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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Multimode turbulent flow measurements using magnetic resonance imaging- and laser-based techniques and computational fluid dynamics simulations

We studied the flow field characteristics of a turbulent flow over a regularized cube array with a perpendicular injection flow through the floor between the second and third cubical elements, representing the complex flow interactions of a 3D jet and the wake flows behind cubical obstacles. Four different experimental measurements were performed: two magnetic resonance imaging-based measurements for three-dimensional three-component velocity (MRV) and concentration (MRC) and two laser-based techniques, particle image velocimetry (PIV) and planar laser-induced fluorescence (PLIF), for two-dimensional two-component velocity and concentration measurement, respectively. The mainstream Reynolds number is Re = 15 000⁠, based on the primary inlet velocity U m and channel height D H ⁠, whereas the injector Reynolds number is Re j = 3400⁠, based on the injector velocity U j and the injector's exit width D j ⁠. Numerical simulations were performed for the studied flow configuration of turbulent flow over a regularized cube array using Reynolds-averaged Navier–Stokes (RANS) and large-eddy simulation (LES) approaches. Results obtained from experimental measurements—including MRV, MRC, PIV, and PLIF—as well as RANS and LES simulations are discussed and compared along several horizontal and vertical planes of the studied configuration. In addition, 3D turbulent flow structures, such as leading-edge vortex, horseshoe vortex, and jet shear-layer vortex, and the isosurfaces of scalar concentration successfully revealed by MRV and MRC techniques were found to be in very good agreement with those 3D features extracted from RANS and LES simulations. In conclusion, the high-resolution experimental and numerical database obtained from this study could be useful for validation and verification of numerical codes.

Computational fluid dynamics↗
DOE OSTI2022

Machine learning molecular dynamics simulations toward exploration of high-temperature properties of nuclear fuel materials: case study of thorium dioxide

Predicting materials properties of nuclear fuel compounds is a challenging task in materials science. Their thermodynamical behaviors around and above the operational temperature are essential for the design of nuclear reactors. However, they are not easy to measure, because the target temperature range is too high to perform various standard experiments safely and accurately. Moreover, theoretical methods such as first-principles calculations also suffer from the computational limitations in calculating thermodynamical properties due to their high calculation-costs and complicated electronic structures stemming from f-orbital occupations of valence electrons in actinide elements. Here, we demonstrate, for the first time, machine-learning molecular-dynamics to theoretically explore high-temperature thermodynamical properties of a nuclear fuel material, thorium dioxide. The target compound satisfies first-principles calculation accuracy because f-electron occupation coincidentally diminishes and the scheme meets sampling sufficiency because it works at the computational cost of classical molecular-dynamics levels. We prepare a set of training data using first-principles molecular dynamics with small number of atoms, which cannot directly evaluate thermodynamical properties but captures essential atomistic dynamics at the high temperature range. Then, we construct a machine-learning molecular-dynamics potential and carry out large-scale molecular-dynamics calculations. Consequently, we successfully access two kinds of thermodynamic phase transitions, namely the melting and the anomalous λ transition induced by large diffusions of oxygen atoms. Furthermore, we quantitatively reproduce various experimental data in the best agreement manner by selecting a density functional scheme known as SCAN. Our results suggest that the present scale-up simulation-scheme using machine-learning techniques opens up a new pathway on theoretical studies of not only nuclear fuel compounds, but also a variety of similar materials that contain both heavy and light elements, like thorium dioxide.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Molecular dynamics simulations of reflection and sputtering behavior of boron under deuterium ion irradiation

Boronization is a commonly used method of wall conditioning in fusion reactors. The application of boron films to the plasma-facing materials results in enhanced plasma performance due to the reduction of intrinsic impurities. This is primarily driven by a reduction in oxygen content that is chemically trapped in the boron film. The reactive nature of these boron films also raises questions concerning interactions with hydrogen isotopes. In this work, boron-deuterium interactions were studied using molecular dynamics (MD). Reactive force field potentials were used to model the chemical interactions between B and D. An amorphous boron substrate was irradiated by D atoms at varying incident energies, 10 eV < E i < 150 eV and angles, 0° < α < 85°. The reflection probability was calculated and compared to results from the commonly-used binary collision approximation (BCA) method. This comparison found that the BCA underestimated the reflection probability at E i < 35 eV and α > 45 ∘ . The source of this discrepancy was found to be the surface binding energy model. The BCA calculation with an isotropic surface binding energy model was more closely aligned to the MD result. This, in combination with a correction function based on the MD results allows for corrections to the reflection probability of deuterium impinging on boron surfaces. The sputtering of the substrate material was also studied. While this study did not contain sufficient events to quantitatively describe the sputtering behavior, some qualitative results emerged: namely, chemical sputtering of B and D-containing molecules (BD, BD 2 , BD 3 ) at low ( < 20 eV) incident deuterium energies. This result suggests that chemical sputtering could be a significant factor in limiting boron coating lifetime when exposed to lower ion energies, such as those in detached plasmas. The results show that chemical interactions should be taken into account when modeling the interactions between D ions and B surfaces.

Boron↗
DOE OSTI2014

Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride

Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'••• O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Here, the calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.

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

Computational Fluid Dynamics Simulations of Glass Vitrification Refractory Coupon Tests

The Waste Treatment and Immobilization Plant (WTP) at the Hanford site is nearing the start of the Direct-Feed Low-Activity Waste (DFLAW) operations. DFLAW is destined to convert a pretreated low activity waste portion of the 56 million gallons of tank waste into a stable solid glass. In the subsequent decade completion of the high-level waste (HLW) facility is anticipated. Sustained operational missions of both LAW and HLW melter facilities are expected over multiple decades. In high-temperature glass melters, the refractory lining corrodes over time, which could potentially be an issue for longer term operations, this refractory corrosion is higher at the level of the glass-air interface due to surface tension driven flow. The glass viscosity, melt pool temperature, and glass chemical composition can impact the rate at which the refractory corrodes. This rate is important to quantify for the various waste glasses to be produced at the WTP since the integrity of the refractory should not be a limiting factor affecting the lifetime of the melter. To this end, a series of glasses representative of the first batches of waste glass produced by the WTP will be melted in small-scale crucibles with Monofrax® K-3 coupons inserted. The corrosion of the K-3 will be measured in the melt and at the meltline (or neckline). A model for the corrosion rate will be constructed and implemented into a previously developed framework for a computational fluid dynamics (CFD) model of the full-scale WTP. To assist with experimental design and validate the implementation of the model in the full-scale melter, CFD simulations of the small-scale crucible tests were performed. The bubbling that occurs in the small-scale crucible is initially validated here with a model that uses silicone oil at room temperature. The viscosity of the oil ranges from 1 to 100 Pa•s, which corresponds to operating glass pool temperatures near 1150 °C down to idling temperatures near 950 °C. The simulation results show good agreement with the bubble sizes that form during experiments. CFD modeling of the crucible setup was used to determine bubbling characteristics to match the range of near-wall velocities expected in the full-scale WTP. This study presents the initial CFD modeling results, corrosion testing plan, and some preliminary corrosion samples with an outline for the next steps for the development of the corrosion model.

Abboud, Alexander W. [Idaho National Lab]↗
DOE OSTI2021

All-Atom Molecular Dynamics Simulations of the Temperature Response of Densely Grafted Polyelectrolyte Brushes

Water acts a “good” solvent for most polyelectrolyte (PE) systems due to its high dielectric strength. Theoretical and experimental studies have highlighted some remarkably unconventional properties of strongly water-swollen PE brushes such as a reduction in brush height with increase in temperature. However, an understanding of the atomistic-scale response of the grafted PE chains as well as the local arrangement and organization of the brush-supported counterions and water molecules to changes in temperature is missing. Here, we conduct an all-atom molecular dynamics (MD) study to probe the influence of temperature on the “microstructure” of densely grafted, fully ionized polyacrylic acid (PAA) brushes. The atomistic insights obtained from our study shed light on prior experimental observations and elucidate the key role played by changes in hydrogen bonding network in dictating the hydrophilicity of the brushes. In addition to the temperature-mediated reduction in height of the PE brush layer, we study the influence of temperature on several properties of the brush-supported water molecules such as the number distribution and kinetics of water-water and water-PE hydrogen bonds (HBs), mass density, orientational tetrahedral order parameter, and the activation energy associated with the self-diffusion of water. The effect of temperature on the properties of the brush-trapped counterions is also quantified via changes in their solvation structure, counterion-water radial distribution function (RDF), and the translational mobility. Our findings unravel several hitherto unknown phenomena such as the enhanced propensity for attaining PE brush-induced “water-in-salt”-like scenarios at elevated temperatures, and an increase in the activation energy for the self-diffusion of water with increase in the degree of PE brush-induced nanoconfinement (from ‘bulk water’ to ‘sparsely grafted PE brushes’ to ‘densely grafted PE brushes’). Further, we anticipate that this work will be helpful in improving our predictive capabilities of the temperature response of water-swollen PE brushes, which would be instrumental for better design of several PE brush systems used in a multitude of applications.

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

Preliminary Tests and Beam Dynamics Simulations of a Straight-Merger Beamline

Beamlines capable of merging beams with different energies are critical to many applications related to advanced accelerator concepts and energy-recovery linacs (ERLs). In an ERL, a low-energy "fresh" bright bunch is generally injected into a superconducting linac for acceleration using the fields established by a decelerated "spent" beam traveling on the same axis. A straight-merger system composed of a selecting cavity with a superimposed dipole magnet was proposed and recently test at AWA. This paper reports on the experimental results obtained so far along with detailed beam dynamics investigations of the merger concept and its ability to conserve the beam brightness associated with the fresh bunch.

Al Marzouk, A. A.↗
DOE OSTI2015

Structure, dynamics and stability of water/scCO 2 /mineral interfaces from ab initio molecular dynamics simulations

Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivity and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO 2 . Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca 2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO 2 ) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences (R.R.), and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle. Computational resources were provided by PNNL’s Platform for Institutional Computing (PIC), the W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Quantum dynamical simulation of the scattering of Ar from a frozen LiF(100) surface based on a first principles interaction potential

In-plane two and three dimensional diffraction patterns are computed for the vertical scattering of an Ar atom from a frozen LiF(100) surface. Suitable collimation of the incoming wavepacket serves to reveal the quantum mechanical diffraction. The interaction potential is based on a fit to an ab initio potential calculated using density functional theory with dispersion corrections. Due to the potential coupling found between the two horizontal surface directions, there are noticeable differences between the quantum angular distributions computed for two and three dimensional scattering. The quantum results are compared to analogous classical Wigner computations on the same surface and with the same conditions. The classical dynamics largely provides the envelope for the quantum diffractive scattering. The classical results also show that the corrugation along the [110] direction of the surface is smaller than along the [100] direction, in qualitative agreement with experimental observations of unimodal and bimodal scattering for the [110] and [100] directions, respectively.

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

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

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

Probing pH-Dependent Dehydration Dynamics of Mg and Ca Cations in Aqueous Solutions with Multi-Level Quantum Mechanics/Molecular Dynamics Simulations

The dehydration of aqueous calcium and magnesium cations is the most fundamental process controlling their reactivity in chemical and biological phenomena, such as the formation of ionic solids or passing through ion channels. It holds particular relevance in light of recent advancements in the development of carbon capture techniques that rely on mineralization for long-term carbon storage. Specifically, dehydration of Ca 2+ and Mg 2+ is a key step in proposed carbon capture processes aiming to exploit the relatively high concentration of dissolved carbon dioxide in seawater via the formation of carbonate minerals from solvated Ca 2+ and Mg 2+ cations for sequestration and storage. Nevertheless, atomic-scale understanding of the dehydration of aqueous Ca 2+ and Mg 2+ cations remains limited. Here, we utilize rare event sampling via density functional theory molecular dynamics and embedded wavefunction theory calculations to elucidate the dehydration dynamics of aqueous Ca 2+ and Mg 2+ . Emphasis is placed on the investigation of the effect pH has on the stability of the different coordination environments. Here, our results reveal significant differences in the dehydration dynamics of the two cations and provide insight into how they may be modulated by pH changes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Background Genome-scale models of metabolism and macromolecular expression (ME models) enable systems-level computation of proteome allocation coupled to metabolic phenotype. Results We develop DynamicME, an algorithm enabling time-course simulation of cell metabolism and protein expression. DynamicME correctly predicted the substrate utilization hierarchy on a mixed carbon substrate medium. We also found good agreement between predicted and measured time-course expression profiles. ME models involve considerably more parameters than metabolic models (M models). We thus generate an ensemble of models (each model having its rate constants perturbed), and then analyze the models by identifying archetypal time-course metabolite concentration profiles. Furthermore, we use a metaheuristic optimization method to calibrate ME model parameters using time-course measurements such as from a (fed-) batch culture. Finally, we show that constraints on protein concentration dynamics (“inertia”) alter the metabolic response to environmental fluctuations, including increased substrate-level phosphorylation and lowered oxidative phosphorylation. Conclusions Overall, DynamicME provides a novel method for understanding proteome allocation and metabolism under complex and transient environments, and to utilize time-course cell culture data for model-based interpretation or model refinement.

Mathematical & Computational Biology↗
DOE OSTI2021

Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation

The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, are responsible for their function and malfunction. Misfolding of α-synuclein can lead to neurodegenerative diseases, and the ability to study their conformations and those of other intrinsically disordered proteins under varying physiological conditions can be crucial to understanding and preventing pathologies. In contrast to well-folded peptides, a consensus feature of IDPs is their low hydropathy and high charge, which makes their conformations sensitive to pH perturbation. We examine a prominent member of this subset of IDPs, α-synuclein, using a divide-and-conquer scheme that provides enhanced sampling of IDP structural ensembles. We constructed conformational ensembles of α-synuclein under neutral (pH ~ 7) and low (pH ~ 3) pH conditions and compared our results with available information obtained from smFRET, SAXS, and NMR studies. Specifically, α-synuclein has been found to in a more compact state at low pH conditions and the structural changes observed are consistent with those from experiments. We also characterize the conformational and dynamic differences between these ensembles and discussed the implication on promoting pathogenic fibril formation. We find that under low pH conditions, neutralization of negatively charged residues leads to compaction of the C-terminal portion of α-synuclein while internal reorganization allows α-synuclein to maintain its overall end-to-end distance. Here, we also observe different levels of intra-protein interaction between three regions of α-synuclein at varying pH and a shift towards more hydrophilic interactions with decreasing pH.

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

Confinement Effects on Proton Transfer in TiO 2 Nanopores from Machine Learning Potential Molecular Dynamics Simulations

Improved understanding of proton transfer in nanopores is critical for a wide range of emerging applications, yet experimentally probing mechanisms and energetics of this process remains a significant challenge. To help reveal details of this process, we developed and applied a machine learning potential derived from first-principles calculations to examine water reactivity and proton transfer in TiO 2 slit-pores. Here, we find that confinement of water within pores smaller than 0.5 nm imposes strong and complex effects on water reactivity and proton transfer. Although the proton transfer mechanism is similar to that at a TiO 2 interface with bulk water, confinement reduces the activation energy of this process, leading to more frequent proton transfer events. This enhanced proton transfer stems from the contraction of oxygen–oxygen distances dictated by the interplay between confinement and hydrophilic interactions. Our simulations also highlight the importance of the surface topology, where faster proton transport is found in the direction where a unique arrangement of surface oxygens enables the formation of an ordered water chain. In a broader context, our study demonstrates that proton transfer in hydrophilic nanopores can be enhanced by controlling pore size, surface chemistry, and topology.

36 MATERIALS SCIENCE↗
DOE OSTI2012

A comparison of methods for melting point calculation using molecular dynamics simulations

Accurate and efficient prediction of melting points for complex molecules is still a challenging task for molecular simulation, although many methods have been developed. Four melting point computational methods, including one free energy-based method (the pseudo-supercritical path (PSCP) method) and three direct methods (two interface-based methods and the voids method) were applied to argon and a widely studied ionic liquid 1-n-butyl-3-methylimidazolium chloride ([BMIM][Cl]). The performance of each method was compared systematically. All the methods under study reproduce the argon experimental melting point with reasonable accuracy. For [BMIM][Cl], the melting point was computed to be 320 K using a revised PSCP procedure, which agrees with the experimental value 337-339 K very well. However, large errors were observed in the computed results using the direct methods, suggesting that these methods are inappropriate for large molecules with sluggish dynamics. The strengths and weaknesses of each method are discussed. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3702587]

Zhang, Y↗
DOE OSTI2022

Mechanism of Solid Electrolyte Interphase Formation on Lithium Anodes Studied by Molecular Dynamics Simulations

We investigated the initial formation of the SEI on lithium-metal anodes in presence of several electrolyte compositions using ReaxFF, in absence of a bias potential. We observed the formation of well-defined regions with different density and oxidation states of Li. Dissolution of Li metal atoms results in an uneven distribution of Li in the liquid phase. The electrolyte decomposition mechanism was studied for various electrolyte mixtures. Overall, the reaction mechanisms observed with ReaxFF are in good agreement with previous reports using DFT. However, we found some discrepancies in specific predictions by the ReaxFF that should be addressed in future work.

25 ENERGY STORAGE↗
DOE OSTI2016

Neutron scattering of residual hydrogen in 1,4-dioxane d 8 liquid: Understanding measurements with molecular dynamics simulations

That incoherent scattering from protiated molecular liquids adds a constant background to the measured scattering intensity is well-known, but less appreciated is the fact that coherent scattering is also induced by the presence of hydrogen in a deuterated liquid. In fact, the scattering intensity can be very sensitive, in the small-q region, with respect to the amounts and distribution of residual H in the system. We used 1,4-dioxane liquid to demonstrate that the partial structure factors of the HD and DD atom pairs contribute significantly to intermolecular scattering and that uncertainty in the extent of deuteration account for discrepancies between simulations and measurements. Both contributions to uncertainty have similar magnitudes: scattering interference of the hydrogen–deuterium pair, and complementary interference from the deuterium–deuterium pair by virtue of chemical inhomogeneity. This situation arises in practice since deuteration of liquids is often 99% or less. A combined experimental and extensive computational study of static thermal neutron scattering of 1,4-dioxane demonstrates the foregoing. We show, through simulations, that the reason for the differences is the content of protiated dioxane (vendors quote 1%). We estimate that up to 5% (at 298 K and at 343 K) protiated molar fraction may be involved in generating the scattering differences. Finally, we find that the particular distribution of hydrogen in the protiated molecules affects the results significantly; here, we considered molecules to be either fully protiated or fully deuterated. This scenario best reconciles the computational and experimental results, and leads us to speculate that the deuteration synthesis process tends to leave a molecule either fully deuterated or fully protiated. As a result, we have used 1,4-dioxane as a model liquid, the effects described in this study extend to similar liquids, and similar systematic experimental/computational studies can be performed to either understand measurements or calibrate/validate molecular dynamics models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗