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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Atomic Diffusion, Segregation, and Grain Boundary Migration in Nickel-Based Alloys from Molecular Dynamics Simulations

Grain boundary diffusion and metal mobility in alloys control material performance in many applications and yet remain poorly understood at a mechanistic level. With advances in accessible time and length scales for computational molecular simulations, and recent force field developments, we now possess tools to help unravel those mechanisms. Using large-scale molecular dynamics simulations, here we examined vacancy-mediated diffusion processes in Ni-5Cr alloy with low and high-energy grain boundaries. We show that atomic diffusion inside the grain boundary plane is about four times higher than bulk diffusion, at any temperature, and exhibits a typical Arrhenius behavior with a very small energy barrier (0~.8 eV for Cr and 0.7 eV for Ni within 1300-1600 K). Additionally, the fastest diffusing species inverts; Cr diffusion was faster than Ni in the bulk but slower in the grain boundaries. This is attributed to the creation of high cohesive energy clusters of Cr at the grain boundary. Grain boundary migration was also observed to be temperature dependent and appears to be two times higher in the 5% Cr alloy than in pure Ni, highlighting the important role of the alloying element on grain boundary motion.

Simonnin, Pauline GN↗
DOE OSTI2020

Reactive Molecular Dynamics Simulations and Quantum Chemistry Calculations To Investigate Soot-Relevant Reaction Pathways for Hexylamine Isomers

Sooting tendencies of a series of nitrogen-containing hydrocarbons (NHCs) have been recently characterized experimentally using the yield sooting index (YSI) methodology. This work aims to identify soot-relevant reaction pathways for three selected C6H15N amines, namely, dipropylamine (DPA), diisopropylamine (DIPA), and 3,3-dimethylbutylamine (DMBA) using ReaxFF molecular dynamics (MD) simulations and quantum mechanical (QM) calculations and to interpret the experimentally observed trends. ReaxFF MD simulations are performed to determine the important intermediate species and radicals involved in the fuel decomposition and soot formation processes. QM calculations are employed to extensively search for chemical reactions involving these species and radicals based on the ReaxFF MD results and also to quantitatively characterize the potential energy surfaces. Specifically, ReaxFF simulations are carried out in the NVT ensemble at 1400, 1600, and 1800 K, where soot has been identified to form in the YSI experiment. These simulations account for the interactions among test fuel molecules and pre-existing radicals and intermediate species generated from rich methane combustion, using a recently proposed simulation framework. ReaxFF simulations predict that the reactivity of the amines decrease in the order DIPA > DPA > DMBA, independent of temperature. Both QM calculations and ReaxFF simulations predict that C2H4, C3H6, and C4H8 are the main nonaromatic soot precursors formed during the decomposition of DPA, DIPA, and DMBA, respectively, and the associated reaction pathways are identified for each amine. Both theoretical methods predict that sooting tendency increases in the order DPA, DIPA, and DMBA, consistent with the experimentally measured trend in YSI. This work demonstrates that sooting tendencies and soot-relevant reaction pathways of fuels with unknown chemical kinetics can be identified efficiently through combined ReaxFF and QM simulations. Overall, predictions from ReaxFF simulations and QM calculations are consistent, in terms of fuel reactivity, major intermediates, and major nonaromatic soot precursors.

fuel decomposition↗
DOE OSTI2021

InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics

Interactive molecular dynamics in virtual reality (IMD-VR) simulations provide a digital molecular playground for students as an alternative or complement to traditional molecular modeling kits or 2D illustrations. Previous IMD-VR studies have used molecular mechanics to enable simulations of macromolecules such as proteins and nanostructures for the classroom setting with considerable success. Here, we present the InteraChem molecular visualizer, intended for reactive IMD-VR simulation using semiempirical and ab initio methods. InteraChem visualizes not only the molecular geometry but also (1) isosurfaces such as molecular orbitals and electrostatic potentials and (2) two-dimensional graphs of time-varying simulation quantities such as kinetic/potential energy, internal coordinates, and user-applied force. Additionally, InteraChem employs speech recognition to facilitate user interaction and introduces a novel “atom happiness” visualization using emojis to indicate the energetic feasibility of a particular bonding arrangement. Furthermore, we include a set of accompanying exercises that we have used to teach chemical reactivity in small molecular systems.

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

Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.

Hsu, Darren J.↗
DOE OSTI2021

Insights into Spontaneous Solid Electrolyte Interphase Formation at Magnesium Metal Anode Surface from Ab Initio Molecular Dynamics Simulations

Spontaneous chemical reactivity at multivalent (Mg, Ca, Zn, Al) electrode surfaces is critical to solid electrolyte interphase (SEI) formation, and hence, directly affects the longevity of batteries. Here, we report an investigation of the reactivity of 0.5 M Mg(TFSI)2 in 1,2-dimethoxyethane (DME) solvent at a Mg(0001) surface using ab initio molecular dynamics (AIMD) simulations and detailed Bader charge analysis. Based on the simulations, the initial degradation reactions of the electrolyte strongly depend on the structure of the Mg(TFSI)2 species near the anode surface. At the surface, the dissociation of Mg(TFSI)2 species occurs via cleavage of the N-S bond for the solvent separated ion pair (SSIP) and via cleavage of the C-S bond for the contact ion pair (CIP) configuration. In the case of the CIP, both TFSI anions undergo spontaneous bond dissociation reactions to form atomic O, C, S, F, and N species adsorbed on the surface of the Mg anode. These products indicate that the initial SEI layer formed on the surface of the pristine Mg anode consists of a complex mixture of multiple components such as oxides, carbides, sulfides, fluorides, and nitrides. We believe that the atomic level insights gained from these simulations will lay the groundwork for the rational design of tailored and functional interphases that are critical for the success of multivalent battery technology.

Agarwal, Garvit↗
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 OSTI2021

New insights into the mechanism governing the elasticity of calcium silicate hydrate gels exposed to high temperature: A molecular dynamics study

When exposed to fire, the integrity of cement-based materials is governed by thermally-induced changes in the mechanical properties of their binding phase, i.e., the calcium–silicate–hydrate (C–S–H) gel. However, the effect of temperature on the structure, density, and mechanical properties of C–S–H remains only partially known. Here, based on reactive molecular dynamics simulations, we reveal the nature of thermally-induced damage in C–S–H gels. In general, we show that, at the atomic scale, exposure to high temperature results in partial dehydration, volumetric shrinkage, disordering, and stiffening in the C–S–H grains. However, we show that the thermal response of C–S–H strongly depends on its chemical composition, wherein C–S–H systems associated with lower Ca/Si molar ratios are able to undergo higher temperatures before amorphization. Based on these results, we demonstrate that the stiffness of C–S–H gels (i.e., including porosity—as probed by nanoindentation) is governed by a competition between the stiffening of the grains and the decrease in packing density—wherein the latter eventually become predominant.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structure/property relationship of semicrystalline polymers during tensile deformation: a molecular dynamics approach

Molecular dynamics (MD) simulation with an ab initio numerical model is conducted to study the structure–property relationship of semicrystalline polymers during uniaxial deformation. The effects of chain length, temperature, and strain rate on mechanical properties are discussed. The influences of microstructural evolution such as bond length, entanglement density, and chain orientation are also studied quantitatively. The temperature will greatly affect the chain conformation in amorphous domains, and the results revealed that the interaction of amorphous and crystalline domains played a crucial role during stretching. Accordingly, the yielding of semicrystalline polymers follows different mechanisms at temperatures above and below T g . A melt-recrystallization scheme is observed during yielding at higher temperatures, while destruction of crystal structures is observed at lower temperatures at the yield point. The correlated effects of different temperatures and strain rates on mechanical properties are examined. This research is part of our efforts to develop a digital twin of a real experiment for efficient optimization of polymer material properties.

36 MATERIALS SCIENCE↗
NASA NTRSDate not supplied

Surrogate Fuel Chemistry from ReaxFF Molecular Dynamics

Reactive molecular dynamics with ReaxFF simulations are used to study the chemistry of four component jet fuel mixtures of n-dodecane, iso-octane, n-propylbenzene, and mesitylene. ReaxFF does not require knowledge of the chemistry a priori providing insight into reactions otherwise not seen in established chemical kinetic mechanisms. The results show that a difference in the local chemical environment can change the fuel decomposition pathways across the surrogate mixtures where the same fuel species are used. These simulations highlight the need to consider cross-chemical interactions in chemical kinetic mechanism development and the importance of resonance stabilized polyaromatic hydrocarbon reactions for soot growth and formation. A method for predicting the threshold sooting index from the carbon species formed at the end of the simulations is established. The results of the simulations are consistent with measurements of the threshold sooting index with the predicted values within 20% of the measured data

Surrogate Fuels↗
DOE OSTI2022

Pathways for Electron Transfer at MgO–Water Interfaces from Ab Initio Molecular Dynamics

The nature of electron transfer across metal oxide–water interfaces depends significantly on the band gap of the oxide and its band edge energies relative to the potentials of relevant aqueous redox couples. Here we focus on the water interface with MgO, a prototypical wide band gap oxide whose conduction band edge is close in energy to that of water. We investigate the behavior of an excess electron at and out of equilibrium near the interface using ab initio molecular dynamics based on hybrid density functional theory. Our simulations show that under equilibrium conditions the excess electron (donated by an Al impurity in MgO) localizes to a midgap defect state comparable in energy and shape to a hydrated electron in bulk water. To characterize the electron transfer from the conduction band of MgO to interfacial product states, we dope near-equilibrium configurations of the pristine MgO–water system with Al and run short trajectories of these instantaneously out-of-equilibrium systems. Here we observe two distinct products associated with the excess electron: a surface-localized electron (e surf –) and an aqueous hydrogen radical (H • ). The H • pathway exhibits a much higher activation barrier despite being more exoergic, making e surf – the kinetic product. Our characterization of the pathways on the basis of Marcus theory is consistent with the poor observed utility of MgO for water radiolysis. Moreover, we anticipate that the computational framework employed here will be broadly applicable to assessing electron transfer mechanisms at aqueous, photocatalytic interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Enhancing the formation of ionic defects to study the ice Ih/XI transition with molecular dynamics simulations

Ice Ih, the common form of ice in the biosphere, contains proton disorder. Its proton-ordered counterpart, ice XI, is thermodynamically stable below 72 K. However, the formation of ice XI is kinetically hindered, and experimentally it is obtained by doping with KOH. Doping creates ionic defects that promote the migration of protons and the associated change in proton configuration. In this article, we mimic the effect of doping with a bias potential that enhances the formation of ionic defects in molecular dynamics simulations. The recombination of the ions thus formed proceeds through fast migration of the hydroxide along hydrogen bond loops, providing a physical and expedite way to change the proton configuration. Here, a key ingredient of this approach is a machine learning potential trained with density functional theory data and capable of modelling molecular dissociation. We exemplify the usefulness of this idea by studying the order-disorder transition using an appropriate order parameter that distinguishes the proton environments in ice Ih and XI. We calculate the changes in free energy, enthalpy, and entropy associated with the transition. Our estimated entropy agrees with experiment within the error bars of the calculation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗