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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

EDIPIC-2D

EDIPIC codes were developed for simulation of kinetic effects in low-temperature plasmas. They can be used for simulation of plasmas in electrostatic approximation and include many atomistic and plasma-surface interaction processes needed for simulations of low temperature plasmas. These codes include a detailed model of secondary electron emission induced by electrons and ions. The Monte-Carlo model of electron-neutral collisions and the Langevin model of Coulomb collisions for electrons are also implemented.

Sydorenko, Dmytro↗
DOE OSTI2024

Atomistic, macromolecular model of the Populus secondary cell wall informed by solid-state NMR

Plant secondary cell walls (SCWs) are composed of a heterogeneous interplay of three major biopolymers: cellulose, hemicelluloses, and lignin. Details regarding specific intermolecular interactions and higher-order architecture of the SCW superstructure remain ambiguous. Here, we use solid-state nuclear magnetic resonance (ssNMR) measurements to infer refined details about the structural configuration, intermolecular interactions, and relative proximity of all three major biopolymers within air-dried Populus wood. To enhance the utility of these findings and enable evaluation of hypotheses in a physics-based environment in silico, the NMR observables are articulated into an atomistic, macromolecular model for biopolymer assemblies within the plant SCW. Through molecular dynamics simulation, we quantitatively evaluate several variations of atomistic models to determine structural details that are corroborated by ssNMR measurements.

09 BIOMASS FUELS↗
DOE OSTI2025

Combined molecular and spin dynamics simulation of BCC iron with vacancy defects

Utilizing an atomistic computational model, which handles both translational and spin degrees of freedom, combined molecular and spin dynamics simulations have been performed to investigate the effect of vacancy defects on spin wave excitations in ferromagnetic iron. Fourier transforms of space- and time-displaced correlation functions yield the dynamic structure factor, providing characteristic frequencies and lifetimes of the spin wave modes. A comparison of the system with a 5% vacancy concentration with pure lattice data shows a decrease in frequency and a decrease in lifetime for all transverse spin wave excitations observed. In addition, the clearly defined transverse spin wave excitations are distorted with the introduction of vacancy defects, and we observe reduced excitation lifetimes due to increased magnon–magnon scattering. We observe further evidence of increased magnon–magnon scattering, as the peaks in the longitudinal spin wave spectrum become less distinct. Finally, similar impacts are observed in the vibrational subsystem, with a decrease in characteristic phonon frequency and flattening of lattice excitation signals due to vacancy defects.

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

Multiscale Modeling of Vinyl-Addition Polynorbornenes: The Effect of Stereochemistry

Vinyl-addition polynorbornenes are candidates for designing high-performance polymers due to unique characteristics, which include a high glass transition temperature associated with a rigid backbone. Recent studies have established that the processability and properties of these polymers can be fine-tuned by using targeted substitutions. However, synthesis with different catalysts results in materials with distinct properties, potentially due to the presence of various stereoisomers that are difficult to quantify experimentally. Herein, we develop all-atom models of polynorbornene oligomers based on classical force fields and density functional theory. To establish the relationship between chemical architecture, chain conformations, and melt structure, we perform detailed molecular dynamics simulations with the fine-tuned atomistic force field and propose simpler coarse-grained descriptions to address the high molecular weight limit. All-atom simulations of oligomers suggest high glass transition temperatures in the range of 550–600 K. In the melt state (800 K), meso chains form highly rigid extended coils (C∞≈11) with amorphous structural characteristics similar to the X-ray diffraction data observed in the literature. In contrast, simulations with racemo chains predict highly helical tubular chain conformations that could promote assembly into crystalline structures.

Polymer Science↗
DOE OSTI2021

Microstructural impacts on ionic conductivity of oxide solid electrolytes from a combined atomistic-mesoscale approach

Abstract Although multiple oxide-based solid electrolyte materials with intrinsically high ionic conductivities have emerged, practical processing and synthesis routes introduce grain boundaries and other interfaces that can perturb primary conduction channels. To directly probe these effects, we demonstrate an efficient and general mesoscopic computational method capable of predicting effective ionic conductivity through a complex polycrystalline oxide-based solid electrolyte microstructure without relying on simplified equivalent circuit description. We parameterize the framework for Li 7- x La 3 Zr 2 O 12 (LLZO) garnet solid electrolyte by combining synthetic microstructures from phase-field simulations with diffusivities from molecular dynamics simulations of ordered and disordered systems. Systematically designed simulations reveal an interdependence between atomistic and mesoscopic microstructural impacts on the effective ionic conductivity of polycrystalline LLZO, quantified by newly defined metrics that characterize the complex ionic transport mechanism. Our results provide fundamental understanding of the physical origins of the reported variability in ionic conductivities based on an extensive analysis of literature data, while simultaneously outlining practical design guidance for achieving desired ionic transport properties based on conditions for which sensitivity to microstructural features is highest. Additional implications of our results are discussed, including a possible connection between ion conduction behavior and dendrite formation.

25 ENERGY STORAGE↗
DOE OSTI2020

Simulation of Inelastic Neutron Scattering Spectra Directly from Molecular Dynamics Trajectories

Inelastic neutron scattering (INS) is a widely used technique to study atomic and molecular vibrations. With the increasing complexity of materials and thus the INS spectra, being able to simulate the spectra from various atomistic models becomes an essential step and also a major bottleneck for INS data analysis. The conventional approach using density functional theory and lattice dynamics often falls short when the materials of interest are complex (e.g., defective, disordered, heterogeneous, amorphous, large-scale), for which molecular dynamics driven by an interatomic force field is a more common approach. In this paper, we demonstrate a method to directly convert molecular dynamics trajectories into simulated INS spectra, including not only fundamental but also higher order excitations. In this work, the results are compared with data collected on various representative samples from different neutron spectrometers. This development will open great opportunities by providing the key tool to perform in-depth analysis of INS data and to validate and optimize computer models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRSDate not supplied

REACTER: A Heuristic Method for Reactive Molecular Dynamics

REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.

polymer simulations, molecular dynamics↗
DOE OSTI2020

A comparative study of the effectiveness of empirical potentials for molecular dynamics simulations of borosilicate glasses

Despite their practical importance, atomistic modeling of B 2 O 3 containing glasses have been challenging due to the lack of reliable empirical potentials. Fortunately, a few recent developments have shown promises to simulate these glasses where the boron coordination has complex and non-linear dependence on glass composition. This work aims to provide an evaluation of the effectiveness of three recently developed potentials by a systematic study of a series (~20) of sodium borosilicate glasses with constant K (ratio of [SiO 2 ]/[B 2 O 3 ]) =2 and varying R (ratio of [Na 2 O]/[B 2 O 3 ] ranging from 0.1 to 4) values and several sodium boroaluminosilicate glasses. A comparative assessment was established on the basis of the short- and medium-range structure features, such as boron N 4 values, total correlation functions, bond angle distribution, oxygen speciation, and mechanical properties using experimental or well-established models as criteria. Furthermore, this work provides insights on the choices of empirical potentials for MD simulations of borosilicate glasses and gives directions of future potential development and refining.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Effects of surface vacancy-adatom pair formation on PFC tungsten surface morphological response

Abstract We report a simulation study of the effect of He-irradiation-induced surface vacancy-adatom pair formation on the surface morphological evolution of plasma-facing component (PFC) tungsten and examine a number of factors that impact such evolution. Our analysis is based on self-consistent dynamical simulations according to an atomistically-informed, continuum-scale surface evolution model that has been developed following a hierarchical multiscale modeling strategy and can access the spatiotemporal scales of relevance to fuzz formation. The model accounts for the flux of surface adatoms generated as a result of the surface vacancy-adatom pair formation effect upon He implantation, which contributes to the anisotropic growth of surface nanostructural features due to the different rates of adatom diffusion along and across step edges of islands on the tungsten surface. We have carried out atomic-scale computations of optimal diffusion pathways along and across island step edges on the W(110) surface and calculated Ehrlich–Schwoebel (ES) barriers in adatom diffusion along and across such step edges. This aspect of surface adatom diffusion contributes to anisotropic surface atomic fluxes, terrace and step diffusive currents, and has been incorporated into our PFC surface evolution model, which predicts the formation of preferentially aligned nanoridge stripe patterns on the PFC surface. We establish that these anisotropic diffusive currents accelerate nanotendril growth on the PFC surface and the onset of surface nanostructure pattern formation. We also explore systematically the dependence of the PFC surface morphological response on the surface temperature and He ion incident flux, characterize in detail the resulting surface topographies and growth kinetics, and compare the predicted surface morphologies with experimental observations. Our simulation predictions for the emerging surface nanostructure patterns under certain plasma exposure conditions are consistent with experimental findings in the literature.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Te/CdTe and Al/CdTe Interfacial Energy Band Alignment by Atomistic Modeling

A synergistic approach that incorporates first-principles atomistic modeling with numerical device simulations is used to systematically evaluate the role of heterointerfaces within metal-chalcogenide-based photovoltaic technologies. Two interfaces involving either a tellurium back contact or aluminum back electrode combined with a cadmium telluride absorber layer within cadmium-telluride-based thin-film solar cells are investigated on an atomic scale to determine the mechanisms contributing to variations in device performance. Electronic structures and predicted charge transport behavior with respect to cadmium and tellurium termination of the absorber layer are studied along the polar oriented CdTe{111} facets. The computational methodology reveals a noticeable contrast between the Schottky barrier forming Al/CdTe interface versus the Type I Te/CdTe heterojunction. Greater band bending features are exhibited by the cadmium termination as opposed to the tellurium termination for each interface case. Subsequent device modeling suggests that 3.6% higher photovoltaic conversion efficiency is achievable for the cadmium termination relative to the tellurium termination of the Te/CdTe interface. Based strictly on an idealistic representation, both interface models show the importance of atomic-scale interfacial properties for cadmium telluride solar cell device performance with their bulk properties being validated in comparison to published experimental data. Here, the synergistic approach offers a suitable method to analyze solar cell interfaces through a predictive computational framework for the engineering and optimization of metal-chalcogenide-based thin-film photovoltaic technologies.

Green’s function↗
DOE OSTI2026

When does global attention help: a unified empirical study on atomistic graph learning

Graph neural networks (GNNs) are widely used as surrogates for costly experiments and first-principles simulations to study the behavior of compounds at atomistic scale, and their architectural complexity is constantly increasing to enable the modeling of complex physics. While most recent GNNs combine more traditional message passing neural networks (MPNNs) layers to model short-range interactions with more advanced graph transformers (GTs) with global attention mechanisms to model long-range interactions, it is still unclear when global attention mechanisms provide real benefits over well-tuned MPNN layers due to inconsistent implementations, features, or hyperparameter tuning. We introduce the first unified, reproducible benchmarking framework–built on HydraGNN–that enables seamless switching among four controlled model classes: MPNN, MPNN with chemistry/topology encoders, GPS-style hybrids of MPNN with global attention, and fully fused localglobal models with encoders. Using seven diverse open-source datasets for benchmarking across regression and classification tasks, we systematically isolate the contributions of message passing, global attention, and encoder-based feature augmentation. Our study shows that encoder-augmented MPNNs form a robust baseline, while fused localglobal models yield the clearest benefits for properties governed by long-range interaction effects. We further quantify the accuracycompute trade-offs of attention, reporting its overhead in memory. Together, these results establish the first controlled evaluation of global attention in atomistic graph learning and provide a reproducible testbed for future model development.

Equivariant graph neural networks↗
DOE OSTI2022

Investigation of fracture in porous materials: a phase-field fracture study informed by ReaxFF

Microscopic features (e.g, pore shapes, sizes, and distribution) in porous material substantially affect the overall mechanical properties such as stiffness and strength. In turn, these material properties determine the macroscopic behaviors of fracture in the porous material. In certain cases, macroscopic properties can be derived from the porous skeleton and void ratio (i.e., porosity), but in many other cases, such derivation is a challenging task. This paper presents a numerical investigation of microporosity and micropore shapes effect on the macrofracture behavior in porous amorphous silica. For this study, we extend the recently-proposed combined molecular dynamic (MD) and phase-field (PF) fracture modeling approach by including different pore shapes in the atomistic domain. In the MD simulations, we adopt ReaxFF to evaluate the material properties, where four different micropore cases are considered. Based on the material properties derived from MD simulations, the macrofracture propagation of porous media is studied using hybrid PF simulation. In the characterization of the pore structure, the concept of pore ligament is proposed to relate the pore shape and the critical energy release rate. Two classical fracture problems were used to evaluate the effect of pore shape on the macrofracture behavior. The results of the case study show that although the micropore shapes change the macrofracture behaviors, these effects vary with the geometry and loading conditions of macroscopic boundary value problems. Furthermore, the case study also shows that the influence of micropore structure can be captured at the macroscopic level through the material properties derived from the MD simulations.

42 ENGINEERING↗
DOE OSTI2021

Influence of Hydrogen Isotopes on Vacancy Formation and Antisite Defect Diffusion in Palladium and Vanadium Metals

Density functional theory calculations are performed to study the interaction between hydrogen isotopes, vacancy, and antisite defects in Pd and V. Various defect configurations and defect-defect distances are systematically explored. Binding energies and migration energy barriers are calculated and tabulated. The study provides atomistic data for subsequent mesoscale simulations of tritium, vacancy, and antisite diffusion. In Pd, a strong binding is found between a vacancy and tritium (0.16 eV). This tritium binding increases the thermal concentration of vacancies by a factor of ~10 at 500 ?C. The increase in vacancy concentration enhances V antisite diffusion in Pd by a factor of ~6 at 500 ?C. The influence of tritium is even stronger in V, with a tritium and vacancy binding energy of 0.38 eV. Such a strong binding increases the thermal concentration of vacancies by a factor of ~300 at 500 ?C. The increase in vacancy concentration enhances Pd antisite diffusion in V by a factor of ~640 at 500 ?C. Vanadium and Pd exhibit a strong driving force to intermix with a formation energy of -1.57 eV for V antisite in Pd and -1.05 eV for Pd antisite in V. The results suggest vanadium diffusion into Pd is energetically stronger than the reverse. Zero-point-energy corrections are taken into account and calculations for hydrogen and tritium are presented.

Setyawan, Wahyu↗
DOE OSTI2024

New insights on the effects of chemistry and temperature on α’ precipitation during aging of FeCrAl alloys

Here, the effect of Al on α' precipitation in FeCrAl alloys was studied through thermal aging of several model binary FeCr and FeCrAl alloys with Cr content of 13 wt.%, 17 wt.%, and 25 wt.% with and without 5.5 wt.% Al. Aging was performed up to 1,000h at varying temperatures from 400-500°C. At 400°C no age hardening was observed due to slow kinetics at this temperature. For both the 17Cr and 25Cr alloys, the addition of Al shows a lowering of the miscibility gap, consistent with other reports in literature. Interestingly, however, for the 25Cr alloys the addition of Al in the FeCrAl ternary alloy accelerated α' precipitation below the miscibility gap. Such enhanced precipitation has also been predicted by our atomistic kinetic Monte Carlo (AKMC) simulations. While previous literature has often focused on Al suppressing α', here we show that while Al can lower the miscibility gap in the Fe-Cr ferritic system thermodynamically, it may also enhance the kinetics of precipitation.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins

Here, we outline recent developments in artificial intelligence (AI) and machine learning (ML) techniques for integrative structural biology of intrinsically disordered proteins (IDP) ensembles. IDPs challenge the traditional protein structure-function paradigm by adapting their conformations in response to specific binding partners leading them to mediate diverse, and often complex cellular functions such as biological signaling, self-organization and compartmentalization. Obtaining mechanistic insights into their function can therefore be challenging for traditional structural determination techniques. Often, scientists have to rely on piecemeal evidence drawn from diverse experimental techniques to characterize their functional mechanisms. Multiscale simulations can help bridge critical knowledge gaps about IDP structure-function relationships - however, these techniques also face challenges in resolving emergent phenomena within IDP conformational ensembles. We posit that scalable statistical inference techniques can effectively integrate information gleaned from multiple experimental techniques as well as from simulations, thus providing access to atomistic details of these emergent phenomena.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Origin and Suppression of Beam Damage-Induced Oxygen-K Edge Artifact from γ-Al 2 O 3 using Cryo-EELS

Gamma-alumina (γ-Al 2 O 3 ), like other low-Z oxides, is readily damaged when exposed to an electron beam. This typically results in the formation of a characteristic pre-edge peak in the oxygen-K edge of electron energy-loss spectra (EELS) acquired during or after the damage process. This artifact can mask the presence of intrinsic O-K edge fine structure that would reveal chemical properties of the material; therefore, its suppression is key. In this work, we systematically investigate the conditions that give rise to the damage-induced O-K pre-edge peak and show that it can be effectively suppressed by performing EELS experiments at cryogenic (cryo) temperatures. Prolonged exposure of γ-Al 2 O 3 to a focused electron beam results in a hole bored through the sample; this was used as a reproducible beam damage condition. O-K edge EELS spectra were collected from a single-crystal γ-Al 2 O 3 sample both during and after focused 2 electron beam hole drilling, and at room and cryo temperatures, using a monochromated scanning transmission electron microscope (STEM). Furthermore, the characteristic 531 eV pre-edge peak visible in the room temperature EELS spectra was completely suppressed in the cryo-EELS spectra, even in the presence of a visible drilled hole. We then correlated these experimental observations with multiple-scattering EELS simulations to determine the likely atomistic origin of the damage-induced O-K pre-edge peak. The findings indicate that the pre-edge peak is caused primarily by the presence of surface O dimer (O-O) bonds formed during beam damage, and that operating at cryo temperature suppresses the formation of surface O-O bonds, thus preventing formation of the O-K pre-edge peak. Additionally, Al-L 2,3 edge EELS spectra revealed Al loss primarily from tetrahedral sites during hole drilling.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Confinement-Driven Heterogeneous Benzene Crystallization in Silica Nanopores

Nanoconfinement alters the thermodynamics, dynamics, and kinetics of fluids hosted in nanoscale solid nanopores to an extent that depends on the characteristics of the confining space and the chemistry of the confined fluids. Confinement-induced alterations in the phase behavior of confined energetic fluids under high pressure or low temperature are highly relevant to subsurface and subsea phenomena such as fluid flow in porous media, hydrate formation and dissociation, and gas storage capacity. Although extensive efforts have been directed toward understanding the phase behavior of confined fluids, the role of solid-liquid interfaces in the phase transitions of organic liquids has not been resolved yet. Here, we explore the onset and growth of benzene crystallization confined in 6 nm sized SBA-15 silica nanopores in the temperature range 300-200 K using in situ extended range small-angle and wide-angle X-ray scattering (SAXS/WAXS) measurements and atomistic classical molecular dynamics (MD) simulations. The crystallization onset of confined benzene depresses to 265 K compared to the freezing point of bulk benzene ( ~278 K), followed by the continuous growth of the emerged crystals in the pore space with complete crystallization at 200 K. The orientation of the emerged benzene crystals is dominated by parallel (π-π stacking) and perpendicular (T-shape stacking) orientations along the cylindrical pore radius and pore length, respectively. The onset of benzene crystals occurs heterogeneously on the pore surface and grows continuously toward the pore center. Further, confined benzene undergoes a dynamical crossover from fragile to strong dynamics behavior, inferred from the rotational and translational diffusion. The insights provided by this study have significant implications for the phase transitions of confined organic liquids that are relevant to a wide range of applications in the biological, geological, environmental, and chemical fields.

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

Structural Properties of [N1888][TFSI] Ionic Liquid: A Small Angle Neutron Scattering and Polarizable Molecular Dynamics Study

In this study, we investigate the quaternary ammonium-based ionic liquid (QAIL), methyltrioctylammonium bis(trifluoromethylsulfonyl)imide, [N 1888 ][TFSI], utilizing small angle neutron scattering (SANS) measurements and polarizable molecular dynamics (MD) simulations to characterize the shortand long-range liquid structure. Scattering structure factors show signatures of three length scales in reciprocal space indicative of alternating polarity (k ~ 0.44 Å –1 ), charge (k ~ 0.75 Å –1 ), and neighboring or adjacent (k ~ 1.46 Å –1 ) domains. Excellent agreement between simulation and experimental scattering structure factors validates various simulation analyses that provide detailed atomistic characterization of the different length scale correlations. The first solvation shell structure is illustrated by obtaining radial, angular, dihedral, and combined distribution functions, where two dominant spatial motifs, N + ···N – and N + ···O – , compete for optimal packing around the polar head of the [N 1888 ] + cation. Intermediate and long-range structures are governed by the balance between local electroneutrality and octyl chain networking, respectively. By computing the charge-correlation structure factor, S ZZ , and the spatial extent of the octyl chain network using graph theory, the bulk-phase structure of [N 1888 ][TFSI] is characterized in terms of electrostatic screening and apolar domain formation length scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗