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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Unveiling the Structure and Dynamics of Water Confined in Colloidal Boehmite Suspensions

Thin fluid layers confined between nanoparticles play an important role in several natural and industrial systems, including radioactive wastes stored in tanks at the U.S. Department of Energy’s Hanford site. Multimodal neutron and computational approaches have been integrated to examine the properties of one, two, and four layers of water (H 2 O or D 2 O) on nanoparticulate, hydrous, or deuterated boehmite (γ-AlOOH or γ-AlOOD). Exposure of deuterated boehmite to H 2 O at 90 °C yielded rapid H/D isotopic exchange likely driven by a Grotthus-like proton-hopping mechanism. The in-plane and out-of-plane vibrations of the structural hydroxyls involved in this exchange were observed for both the hydrated and deuterated boehmite. These observations were confirmed by molecular dynamics simulations that also showed that single water molecules on the (010) surface bond to the structure via four bonds: two from hydrogens (deuteriums) on the water to surrounding oxygens and two from the water’s oxygen to surrounding OD/OH. Bulk water-like properties began to appear once four monolayers of water had been added, but steric crowding limited water diffusion rates once two monolayers had been added. The super-Arrhenius temperature dependence observed at four monolayers indicated glass-like behavior in a well-formed hydrogen-bonding network. Such a network is not sufficiently developed, however, when the surface water coverage is less than four layers. In conclusion, the unique nature of these layers can provide critical information for understanding forces between particles in proximity, and resultant effects on suspension rheology.

Anovitz, Lawrence M. [Oak Ridge National Laborator↗
DOE OSTI2026

Data-driven particle dynamics: Structure-preserving coarse-graining for emergent behavior in non-equilibrium systems

Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems are coarse-grained into low-dimensional models, the entropic loss of information leads to emergent physics which are dissipative, history-dependent, and stochastic. To machine learn coarse-grained dynamics from time-series observations of particle trajectories, we propose a framework using the metriplectic bracket formalism that preserves these properties by construction; most notably, the framework guarantees discrete notions of the first and second laws of thermodynamics, conservation of momentum, and a discrete fluctuation-dissipation balance crucial for capturing non-equilibrium statistics. We introduce the mathematical framework abstractly before specializing to a particle discretization. As labels are generally unavailable for entropic state variables, we introduce a novel self-supervised learning strategy to identify emergent structural variables. We validate the method on benchmark systems and demonstrate its utility on two challenging examples: (1) coarse-graining star polymers at challenging levels of coarse-graining while preserving non-equilibrium statistics, and (2) learning models from high-speed video of colloidal suspensions that capture coupling between local rearrangement events and emergent stochastic dynamics. We provide open-source implementations in both PyTorch and LAMMPS, enabling large-scale inference and extensibility to diverse particle-based systems.

Computational Engineering, Finance, and Science (c↗
DOE OSTI2020

Insights into the Structure and Dynamics of Metal–Organic Frameworks via Transmission Electron Microscopy

Metal–organic frameworks (MOFs) are hybrid materials composed of metal ions and organic linkers featuring high porosity, crystallinity, and chemical tunability at multiple length scales. Here, a recent advancement in transmission electron microscopy (TEM) and its direct application to MOF structure–property relationships have changed how we consider rational MOF design and development. Herein, we provide a perspective on TEM studies of MOFs and highlight the utilization of state-of-the-art TEM technologies to explore dynamic MOF processes and host–guest interactions. Additionally, we provide thoughts on what the future holds for TEM in the study of MOFs.

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

Capturing the generation and structural transformations of molecular ions

Molecular ions are ubiquitous and play pivotal roles in many reactions, particularly in the context of atmospheric and interstellar chemistry. However, their structures and conformational transitions, particularly in the gas phase, are less explored than those of neutral molecules owing to experimental difficulties. A case in point is the halonium ions, whose highly reactive nature and ring strain make them short-lived intermediates that are readily attacked even by weak nucleophiles and thus challenging to isolate or capture before they undergo further reaction. Here we show that mega-electronvolt ultrafast electron diffraction (MeV-UED), used in conjunction with resonance-enhanced multiphoton ionization, can monitor the formation of 1,3-dibromopropane (DBP) cations and their subsequent structural dynamics forming a halonium ion. We find that the DBP + cation remains for a substantial duration of 3.6 ps in aptly named ‘dark states’ that are structurally indistinguishable from the DBP electronic ground state. The structural data, supported by surface-hopping simulations and ab initio calculations, reveal that the cation subsequently decays to iso-DBP + , an unusual intermediate with a four-membered ring containing a loosely bound bromine atom, and eventually loses the bromine atom and forms a bromonium ion with a three-membered-ring structure. We anticipate that the approach used here can also be applied to examine the structural dynamics of other molecular ions and thereby deepen our understanding of ion chemistry.

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

Mapping structures and dynamics with frequency-correlated diffusion exchange

Understanding molecular motion in diffusion-driven complex environments is critical for designing sustainable materials and improving chemical processes. Here, we introduce a multidimensional nuclear magnetic resonance (NMR) method that captures how molecular populations exchange across different dynamic regimes. By extending the modulated gradient spin-echo technique to include frequency-frequency correlations, our approach reveals diffusion pathways that are otherwise obscured in heterogeneous systems. Implemented on a unilateral NMR magnet, the method eliminates gradient pulsing constraints and accesses dynamics in the kilohertz regime. We apply this technique to swelling and acid-catalyzed deconstruction of cross-linked and linear polymers to observe how structural heterogeneity evolves over time. By linking molecular motion to topology and chemical state, we extract physical metrics such as fractal surface dimensionality and reaction wavefront velocity, properties inaccessible with standard diffusion measurements. This work expands the capabilities of NMR for probing soft matter, with implications for polymer recycling and materials design.

Fricke, Sophia N. [University of California, Berke↗
DOE OSTI2023

Rheological dynamics and structural characteristics of supramolecular assemblies of β-cyclodextrin and sulfonic surfactants

Cyclodextrins are highly functional compounds with a hydrophobic cavity capable of forming supramolecular inclusion complexes with various classes of molecules including surfactants. The resultant rich nanostructures and their dynamics are an interesting research problem in the area of soft condensed matter and related applications. In this paper, we report novel dynamical supramolecular assemblies based on the complexation of β-cyclodextrin with 3 different sulfonic surfactants, which are sodium hexadecylsulfate, sodium dodecylbenzenesulfonate, and myristyl sulfobetaine. It was observed that a β-cyclodextrin : surfactant/2 : 1 molar ratio was ideal for inducing axial growth and imparting large viscosities in the suspensions. Such complexation processes were accompanied by intriguing nanostructural phase behaviors and rheological properties that were very sensitive to the molecular architecture of sulfonic surfactants. The presence of an amino group in the head group of the surfactant allowed for large viscosities that reached 2.4 × 10 4 Pa s which exhibited gel-like behavior. In contrast, smaller viscosity values with a lower consistency index were observed when a bulky aromatic ring was present instead. DIC microscopy was used to visually probe the microstructure of the systems with respect to sulfonate molecular architecture. Additionally, surface tension measurements, and FTIR and NMR spectroscopies were used to gain insights into the nature of interactions that lead to the complexation and nanostructural characteristics. Finally, mechanics correlating the supramolecular morphologies to the rheological properties were proposed.

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

Lattice structure and dynamics of sparse molecular crystals: OsO4 and RuO4

This dataset contains input and output files from DFT simulations used to reproduce the electronic and phonon calculations of bulk and molecular OsO₄ and RuO₄. The files include data from initial electronic structure and phonon calculations performed using different functionals: PBE, PBEsol, and vdW-DF-optB86b. The computed phonon frequencies are compared with Raman crystal and gas-phase frequencies from existing literature, while the calculated phonon density of states (PhDOS) is compared with experimental PhDOS data.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination

To understand the dynamic structure–function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.

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

Resolving electrochemically triggered topological defect dynamics and structural degradation in layered oxides

Understanding topological defects-controlled structural degradation of layered oxides—a key cathode material for high-performance lithium-ion batteries—plays a critical role in developing next-generation cathode materials. Here, by constructing a nanobattery in an electron microscope enabling atomic-scale monitoring of electrochemcial reactions, we captured the electrochemically driven atomistic dynamics and evolution of dislocations—a most important topological defect in material. We deciphered how dislocations nucleate, move, and annihilate within layered cathodes at the atomic scale. Specifically, we found two types of dislocation configurations, i.e., single dislocations and dislocation dipoles. Both pure dislocation glide/climb and mixed motions were captured, and the dislocation glide and climb velocities were first experimentally measured. Moreover, dislocation activity-mediated structural degradation such as crack nucleation, phase transformation, and lattice reorientation was unraveled. Our work provides deep insights into the atomistic dynamics of electrochemically driven dislocation activities in layered oxides.

Wang, Chunyang (ORCID:0000000184613952)↗
DOE OSTI2023

Elucidating Structural Transition Dynamics in the Magnesium Cathode MgCr 2 O 4

Multivalent batteries, e.g., those based on magnesium (Mg), are promising candidates for next-generation energy storage due to their high volumetric energy densities and low cost. However, the corresponding ion migration and structural transition mechanisms are often linked and difficult to observe directly. Here, in this paper, we report the direct investigation of atomic transport pathways of cations in spinel magnesium chromate (MgCr 2 O 4 ) by using aberration-corrected scanning transmission electron microscopy (STEM). Cr atoms are directly observed to reversibly occupy the otherwise vacant octahedrally coordinated interstitial sites, passing through tetrahedral sites normally occupied by Mg. Furthermore, imaging and electron energy loss spectroscopy show that electron irradiation induces the formation of Mg and O vacancies, facilitating the migration of Cr and leading to an irreversible phase transition. These results demonstrate the ability of STEM to capture the pathway of deleterious point defects that can result in undesirable phase transitions.

25 ENERGY STORAGE↗
DOE OSTI2021

Nutrient availability and senescence spatially structure the dynamics of a foundation species

Significance Landscapes are spatially heterogeneous, and the measurement of spatial pattern is dependent upon observation scale. Understanding plant populations requires assessing their extrinsic interactions with the environment as well as intrinsic biological processes and has been difficult because of the inability to track both plant abundance and health on appropriate scales. We introduce remote sensing observations that assess the abundance and health of giant kelp, an important ecosystem-structuring species, over regional and local scales. We find that both extrinsic nutrient availability and intrinsic senescence processes regulate population dynamics but on regional and local scales, respectively. This suggests that future satellite missions will be able to assess plant abundance and health and their interactions with the environment on local to global scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Structural and dynamic mechanisms of GABA A receptor modulators with opposing activities

γ-Aminobutyric acid type A (GABA A ) receptors are pentameric ligand-gated ion channels abundant in the central nervous system and are prolific drug targets for treating anxiety, sleep disorders and epilepsy. Diverse small molecules exert a spectrum of effects on γ-aminobutyric acid type A (GABA A ) receptors by acting at the classical benzodiazepine site. They can potentiate the response to GABA, attenuate channel activity, or counteract modulation by other ligands. Structural mechanisms underlying the actions of these drugs are not fully understood. Here we present two high-resolution structures of GABA A receptors in complex with zolpidem, a positive allosteric modulator and heavily prescribed hypnotic, and DMCM, a negative allosteric modulator with convulsant and anxiogenic properties. These two drugs share the extracellular benzodiazepine site at the α/γ subunit interface and two transmembrane sites at β/α interfaces. Structural analyses reveal a basis for the subtype selectivity of zolpidem that underlies its clinical success. Molecular dynamics simulations provide insight into how DMCM switches from a negative to a positive modulator as a function of binding site occupancy. Together, these findings expand our understanding of how GABA A receptor allosteric modulators acting through a common site can have diverging activities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Real-time Atomic-scale Visualization of Reversible Copper Surface Activation during the CO Oxidation Reaction

Dynamic structural and chemical information of catalyst surface during a catalytic reaction is critical for deciphering the mechanisms governing the properties of catalysts. Transition-metal based catalysts have emerged as an important alternative to noble metal catalysts, but their catalytic mechanism remains largely elusive, complicated by dynamic structure and valence evolution. Herein, by using in situ aberration-corrected environmental transmission electron microscopy, we capture, for the first time at atomic level, the dynamic evolution of Cu surface during CO oxidation reaction. We discovered that, under reaction condition, the Cu surface is activated, typically involving 2-3 atomic layers with the formation of a reversible meta-stable phase that only exists during catalytic reactions. Further, we reveal the distinctive role of CO and O2 in the surface activation, featuring CO exposure to lead to surface roughening and consequently formation of low-coordinated Cu atoms, while O2 exposure to induce quasi-crystalline CuOx phase. Corrugated by DFT calculations, we rationalize crystalline CuOx reversibly transforms into the amorphous phase, acting as an active species to facilitate the interaction of gas reactants and catalyzing CO oxidation.

Luo, Langli↗
DOE OSTI2025

Imaging the photochemistry of cyclobutanone using ultrafast electron diffraction: Experimental results

We investigated the ultrafast structural dynamics of cyclobutanone following photoexcitation at λ = 200 nm using gas-phase megaelectronvolt ultrafast electron diffraction. Our investigation complements the simulation studies of the same process within this special issue. It provides information about both electronic state population and structural dynamics through well-separable inelastic and elastic electron scattering signatures. We observe the depopulation of the photoexcited S 2 state of cyclobutanone with n3s Rydberg character through its inelastic electron scattering signature with a time constant of (0.29 ± 0.2) ps toward the S 1 state. The S 1 state population undergoes ring-opening via a Norrish Type-I reaction, likely while passing through a conical intersection with S 0 . The corresponding structural changes can be tracked by elastic electron scattering signatures. These changes appear with a delay of (0.14 ± 0.05) ps with respect to the initial photoexcitation, which is less than the S 2 depopulation time constant. This behavior provides evidence for the ballistic nature of the ring-opening once the S 1 state is reached. The resulting biradical species react further within (1.2 ± 0.2) ps via two rival fragmentation channels yielding ketene and ethylene, or propene and carbon monoxide. Furthermore, our study showcases the value of both gas-phase ultrafast diffraction studies as an experimental benchmark for nonadiabatic dynamics simulation methods and the limits in the interpretation of such experimental data without comparison with such simulations.

Carbon monoxide↗
DOE OSTI2026

Structure and Dynamics of Water Confined in Transition Metal Carbide MXenes: Implications for Electrochemical Applications

Two-dimensional transition metal carbides and nitrides (MXenes) are an important family of electrochemically active 2D materials. MXenes combine high conductivity with hydrophilicity, making them attractive materials for many applications, including electrochemical energy storage, sensing, desalination, and others. In order to better understand the role of structure on MXene properties, here, we investigated the vibrational properties and diffusion of water in MXenes with differing layer thicknesses and transition metal compositions using inelastic, quasi-elastic, and small-angle neutron scattering. We found that all of the Mo-containing MXenes studied here exhibited comparable vibrational dynamics and diffusion coefficients to each other and to previously studied Ti 3 C 2 T x . However, Ti 2 CT x was distinguished by its faster diffusion and more hydroxyl groups compared to the other MXenes studied. These results can help guide the selection of appropriate MXenes for energy storage and electrochemical water purification applications.

MXenes↗
DOE OSTI2021

Redox Mediated Control of Electrochemical Potential in Liquid Cell Electron Microscopy

Liquid cell electron microscopy enables the study of nanoscale transformations in solvents with high spatial and temporal resolution, but for the technique to achieve its potential requires a new level of control over the reactivity caused by radical generation under electron beam irradiation. An understanding of how to control electron-solvent interactions is needed to further advance the study of structural dynamics for complex materials at the nanoscale. Additionally, we developed an approach that scavenges radicals with redox species that form well-defined redox couples and control the electrochemical potential in situ . This approach enables the observation of electrochemical structural dynamics at near-atomic resolution with precise control of the liquid environment. Analysis of nanocrystal etching trajectories indicates that this approach can be generalized to several chemical systems. The ability to simultaneously observe heterogeneous reactions at near-atomic resolution and precisely control the electrochemical potential enables the fundamental study of complex nanoscale dynamics with unprecedented detail.

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

MECHANICAL SHOCK AND VIBRATION ANALYSIS OF SPENT NUCLEAR FUEL CARRIED BY THE ATLAS RAILCAR

Researchers at Pacific Northwest National Laboratory have completed a structural-dynamic analysis of spent nuclear fuel subjected to the mechanical shock and vibration environment that is anticipated during normal conditions of transport in casks carried by the Atlas railcar. The Atlas railcar is a new railcar design that is being developed specifically for the purpose of carrying spent nuclear fuel casks. The analysis used best-estimate railcar dynamics models of the Atlas railcar and considered 17 different spent nuclear fuel transportation cask systems, representing the current fleet of cask options. This work used NUCARS, a specialized railcar dynamics explicit finite element code to calculate railcar dynamic response to prescribed speeds and track configurations. The railcar dynamics models provided cask transient motion for a wide range of speeds and track conditions, generating a relatively large database of potential cask motion. All of the cask motion transients were then applied as loading conditions to LS-DYNA structural-dynamic models of a single fuel rod. The analyses predict that the Equipos Nucleares S.A./U.S. Department of Energy (ENSA/DOE) multimodal transportation test of 2017 provided a relatively stronger vibration environment than is expected from the Atlas railcar. This paper describes the analysis methods, the analysis results, and compares the results of the Atlas transportation analysis to the test results and analyses of the ENSA/DOE multimodal transportation test of 2017.

Klymyshyn, Nicholas A.↗
DOE OSTI2023

The Migdal effect in semiconductors for dark matter with masses below ~ 100 MeV

Dark matter scattering off a nucleus has a small probability of inducing an observable ionization through the inelastic excitation of an electron, called the Migdal effect. We use an effective field theory to extend the computation of the Migdal effect in semiconductors to regions of small momentum transfer to the nucleus, where the final state of the nucleus is no longer well described by a plane wave. Our analytical result can be fully quantified by the measurable dynamic structure factor of the semiconductor, which accounts for the vibrational degrees of freedom (phonons) in a crystal. We show that, due to the sum rules obeyed by the structure factor, the inclusive Migdal rate and the shape of the electron recoil spectrum is well captured by approximating the nuclei in the crystal as free ions; however, the exclusive differential rate with respect to energy depositions to the crystal depends on the phonon dynamics encoded in the dynamic structure function of the specific material. Our results now allow the Migdal effect in semiconductors to be evaluated even for the lightest dark matter candidates (m χ ≳ 1 MeV) that can kinematically excite electrons.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗