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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 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Scientific machine learning for modeling and simulating complex fluids

The formulation of rheological constitutive equations—models that relate internal stresses and deformations in complex fluids—is a critical step in the engineering of systems involving soft materials. While data-driven models provide accessible alternatives to expensive first-principles models and less accurate empirical models in many engineering disciplines, the development of similar models for complex fluids has lagged. The diversity of techniques for characterizing non-Newtonian fluid dynamics creates a challenge for classical machine learning approaches, which require uniformly structured training data. Consequently, early machine-learning based constitutive equations have not been portable between different deformation protocols or mechanical observables. Here, we present a data-driven framework that resolves such issues, allowing rheologists to construct learnable models that incorporate essential physical information, while remaining agnostic to details regarding particular experimental protocols or flow kinematics. These scientific machine learning models incorporate a universal approximator within a materially objective tensorial constitutive framework. By construction, these models respect physical constraints, such as frame-invariance and tensor symmetry, required by continuum mechanics. We demonstrate that this framework facilitates the rapid discovery of accurate constitutive equations from limited data and that the learned models may be used to describe more kinematically complex flows. This inherent flexibility admits the application of these “digital fluid twins” to a range of material systems and engineering problems. We illustrate this flexibility by deploying a trained model within a multidimensional computational fluid dynamics simulation—a task that is not achievable using any previously developed data-driven rheological equation of state.

Science & Technology - Other Topics↗
DOE OSTI2020

Surface Hydration and Hydroxyl Configurations of Gibbsite and Boehmite Nanoplates

Discontinuation of the bulk structure at the interface between metal oxide particles and water leads to altered bonding characteristics and unique facet-dependent molecular environments. Surface hydration and consequent hydroxylation adds further complexity to the interface, details that for metal (oxy)hydroxides are especially difficult to isolate from the background signal of bulk structural hydroxyls. Here we probe for the first time the hydroxylation and hydration structures on basal surfaces of gibbsite (?-Al(OH)3) and boehmite (?-AlOOH) nanoplates at ambient conditions, using the interface-sensitive technique vibrational sum frequency generation spectroscopy (VSFG). Hydroxyl stretching modes at the interfaces with adsorbed water layers compared directly to Raman and infrared bulk modes show that while gibbsite surface frequencies were sharp and nearly identical to those in the bulk, boehmite surface hydroxyls displayed a very different broad spectrum of states. Ab initio molecular dynamics simulations of both basal surfaces with and without hydration waters reveal that gibbsite surface hydroxyls interact only weakly with overlying hydration waters remaining essentially unperturbed, whereasthose on boehmite can interact more strongly facilitated by higher configurational degrees of freedom at the interface. The findings clearly unveil substantial differences in the hydrated interfacial dynamics of these two otherwise similar materials, with implications for their interfacial chemistry and wettability.

Sassi, Michel JPC↗
DOE OSTI2023

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗
DOE OSTI2021

JSPEC: A Program for IBS and Electron Cooling Simulation

Intrabeam scattering is an important collective effect that can deteriorate the properties of a high-intensity beam, and electron cooling is a method to mitigate the IBS effect. JSPEC (JLab Simulation Package for Electron Cooling) is an open-source program developed at Jefferson Lab, which simulates the evolution of the ion beam under the IBS and/or the electron cooling effect. JSPEC has been benchmarked with BETACOOL and experimental data. In this report, we will introduce the features of JSPEC, including the friction force calculation, the IBS expansion rate and electron cooling rate calculation, and the beam-dynamic simulations for the electron cooling process; explain how to set up the simulations in JSPEC; and demonstrate the benchmarking results.

Zhang, He↗
DOE OSTI2022

Isotropic-to-Nematic Transition in Salt-Free Polyelectrolyte Coacervates from Coarse-Grained Simulations

Recent interest in complex coacervation between oppositely charged polyelectrolytes (PEs) has been fueled by its relevance to biology in the context of membraneless organelle formation within living cells. For PEs with limited flexibility (such as double-stranded DNA), theoretical treatments and recent experiments have reported the emergence of liquid crystalline order (LCO) within the resulting coacervate phases. In this work, we study the underlying physics of this phenomenon using coarse-grained molecular dynamics simulations of symmetric semiflexible-semiflexible and asymmetric semiflexible-flexible coacervates. By comparing coacervates with the corresponding semidilute solutions of neutral polymers, we demonstrate that the presence of Coulomb interactions in coacervates facilitates orientational ordering, in agreement with theoretical predictions. Quantitative comparisons between our simulations and theory indicate that, for asymmetric nematic coacervates, the strong orientational ordering of stiff polyanions induces a weak ordering of the flexible polycations-an effect that was not anticipated by available theoretical studies. Simulations reveal that, for nematic coacervates, the preferred orientation of the PE chains at the liquid-liquid coacervate-supernatant interface is parallel, and the alignment of semiflexible PEs is homogeneous. The results presented here provide new molecular-level insights into the intracoacervate LCO and will help motivate further experimental and theoretical activities in this area.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Ion Solvation and Hydrogen Bonding in Liquid Electrolytes

The primary goal of the proposed research was to explore the use of far-infrared (FIR) spectroscopy for providing new informal on about the solvation structure and dynamics of small ions such as Li + , Na + , and Mg 2+ in electrolyte solutions commonly used in energy-related applications. Classical and ab initio molecular dynamics simulations were to be carried out together with spectroscopic measurements to aid interpretation of the spectra generated.

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

Development of $\mathrm{AMOEBA}$ Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands

Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. In this report we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La 3+ ) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La 3+ –ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La 3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion–water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion–protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.

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

Relevance of structural defects to the mechanism of mechanical deformation in metallic glasses

Abstract It is known that deformation in disordered materials such as metallic glasses and supercooled liquids occurs via the cooperative rearrangement of atoms or constituent particles at dynamical heterogeneities, commonly regarded as point-like defects. We show via molecular-dynamics simulations that there is no apparent relationship between atomic rearrangements and the local atomic environment as measured by the atomic-level stresses, kinetic and potential energies, and the per-atom Voronoi volume. In addition, there is only a weak correlation between atomic rearrangements and the largest and smallest eigenvalues of the dynamical matrix. Our results confirm the transient nature of dynamical heterogeneities and suggest that the notion of defects may be less relevant than that of a propensity for rearrangement.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Detailed Simulations of a Three-Stage Supercritical Carbon Dioxide Axial Compressor with a Focus on the Shrouded Stator Cavities Flow

This paper describes the findings of detailed simulations performed to investigate the impact of seal teeth cavity leakage flow on the aerodynamic and thermal performance of a three-stage supercritical CO 2 axial compressor. The study compares a shrouded stator configuration (with cavities) to a cantilevered stator configuration (without cavities) to highlight their differences. High-fidelity computational fluid dynamics simulations were performed using non-linear harmonic (NLH) and mixing plane assumptions, considering various possible rotor/stator interface configurations for mixing plane calculations. The key performance parameters for each case were compared, and the best-performing configuration selected for further analysis. The individual stage performance parameters are also examined and compared between the cantilevered and shrouded configurations. It was observed that in the shrouded case, the leakage flow enters the cavity downstream of the stator trailing edge and gets entrained into the primary flow upstream of the stator, leading to boundary layer changes at the hub and degradation of stator and downstream rotor performance. Vortical flow structures were also observed in the stator wells, which tended to change the flow angles around the region, thereby affecting mixing and velocity distribution, resulting in a slight deterioration of compressor performance. Additionally, the study examines windage heating due to shear work from rotating walls, including the seal teeth surface. The amount of shear work done on the leakage flow and the corresponding rise in fluid temperature were quantified, tabulated, and further compared with a simple analytical model, showing good agreement between them and, hence, validating the numerical approach used.

42 ENGINEERING↗
DOE OSTI2021

Ab-Initio Simulation Studies of Cr Solvation in Fluoride Molten Salts

Understanding molten salt chemistry is essential in ongoing research of the molten salt nuclear reactor (MSR). In this context, detailed understanding of the mechanisms underlying selective oxidation of metal species, such as Cr, is required to guide the design of effective corrosion mitigation strategies in molten salts. An important starting point for such mechanistic understanding is knowledge of the solvation structure and its role in controlling metal speciation. In this work, we use ab initio molecular dynamics simulations to study the short-range (on the scale of the nearest-neighbor bond lengths) and medium-range (over length scales of several neighbor spacings) structure in three different fluoride melts with and without Cr addition; namely, 2KF-NaF, 2LiF-BeF 2 , and 3LiF-AlF3. We find that Cr 0 ,Cr 2+ ,Cr 3+ can each be coordinated by different numbers of F-, with the variance in coordination number decreasing as oxidation state increases, and that these coordination geometries are largely independent of solvent. The manner by which Cr changes the medium-range structure, however, is found to be solvent-dependent. While 2KF-NaF melts show short and medium range order that is highly dynamic, 2LiF-BeF 2 and 3LiF-AlF 3 are characterized by molecular associates that are relatively long-lived that organize into oligomer structures on larger length scales. Rather than being solvated by F- ions alone, we find that Cr can incorporate into and be solvated within this oligomer structure. Fluoroacidity, alone, may therefore prove too simple a metric for assessing the corrosivity of molten fluorides. As our work suggests, the ability of Cr to solvate must be understood in the context of the short- and medium-range structure of the solvent.

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

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence–structure–function relations remain poorly characterized. Here, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 20 3 = 8000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.

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

Solvent effects on extractant conformational energetics in liquid–liquid extraction: a simulation study of molecular solvents and ionic liquids

Extractant design in liquid–liquid extraction (LLE) is a research frontier of metal ion separations that typically focuses on the direct extractant–metal interactions. However, a more detailed understanding of energetic drivers of separations beyond primary metal coordination is often lacking, including the role of solvent in the extractant phase. In this work, we propose a new mechanism for enhancing metal-complexant energetics with nanostructured solvents. Using molecular dynamics simulations with umbrella sampling, we find that the organic solvent can reshape the energetics of the extractant's intramolecular conformational landscape. Here, we calculate free energy profiles of different conformations of a representative bidentate extractant, n-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four different solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]). By promoting reorganization of the extractant molecule into its binding conformation, our findings reveal how particular solvents can ameliorate this unfavorable step of the metal separation process. In particular, the charge alternating nanodomains formed in ILs substantially reduce the free energy penalty associated with extractant reorganization. Importantly, using alchemical free energy calculations, we find that this stabilization persists even when we explicitly include the extracted cation. These findings provide insight into the energetic drivers of metal ion separations and potentially suggest a new approach to designing effective separations using a molecular-level understanding of solvent effects.

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

Elucidating the Solvation Structures and Dynamics in Iron-Based TFSI – Aqueous Systems

This study investigates the solvation structures and dynamics of bis(trifluoromethanesulfonyl)imide (TFSI – )-based aqueous electrolytes, focusing on Fe(TFSI) 2 and Fe(TFSI) 3 . Using advanced characterization techniques, including small-angle X-ray scattering, molecular dynamics simulations, Raman spectroscopy, Fourier-transform infrared spectroscopy, and nuclear magnetic resonance, we elucidate how the electrolyte concentration influences ion association, solvation structures, and transport properties. Furthermore, our findings show that higher electrolyte concentrations promote the formation of contact ion pairs and anion networks, leading to reduced ion mobility and altered hydrogen-bonding dynamics. These insights provide a deeper understanding of solvation phenomena in TFSI-based electrolytes and contribute to the development of efficient and environmentally friendly iron electrodeposition processes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Dynamically Formed Active Sites on Liquid Boron Oxide for Selective Oxidative Dehydrogenation of Propane

Boron-based catalysts have been shown to be both active and selective for driving the oxidative dehydrogenation of propane (ODHP) without the use of precious metals. This reaction occurs at temperatures that melt the oxide catalyst which challenges our ability to identify the liquid structures of the boron oxide phase under reaction conditions, hindering the understanding of its active sites and reaction mechanism. By combining ab initio molecular dynamics simulation, in-situ Raman characterization, and microkinetic modeling, we propose that the di-coordinated boron sites (BO2) in liquid boron oxide are the active species for O2 activation under reaction conditions. The formed peroxy-like species (>B-O-O-B<) can be viewed as a moderate oxidant for ODHP. The dynamical >B-O* dangling bond originated from >B-O-O-B< site as well as the liquid B2O3 structure itself, plays a critical role in the abstraction of H atoms from propane (C3H7 radical formation). Microkinetic modeling reveals C3H7 radical formation to be the main rate controlling step (~75% degree of rate control) with the dehydration of boron hydroxyls (B-OHs) to recover the di-coordinated boron active sites controlling the remainder of the rate (~25% degree of rate control). Moreover, the activation barriers are found to strongly depend upon the surface B-OH concentration. These findings provide significant insights into the active site and reaction mechanisms on boron-based catalysts for ODHP and underlie the importance of understanding the liquid nature of the catalyst to account for the catalytic activity.

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

Solving Newton’s equations of motion with large timesteps using recurrent neural networks based operators

Classical molecular dynamics simulations are based on solving Newton’s equations of motion. Using a small timestep, numerical integrators such as Verlet generate trajectories of particles as solutions to Newton’s equations. We introduce operators derived using recurrent neural networks that accurately solve Newton’s equations utilizing sequences of past trajectory data, and produce energy-conserving dynamics of particles using timesteps up to 4000 times larger compared to the Verlet timestep. We demonstrate significant speedup in many example problems including 3D systems of up to 16 particles.

Newton’s equations↗
DOE OSTI2023

Arrested coarsening and large density fluctuations in driven particle mixtures in two dimensions

Abstract Using molecular dynamics simulations, we study a driven, nonadditive binary mixture of spherical particles confined to move in two dimensions and immersed in an explicit solvent consisting of point particles with purely repulsive interactions. We show that, without a drive, the mixture of spherical particles phase separates and coarsens with kinetics consistent with an Ising-like conserved dynamics. Conversely, when the drive is applied, the coarsening is arrested and the system develops large density fluctuations. We show that the drive creates domains of a characteristic size which decreases with an increasing force. Furthermore, we find that these domains are anisotropic and can be oriented either parallel or perpendicular to the drive direction. Finally, we connect our findings to existing theories of strongly-driven systems, pointing out the importance of introducing the explicit solvent particles to break the Galilean invariance of the system.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Shapiro steps observed in a two-dimensional Yukawa solid modulated by a one-dimensional vibrational periodic substrate

Depinning dynamics of a two-dimensional (2D) solid dusty plasma modulated by a one-dimensional (1D) vibrational periodic substrate are investigated using Langevin dynamical simulations. As the uniform driving force increases gradually, from the overall drift velocity varying with the driving force, four significant Shapiro steps are discovered. The data analysis results indicate that, when the ratio of the frequency from the drift motion over potential wells to the external frequency from the modulation substrate is close to integers, dynamic mode locking occurs, corresponding to the discovered Shapiro steps. In conclusion, around both termini of the first and fourth Shapiro steps, the transitions are found to be always continuous, however, the transition between the second and third Shapiro steps is discontinuous, probably due to the different arrangements of particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗