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At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Patchy particle model of hydrated amorphous silica

Glasses corroded in static aqueous conditions typically reach a slow, residual rate of dissolution as a result of the complex interplay between multiple processes. While intrinsically suited to address this problem, Monte Carlo (MC) models developed to date have relied on lattices to describe the amorphous structure of glass and are thus unable to reproduce the residual rate of glass corrosion. A recently developed MC approach based on amorphous structures derived from molecular dynamics simulations offers a solution [Kerisit and Du J. Non-Cryst. Solids 522 (2019) 119601], but it requires a simple model that can rapidly relax the glass-water interface upon each dissolution/condensation event to retain the ability of MC simulations to reach large spatial and temporal scales. To this end, a patchy particle model of hydrated amorphous silica was developed and evaluated against atomistic simulations in this work. Models of water and amorphous silica were first developed separately, and cross terms were then defined to enable simulations of hydrated amorphous silica structures with varying water content. While the nature of its interaction potential prevents the patchy particle model from reproducing simultaneously the structure and dynamics of the systems of interest with a single set of parameters, it described well the connectivity of hydrated amorphous silica structures and the local coordination geometry of individual species. Therefore, this model opens the door to MC simulations of the residual rate of glass corrosion and offers an alternative to atomistic models to investigate the evolution of silica gels over large spatial and temporal scales.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS2014

The Surface Compositions of Pluto and Charon

The surface of Pluto as it is understood on the eve of the encounter of the New Horizons spacecraft (mid-2015) consists of a spatially heterogeneous mix of solid N2, CH4, CO, C2H6, and an additional component that imparts color, and may not be an ice. The known molecular ices are detected by near-infrared spectroscopy. The N2 ice occurs in the hexagonal crystalline b-phase, stable at T greater than 35.6 K. Spectroscopic evidence for wavelength shifts in the CH4 bands attests to the complex mixing of CH4 and N2 in the solid state, in accordance with the phase diagram for N2 + CH4. Spectra obtained at several aspects of Plutos surface as the planet rotates over its 6.4-day period show variability in the distribution of CH4 and N2 ices, with stronger CH4 absorption bands associated with regions of higher albedo, in correlation with the visible rotational light curve. CO and N2 ice absorptions are also strongly modulated by the rotation period; the bands are strongest on the anti-Charon hemisphere of Pluto. Longer term changes in the strengths of Plutos absorption bands occur as the viewing geometry changes on seasonal time-scales, although a complete cycle has not been observed. The non-ice component of Plutos surface may be a relatively refractory material produced by the UV and cosmic-ray irradiation of the surface ices and gases in the atmosphere, although UV does not generally penetrate the atmospheric CH4 to interact with the surface. Laboratory simulations indicate that a rich chemistry ensues by the irradiation of mixtures of the ices known to occur on Pluto, but specific compounds have not yet been identified in spectra of the planet. Charons surface is characterized by spectral bands of crystalline H2O ice, and a band attributed to one or more hydrates of NH3. Amorphous H2O ice may also be present; the balance between the amorphization and crystallization processes on Charon remains to be clarified. The albedo of Charon and its generally spatially uniform neutral color indicate that a component, not yet identified, is mixed in some way with the H2O and NH3nH2O ices. Among the many known small bodies in the transneptunian region, several share characteristics with Pluto and Charon, including the presence of CH4, N2, C2H6, H2O ices, as well as components that yield a wide variety of surface albedo and color. The New Horizons investigation of the Pluto-Charon system will generate new insight into the physical properties of the broader transneptunian population, and eventually to the corresponding bodies expected in the numerous planetary systems currently being discovered elsewhere in the Galaxy.

surface composition↗
DOE OSTI2021

Structure of the human SAGA coactivator complex

The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP 6 ) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Recombination of Autodissociated Water Ions in a Nanoscale Pure Water Droplet

The recombination of water ions has diverse scientific and practical implications, ranging from acid-base chemistry and biological systems to planetary environments and applications in fuel cell and carbon conversion technologies. While spatial confinement affects the physicochemical properties of water dynamics, its impact on the recombination process has rarely been studied. In this work, we investigate the dynamics of water, the water ion distribution, and the ion recombination process in water droplets as a function of droplet size through molecular dynamics simulations and adaptive quantum mechanical/molecular mechanical calculations. We compare the dynamics of recombination in water droplet sizes ranging from 100 to 18 000 waters, both in their interiors and on their surfaces. We found that the self-diffusion of water dramatically decreases in droplets with a diameter below 2.2 nm. Using a classical RexPoN force-field, we found that the ions in 1000 H2O's spend almost 50% of the time on the surface and 0.5 nm beneath it with a slight preference for OH- ion to reside longer on the surface. We estimate that, on average, recombination in these drops occurs at 400 ps in 1000 H2O's and 1 ns in 3000 H2O's. We also found that recombination is not limited by the local structure of the surface or the size of the droplet but can be influenced by the geometry of the water wire connecting the ions as they approach each other, which can often prevent recombination. Our results provide insights to the reaction microenvironments presented by nanoscopic water droplets.

Kwon, Soonho↗
DOE OSTI2020

Controlling light emission by engineering atomic geometries in silicon photonics

By engineering atomic geometries composed of nearly 1000 atomic segments embedded in micro-resonators, we observe Bragg resonances induced by the atomic lattice at the telecommunication wavelength. The geometrical arrangement of erbium atoms into a lattice inside a silicon nitride (SiN) microring resonator reduces the scattering loss at a wavelength commensurate with the lattice. We confirm dependency of light emission to the atomic positions and lattice spacing and also observe Fano interference between resonant modes in the system.

42 ENGINEERING↗
DOE OSTI2020

Crystallography of Reactive Intermediates

Metal–ligand (M–L) multiply bonded complexes hold a central place in inorganic chemistry and catalysis: From fundamental and historical perspectives, these species have played a critical role in the articulation of important bonding principles (i.e. the vanadyl ion in the development of molecular orbital theory); from a practical perspective, these species are critical intermediates in a variety of chemical reactions (i.e. N 2 and O 2 reduction, H 2 O oxidation, and C–H functionalization). For many high-valent, early metal complexes, overlap of ligand-based electrons with vacant π-symmetry orbitals leads to strong M–L multiple bonds. The stability of these species enables straightforward characterization with a suite of standard spectroscopic and diffraction-based experiments. Mid- and late-transition metal complexes, with attendant higher d-electron counts, often support more reactive M–L multiply bonded fragments. The reactivity of these species simultaneously renders them attractive intermediates for catalysis but challenging synthetic targets to observe and characterize. A number of important strategies have been advanced to enable experimental characterization of mid- to late-metal–ligand multiply bonded species. Synthetic manipulation of the coordination geometry and ligand donicity, as well as introduction of sterically encumbering ligands, have each emerged as powerful methods to tame the inherent reactivity of kinetically labile M–L multiple bonds. While these efforts have resulted in families of well-characterized complexes and provided critical insights regarding structure and bonding, the synthetic derivatization required to stabilize M–L fragments of interest often obviates the substrate functionalization activity relevant to catalysis. Photochemical synthesis of reactive species provides a conceptually attractive strategy to generate reactive M–L fragments under conditions compatible with time-resolved or cryogenic steady-state characterization, and photogeneration has enabled observation of a number of reactive M–L fragments. The suite of tools available to characterize photogenerated reactive species is often more limited than typical for kinetically stabilized complexes and structural characterization is typically not possible. Recently, photocrystallographic experiments, in which reactive M–L multiply bonded intermediates are generated within single-crystal matrices, have been advanced as a strategy to interrogate the structures of reactive intermediates in C–H functionalization. Lastly, this Comment describes the historical antecedents to these experiments, highlights examples of photocrystallographic characterization of reactive intermediates, and discusses future opportunities.

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

Field-gradient measurement using a Stern-Gerlach atomic interferometer with butterfly geometry

Atomic interferometers have been studied as a promising device for precise sensing of external fields. Among various configurations, a particular configuration with a butterfly-shaped geometry has been designed to sensitively probe field gradients. Here, we introduce a Stern-Gerlach (SG) butterfly interferometer by incorporating magnetic field in the conventional butterfly-shaped configuration. Atomic trajectories of the interferometer can be flexibly adjusted by controlling magnetic fields to increase the sensitivity of the interferometer, while the conventional butterfly interferometer using Raman transitions can be understood as a special case. We also show that the SG interferometer can keep high contrast against a misalignment in position and momentum caused by the field gradient.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2012

Studies of Supernovae, SNR, and Dust with the James Webb Space Telescope

The james Webb Space Telescope (JWST) will provide breakthrough capabilities for the study of supernovae and supernova remnants, as well as many other science objectives. JWST is a large aperture, cryogenic, infrared-optimized general purpose space observatory under construction by NASA, ESA, and CSA for launch in 2018. The JWST instrumentation will provide imaging, coronagraphy, and spectroscopy between 6000A to 29 microns. This spectral region contains many atomic, molecular, and particulate diagnostics that are especially relevant for the study of dust formation. The spectroscopic capabilities include velocity resolution down to approx. 100 km/sec, a near-IR multi-object spectrograph with a approx. 3x3 arcmin field of view array of approx. 250,000 addressable shutters, and near-IR and mid-IR approx. 3x3 arcsec integral field units. The JWST telescope will have a 6.5m-diameter segmented primary mirror and will be diffraction-limited at 2 microns (PSF FWHM - 0.07 arcsec). The imaging and spectroscopic sensitivities will be about 100x lower than previous capabilities in the near- and mid-IR. The JWST observatory will be placed in a L2 orbit by an Ariane 5 launch vehicle provided by ESA. The JWST telescope and instruments will be passively cooled to approx. 40K by a sunshield that will be unfolded after launch. The sunshield geometry limits the JWST pointing on the sky to be between 85 deg and 135 deg from the Sun. The observatory is designed for a 5-year prime science mission, with consumables for 10 years of science operations, and a Target of Opportunity response time of 48 hours.

Sonneborn, George↗
DOE OSTI2023

De novo design of protein structure and function with RFdiffusion

Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.

Science & Technology - Other Topics↗
DOE OSTI2022

Smoothed particle hydrodynamics modeling and analysis of oxide reduction process for uranium oxides

A common kinetic feature for oxide reduction chemical/electrochemical processes is oxygen transport via a porous metallic layer, which has been considered as a rate-determining step for reducing uranium oxides to metallic uranium. Accounting this kinetic behavior must involve the resolution of the moving reactive interface between shrinking oxide and expanding metal phases. This study presents a numerical model using smoothed particles hydrodynamics (SPH) to effectively deal with the evolution of the shrinking core reaction interface and oxygen transport via mass transfer of lithium oxide (Li 2 O) species in multiple mass transfer domains. We successfully validated the proposed model against a theoretical derivation for the oxide reduction process handling a shrinking oxide core with molten salt and metal ash medium on a simple planar geometry. Armed with successful validation results, the model examined a realistic reactant geometry to extend the arguments beyond the one-dimensional analyses, allowing the proposed model to apply to general application scenarios with multi-dimensional geometry. Here, this study demonstrated that the proposed model could simulate and evaluate an arbitrary reaction basket design without iterative experimental trials, which is prohibitive for a scaled high-temperature molten salt study in an inert environment. The construct potentially provides not only deep insights on multiphysics behaviors governing the process dynamics but also a robust framework for evaluating and screening candidate basket designs in the most cost-effective manner.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Self-Isolated Raman Lasing with a Chiral Dielectric Metasurface

The light sources that power photonic networks are small and scalable, but they also require the incorporation of optical isolators that allow light to pass in one direction only, protecting the light source from damaging backreflections. Unfortunately, the size and complex integration of optical isolators makes small-scale and densely integrated photonic networks infeasible. Here, we overcome this limitation by designing a single device that operates both as a coherent light source and as its own optical isolator. Our design relies on high-quality-factor dielectric metasurfaces that exhibit intrinsic chirality. By carefully manipulating the geometry of the constituent silicon metaatoms, we design three-dimensionally chiral modes that act as optical spin-dependent filters. Using spin-polarized Raman scattering together with our chiral metacavity, we demonstrate Raman lasing in the forward direction, while the lasing action is suppressed by over an order of magnitude for reflected light. Our high-$\textit{Q}$ chiral metasurface design presents a new approach toward compactly isolating integrated light sources by directly tailoring the emission properties of the light source itself.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Molecular structure models of amorphous bismuth and cerium carboxylate catalyst precursors

As our societal need for materials and energy has grown, so has our need for catalyst processes in hydrogen production. A major function in these applications, for both homogenous and heterogeneous catalysis processes, is the synthesis of an active metal catalyst. It must first be soluble to control the physical properties of the metal being used. Recent work in metal precursors has begun to turn toward these metal carboxylate types of material. Here, structural models are proposed for bismuth 2-ethylhexanoate and 2,2-dimethyloctanoate and cerium 2-ethylhexanoate. The bismuth compounds have been characterized at different ratios of bismuth to carboxylate as solutions of the free acids. Their structures are most consistent with a Bi 4 (RCO 2 ) 12 motif where the Bi ions are arranged in a flattened tetrahedron with Bi – Bi distances of about 4.3 Å. There is evidence for Bi – O – Bi linkages at low free acid concentrations. The cerium compound is most consistent with a linear tetracerium molecule where the Ce – Ce distances repeat at about 4.3 Å out to 16.4 Å. The models were generated by analogy with known crystal structures and compared to high-energy x-ray scattering data. To further evaluate the models, DFT calculations were made, and the equilibrium geometries were compared. The vibrational spectra calculated from those geometries are presented and compared to the experimental results. Magnetization vs. temperature data was collected on the cerium compound, and its behavior was consistent with the proposed model. A geometrical approach to determining the dimensionality and relative positions of the metal ions in these structures is presented.

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

Materials Data on Fe2(SO7)3 by Materials Project

FeO6(Fe(SO5)2)3(O2)3 is Tungsten Carbide-like structured and crystallizes in the trigonal P-31c space group. The structure is zero-dimensional and consists of two chebi:30649 molecules, six molecular oxygen molecules, and two Fe(SO5)2 clusters. In each Fe(SO5)2 cluster, there are two inequivalent Fe sites. In the first Fe site, Fe is bonded to six equivalent O atoms to form FeO6 octahedra that share corners with six equivalent SO4 tetrahedra. All Fe–O bond lengths are 2.02 Å. In the second Fe site, Fe is bonded to six O atoms to form FeO6 octahedra that share corners with three equivalent SO4 tetrahedra. There is three shorter (1.78 Å) and three longer (1.94 Å) Fe–O bond length. S is bonded to four O atoms to form SO4 tetrahedra that share corners with two FeO6 octahedra. The corner-sharing octahedra tilt angles range from 42–46°. There are a spread of S–O bond distances ranging from 1.46–1.53 Å. There are five inequivalent O sites. In the first O site, O is bonded in a single-bond geometry to one Fe atom. In the second O site, O is bonded in a distorted bent 120 degrees geometry to one Fe and one S atom. In the third O site, O is bonded in a single-bond geometry to one S atom. In the fourth O site, O is bonded in a distorted bent 150 degrees geometry to one Fe and one S atom. In the fifth O site, O is bonded in a single-bond geometry to one S atom.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Geometric control of emergent antiferromagnetic order in coupled artificial spin ices

Artificial spin ices (ASIs) composed of coupled nanomagnets offer the possibility to create designer geometrical frustration and manipulate inter-nanomagnet interactions. In particular, by using a dimer motif consisting of two strongly coupled single-domain nano magnets as a building block, we can control and realize intriguing antiferromagnetic physical states in which the magnetic charge is not conserved. Here we create a dimer kagome ASI system within which the antiferromagnetic order is controlled by tuning lattice geometry. Different disordered antiferromagnetic phases and the inter-nanomagnet interactions are visualized directly in demagnetized lattices with different lattice parameters. Monte Carlo simulations establish that the collective ground state consists of disordered antiferromagnetic dimers across the lattice when the intra-dimer interaction is dominant. However, for lattices governed by intra-triad-unit interactions, the ground state exhibits a longrange spin-ordered state in which the vertex magnetic charge is uniform across all triads.

36 MATERIALS SCIENCE↗
NASA NTRS1994

Local shear instabilities in weakly ionized, weakly magnetized disks

We extend the analysis of axisymmetric magnetic shear instabilities from ideal magnetohydrodynamic (MHD) flows to weakly ionized plasmas with coupling between ions and neutrals caused by collisions, ionization, and recombination. As part of the analysis, we derive the single-fluid MHD dispersion relation without invoking the Boussinesq approximation. This work expands the range of applications of these instabilities from fully ionized accretion disks to molecular disks in galaxies and, with somewhat more uncertainty, to protostellar disks. Instability generally requires the angular velocity to decrease outward, the magnetic field strengths to be subthermal, and the ions and neutrals to be sufficiently well coupled. If ionization and recombination processes can be neglected on an orbital timescale, adequate coupling is achieved when the collision frequency of a given neutral with the ions exceeds the local epicyclic freqency. When ionization equilibrium is maintained on an orbital timescale, a new feature is present in the disk dynamics: in contrast to a single-fluid system, subthermal azimuthal fields can affect the axisymmetric stability of weakly ionized two-fluid systems. We discuss the underlying causes for this behavior. Azimuthal fields tend to be stabilizing under these circumstances, and good coupling between the neutrals and ions requires the collision frequency to exceed the epicyclic frequency by a potentially large secant factor related to the magnetic field geometry. When the instability is present, subthermal azimuthal fields may also reduce the growth rate unless the collision frequency is high, but this is important only if the field strengths are very subthermal and/or the azimuthal field is the dominant field component. We briefly discuss our results in the context of the Galactic center circumnuclear disk, and suggest that the shear instability might be present there, and be responsible for the observed turbulent motions.

Blaes, Omer M.↗
DOE OSTI2020

Understanding the Interplay between the Nonvalence and Valence States of the Uracil Anion upon Monohydration

In this work we present an ab initio investigation into the effect of monohydration on the interaction of uracil with low energy electrons. Electron attachment and photodetachment experimental studies have previously shown dramatic changes in uracil upon solvation with even a single water molecule, due to an inversion of the character of the ground state of the anion. Here we explore the interplay between the nonvalence and valence states of the uracil anion, as a function of geometry and site of solvation. Our model provides unambiguous interpretation of previous photoelectron studies, reproducing the binding energies and photoelectron images for bare uracil and a single isomer of the U•(H 2 O) 1 cluster. Furthermore, the results of this study provide insight into how electrons may attach to hydrated nucleobases. These results lay the foundations for further investigations into the effect of microhydration on the electronic structure and electron capture dynamics of nucleobases.

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

Out-of-time-order correlators bridge classical transport and quantum dynamics

The out-of-time-order correlator (OTOC) has emerged as a central tool for quantifying decoherence across wide-ranging physical platforms. Here, we demonstrate its direct measurement in a classical ensemble using nuclear magnetic resonance with a modulated gradient spin echo sequence and extend the method into a multidimensional correlation to track exchange phenomena. Position is encoded through magnetic field gradients and momentum through the velocity autocorrelation function, enabling experimental access to OTOCs for proton motion confined within the self-similar lattice of the metal–organic framework MOF-808. Here, water confined to specified geometries within the MOF pores gives rise to spatially distinct diffusive eigenmodes with characteristic relative entropies. We demonstrate that periodic radio frequency driving combined with gradient modulation yields entropy evolution through the selection of distinct diffusion modes. Frequency-resolved diffusion spectra connect these entropy dynamics to classical heat exchange laws, revealing how operational features of quantum systems are mirrored in confined, macroscopic spin ensembles.

Fricke, Sophia N. [University of California, Berke↗
DOE OSTI2026

Learning interpretable surface elasticity properties from bulk properties via neural network equation learners

Surface elasticity is central to understanding the mechanics and stability of surfaces and interfaces. It is characterized by quantities such as surface tension, residual surface stress, and surface stiffness. However their analytical expressions are typically difficult to derive from atomistic data, and depend strongly on modeling choices. This work presents a neural network-based equation learner which combines customized activation functions and connection-based pruning to discover parsimonious, closed-form equations for surface elasticity from atomistic simulations. Applying the method to seven face-centered cubic (FCC) metals, our equation learner uncovers interpretable equations that describe both low-Miller index and high-Miller index surface properties, capturing long-tail property distributions accurately. The discovered expressions are decoupled into two components: a universal, geometry-driven orientation function, and material-specific baseline coefficients. We find that lower-order properties such as surface tension are fundamentally geometry dependent, while higher-order properties such as surface stress and elasticity show more complex geometry and material dependence. We also relate material dependent coefficients to bulk properties, forming a clear map from bulk material properties to surface elasticity. Overall, this approach demonstrates that interpretable neurosymbolic machine learning can bridge the gap between atomistic simulations and physical laws, enabling the discovery of generalizable structure–property relationships for materials science phenomena such as surface elasticity.

Equation learning↗