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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Application of First-Principles-Based Artificial Neural Network Potentials to Multiscale-Shock Dynamics Simulations on Solid Materials

The use of artificial neural network (ANN) potentials trained with first-principles calculations has emerged as a promising approach for molecular dynamics (MD) simulations encompassing large space and time scales while retaining first-principles accuracy. To date, however, the application of ANN-MD has been limited to near-equilibrium processes. Here we combine first-principles-trained ANN-MD with multiscale shock theory (MSST) to successfully describe far-from-equilibrium shock phenomena. Overall, our ANN-MSST-MD approach describes shock-wave propagation in solids with first-principles accuracy but a 5000 times shorter computing time. Accordingly, ANN-MD-MSST was able to resolve fine, long-time elastic deformation at low shock speed, which was impossible with first-principles MD because of the high computational cost. This work thus lays a foundation of ANN-MD simulation to study a wide range of far-from-equilibrium processes.

36 MATERIALS SCIENCE↗
NASA NTRS1997

Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

Jaffe, Richard↗
DOE OSTI2023

Structural Changes to the Gd‐DTPA Complex at Varying Ligand Protonation State

Abstract Diethylenetriaminepentaacetic acid (DTPA) is a chelating agent whose complex with the Gd 3+ ion is used in medical imaging. DTPA is also used in lanthanide‐actinide separation processes. As protonation of the DTPA ligand can facilitate dissociation of the Gd 3+ ion from the Gd‐DTPA complex, this work investigates the coordination structures of the aqueous Gd 3+ ion and its environment when chelated by DTPA in eight different DTPA protonation states. Both classical and ab initio molecular dynamics (MD) simulations are conducted to model the solvated complexes. Extended X‐ray absorption fine structure (EXAFS) measurements of the Gd 3+ aqua ion, and the Gd‐DTPA complex at pH 1 and 11, are compared to EXAFS spectra predicted from the MD simulations to verify the accuracy of the MD structures. The findings of this work provide atomic‐level details into the fluctuating Gd‐DTPA complex environment as the DTPA ligand gradually detaches from the Gd 3+ ion with increased protonation.

Chemistry↗
DOE OSTI2022

Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin

Serum albumin is the most abundant protein in blood plasma, and it is involved in multiple biological processes. Serum albumin has recently been adapted for improving biomaterial integration with bone tissue, and studies have shown the importance of this protein in bone repair and regeneration. However, the mechanism of action is not yet clear. In stark contrast, other studies have demonstrated that albumin blocks cell adhesion to surfaces, which is seen as a limitation to its bone healing role. These apparent contradictions suggest that the conformation of albumin facilitates its bioactivity, leading to enhanced bone repair. Serum albumin is known to play a major role in maintaining the calcium ion concentration in blood plasma. Due to the prevalence of calcium at bone repair and regeneration sites, it has been hypothesized that calcium binding to serum albumin triggers a conformational change, leading to bioactivity. In the current study, molecular modeling approaches including molecular docking, atomic molecular dynamics (MD) simulation, and coarse-grained MD simulation were used to test this hypothesis by investigating the conformational changes induced in bovine serum albumin by interaction with calcium ions. The computational results were qualitatively validated with experimental Fourier-transform infrared spectroscopy analysis. We find that free calcium ions in solution transiently bind with the three major loops in albumin, triggering a conformational change where N-terminal and C-terminal domains separate from each other in a partial unfolding process. The separation distance between these domains was found to correlate with the calcium ion concentration. The experimental data support the simulation results showing that albumin has enhanced conformational heterogeneity upon exposure to intermediate levels of calcium, without any significant secondary structure changes.

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

First-Principles Simulations of CuCl in High-Temperature Water Vapor

Experimental data suggest that the solubility of copper in high-temperature water vapor is controlled by the formation of hydrated clusters of the form CuCl(H 2 O) n , where the average number of water molecules in the cluster generally increases with increasing density [Migdisov, A. A.; et al. Geochim. Cosmochim. Acta2014, 129, 33–53]. However, the precise nature of these clusters is difficult to probe experimentally. Moreover, there are some discrepancies between experimental estimates of average cluster size and prior simulation work [Mei, Y. Geofluids2018, 2018, 4279124]. Here, we have performed first-principles Monte Carlo (MC) and molecular dynamics (MD) simulations to explore these clusters in finer detail. We find that molecular dynamics is not the most appropriate technique for studying aggregation in vapor phases, even at relatively high temperatures. Specifically, our MD simulations exhibit substantial problems in adequately sampling the equilibrium cluster size distribution. In contrast, MC simulations with specialized cluster moves are able to accurately sample the phase space of hydrogen-bonding vapors. At all densities, we find a stable, slightly distorted linear H 2 O–Cu–Cl structure, which is in agreement with the earlier simulations, surrounded by a variable number of water molecules. The surrounding water molecules do not form a well-defined second solvation shell but rather a loose network of hydrogen-bonded water with molecular CuCl on the outside edge of the water cluster. We also find a broad distribution of hydration numbers, especially at higher densities. In contrast to previous simulation work but in agreement with experimental data, we find that the average hydration number substantially increases with increasing density. Moreover, the value of the hydration number depends on the choice of cluster definition.

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

Recreating Giants Impacts in the Laboratory: Shock Compression of MgSiO 3 Bridgmanite to 14 Mbar

Understanding giant impacts requires accurate description of how extreme pressures and temperatures affect the physical properties of the constituent materials. Here, we report shock experiments on two polymorphs of MgSiO 3 : enstatite and bridgmanite (perovskite) crystals.We obtain pressure-density shock equation of state to 14 Mbar and more than 9 g/cm 3 , a 40% increase in density from previous data on MgSiO 3 . Density-functional-theory molecular dynamics (DFT-MD) simulations provide predictions for the shock Hugoniot curves for bridgmanite and enstatite and suggest that the Grüneisen parameter decreases with increasing density. The good agreement between the simulations and the experimental data, including for the shock temperature along the enstatite Hugoniot reveals that DFT-MD simulations reproduce well the behavior of dense fluid MgSiO 3 .We also reveal a high optical reflectance indicative of a metal-like electrical conductivity which supports the hypothesis that magma oceans may contribute to planetary magnetic field generation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Multiscale Machine-Learned Modeling Infrastructure

The Multiscale Machine-Learned Modeling Infrastructure (MuMMI) is a multiscale workflow management infrastructure that can concurrently orchestrate thousands of molecular dynamics (MD) simulations operating at different time and/or length scales, spanning nanoseconds to seconds and nanometers to micrometers. MuMMI uses machine learning (backed by biology experiments) to guide a massive ensemble of MD simulations that capture biologically relevant time and length scales with unprecedented resolution. MuMMI supports multiple MD codes such as GROMACS and ddcMD and can be fully deployed using the HPC package manager Spack. MuMMI has been used in many publications to run hundreds of thousands simulations, leading to significant biology breakthroughs.

Di Natale, Francesco [Lawrence Livermore National ↗
DOE OSTI2024

Structural and Spectroscopic Properties of Butanediol-Modified Boehmite Materials

Glycoboehmite (GB) materials are synthesized by a solvothermal reaction to form layered aluminum oxyhydroxide (boehmite) modified by intercalated butanediol molecules. These hybrid materials offer a platform to design materials with potentially novel sorption, wetting, and catalytic properties. Several synthetic methods have been used, resulting in different structural and spectroscopic properties, but atomistic detail is needed to determine the interlayer structure to explore the synthetic control of GB materials. Here, in this study, we use classical molecular dynamics (MD) simulations to compare the structural properties of GB interlayers containing chemisorbed butanediol molecules as a function of diol loading. Accompanying quantum (density functional theory, DFT) static calculations and MD simulations are used to validate the classical model and compute the infrared spectra of various models. Classical MD results reveal the existence of two unique interlayer environments at higher butanediol loading, corresponding to smaller (cross-linked) and expanded interlayers. DFT-computed infrared spectra reveal the sensitivity of the aluminol O–H stretch frequencies to the interlayer environment, consistent with the spectrum of the synthesized material. Insight from these simulations will aid in the characterization of the newly synthesized GB materials.

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

On the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysis

Computational workflows that combine molecular dynamics (MD) simulations and emerging data-centric (DC) methods can accelerate the screening and analysis of solvent systems experimentally and computationally. Here, MD simulations provide atomic positions and velocities of reactant, solvent, and catalyst materials that can be manipulated into data representations that in turn can be used by DC techniques to conduct predictive modeling, feature extraction, and experimental design. For liquid-phase catalytic applications, emerging DC techniques such as Convolutional and Graph Neural Networks (CNN/GNN), Topological Data Analysis (TDA), and Active Learning (AL) can leverage MD and experimental data to quickly predict solvent effects on reaction outcomes. For instance, in recent studies, 3D solvent environments obtained with MD have been exploited by CNNs to predict experimental reaction rates for homogeneous acid-catalyzed lignocellulosic processes. In this perspective, we discuss basic principles of DC methods and how these can be combined with MD to enable high-throughput screening of solvent selection for diverse catalysis applications.

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

Understanding the Surprising Ionic Conductivity Maximum in Zn(TFSI) 2 Water/Acetonitrile Mixture Electrolytes

Aqueous electrolytes composed of 0.1 M zinc bis-(trifluoromethyl-sulfonyl)-imide (Zn-(TFSI) 2 ) and acetonitrile (ACN) were studied using combined experimental and simulation techniques. The electrolyte was found to be electrochemically stable when the ACN V% is higher than 74.4. In addition, it was found that the ionic conductivity of the mixed solvent electrolytes changes as a function of ACN composition, and a maximum was observed at 91.7 V% of ACN although the salt concentration is the same. This behavior was qualitatively reproduced by molecular dynamics (MD) simulations. Detailed analyses based on experiments and MD simulations show that at high ACN composition the water network existing in the high water composition solutions breaks. As a result, the screening effect of the solvent weakens and the correlation among ions increases, which causes a decrease in ionic conductivity at high ACN V%. Furthermore, this study provides a fundamental understanding of this complex mixed solvent electrolyte system.

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

Si–Cl 2 –Ar + Atomic Layer Etching Window: A Fundamental Study Using Molecular Dynamics Simulations and a Reduced Order Model

Silicon (Si) atomic layer etching (ALE) by alternating exposure to chlorine gas (Cl 2 ) and argon ions (Ar + ) is studied by using molecular dynamics (MD) simulations and a reduced order model (ROM). Here, the purpose of this study is to elucidate the properties of the ALE window, a range of ion energies where the amount of Si etched over a series of cycles is nonzero and nearly independent of ion energy. Experimental studies of the Si–Cl 2 –Ar + ALE system report contradictory results related to the ALE window’s ion energy range. Both MD simulations and the ROM show that there is an ALE window present from approximately 15 to 20 eV for normal incidence argon ions. The Si–Cl 2 –Ar + system, therefore, exhibits a narrow ALE window. The amount of Si etched per cycle is less than one atomic layer because of the higher etch yield of Cl atoms relative to atomic Si and silicon chlorides. A modified version of the ROM with an artificially increased Si physical sputtering threshold energy expands the ALE window, illustrating the importance of the difference in chemical and physical sputtering threshold energies in the ALE window energy range. The ROM is also used to examine the dependence of the EPC on the Ar + ion fluence.

energy↗
DOE OSTI2023

Molecular dynamics study of primary damage in the near-surface region in nickel

In this work, we carried out a large-scale molecular dynamics (MD) simulation to elucidate the effect of the free surface on the defect production of displacement cascades in pure nickel. These MD simulations were performed both in the bulk and near-surface regions with primary knock-on atom (PKA) energies of E PKA = 1, 5, or 10 keV and at temperatures T = 300, 425, or 525 K. Additionally, for every (T, E PKA ), near-surface cascade simulations were performed as a function of depth. In the near-surface simulations, assuming isotropic neutron fluence, the PKAs were initiated in random directions, including toward and parallel to the free surface. For both the near-surface and bulk cascades, the effect of E PKA and T on the defect production is similar. In both cases, the defect production increases with E PKA , but the temperature has minimal effect. However, the production and clustering of vacancies are higher for near-surface cascades, and they decrease with increasing depth. In contrast, the production and clustering of self-interstitial atoms are lower and increase with depth. Eventually, the production and clustering of both defect types approach bulk cascade-like behavior, and the depth at which this occurs increases with E PKA , but is independent of temperature.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Probing phonon focusing, thermomechanical behavior, and moiré patterns in van der Waals architectures using surface acoustic waves

Surface acoustic waves (SAWs) propagate along solid-air, solid-liquid, and solid-solid interfaces. Their characteristics depend on the elastic properties of the solid. Combining transmission electron microscopy (TEM) experiments with molecular dynamics (MD) simulations, we probe atomic environments around intrinsic defects that generate SAWs in vertically stacked two-dimensional (2D) bilayers of MoS 2 . Our joint experimental-simulation study provides insights into SAW-induced structural and dynamical changes and thermomechanical responses of MoS 2 bilayers. Using MD simulations, we compute mechanical properties from the SAW velocity and thermal conductivity from thermal diffusion of SAWs. The results for Young’s modulus and thermal conductivity of an MoS 2 monolayer are in good agreement with experiments. The presence of defects, such as nanopores which generate SAWs, reduces the thermal conductivity of 2D-MoS 2 by an order of magnitude. We also observe dramatic changes in moiré patterns, phonon focusing, and cuspidal structures on 2D-MoS 2 layers.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Modified Lucas-Washburn theory for fluid filling in nanotubes

Ultrafast water transport in carbon nanotubes (CNTs) has drawn a great deal of attention in a number of applications, such as water desalination, power generation, and biomolecule detection. With the recent experimental advances in water filling of isolated CNTs, the Lucas-Washburn theory for capillary rise in tubes needs to be revisited for a better understanding of the physics and dynamics of water filling in CNTs. Here, the Lucas-Washburn theory is corrected for the hydrodynamic entrance effects as well as the variation of capillary pressure and hydrodynamic properties with the radius and length of CNTs. Due to the large slippage in CNTs, inclusion of the entrance effects is important particularly for the initial stages of filling where a L ∝ t scaling, as opposed to L 2 ∝ t , is observed in our molecular dynamics (MD) simulations. The corrected Lucas-Washburn theory is shown to predict the water filling dynamics in CNTs as observed in MD simulations. With the corrected theory, we achieve a better understanding of capillary rise and water filling dynamics in CNTs.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Effective Fragment Potential-Based Molecular Dynamics Studies of Diffusion in Acetone and Hexane

To facilitate more reliable descriptions of transport properties in liquids, molecular dynamics (MD) simulations are performed based on the effective fragment potential (EFP) method derived from first-principles quantum mechanics (in contrast to MD based upon empirically fitted potentials). The EFP method describes molecular interactions in terms of Coulomb, polarization/induction, dispersion, exchange-repulsion, and charge-transfer interactions. The EFP MD simulations described in this paper, performed on hexane and acetone, are able to track the mean-square displacement of molecules for sufficient time to reliably extract translational diffusion coefficients. Finally, the results reported here are in reasonable agreement with experiment.

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

Calculation of self-diffusion coefficients in supercritical carbon dioxide using mean force kinetic theory

This paper presents an application of mean force kinetic theory (MFT) to the calculation of the self-diffusivity of CO 2 in the supercritical fluid regime. Two modifications to the typical application of MFT are employed to allow its application to a system of molecular species. Therefore, the first is the assumption that the inter-particle potential of mean force can be obtained from the molecule center-of-mass pair correlation function, which in the case of CO 2 is the C–C pair correlation function. The second is a new definition of the Enskog factor that describes the effect of correlations at the surface of the collision volume. The new definition retains the physical picture that this quantity represents a local density increase, resulting from particle correlations, relative to that in the zero density homogeneous fluid limit. These calculations are facilitated by the calculation of pair correlation functions from molecular dynamics (MD) simulations using the FEPM2 molecular CO2 model. The self-diffusivity calculated from theory is in good agreement with that from MD simulations up to and slightly beyond the density at the location of the Frenkel line. The calculation is compared with and is found to perform similarly well to other commonly used models but has a greater potential for application to systems of mixed species and to systems of particles with long range interatomic potentials due to electrostatic interactions.

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

Molecular-Level Insights into the NMR Relaxivity of Gadobutrol Using Quantum and Classical Molecular Simulations

MRI is an indispensable diagnostic tool in modern medicine; however, understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge, hindering the molecular-guided development of more effective contrast agents. By using quantum-based polarizable force fields, the first-of-its-kind molecular dynamics (MD) simulations of Gadobutrol are reported where the 1 H NMR longitudinal relaxivity r 1 of the aqueous phase is determined without any adjustable parameters. The MD simulations of r 1 dispersion (i.e., frequency dependence) show good agreement with measurements at frequencies of interest in clinical MRI. Importantly, the simulations reveal key insights into the molecular level processes leading to r 1 dispersion by decomposing the NMR dipole–dipole autocorrelation function G(t) into a discrete set of molecular modes, analogous to the eigenmodes of a quantum harmonic oscillator. The molecular modes reveal important aspects of the underlying mechanisms governing r 1 , such as its multiexponential nature and the importance of the second eigenmodal decay. By simply analyzing the MD trajectories on a parameter-free approach, the Gadobutrol simulations show that the outer-shell water contributes ∼50% of the total relaxivity r 1 compared to the inner-shell water, in contrast to simulations of (nonchelated) gadolinium-aqua where the outer shell contributes only ∼15% of r 1 . The deviation between simulations and measurements of r 1 below clinical MRI frequencies is used to determine the low-frequency electron-spin relaxation time for Gadobutrol, in good agreement with independent studies.

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

Sensitivity of Dislocation-GB interactions to simulation setups in atomistic models

Dislocation-grain boundary (GB) interactions play an integral role in strengthening of crystalline materials, and are dependent on external loading conditions and atomic arrangements at the grain boundary. While molecular dynamics (MD) simulations can provide critical insights into relationships between these parameters and the exact interaction, the outcomes are sensitive to the computational setup. Here, in this work, we explore the effect of computational setup (system size, GB orientation and boundary conditions) on stress-controlled dislocation-grain boundary (DGB) reactions using MD simulations for a well-studied copper symmetric $\langle$1 1 2$\rangle$ tilt boundary. The study demonstrates that the DGB reactions (pinning, absorption, transmission, etc.) are sensitive to the system size and the orientation of the GB to the applied stress. Additionally, the current work shows that there is a critical system size for the dislocation-grain boundary reaction stresses to converge, one which was found to be much larger than the setups in comparable MD studies. This was attributed to the specific stress states and the influence of surfaces, fixed or free, as these computational setups are modified. Finally, a stress-controlled setup with minimal model artifacts is examined, and the effect of coupled Schmid and non-Schmid stress components on the dislocation-GB reactions are discussed.

36 MATERIALS SCIENCE↗