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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 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Molecular Dynamics Simulations of Supercritical Carbon Dioxide and Water using TraPPE and SWM4-NDP Force Fields

The increased levels of carbon dioxide (CO 2 ) emissions due to the combustion of fossil fuels and the consequential impact on global climate change have made CO 2 capture, storage, and utilization a significant area of focus for current research. In most electrochemical CO 2 applications, water is used as a proton donor due to its high availability and mobility and use as a polar solvent. Additionally, supercritical CO 2 is a promising avenue for electrochemical applications due to its unique chemical and physical properties. Consequently, understanding the interactions between water and supercritical CO 2 is of great importance for future electrochemical applications. Molecular dynamics (MD) simulation is a powerful tool that enables atomistic-resolution dynamics of molecular systems, which can complement and guide future experimental investigations. This study employed atomistic MD to study the cosolubilities, codiffusivities, and structure of supercritical CO 2 and water systems, with a polarizable water model (SWM4-NDP) and a nonpolarizable CO 2 model (TraPPE). Additionally, ab initio MD simulations were used to better understand how atomistic polarizable/nonpolarizable models compare to explicit modeling of electron densities. The polarizable water model exhibited substantial improvement in water-associated properties. In conclusion, we anticipate the development of a compatible polarizable CO 2 model to yield similar improvement, providing a pathway for realizing novel high-pressure electrochemical systems.

25 ENERGY STORAGE↗
DOE OSTI2023

Nucleation-mediated reshaping of facetted metallic nanocrystals: Breakdown of the classical free energy picture

Shape stability is key to avoiding degradation of performance for metallic nanocrystals synthesized with facetted non-equilibrium shapes to optimize properties for catalysis, plasmonics, and so on. Reshaping of facetted nanocrystals is controlled by the surface diffusion-mediated nucleation and growth of new outer layers of atoms. Here, Kinetic Monte Carlo (KMC) simulation of a realistic stochastic atomistic-level model is applied to precisely track the reshaping of Pd octahedra and nanocubes. Unexpectedly, separate constrained equilibrium Monte Carlo analysis of the free energy profile during reshaping reveals a fundamental failure of the classical nucleation theory (CNT) prediction for the reshaping barrier and rate. Why? Nucleation barriers can be relatively low for these processes, so the system is not locally equilibrated before crossing the barrier, as assumed in CNT. This claim is supported by an analysis of a first-passage problem for reshaping within a master equation framework for the model that reasonably captures the behavior in KMC simulations.

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

Mapping the structural–mechanical landscape of amorphous carbon with ReaxFF molecular dynamics

We use ReaxFF molecular dynamics (MD) to investigate the relationship between structural and mechanical properties in bulk and nanostructured amorphous carbon (a-C). The liquid-quench MD method is used to generate isotropic bulk samples with mass densities ranging from 0.96 to 3.29 g/cm3. Structural analysis identifies two types of structures with distinct short- and medium-range order: lower-density sp2-dominated a-C, which is characterized by a bimodal ring-size distribution, and higher-density sp3-dominated tetrahedral amorphous carbon (ta-C), exhibiting a unimodal ring-size distribution. Stress–strain MD simulations and analysis reveal how an atomistic structure impacts elastic properties and post-yield atomic rearrangements. All stretched structures demonstrate elastic isotropy and plasticity driven by a ring-size expansion mechanism reflected in changes in ring statistics. The plastic region is substantially larger in ta-C than in a-C due to the post-yield shift from sp3 to sp2 C dominant bonding. In both a-C and ta-C, ultimate failure occurs when a reactive crack, traversed by long sp chains, forms and propagates predominantly perpendicular to the direction of the applied strain. Oxygen infiltration into the fractured region significantly reduces stress resistance, primarily through the early rupture of long sp chains. MD simulations and analysis are extended to a-C slabs, a-C nanotubes, and partially a-C nanotubes. The latter nanostructure highlights the differences between the elastically isotropic a-C walls, which develop circumferential cracking, and the crystalline walls, which tear along crystallographic directions. These results provide a strong foundation for further computational characterization of a-C materials.

Dernov, A. (ORCID:0009000004220973)↗
DOE OSTI2022

ezAlign

The ezAlign is aimed at clustering coarse grain simulation to find common or uncommon occurrences and convert coarse (CG) grained coordinate and topology files to atomistic formats. We use a PointNet based approach to map individual frames of simulation to points in a latent space. These points are then clustered using a variety of clustering methods. Clusters are analyzed to associate them with states in the simulation. Frames can be chosen from these clusters based on proximity to cluster centers. ezAlign takes CG coordinate and topology files and converts and outputs their corresponding atomistic formats using an alignment and relaxation procedure. ezAlign is designed to convert complex, solvated biological systems including lipid membranes with drug-like molecules using GROMACS. A GROMACS checkpoint (.cpt) file is also outputted to enable continuation simulations that retain the equilibrated atomic velocities. Independent atomistic coordinates and topologies for every molecule must already be included in ezAlign/files. A number of commonly simulated biological molecules are currently provided.

Bennett, WilliamF.↗
DOE OSTI2026

Rotation of Crystal Seed During Early Stages of Growth Reveals the Anisotropy of Glass Matrix

Glass-ceramics are a highly valuable class of materials that are needed for realizing many high-tech as well as consumer products. They are made by controlling crystallization of glass. Theoretical atomistic insights obtained using molecular dynamics simulations in this work reveal that crystal seeds can spontaneously rotate within glass at high temperatures due to anisotropic forces at the glass-crystal interface. This rotation challenges the long‐held view of glass as isotropic solid, and highlights how atomic‐scale inhomogeneities influence crystal growth and microstructure, hence the physical properties glass‐ceramics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Deciphering the non-linear impact of Al on chemical durability of silicate glass

The role of Al in aluminosilicate glasses remains somewhat a mystery: at low concentrations, it increases the resistance to hydrolysis of the glass, whereas at high concentrations an opposite effect is observed. To understand the origin of the phenomenon on a fundamental atomistic scale, we performed 577 MD simulations and applied potential mean force (PMF) calculations to estimate the activation barriers for hydrolysis and to statistically correlate them with local structural features of the glass. Models of pure silicate and aluminosilicate glasses are constructed and investigated. PMF simulation results are further validated by the experimental measurements and revealed that Al is very easy to dissociate, but it also increases the glass chemical durability through significantly increasing both the strength of Si and network connectivity of the glass. In contrast, at high Al concentration, preferential dissolution of Al weakens the silicate network, which it supposes to strengthen, and so the glass resistance becomes poor. Through PMF calculations, we evaluated the activation barriers for dissociating bonds around Al as 0.49 eV, which is less than a half of the energy to dissociate bonds around Si in pure silicate (1.22 eV) and around Si in aluminosilicate glass (1.34 eV), all these energy differences being statistically significant. Molecular structural level investigation revealed that Si with Al as a second neighbor in the glass network has a significantly higher activation energy for dissociation than Si in pure silicate glass. Furthermore, the proposed approach opens the way to the development of quantitative predictive models of glass durability.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Resonant interaction between phonons and PbTe/PbSe (001) misfit dislocation networks

Here this work aims at a quantitative and mechanistic understanding of the dynamic process of the phonon-dislocation interaction in PbTe/PbSe (001) heterostructures using the Concurrent Atomistic-Continuum (CAC) method as the simulation tool. The misfit dislocation network and the atomic-scale dislocation core structure obtained in the simulations are found to agree reasonably well with the experimental observations of the PbTe/PbSe (001) interface. Through visualizing the dynamic interaction between phonons and dislocations, as well as quantifying the dislocation vibration amplitude, the phonon energy transmission, and the thermal resistance of the misfit interfaces, this work has illustrated and quantified two mechanisms for phonon-dislocation interaction: (1) phonon scattering by the strain field of dislocations, and (2) phonon scattering by dislocations that vibrate via the local modes of a dislocation network; the latter, leads to resonant phonon-dislocation interaction, which is manifested as local maxima of out-of-phase vibration of the atoms on the two sides of the slip plane, leading to local minima of the energy transmission in the heterostructure that contains one interface. The local vibrational modes are found to be excited only by shear stress induced by transverse phonons. Among various resonant modes, the one with the lowest frequency has the strongest effect. This work has also demonstrated the collective motion of dislocations under ultrafast phonon pulses. In addition, the dynamic properties of the misfit dislocation network localized within one interface are found to be significantly altered by the presence of misfit dislocations at other interfaces, thus further confirming the cooperative dynamic nature of the motion of dislocations and phonons.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Stress-dominated growth of two-dimensional materials on nonplanar substrates

Curved features are ubiquitous on solid surfaces, but the effect of surface curvatures on growth of two-dimensional (2D) materials has not yet been established. Using a newly developed method based on the Metropolis algorithm and taking graphene as a prototype, we find that a curved feature on substrates can result in a variety of topological defects in 2D materials. As the feature's size increases by just nanometers, the defects can vary from adatoms, dislocation pairs, and grain boundary scars to long-range grain boundaries, in contrast to previously reported defect-free modes of rigid colloidal crystals growing on spheres. We identify an important role of curvature-induced lattice stress in lowering the growth rate over the curved features and driving a plastic instability in the materials. When the feature's size increases to several nanometers, the stress effect is compromised by an enhanced effect of geodesic curvature, yielding long-range grain boundaries as a result of increased local growth rate on the feature with respect to that on flat regions. Here we further provide a ‘phase diagram’ of defects that helps to guide a rational choice of geometrical parameters of features towards the growth of high-quality 2D materials as well as controllable creation of topological defects.

36 MATERIALS SCIENCE↗
DOE OSTI2025

From Micro-environments to Macroscopic Effects: How the Alkaline Hydrogen Evolution Reaction Drives Cu Cathodic Corrosion

Cathodic corrosion of copper (Cu) has posed a significant challenge for over a century, impeding various technological progresses such as electrochemical conversion of CO 2 (eCO 2 RR) into fuels and other value-added carbon products. Here, in this study, employing a combined Density Functional Theory (DFT) and kinetic Monte Carlo (kMC) simulation approach, we delve into the atomistic level mechanism driving this phenomenon in Cu. Our hypothesis posits the pivotal role of alkaline hydrogen evolution reaction (HER) in facilitating cathodic corrosion in Cu. We rigorously develop a pH-dependent hydroxide (OH) adsorption mechanism and calculate the equilibrium OH coverage (𝜃 OH ) at varying pH levels, the thermodynamic stability of subsurface oxygen (O sub ), as well as the Cu-vacancy mediated diffusion of subsurface oxygens (O sub ). Through comprehensive analysis, we establish correlation among various microenvironments, including oxygen diffusion in subsurface layers, pH-dependent OH adsorption, and Cu dissolution into the electrolyte as (Cu-OH) complexes. Furthermore, our investigation explores the correlation between surface coordination environment of active sites and cathodic corrosion of Cu. Finally, by integrating DFT-derived thermodynamic data into a kMC model, we successfully predict the formation of experimentally observed corrosion pits on Cu-surfaces. This combined approach not only advances our fundamental understanding of Cu cathodic corrosion but also offers insights crucial for developing effective corrosion mitigation strategies.

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

Lithium crystallization at solid interfaces

Understanding the electrochemical deposition of metal anodes is critical for high-energy rechargeable batteries, among which solid-state lithium metal batteries have attracted extensive interest. A long-standing open question is how electrochemically deposited lithium-ions at the interfaces with the solid-electrolytes crystalize into lithium metal. Here, using large-scale molecular dynamics simulations, we study and reveal the atomistic pathways and energy barriers of lithium crystallization at the solid interfaces. In contrast to the conventional understanding, lithium crystallization takes multi-step pathways mediated by interfacial lithium atoms with disordered and random-closed-packed configurations as intermediate steps, which give rise to the energy barrier of crystallization. This understanding of multi-step crystallization pathways extends the applicability of Ostwald’s step rule to interfacial atom states, and enables a rational strategy for lower-barrier crystallization by promoting favorable interfacial atom states as intermediate steps through interfacial engineering. Our findings open rationally guided avenues of interfacial engineering for facilitating the crystallization in metal electrodes for solid-state batteries and can be generally applicable for fast crystal growth.

25 ENERGY STORAGE↗
DOE OSTI2023

Computational investigation of hysteresis and phase equilibria of n-alkanes in a metal-organic framework with both micropores and mesopores

Abstract Adsorption hysteresis is a phenomenon related to phase transitions that can impact applications such as gas storage and separations in porous materials. Computational approaches can greatly facilitate the understanding of phase transitions and phase equilibria in porous materials. In this work, adsorption isotherms for methane, ethane, propane, and n-hexane were calculated from atomistic grand canonical Monte Carlo (GCMC) simulations in a metal-organic framework having both micropores and mesopores to better understand hysteresis and phase equilibria between connected pores of different size and the external bulk fluid. At low temperatures, the calculated isotherms exhibit sharp steps accompanied by hysteresis. As a complementary simulation method, canonical (NVT) ensemble simulations with Widom test particle insertions are demonstrated to provide additional information about these systems. The NVT+Widom simulations provide the full van der Waals loop associated with the sharp steps and hysteresis, including the locations of the spinodal points and points within the metastable and unstable regions that are inaccessible to GCMC simulations. The simulations provide molecular-level insight into pore filling and equilibria between high- and low-density states within individual pores. The effect of framework flexibility on adsorption hysteresis is also investigated for methane in IRMOF-1.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Machine learning using host/guest energy histograms to predict adsorption in metal–organic frameworks: Application to short alkanes and Xe/Kr mixtures

A machine learning (ML) methodology that uses a histogram of interaction energies has been applied to predict gas adsorption in metal–organic frameworks (MOFs) using results from atomistic grand canonical Monte Carlo (GCMC) simulations as training and test data. In this work, the method is first extended to binary mixtures of spherical species, in particular, Xe and Kr. In addition, it is shown that single-component adsorption of ethane and propane can be predicted in good agreement with GCMC simulation using a histogram of the adsorption energies felt by a methyl probe in conjunction with the random forest ML method. Here, the results for propane can be improved by including a small number of MOF textural properties as descriptors. We also discuss the most significant features, which provides physical insight into the most beneficial adsorption energy sites for a given application.

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

Pressure-induced polyamorphic transition in CaA l 2 O 4 glass

In situ high-pressure ultrasonic velocity measurements of CaAl 2 O 4 glass reveal abrupt irreversible discontinuities in the elastic wave velocities at ~8–10 GPa. Total structure factor and pair distribution functions measured by synchrotron x-ray diffraction show a rapid change in the intermediate range structure attributed to a rearrangement of calcium ions over this narrow pressure region. Atomistic models obtained from molecular dynamics simulations reveal that this intermediate range structure is explained by a transition of Ca–O void radius distribution from a bimodal distribution with peaks at ~2.1 and ~2.4 Å to a single distribution centered at ~2.1 Å. Further, these abrupt structural changes involving the rapid increase in elastic wave velocity are markedly different to the continuous transformations observed in conventional network-forming glasses, such as SiO 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Processes at lithium-hydride/deuteride surfaces upon low energy impact of H/D

Sputtering, reflection, and retention processes at amorphous and crystalline lithium hydride surfaces due to impact of low energy (1–100 eV) hydrogen and deuterium atoms over the range of 0 o −85 o angle of incidence at 300 K surface temperature were investigated by atomistic computational methods. Classical molecular dynamics simulations were performed with improved reactive bond-order force field (ReaxFF) potentials that include long-range polarization effects. In addition to probabilities of surface processes, the energy and angular spectra of ejected particles were obtained. Comparison of these results with those previously obtained on pristine lithium surfaces indicates the importance of saturation of the Li surface and near-surface region with hydrogen. We show that such saturation, which is typical in both laboratory and fusion device experiments with lithium coating of the plasma-facing surfaces, significantly changes the surface processes with hydrogen irradiation in the understudied low-energy region of impact energies.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV

The design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications.

Conti, Simone (ORCID:000000017986567X)↗
DOE OSTI2025

Combining Reactive Quantum-Mechanical Molecular-Dynamics Simulations with Mutagenesis, Crystallography, and Enzyme Kinetics to Reveal Plausible Steps of Isocyanide Hydratase Catalysis

A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but trade-offs between accuracy and computational cost have limited their use. We previously developed extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) methods that leverage a negligible compromise in accuracy to substantially decrease the cost of QMD simulations. Here, we develop a reactive QMD approach using the latest XL-BOMD formulation, which enables efficient simulations of highly reactive systems, and use it to investigate mechanisms of intermediate formation in isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenyl isocyanide, forming a thioimidate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation and suggested a possible role of Asp17 as a proton donor in the early phase of ICH catalysis. To test whether the pathway seen using the reactive QMD approach might be relevant to ICH catalysis, we performed X-ray crystallography and pre-steady-state enzyme kinetics studies of wild-type and D17N mutant ICH. Both the structure and kinetics are sensitive to the D17N mutation in a manner that is consistent with the order of the reaction steps seen in the simulations. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate model reactions for the design of experiments that provide information about enzyme mechanisms involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Creation of an Fe 3 P Schreibersite Density Functional Tight Binding Model for Astrobiological Simulations

The mineral schreibersite, e.g., Fe 3 P, is commonly found in iron-rich meteorites and could have served as an abiotic phosphorus source for prebiotic chemistry. However, atomistic calculations of its degradation chemistry generally require quantum simulation approaches, which can be too computationally cumbersome to study sufficient time and length scales for this process. In this regard, we have created a computationally efficient semiempirical quantum density functional tight binding (DFTB) model for iron and phosphorus-containing materials by adopting an existing semiautomated workflow that represents many-body interactions by linear combinations of Chebyshev polynomials. Here, we have utilized a relatively small training set to optimize a DFTB model that is accurate for schreibersite physical and chemical properties, including its bulk properties, surface energies, and water absorption. We then show that our model shows strong transferability to several iron phosphide solids as well as multiple allotropes of iron metal. Our resulting DFTB parametrization will allow us to interrogate schreibersite aqueous decomposition at longer time and length scales than standard quantum approaches, providing for more detailed investigations of its role in prebiotic chemistry on early Earth.

36 MATERIALS SCIENCE↗