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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Coarse-grained molecular dynamics simulation of solvent-dependent cellulose nanofiber interactions

Associations between cellulose are important both in biofuel production and in the use of cellulose for biomaterials. Cellulose nanofibers (CNFs) are sustainable, strong, light-weight alternatives to traditional materials in manufacturing, but are challenging to obtain due to irreversible aggregation in solution during preparative fibrillation. Therefore, it is imperative to understand the underlying factors driving aggregation with a view to designing solvents that can effectively compete with interfiber interactions, hence reducing aggregation. Molecular dynamics (MD) simulation at atomic detail can provide useful information on local interactions. However, the length and timescales accessible are too short to fully capture association processes. Here, we provide a method for accessing the longer length and timescales required using coarse-grained (CG) MD simulations with a MARTINI force field to calculate the interaction behavior of CNFs in three selected solvents: NaOH-urea-water, acetone, and neat water. The CG results are consistent with our prior all-atom MD and with previous experimental results. While acetone is found not to be an effective solvent, urea and ionic moieties in NaOH-urea-water not only solvate the fibrils but also improve the confinement of water molecules around them as shown by the solvent residence times and mean-square displacements. Overall, the presence of urea and ions reduces the likelihood of aggregation in multi-CNF systems relative to neat water irrespective of whether the hydrophobic or hydrophilic CNF surfaces are interacting. In conclusion, the CG method shows clear promise for selecting potential high-performance solvents for experimental prioritization in bioenergy and biomaterials research in a relatively fast manner as well as for understanding the aggregation and rheological behavior of CNF-solvent systems.

aggregation↗
DOE OSTI2021

Modelling dust transport in DIII-D with DTOKS-Upgrade

Comprehensive upgrades to the dust transport code Dust in TOKamaks (DTOKS) that extend the plasma-dust interaction model are presented and compared with recent measurements of dust transport in DIII-D. Simulations incorporating variation in physical properties of graphite dust with temperature and size in a stationary plasma background suggest a substantial decrease in lifetimes due principally to thermal expansion. The trajectories of 53 dust grains identified from analysis of visible camera data taken across two similar shots were used to measure the dust particle velocity distributions. Dust tracks terminated mostly at the outer divertor strike point having a mean observation time of 2.1 ± 0.4 ms. Stochastic modelling of 200 graphite dust particles in the DIII-D tokamak performed with DTOKS-U using plasma simulations generated by OEDGE found similar behaviour, with particles ablating rapidly after acquiring a positive charge in the region close to the outer strike point, creating an acute source of neutral carbon atoms. The simulated mean lifetime, 11 ± 2 ms, showed approximate agreement with experimental observation when corrected by accounting for dust visibility and ignoring the longest trajectories 1.5 ± 0.2 ms. Synthetic diagnostic data generated from coupling the results of DTOKS-U with the visualisation software Calcam offers a powerful new tool for validation of simulations and predictive calculations of dust dynamics.

Physics↗
DOE OSTI2021

Bayesian force fields from active learning for simulation of inter-dimensional transformation of stanene

Abstract We present a way to dramatically accelerate Gaussian process models for interatomic force fields based on many-body kernels by mapping both forces and uncertainties onto functions of low-dimensional features. This allows for automated active learning of models combining near-quantum accuracy, built-in uncertainty, and constant cost of evaluation that is comparable to classical analytical models, capable of simulating millions of atoms. Using this approach, we perform large-scale molecular dynamics simulations of the stability of the stanene monolayer. We discover an unusual phase transformation mechanism of 2D stanene, where ripples lead to nucleation of bilayer defects, densification into a disordered multilayer structure, followed by formation of bulk liquid at high temperature or nucleation and growth of the 3D bcc crystal at low temperature. The presented method opens possibilities for rapid development of fast accurate uncertainty-aware models for simulating long-time large-scale dynamics of complex materials.

Chemistry↗
DOE OSTI2022

Advanced Physics Models for Particle-Particle Interactions (UCD final report)

The LDRD "Advanced Physics Models for Particle-Particle Interactions” collaborative research with Professor Jennifer Sinclair Curtis and PhD student Chanh Nguyen at the University of California, Davis involved meso-scale, discrete element method (DEM) modeling of micron-sized particles impacting a substrate. Using DEM, physical insight into the details of particle response upon impact can be obtained. Such details provide the type of information necessary to enhance existing continuum or macro-scale simulation tools so that modeling for material strength and particle breakage models is based on particle physics versus empirical relationships. While molecular dynamics simulations of atoms can also provide physical insight into the particle response to impact, the scale of particles that are treated is on the order of angstroms, not microns. This study gives evidence to the ability of the DEM simulation technique to provide such fundamental, detailed insight for micron-sized particles as a function of particle properties and impact velocity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Enhanced analysis of experimental x-ray spectra through deep learning

X-ray spectroscopic data from high-energy-density laser-produced plasmas has long required thorough, time-consuming analysis to extract meaningful source conditions. There are often confounding factors due to rapidly evolving states and finite spatial gradients (e.g., the existence of multi-temperature, multi-density, multi-ionization states, etc.) that make spectral measurements and analysis difficult. Here, in this paper, we demonstrate how deep learning can be applied to enhance x-ray spectral data analysis in both speed and intricacy. Neural networks (NNs) are trained on ensemble atomic physics simulations so that they can subsequently construct a model capable of extracting plasma parameters directly from experimental spectra. Through deep learning, the models can extract temperature distributions as opposed to single or dual temperature/density fits from standard trial-and-error atomic modeling at a significantly reduced computational cost compared to traditional trial-and-error methods. These NNs are envisioned to be deployed with high repetition rate x-ray spectrometers in order to provide detailed real-time analysis of experimental spectra.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Isolating Chemical Reaction Mechanism as a Variable with Reactive Coarse-Grained Molecular Dynamics: Step-Growth versus Chain-Growth Polymerization

Here we present a general approach to isolate chemical reaction mechanism as an independently controllable variable across chemically distinct systems. Modern approaches to reduce the computational expense of molecular dynamics simulations often group multiple atoms into a single “coarse-grained” interaction site, which leads to a loss of chemical resolution. In this work we convert this shortcoming into a feature and use identical coarse-grained models to represent molecules that share nonreactive characteristics but react by different mechanisms. As a proof of concept, we use this approach to simulate and investigate distinct, yet similar, trifunctional isocyanurate resin formulations that polymerize by either chain- or step-growth. Because the underlying molecular mechanics of these models are identical, all emergent differences are a function of the reaction mechanism only. We find that the microscopic morphologies resemble related all-atom simulations and that simulated mechanical testing reasonably agrees with experiment.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Modeling of Atom Interferometer Accelerometer

This report presents the theoretical effort to model and simulate the atom-interferometer accelerometer operating in a highly mobile environment. Multitudes of non-idealities may occur in such a rapidly-changing environment with a large acceleration whose amplitude and direction both change quickly. We studied the undesired effect of high mobility in the atom-interferometer accelerator in a detailed model and a simulator. The undesired effects include the atom cloud's movement during Raman pulses, the Doppler effect due to the relative movement between the atom-cloud and the supporting platform, the finite atom cloud temperature, and the lateral movement of the atom cloud. We present the relevant feed-forward mitigation strategies for each identified non-ideality to neutralize the impact and obtain accurate acceleration measurements.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics

Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent K C modulus for bilayer bending. Our results show a strong correlation with K C values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Local Electric Field Effects on Water Dissociation in Bipolar Membranes Studied Using Core–Shell Catalysts

The local electric field strength is thought to affect the rate of water dissociation (WD) in bipolar membranes (BPMs) at the catalyst–nanoparticle surfaces. Here, we study core–shell nanoparticles, where the core is metallic, semiconducting, or insulating, to understand this effect. The nanoparticle cores were coated with a WD catalyst layer (TiO2 or HfO2) via atomic layer deposition (ALD), and the morphology was imaged with transmission electron microscopy. Irrespective of the core material, these core–shell catalysts displayed comparable WD overpotentials at optimal mass loading, despite the hypothesized differences in the electric field strength across the catalyst particle suggested by continuum electrostatic simulations. Substantial atomic interdiffusion between the core and shell was ruled out by X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and diffuse reflectance optical measurements. However, the optimal mass loading of catalyst was roughly 1 order of magnitude higher for the conductive and high dielectric core materials than for the low dielectric insulating cores. These findings are consistent with the hypothesis that electric field screening within the core material focuses the electric field drop between particles such that larger film thicknesses can be tolerated. Collectively, these data support the idea that it is the local electric field at the molecular level that controls proton-transfer rates and that the metal core/dielectric-shell constructs introduced here modulate that field. Further materials and synthetic design may enable optimization of the electric field strength across the proton-transfer trajectory at the material surface.

Sarma, Prasad V↗
DOE OSTI2023

Bicrystallography-informed Frenkel–Kontorova model for interlayer dislocations in strained 2D heterostructures

In recent years, van der Waals (vdW) heterostructures and homostructures, which consist of stacks of two-dimensional (2D) materials, have risen to prominence due to their association with exotic quantum phenomena originating from correlated electronic states harbored by them. Atomistic scale relaxation effects play an extremely important role in the electronic scale quantum physics of these systems, providing means of manipulation of these materials and allowing them to be tailored for emergent technologies. We investigate such structural relaxation effects in this work using atomistic and mesoscale models, within the context of twisted bilayer graphene — a well-known heterostructure system that features moiré patterns arising from the lattices of the two graphene layers. For small twist angles, atomic relaxation effects in this system are associated with the natural emergence of interface dislocations or strain solitons, which result from the cyclic nature of the generalized stacking fault energy (GSFE), that measures the interface energy based on the relative movement of the two layers. Here, in this work, we first demonstrate using atomistic simulations that atomic reconstruction in bilayer graphene under a large twist also results from interface dislocations, although the Burgers vectors of such dislocations are considerably smaller than those observed in small-twist systems. To reveal the translational invariance of the heterointerface responsible for the formation of such dislocations, we derive the translational symmetry of the GSFE of a 2D heterostructure using the notions of coincident site lattices (CSLs) and displacement shift complete lattices (DSCLs). The workhorse for this exercise is a recently developed Smith normal form bicrystallography framework. Next, we construct a bicrystallography-informed and frame-invariant Frenkel–Kontorova model, which can predict the formation of strain solitons in arbitrary 2D heterostructures, and apply it to study a heterostrained, large-twist bilayer graphene system. Our mesoscale model is found to produce results consistent with atomistic simulations. We anticipate that the model will be invaluable in predicting structural relaxation and for providing insights into various heterostructure systems, especially in cases where the fundamental unit cell is large and therefore, atomistic simulations are computationally expensive.

2D heterostructures↗
DOE OSTI2023

Electrochemical C–N Bond Formation within Boron Imidazolate Cages Featuring Single Copper Sites

Electrocatalysis expands the ability to generate industrially relevant chemicals locally and on-demand with intermittent renewable energy, thereby improving grid resiliency and reducing supply logistics. Herein, we report the feasibility of using molecular copper boron-imidazolate cages, BIF-29(Cu), to enable coupling between the electroreduction reaction of CO 2 (CO 2 RR) with NO 3 – reduction (NO 3 RR) to produce urea with high selectivity of 68.5% and activity of 424 μA cm –2 . Remarkably, BIF-29(Cu) is among the most selective systems for this multistep C–N coupling to-date, despite possessing isolated single-metal sites. The mechanism for C–N bond formation was probed with a combination of electrochemical analysis, in situ spectroscopy, and atomic-scale simulations. We found that NO 3 RR and CO 2 RR occur in tandem at separate copper sites with the most favorable C–N coupling pathway following the condensation between *CO and NH 2 OH to produce urea. In conclusion, this work highlights the utility of supramolecular metal–organic cages with atomically discrete active sites to enable highly efficient coupling reactions.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
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 OSTI2023

Near-surface damage and mixing in Si-Cl 2 -Ar atomic layer etching processes: Insights from molecular dynamics simulations

Silicon-chlorine-argon (Si-Cl 2 -Ar) atomic layer etching (ALE) is simulated using classical molecular dynamics (MD). The simulations provide a detailed view into the near-surface region during ALE processing. Bombardment of Ar + ions creates a mixed amorphous region that significantly differs from the picture of ideal ALE. There is also a significant change in the Si etch yield and the etch product distribution as a function of Ar + ion fluence. The Si etch yield is the highest at the beginning of the bombardment step but eventually decays to the physical sputtering yield. Atomic Cl and silicon chlorides are major etch products at the start of an ion bombardment step, but quickly decay. Atomic Si yields remain relatively constant as a function of Ar + ion fluence. As a result, a new schematic of Si-Cl 2 -Ar ALE is presented in order to emphasize the complex behavior observed in MD simulations.

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

Rainbow scars: From area to volume law

Quantum many-body scars (QMBS) constitute a new quantum dynamical regime in which rare “scarred” eigenstates mediate weak ergodicity breaking. One open question is to understand the most general setting in which these states arise. In this work, we develop a generic construction that embeds a new class of QMBS, rainbow scars, into the spectrum of an arbitrary Hamiltonian. Unlike other examples of QMBS, rainbow scars display extensive bipartite entanglement entropy while retaining a simple entanglement structure. Specifically, the entanglement scaling is volume-law for a random bipartition, while scaling for a fine-tuned bipartition is subextensive. When internal symmetries are present, the construction leads to multiple, and even towers, of rainbow scars revealed through distinctive non-thermal dynamics. Remarkably, certain symmetries can lead rainbow scars to arise in translation-invariant models. To this end, we provide an experimental road map for realizing rainbow scar states in a Rydberg-atom quantum simulator, leading to coherent oscillations distinct from the strictly sub-volume-law QMBS previously realized in the same system.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Oxygen and Proton Transport in Flooded Graphene Pores with N-Dopants and Defects

Reactant transport is an important consideration in the design of ideal electrode structures. For the oxygen reduction reaction catalyzed by Pt/C in proton exchange membrane fuel cell cathodes, O 2 and H + delivery to Pt surfaces and H 2 O transport away are required. Some Pt nanoparticles may only be accessible via micropores that are too small for ionomer molecules to enter, possibly requiring flooding for H + transport. Here, to test if these “buried” Pt particles can play a role in activity through this proposed transport mechanism, we have performed atomic-scale simulations based on reactive force field molecular dynamics with an emphasis on confinement below 20 Å. Diffusion coefficients as a function of the molar concentration and local environment have been evaluated in water domains confined in two-dimensional graphene nanochannels of various channel heights representing a morphological model for micropores in proton exchange fuel cell cathodes. Our study shows that local atomic-scale structures can strongly modify H + , O 2 , and H 2 O transport rates in flooded micropores less than 20 Å in size. We find that there is a critical crossover in diffusion behavior around the 20 Å spacing with larger pores having bulk-like diffusion properties and confinement below 20 Å monotonically decreases diffusion rates. As pore size decreases, we observe locally dispersed water regions that ultimately strand reactants from long-distance transport. These findings suggest that flooded micropores may in fact be viable transport pathways for relevant reactants and products if the pore walls on opposite sides remain separated by ≥10 Å separation. Furthermore, the confinement effect is so strong that N-doping and C-vacancy defects in the C pore wall have only a minimal impact on diffusion rates and their effects are counterintuitively more apparent at larger spacings. These findings provide valuable insight regarding cathode performance and the role “stranded” catalyst particles may play in fuel cell cathodes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

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

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Automated discovery of a robust interatomic potential for aluminum

Machine learning, trained on quantum mechanics (QM) calculations, is a powerful tool for modeling potential energy surfaces. A critical factor is the quality and diversity of the training dataset. Here we present a highly automated approach to dataset construction and demonstrate the method by building a potential for elemental aluminum (ANI-Al). In our active learning scheme, the ML potential under development is used to drive non-equilibrium molecular dynamics simulations with time-varying applied temperatures. Whenever a configuration is reached for which the ML uncertainty is large, new QM data is collected. The ML model is periodically retrained on all available QM data. The final ANI-Al potential makes very accurate predictions of radial distribution function in melt, liquid-solid coexistence curve, and crystal properties such as defect energies and barriers. We perform a 1.3M atom shock simulation and show that ANI-Al force predictions shine in their agreement with new reference DFT calculations.

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

A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)- block -poly(ε-caprolactone) (PEG- b -PCL) micelles

In order to provide the means to predict from molecular dynamics (MD) simulations the structures of copolymer-based micelles in solution, we developed coarse grain force field (CGq FF) parameters for poly(ethylene glycol) (PEG) and for poly(ε-caprolactone) (PCL). A key advance here is the use of quantum mechanics to train the parameters describing the non-bonded (NB) interactions between the CG beads. The functional forms are the same as the MARTINI CG FF so standard MD codes can be used. Our CGq FF describes well the experimentally observed properties for the polymer–air and polymer–water interfaces, indicating the accuracy of the NB interactions. Additionally, the structural properties (density, radius of gyration ( R g ), and end-to-end distance ( h )) match both experiment and all atom (AA) simulations. We illustrate the application of this CGq FF by following the formation of a spherical micelle from 250 chains of PEG 23 - b -PCL 9 diblock copolymer, each block with molecular weight of 1000 Daltons (10 500 beads, corresponding to 123 250 atoms), in a water box with 119 139 water beads (426 553 water molecules).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗