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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Comparison of fixed charge and polarizable models for predicting the structural, thermodynamic, and transport properties of molten alkali chlorides

Results from extensive molecular dynamics simulations of molten LiCl, NaCl, KCl, and RbCl over a wide range of temperatures are reported. Comparison is made between the “Polarizable Ion Model” (PIM) and the non-polarizable “Rigid Ion Model” (RIM). Densities, self-diffusivities, shear viscosities, ionic conductivities, and thermal conductivities are computed and compared with experimental data. In addition, radial distribution functions are computed from ab initio molecular dynamics simulations and compared with the two sets of classical simulations as well as experimental data. Here, the two classical models perform reasonably well at capturing structural and dynamic properties of the four molten alkali chlorides, both qualitatively and often quantitatively. With the singular exception of liquid density, for which the PIM is more accurate than the RIM, there are few clear trends to suggest that one model is more accurate than the other for the four alkali halide systems studied here.

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

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

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

36 MATERIALS SCIENCE↗
DOE OSTI2020

Molecular dynamics and continuum analyses of the electrokinetic zeta potential in nanostructured slit channels

This work presents a theoretical and numerical study of electrokinetic flow and the zeta potential for the case of slit channels with nanoscale surface features of dimensions comparable to the Debye length, by employing molecular dynamics simulations and continuum-level analyses. Additionally, a simple analytical model for considering the average effect of such surface features producing nanoscale roughness is proposed by employing matched asymptotic solutions for the charge density and fluid flow field, and matching conditions that satisfy electroneutrality and the Onsager reciprocal relation between the electroosmotic flow rate and streaming current. The proposed analytical model quantitatively accounts for results from molecular dynamics simulations that consider the presence of ion solvation shells and surface hydration layers. Our analysis indicates that a simultaneous knowledge of the electroosmotic and pressure-driven flow rate or streaming current can be instrumental to unambiguously determine the zeta potential in the presence of nanoscale surface features.

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

Reinforcement learning based hybrid bond-order coarse-grained interatomic potentials for exploring mesoscale aggregation in liquid–liquid mixtures

Exploring mesoscopic physical phenomena has always been a challenge for brute-force all-atom molecular dynamics simulations. Although recent advances in computing hardware have improved the accessible length scales, reaching mesoscopic timescales is still a significant bottleneck. Coarse-graining of all-atom models allows robust investigation of mesoscale physics with a reduced spatial and temporal resolution but preserves desired structural features of molecules, unlike continuum-based methods. Here, we present a hybrid bond-order coarse-grained forcefield (HyCG) for modeling mesoscale aggregation phenomena in liquid–liquid mixtures. The intuitive hybrid functional form of the potential offers interpretability to our model, unlike many machine learning based interatomic potentials. We parameterize the potential with the continuous action Monte Carlo Tree Search (cMCTS) algorithm, a reinforcement learning (RL) based global optimizing scheme, using training data from all-atom simulations. The resulting RL-HyCG correctly describes mesoscale critical fluctuations in binary liquid–liquid extraction systems. cMCTS, the RL algorithm, accurately captures the mean behavior of various geometrical properties of the molecule of interest, which were excluded from the training set. The developed potential model along with the RL-based training workflow could be applied to explore a variety of other mesoscale physical phenomena that are typically inaccessible to all-atom molecular dynamics simulations.

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

Synergetic Effects of Soil Organic Matter Components During Interactions with Minerals

Mineral-associated soil organic matter (SOM) is critical for stabilizing organic carbon and mitigating climate change. However, mineral-SOM interactions at the molecular scale, particularly synergetic adsorption through organic-organic interaction on the mineral surface known as organic multilayering, remain poorly understood. This study investigates the impact of organic multilayering on mineral-SOM interactions, by integrating macroscale experiments and molecular-scale simulations that assess the individual and sequential adsorption of major SOM compounds – lauric acid (lipid), pentaglycine (amino acid), trehalose (carbohydrate), and lignin onto soil minerals. Ferrihydrite, Al-hydroxide, and calcite are exposed to SOM compounds to determine adsorption affinities and binding energies. Results show that lauric acid has 20-40 times higher K d than pentaglycine, following the order K d (ferrihydrite) > K d (Al-hydroxide) >> K d (calcite). Molecular-scale simulations confirm that lauric acid has a higher binding energy (30.8 kcal/mol) on ferrihydrite than pentaglycine (6.0 kcal/mol), attributed to lipid hydrophobicity. The lower binding energy of pentaglycine results from its hydrophilic amide groups, facilitating partitioning into water. Sequential experiments examine how the first layer of lipid or amino acid affects the adsorption of carbohydrate/lignin, which show little or no individual adsorption affinities. Macroscale results reveal that lipid and amino acid adsorption induce ferrihydrite particle repulsion increasing reactive surface area and enhancing carbohydrate/lignin adsorption independently and synergistically through organic multilayering. Molecular-scale results reveal that amino acid adsorbed on ferrihydrite interacts more readily with lignin macroaggregates (preformed in solution) than with individual lignin units, indicating organic multilayering via H-bonding. Further, these findings reveal the molecular mechanisms of SOM-mineral interactions, crucial for enhancing soil carbon stabilization.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Molecular dynamics analysis of particle number fluctuations in the mixed phase of a first-order phase transition

Molecular dynamics simulations are performed for a finite nonrelativistic system of particles with Lennard-Jones potential. We study the effect of liquid-gas mixed phase on particle number fluctuations in coordinate subspace. A metastable region of the mixed phase, the so-called nucleation region, is analyzed in terms of a noninteracting cluster model. Large fluctuations due to spinodal decomposition are observed. They arise due to the interplay between the size of the acceptance region and that of the liquid phase. These effects are studied with a simple geometric model. The model results for the scaled variance of particle number distribution are compared with those obtained from the direct molecular dynamic simulations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Stockmayer fluid simulations for viscosity and glass transition temperature of ionic liquids

We develop a Stockmayer fluid model for molecular dynamics simulations of ionic liquids that captures molecular polarization, ionic conductivity, viscosity, and glass transition temperature, using ethylammonium nitrate (EAN) as an example. The ions in EAN are treated as spheres interacting via the Lennard-Jones potential with an embedded point charge and a permanent dipole moment. We show that our simulation results for EAN are consistent with experimental data and then explore the effects of the molecular parameters on the viscosity of ionic liquids. Our results indicate that viscosity monotonically increases with ionic charge and dipole moment but non-monotonically changes with ionic diameter (or molar volume). This non-monotonic trend arises from the competition among the electrostatic interactions, molecular packing, and size asymmetry between the cation and anion. In conclusion, our model also shows that long-lived ion pairs result in higher viscosities.

Coarse-grained simulations↗
DOE OSTI2026

Towards the Ultimate Strength of Medium‐Entropy Alloys Through Pulsed Lasers

The tensile strength of metals at extreme strain rates is a key predictor of their performance in ballistic and structural impact applications. An important experimental method to reach these extreme strain rates is the use of high-amplitude, short-duration pulsed lasers. The Jupiter Laser Facility at the Lawrence Livermore National Laboratory enabled probing for the first time the mechanical response of several promising High Entropy Alloys at times on the order of nanoseconds (strain rates of ∼10 7 and ∼10 9 s −1 ). The measured strength is in the range of 6 to 10 GPa, ten times the quasistatic value. The mechanisms of plastic deformation and failure were identified and quantified through analysis and molecular dynamics simulation. The reflected wave amplitudes, obtained by VISAR, were used to determine the tensile (spall) stress. The high tensile strength obtained is due to two factors: the strain-rate dependence of plastic flow and the kinetics of void nucleation, growth, and coalescence. The experimental results are compared with an analytical prediction considering both grain-interior and grain-boundary void initiation. Molecular dynamics simulations, conducted at strain rates of 10 8 and 10 9 s −1 , rationalize the experimental results. In conclusion, they provide valuable information about the process of failure evolution, and reveal that grain boundary separation plays a pivotal role in spalling.

Materials science↗
DOE OSTI2024

Solvation Structure of Methanol-in-Salt Electrolyte Revealed by Small-Angle X-ray Scattering and Simulations

The solvation structure of water-in-salt electrolytes was thoroughly studied, and two competing structures—anion solvated structure and anion network—were well-defined in recent publications. To further reveal the solvation structure in those highly concentrated electrolytes, particularly the influence of solvent, methanol was chosen as the solvent for this proposed study. In this work, small-angle X-ray scattering, small-angle neutron scattering, Fourier-transform infrared spectroscopy, and Raman spectroscopy were utilized to obtain the global and local structural information. With the concentration increment, the anion network formed by TFSI - became the dominant structure. Meanwhile, the hydrogen bonds among methanol were interrupted by the TFSI - anion and formed a new connection with them. Further, molecular dynamic simulations with two different force fields (GAFF and OPLS-AA) are tested, and GAFF agreed with synchrotron small-angle X-ray scattering/wide-angle X-ray scattering (SAXS/WAXS) results well and provided insightful information about molecular/ion scale solvation structure. This article not only deepens the understanding of the solvation structure in highly concentrated solutions, but more importantly, it provides additional strong evidence for utilizing SAXS/WAXS to validate molecular dynamics simulations.

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

Recent developments in 3D-printed membranes for water desalination

The recognition of membrane separations as a vital technology platform for enhancing the efficiency of separation processes has been steadily increasing. Concurrently, 3D printing has emerged as an innovative approach to fabricating reverse osmosis membranes for water desalination and treatment purposes. This method provides a high degree of control over membrane chemistry and structural properties. In particular, when compared to traditional manufacturing techniques, 3D printing holds the potential to expedite customization, a feat that is typically achieved through conventional manufacturing methods but often involves numerous processes and significant costs. This review aims to present the current advancements in membrane manufacturing technology specifically tailored for water desalination purposes, with a particular focus on the development of 3D-printed membranes. A comprehensive analysis of recent progress in 3D-printed membranes is provided. However, conducting experimental work to investigate various influential factors while ensuring consistent results poses a significant challenge. To address this, we explore how membrane manufacturing processes and performance can be effectively pre-designed and guided through the use of molecular dynamics simulations. Finally, this review outlines the challenges faced and presents future perspectives to shed light on research directions for optimizing membrane manufacturing processes and achieving optimal membrane performance.

3D printing membranes↗
DOE OSTI2021

Extended Lagrangian Born–Oppenheimer molecular dynamics for orbital-free density-functional theory and polarizable charge equilibration models

We report extended Lagrangian Born–Oppenheimer molecular dynamics (XL-BOMD) is formulated for orbital-free Hohenberg–Kohn density-functional theory and for charge equilibration and polarizable force-field models that can be derived from the same orbital-free framework. The purpose is to introduce the most recent features of orbital-based XL-BOMD to molecular dynamics simulations based on charge equilibration and polarizable force-field models. These features include a metric tensor generalization of the extended harmonic potential, preconditioners, and the ability to use only a single Coulomb summation to determine the fully equilibrated charges and the interatomic forces in each time step for the shadow Born–Oppenheimer potential energy surface. The orbital-free formulation has a charge-dependent, short-range energy term that is separate from long-range Coulomb interactions. This enables local parameterizations of the short-range energy term, while the long-range electrostatic interactions can be treated separately. The theory is illustrated for molecular dynamics simulations of an atomistic system described by a charge equilibration model with periodic boundary conditions. The system of linear equations that determines the equilibrated charges and the forces is diagonal, and only a single Ewald summation is needed in each time step. The simulations exhibit the same features in accuracy, convergence, and stability as are expected from orbital-based XL-BOMD.

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

Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes

Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.

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

Atomic scale understanding of organic anion separations using ion-exchange resins

A combination of ab initio and classical molecular dynamic simulations was used to explore the adsorption/desorption and diffusion characteristics of ion-exchange resins for extraction of organic anions in electrically-driven separation processes. We considered two classes of carboxylate mixtures that are commonly encountered in bioprocessing separations: a short chain fatty acid mixture (acetate/butyrate) and an aromatic mixture (ferulate/coumarate). The suitability of several resin materials including PFC100E, IRC86, PFA444 and IRA67 was interrogated. The decomposition of the interaction energies by the symmetry-adapted perturbation theory and the classical molecular dynamic simulations of organic diffusion together reveal that the geometries of the organic anions and the functional groups of the resins, as well as their Columbic interactions, are the controlling factors in the diffusion process of the organic compounds in these resins. Additionally, classical simulations also show that modifying the functionality of resin beads, the magnitude of electric fields, and the ratio of organic mixtures may provide an effective way to control the diffusion rate and obtain selective separation of these organic mixtures. Finally, a general suggestion for favorable separation conditions is summarized.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Dehydration-Driven Ion Aggregation and the Onset of Gelation in ZnCl2 Solution

A minimal model of ionic aggregation in concentrated ZnCl2 is developed, guided by molecular dynamics simulations with a machine-learned potential. It explicitly incorporates solvent-site depletion, correlated chloride binding, and allows for loops within Zn–Cl clusters. Dehydration drives two coordination-controlled structural changes: a crossover at Z=2 from predominantly isolated Zn-containing species to Cl-bridged clusters and the onset of gelation near Z≈3. The model reproduces the concentration-dependent trends observed in the molecular dynamics simulations with two fitted parameters, while the cluster-size distribution at the highest concentration is consistent with three-dimensional percolation scaling over the accessible range of cluster sizes.

25 ENERGY STORAGE↗
DOE OSTI2024

Improving the reliability of machine learned potentials for modeling inhomogeneous liquids

The atomic-scale response of inhomogeneous fluids at interfaces and surrounding solute particles plays a critical role in governing chemical, electrochemical, and biological processes. Classical molecular dynamics simulations have been applied extensively to simulate the response of fluids to inhomogeneities directly, but are limited by the accuracy of the underlying interatomic potentials. Here, we use neural network potentials (NNPs) trained to ab initio simulations to accurately predict the inhomogeneous responses of two distinct fluids: liquid water and molten NaCl. Although NNPs can be readily trained to model complex bulk systems across a range of state points, we show that to appropriately model a fluid's response at an interface, relevant inhomogeneous configurations must be included in the training data. In order to sufficiently sample appropriate configurations of such inhomogeneous fluids, we develop protocols based on molecular dynamics simulations in the presence of external potentials. We demonstrate that NNPs trained on inhomogeneous fluid configurations can more accurately predict several key properties of fluids—including the density response, surface tension and size-dependent cavitation free energies—for liquid water and molten NaCl, compared to both empirical interatomic potentials and NNPs that are not trained on such inhomogeneous configurations. This work therefore provides a first demonstration and framework to extract the response of inhomogeneous fluids from first principles for classical density-functional treatment of fluids free from empirical potentials.

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

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

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

Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor

Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ~5-50 cm -1 . This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effect of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal/mol -1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.

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

High-resolution neutron time-of-flight measurements for light water at the Spallation Neutron Source (SNS), Oak Ridge National Laboratory

Series of light water inelastic neutron scattering experiments have been made at the Oak Ridge National Laboratory (ORNL), Spallation Neutron Source (SNS) covering temperatures ranging from 295 K to 600 K and pressures of 1 bar and 150 bar. The temperatures and pressures ranges correspond to that of pressurized light water reactors. The inelastic scattering measurements will help the development of light water thermal scattering kernels, also known as S (α,β) thermal scattering law (TSL), in a consistent fashion given the amount and the quality of the measured data. Light water thermal scattering evaluations available in existing nuclear data libraries have certain limitations and pitfalls. This paper introduces the state of the art of the light water thermal scattering cross-section data not only for room temperature but as well as for reactor operating temperatures, i.e. 550 - 600 K. During the past few years there has been a renewed interest in re-investigating the existing TSL models and utilize the recent experimental data or perform molecular dynamics simulations. It should be pointed out that no single TSL evaluation is based entirely on experimental data and one has to rely on TSL models or a combination of both. New TOF measurement of light water at the SNS, with a detailed description of the experimental setup, measurement conditions, and the associated foreseen results is presented in this paper. The analysis of the experimental data would help in validating the existing approach based on old experimental data or based on molecular dynamic simulations using classical water models, knowledge of which is very important to generate TSL libraries at reactor operating conditions.

Leal, Luiz C.↗