihood of a disordered protein ensemble. X-EISD accounts for the uncertainties of a range of experimental data and back-calculation models from structures, including NMR chemical shifts, J-couplings, Nuclear Overhauser Effects (NOEs), paramagnetic relaxation enhancements (PREs), residual dipolar couplings (RDCs), hydrodynamic radii (R h ), single molecule fluorescence Förster resonance energy transfer (smFRET) and small angle X-ray scattering (SAXS). We apply X-EISD to the joint optimization against experimental data for the unfolded drkN SH3 domain and find that combining a local data type, such as chemical shifts or J-couplings, paired with long-ranged restraints such as NOEs, PREs or smFRET, yields structural ensembles in good agreement with all other data types if combined with representative IDP conformers.

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

Unlocking Mesoscopic Disorder in Graphitic Carbon with Spectroelectrochemistry

Intrinsic structural and oxidic defects activate graphitic carbon electrodes towards electrochemical reactions underpinning energy conversion and storage technologies. Yet, these defects can also disrupt the long-range and periodic arrangement of carbon atoms, thus, the characterization of graphitic carbon electrodes necessitates in-situ atomistic differentiation of graphitic regions from mesoscopic bulk disorder. Here, we leverage the combined techniques of in-situ attenuated total reflectance infrared spectroscopy and first-principles calculations to reveal that graphitic carbon electrodes exhibit electric-field dependent infrared activity that is sensitive to the bulk mesoscopic intrinsic disorder. With this platform, we identify graphitic regions from amorphous domains by discovering that they demonstrate opposing electric-field-dependent infrared activity under electrochemical conditions. Our work provides a roadmap for identifying mesoscopic disorder in bulk carbon materials under potential bias.

Disordered graphitic carbon electrodes↗
DOE OSTI2023

Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation

The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent Cα model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Integrative visualization of the molecular structure of a cellular microdomain

Abstract An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus . The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well‐studied example of a cellular condensate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles

Small-angle x-ray scattering (SAXS) is a powerful technique for assessing macromolecular structure. High-throughput SAXS is limited by the time-consuming and, at times, subjective nature of SAXS data interpretation. Here, we present SAXS Assistant, a Python-based script that streamlines SAXS data analysis to extract features for machine learning (ML) and key structural parameters, including the Guinier radius of gyration (R g ), pair distance distribution function (PDDF)-derived R g , maximum particle dimension (D max ), and Kratky plots. The script builds upon BioXTAS RAW and validates reliability via Guinier/PDDF R g agreement, an important indicator of well-measured data sets. For assistance in D max estimation, a multilayer perceptron regressor was trained with 1940 data files from the Small Angle Scattering Biological Data Bank. The model achieved a test set performance R 2 = 0.90 and mean absolute error = 11.7 Å. Training exclusively with experimental data translates analyses from researchers, including experts in the field, to the ML model, which helps assess D max estimations from PDDF. Gaussian mixture model clustering was implemented to classify profiles into structural classes based on entries in the Small Angle Scattering Biological Data Bank. Users may therefore assess the similarity between experimental samples and known biomolecular shapes within the mapped repository entries. This probabilistic clustering aids in quantifying information from Kratky and generating shape-descriptive features. SAXS Assistant accelerates SAXS data analysis through enforced quality control, ML-ready outputs, and flags for low-confidence results. In addition to providing the ability to analyze large data sets at high throughput, this tool is versatile and may serve researchers in both biological and synthetic polymer research fields.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Many organisms evolved strategies to survive desiccation. Plant seeds protect dehydrated embryos from various stressors and can lay dormant for millennia. Hydration is the key trigger to initiate germination, but the mechanism by which seeds sense water remains unresolved. Here we identified an uncharacterized Arabidopsis thaliana prion-like protein we named FLOE1, which phase separates upon hydration and allows the embryo to sense water stress. We demonstrate that biophysical states of FLOE1 condensates modulate its biological function in vivo in suppressing seed germination under unfavorable environments. We find intragenic, intraspecific, and interspecific natural variation in FLOE1 expression and phase separation and show that intragenic variation is associated with adaptive germination strategies in natural populations. This combination of molecular, organismal, and ecological studies uncovers FLOE1 as a tunable environmental sensor with direct implications for the design of drought-resistant crops, in the face of climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enhancing low-temperature sintering in the MgO-LiF system: Mechanistic insights

In the present article, we provide compelling evidence that minor (1 wt%) additions of micron and nanometre-sized LiF particles in MgO decompose leading to free Li diffusing into MgO surfaces enhancing vacancy production during direct current sintering. The addition of nanometre-sized LiF particles leads to a > 500 °C reduction in the sintering temperature and over 99 % theoretical density of final consolidated compacts. Correlating differential scanning calorimetry with in-situ x-ray diffraction, together with Schottky calculations, post sintering electron microscopy and laser induced breakdown spectroscopy, we uncover critical insights into this impressive reduction in sintering temperature. Our quantitative analysis reveals that MgO and LiF interact at low temperatures with the diffusion of Li into the surface of MgO particles due to the intrinsic structural disorder of the LiF and MgO crystallites. Nanometre-sized LiF particles were found to react the most at low temperatures due to their increased structural disorder. Our multimodal characterization points to a Li-promoted densification and sintering mechanism. This impressive reduction in sintering temperature can be harnessed to promote low-temperature fabrication of MgO-based composites for technological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Proton, Electron, and Hydrogen-Atom Transfer Thermodynamics of the Metal–Organic Framework, Ti-MIL-125, Are Intrinsically Correlated to the Structural Disorder

Interfacial charge transfer reactions involving protons and/or electrons are fundamental to heterogeneous catalysis and many other reactions relevant to energy, chemical, and biological sectors. Metal–organic frameworks (MOFs) with redox-active metal-oxo nodes have emerged as candidate materials to examine these reactions with near-atomic-level precision, given their crystalline nature. Here, we employed a colloidally stable, Ti-based MOF, Ti-MIL-125, with different crystal sizes to examine catalytically relevant charge transfer thermodynamics. The Ti 8 (μ 2 -O) 8 (μ 2 -OH) 4 nodes structurally mimic TiO 2 , which has shown some PCET reactivity toward reactions of H 2 , O 2 , and others. In this report, we have demonstrated that a change in crystal size induces different amounts of structural disorder to the Ti-oxo node, further changing the thermodynamics of proton/electron/hydrogen-atom transfer reactions. Using electrochemical open-circuit potential (E OCP ) measurements, we have determined that all crystallites undergo a 1H + /1e – redox reaction, which, given the stoichiometry, can be considered as a net H atom transfer (HAT) reaction. The thermodynamics of this HAT reaction, the Ti 3+ O–H bond dissociation free energy (BDFE), was dependent on the crystal size of the MOF, as the decrease in crystal size induced more structural disorder. Our computational calculations have indicated that this difference in BDFE is due to a local change in the geometry of Ti cations, rather than the commonly invoked defects, such as the “missing-linker” defect sites. Individual proton/electron transfer (PT/ET) thermodynamics were also highly dependent on the crystal sizes. These were probed using pK a or band gaps (E g ), respectively. These findings suggest that, particularly when MOFs are nanosized with a large amount of structural disorder, they should no longer be considered “true” single-site catalysts; this is an implicit, but widespread assumption within the MOF-based catalysis field. Implications of these findings will be contrasted with structurally similar metal oxides like TiO 2 and other redox-active MOFs.

Bond dissociation free energy↗
DOE OSTI2021

A multi-step nucleation process determines the kinetics of prion-like domain phase separation

Compartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize the assembly kinetics of a prototypical prion-like domain with equilibrium techniques that characterize its phase boundaries and the size distribution of clusters prior to phase separation. We find two kinetic regimes on the micro- to millisecond timescale that are distinguished by the size distribution of clusters. At the nanoscale, small complexes are formed with low affinity. After initial unfavorable complex assembly, additional monomers are added with higher affinity. At the mesoscale, assembly resembles classical homogeneous nucleation. Careful multi-pronged characterization is required for the understanding of condensate assembly mechanisms and will promote understanding of how the kinetics of biological phase separation is encoded in biomolecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Complexes of tubulin oligomers and tau form a viscoelastic intervening network cross-bridging microtubules into bundles

Abstract The axon-initial-segment (AIS) of mature neurons contains microtubule (MT) fascicles (linear bundles) implicated as retrograde diffusion barriers in the retention of MT-associated protein (MAP) tau inside axons. Tau dysfunction and leakage outside of the axon is associated with neurodegeneration. We report on the structure of steady-state MT bundles in varying concentrations of Mg 2+ or Ca 2+ divalent cations in mixtures containing αβ-tubulin, full-length tau, and GTP at 37 °C in a physiological buffer. A concentration-time kinetic phase diagram generated by synchrotron SAXS reveals a wide-spacing MT bundle phase (B ws ), a transient intermediate MT bundle phase (B int ), and a tubulin ring phase. SAXS with TEM of plastic-embedded samples provides evidence of a viscoelastic intervening network (IN) of complexes of tubulin oligomers and tau stabilizing MT bundles. In this model, αβ-tubulin oligomers in the IN are crosslinked by tau’s MT binding repeats, which also link αβ-tubulin oligomers to αβ-tubulin within the MT lattice. The model challenges whether the cross-bridging of MTs is attributed entirely to MAPs. Tubulin-tau complexes in the IN or bound to isolated MTs are potential sites for enzymatic modification of tau, promoting nucleation and growth of tau fibrils in tauopathies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

From nonmetal to strange metal at the stripe-percolation transition in La 2 - x Sr x CuO 4

The nature of the normal state of cuprate superconductors continues to stimulate considerable speculation. Of particular interest has been the linear temperature dependence of the in-plane resistivity in the low-temperature limit, which violates the prediction for a Fermi liquid. We present measurements of anisotropic resistivity in La$_{2–x}$Sr$_x$CuO$_4$ that confirm the strange-metal behavior for crystals with doped-hole concentration $p = x > p^* \sim 0.19$ and contrast with the nonmetallic behavior for $p < p^*$. We propose that the changes at $p^*$ are associated with a first-order transition from doped Mott insulator to conventional metal; the transition appears as a crossover due to intrinsic dopant disorder. We consider results from the literature that support this picture; in particular, we present a simulation of the impact of the disorder on the first-order transition and the doping dependence of stripe correlations. Below $p^*$, the strong electronic interactions result in charge and spin stripe correlations that percolate across the CuO 2 planes; above $p^*$, residual stripe correlations are restricted to isolated puddles. Here we suggest that the $T$-linear resistivity results from scattering of quasiparticles from antiferromagnetic spin fluctuations within the correlated puddles. This is a modest effect compared to the case at $p < p^*$, where the data suggest that there are no coherent quasiparticles in the normal state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗