Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “atomic dynamics”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Lattice dynamics, sound velocities, and atomic environments of szomolnokite at high pressure

Complex mixtures of sulfates, silicates, and ice have been observed in a variety of planetary environments on Earth, Mars and the icy satellites of the solar system. Characterizing the properties of the corresponding compositional endmembers is important for understanding the interiors of a range of planetary bodies in which these phases are observed. To measure the electronic and vibrational properties of the pure ferrous iron endmember of the kieserite group, szomolnokite, (FeSO 4 ∙H 2 O), we have performed synchrotron 57 Fe nuclear resonant inelastic and forward scattering experiments in the diamond-anvil cell up to 14.5 GPa. This pressure range covers depths within Earth’s interior relevant to sulfur cycling in subduction zones and the range of pressures expected within icy satellite interiors. We find evidence of crystal lattice softening, changes in elastic properties, and changes in the electric field gradients of iron atoms associated with two structural transitions occurring within the experimental pressure range. Here we apply these findings to icy satellite interiors, including discussion of elastic properties, modeling of ice-sulfate aggregates, and implications for tidal observations.

58 GEOSCIENCES↗
DOE OSTI2023

Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. Here we combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

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

Modification of a force field for molecular dynamics simulations of silicon etching by chlorine atoms

Here, a modified classical molecular dynamics (MD) force field is presented for the interaction between silicon (Si) and chlorine (Cl). The original version of the force field is shown to significantly overestimate the probability of Si etching by thermal Cl atoms. However, the modified force field corrects this problem and results in generally good agreement with experimental data. Further, it is shown that while the modification of the force field improves the prediction of Si spontaneous etching with Cl atoms, it does not degrade predictions of atomic-layer etching of Si with Cl[Formula: see text] molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

From bulk to surface: Structure and dynamics of amorphous alumina from deep potential molecular dynamics

Understanding the atomic-scale structure and dynamics of amorphous oxide surfaces is essential for interpreting their chemical reactivity, mechanical stability, and interfacial behavior, yet direct experimental characterization remains challenging. We employ Deep Potential (DP) molecular dynamics to generate large-scale, ab initio -quality models of amorphous Al 2 O 3 bulk glasses and melt-quenched free surfaces, enabling a quantitative analysis of both structure and relaxation dynamics with statistical confidence inaccessible to direct ab initio simulation. The trained DP model reproduces experimental liquid and glass structure, captures the cooling-rate dependence of the bulk glass transition, and corrects systematic biases in the polyhedral populations predicted by widely used classical force fields. At the free surface, mass density recovers to bulk values over ~10 Å, while local coordination requires a slightly wider subsurface region to fully converge. The outermost layer is oxygen-enriched, exhibits altered polyhedral connectivity with contracted Al–O bonds, and hosts a broad population of under-coordinated motifs (notably AlO 3 and OAl 2 ) whose abundances are governed by glass stability. These under-coordinated surface motifs exhibit distinct vibrational signatures and occur as locally paired Lewis acid and Brønsted base sites consistent with bond-valence compensation, yet remain spatially dispersed rather than aggregating into extended clusters. Despite this pronounced structural heterogeneity, surface relaxation and the glass-transition temperature remain comparable to their bulk counterparts, suggesting that the disordered surface is kinetically stable once formed. Together, these results establish a molecular-level picture of amorphous alumina surfaces and demonstrate the capability of machine-learned potentials to resolve structure–property relationships in disordered oxide interfaces.

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

Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells

Carboxysomes are protein microcompartments found in cyanobacteria, whose shell encapsulates rubisco at the heart of carbon fixation in the Calvin cycle. Carboxysomes are thought to locally concentrate CO 2 in the shell interior to improve rubisco efficiency through selective metabolite permeability, creating a concentrated catalytic center. However, permeability coefficients have not previously been determined for these gases, or for Calvin-cycle intermediates such as bicarbonate (HCO$^–_3$), 3-phosphoglycerate, or ribulose-1,5-bisphosphate. Starting from a high-resolution cryogenic electron microscopy structure of a synthetic β-carboxysome shell, we perform unbiased all-atom molecular dynamics to track metabolite permeability across the shell. The synthetic carboxysome shell structure, lacking the bacterial microcompartment trimer proteins and encapsulation peptides, is found to have similar permeability coefficients for multiple metabolites, and is not selectively permeable to HCO$^–_3$ relative to CO 2 . To resolve how these comparable permeabilities can be reconciled with the clear role of the carboxysome in the CO 2 -concentrating mechanism in cyanobacteria, complementary atomic-resolution Brownian Dynamics simulations estimate the mean first passage time for CO 2 assimilation in a crowded model carboxysome. Despite a relatively high CO 2 permeability of approximately 10 -2 cm/s across the carboxysome shell, the shell proteins reflect enough CO 2 back toward rubisco that 2,650 CO 2 molecules can be fixed by rubisco for every 1 CO 2 molecule that escapes under typical conditions. The permeabilities determined from all-atom molecular simulation are key inputs into flux modeling, and the insight gained into carbon fixation can facilitate the engineering of carboxysomes and other bacterial microcompartments for multiple applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Ion irradiation and modification: The role of coupled electronic and nuclear energy dissipation and subsequent nonequilibrium processes in materials

Understanding material responses to energy deposition from energetic charged particles is important for defect engineering, ion-beam processing, ion-beam analysis and modification, geologic aging, space exploration, and nuclear applications. As an incident ion penetrates a solid, its energy is transferred to electrons and to atomic nuclei of the solid. Much of this electronic energy deposition is subsequently transferred to the atomic structure via electron–phonon (e–ph) coupling, leading to local inelastic thermal spikes in which energy dissipation is influenced by the local environment. In addition, intense ionization can lead to high densities of localized electronic excitations in wide-bandgap materials and ceramics that can affect defect dynamics and atomic mobility. Specifically, energy exchange between electrons and atomic nuclei, along with localized electronic excitations, can lead to substantial competitive (ionization-induced annealing), additive (both electronic and nuclear energy depositions contributing to damage production), and synergistic (more damage than the sums of separate damage processes) effects. Although nonmonotonic effects of the e–ph coupling strength and athermal processes are demonstrated for pre-existing defects and residual damage during ion–solid interactions, there is limited understanding of when such electronic effects must be considered in atomic-scale models of damage production and evolution in a broad variety of materials. Complex ceramics and chemically disordered solid solution alloys with different constituent elements allow a systematic evaluation of defect dynamics and irradiation performance with increasing complexity. Current knowledge regarding tuning of bonding characteristics and chemical disorder to control atomic-level dynamics is reviewed. Although a lack of fundamental understanding obstructs the advancement of reliable predictions for ion beam material modification, it highlights challenges and opens research opportunities. Insights into the complex electronic and atomic correlations with extreme energy deposition will strengthen our ability to design materials and predict ion-irradiation-induced damage in a radiation environment, and they may pave the way to better control fundamental processes and design new material functionalities for advanced technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Real-time observation of multi-electron processes in atoms and diatomic molecules

We report on the implementation of a reliable experimental approach to observe, in real-time, electron dynamics in atoms and molecules at the attosecond time scale. The experimental approach combines a source of shape-controlled attosecond pulses, a stabilized XUV/IR interferometer for time-resolved measurements, and a multi-particle imaging system (Coltrims). In addition, we report new capabilities to control electron dynamics in quantum systems.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Iron surface corrosion in supercritical CO2 at atomic scale investigated by molecular dynamics simulations

Understanding the corrosion behavior of steels in supercritical carbon dioxide (S-CO2) is essential for ensuring the safe application of S-CO2 as a heat-transfer fluid in high-temperature energy systems, including advanced nuclear reactors. In this work, molecular dynamics (MD) simulations using ReaxFF potential are performed to explore the atomic-scale corrosion mechanisms of body-centered cubic iron (BCC-Fe) in S-CO2. The results show that CO2 molecules in S-CO2 decompose at the Fe surface, generating free C and O atoms that form Fe-C and Fe-O bonds and subsequently produce oxides and carbides. Concurrently, Fe atoms dissolve from the surface and diffuse into the S-CO2 region, resulting in interdiffusion of Fe, C and O atoms at the interface. The corrosion-layer thickness calculations show that high pressure and temperature induced by S-CO2 have stronger effects than surface orientation on the corrosion process. In addition, surface Fe atoms undergo substantial displacement under S-CO2 exposure, further accelerating corrosion. When a radiation-induced void is introduced near the Fe surface, the corrosion is enhanced. The void-matrix interface expands the reaction surface area and simultaneously induces corrosion reactions inside the bulk, resulting in a deeper penetration of C and O and thicker corrosion layers. All these results indicate that high-temperature, high-pressure and radiation-induced voids can seriously affect the corrosion of Fe in S-CO2, and must be considered to better use S-CO2 in nuclear facilities.

Li, Wenhua↗
DOE OSTI2024

Atomic-level mechanisms of short-circuit diffusion in materials

This paper reviews the recent progress in understanding the atomic mechanisms of short-circuit diffusion along materials interfaces, such as grain and interphase boundaries, as well as lattice and interfacial dislocations/disconnections. Recent atomistic computer simulations have shown that short-circuit diffusion is dominated by collective atomic rearrangements in the form of strings and rings of mobile atoms. The process is dynamically heterogeneous in space and time and has many features in common with atomic dynamics in supercooled glass-forming liquids. We discuss examples of grain boundary, interphase boundary, and dislocation diffusion in metals and alloys, including the solute effect on the diffusion rates and mechanisms. Interphase boundaries are exemplified by Al–Si interfaces with diverse orientation relationships and atomic structures. The hierarchy of short-circuit diffusion paths in materials is reviewed by comparing the rates of grain boundary, interphase boundary, and dislocation diffusion. Future directions in the field of short-circuit diffusion in defect core regions are discussed.

36 MATERIALS SCIENCE↗
NASA NTRS1972

Dynamics of the molecular and atomic mechanisms for the hydrogen-iodine exchange reaction.

The molecular and atomic mechanisms for the hydrogen-iodine exchange reaction are treated theoretically by means of extensive classical trajectories calculated on a reasonable potential energy surface on which the single adjustable parameter is the iodine-core effective charge. The analysis shows the molecular mechanism to be dynamically forbidden, but gives an over-all rate constant for the atomic mechanism that is in agreement with the experimental values. It is indicated that the formation of a weak H2I complex plays an important dynamical role if the atomic mechanism is limited to reactions with collision complexes involving no more than two hydrogen atoms and two iodine atoms. Excellent agreement with experiment is obtained for the rate constant for the recombination I+I+H2 yields I2+H2 and its negative temperature coefficient.

Raff, L. M.↗
DOE OSTI2023

Dynamic Evolution of Palladium Single Atoms on Anatase Titania Support Determines the Reverse Water–Gas Shift Activity

Research interest in single-atom catalysts (SACs) has been continuously rising. However, the lack of understanding of the dynamic behaviors of SACs during applications hinder catalyst development and mechanistic understanding. Herein, we report on the evolution of active sites over Pd/TiO 2 -anatase SAC (Pd 1 /TiO 2 ) in the reverse water-gas shift (rWGS) reaction. Combining kinetics, in-situ characterization, and theory, we show that at T ≥ 350 °C, the reduction of TiO 2 by H 2 alters the coordination environment of Pd, creating Pd sites with partially cleaved Pd-O interfacial bonds and a unique electronic structure that exhibit high intrinsic rWGS activity through the carboxyl pathway. The activation by H 2 is accompanied by the partial sintering of single Pd atoms (Pd 1 ) into disordered, flat, ~1 nm diameter clusters (Pd n ). The highly active Pd sites in the new coordination environment under H 2 are eliminated by oxidation, which, when performed at high temperature, also re-disperses Pd n and facilitates the reduction of TiO 2 . In contrast, Pd 1 sinters into crystalline, ~5 nm particles (Pd NP ) during CO treatment, deactivating Pd 1 /TiO 2 . During the rWGS reaction, the two Pd evolution pathways co-exist. The activation by H 2 dominates, leading to the increasing rate with time-on-stream, and steady-state Pd active sites similar with the ones formed under H 2 . Finally, this work demonstrates how the coordination environment and nuclearity of metal sites on a SAC evolve during catalysis and pre-treatments, and how their activity is modulated by these behaviors. These insights on SAC dynamics and structure-function relationship are valuable to mechanistic understanding and catalyst design.

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

Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data

The dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D fast Fourier transforms, correlation, and pair distribution functions are explored using the unsupervised linear unmixing, demonstrating the presence of static ordered and dynamic disordered phases and establishing their time dynamics. Here, the deep learning (DL)-based workflow is developed to analyze detailed particle dynamics and explore the evolution of local geometries. Finally, we use a combination of DL feature extraction and mixture modeling to define particle neighborhoods free of physics constraints, allowing for a separation of possible classes of particle behavior and identification of the associated transitions. Overall, this work establishes the workflow for the analysis of the self-organization processes in complex systems from observational data and provides insight into the fundamental mechanisms.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Accurate and efficient parameterization of an atomic cluster expansion (ACE) potential for ammonia under extreme conditions

We present a machine learning interatomic potential for ammonia designed to capture its complex multiphase behavior, including both molecular and superionic phases. The potential is based on the atomic cluster expansion (ACE) formulation and has been parameterized to facilitate high-fidelity molecular dynamics simulations of ammonia under extreme conditions, for pressures up to 100 GPa and for temperatures above 500 K and up to 6000 K. A diverse range of configurations was generated through high-quality ab initio molecular dynamics simulations, covering insulating and superionic ice phases, liquid ammonia, molecular nitrogen (N 2 ) and hydrogen (H 2 ), and metastable compounds that form upon dissociation, including $NH^{+}_{4}$, $H^{+}_{3}$, N 2 H 4 , and N 3 H. We demonstrate that the ammonia ACE potential accurately reproduces experimental and density functional theory predicted isotherms and Hugoniots. Crucially, the potential is able to capture the intricate phase behavior of ammonia, including the transition from insulating molecular fluid to the superionic phase. This work provides a robust interatomic potential that can be used for large-scale, accurate simulations of ammonia under extreme thermodynamic conditions, offering a powerful tool for investigating its behavior in various phases and applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗