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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 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
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

Computational and experimental study of different brines in temperature swing solvent extraction desalination with amine solvents

Rapid global urbanization and high-salinity wastewater disposal from industrial activities have exerted significant pressure on water resources. Over the past few years, temperature swing solvent extraction (TSSE) has been identified as a promising technique to desalinate hypersaline brines. Despite its potential, the TSSE desalination literature has been mainly based on empirical insights, and the limited molecular simulation studies have primarily focused on NaCl brines. Herein, we use molecular dynamics (MD) simulations to study the TSSE desalination of four different brines, namely, KCl, KBr, NaCl, and NaBr using diisopropylamine as the solvent. Based on both bulk and interfacial brine-diisopropylamine MD results, here we investigate the qualitative and quantitative performance of the simulations by benchmarking these results against our experimental evaluations of these same systems. MD results provide satisfactory qualitative agreement with the experimental data of water solubilization in the organic phase and amine solubilization in the aqueous phase for the KBr, KCl, and NaBr brines. Also, the molecular mechanism of solvation of ionic species by water molecules over diisopropylamine suggested by the MD simulations is in agreement with our experimental data. However, larger qualitative and quantitative deviations were observed for the NaCl brines, and this is likely due to polarization and charge transfer effects, as quantified by our quantum chemical calculations.

42 ENGINEERING↗
DOE OSTI2022

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

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

Molecular Insights Into the Ionic Assembly of Poly-Galacturonic Acid Oligomers - Impact of Charge, Ionic Radius, and Polymer Functionalization

Pectin, a major class of matrix polysaccharides present in plant cell walls (PCW), contains widespread anionic saccharides that cross-link in the presence of cations. It modulates important functions such as cell-cell adhesion and determines the PCW's biomechanical properties. It is known that mono-, di-, and tri-valent cations facilitate cross-linking; however, significant knowledge gaps remain in understanding the structure and mechanism of pectin cross-linking. In this study, replica-exchange molecular dynamics (REMD) simulations were employed to elucidate the role of ionic charge, ionic radii, and functional groups on the cross-linking of homogalacturonan (HG), the most abundant pectin molecule. Our enhanced sampling approach in fully solvated environments suggests more effective cross-linking with higher-valent and smaller ions, and that the "zipper" conformation is more favorable than the prevalent "egg-box" conformation. These findings advance our fundamental understanding of pectin matrix structure in PCWs and provide a solid foundation to probe structure-property relationships in pectic polysaccharides.

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

Reactivity of the Hydrated Electron

Hydrated electrons are created in virtually every radiation environment and in many photochemical or electrochemical environments where liquid water is present, so their reaction products and reaction rate constants are naturally important in applications. Thanks to the strong optical absorbance of (e - ) aq , these rate constants are easy to measure, and a large database has been accumulated. It is not generally appreciated that no working theory of hydrated electron reaction rates presently exists. We discuss key experimental observations of hydrated electron reactions in the context of recent progress in theoretical and simulation developments toward understanding them, made possible by ever increasing computational power.

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

Simulation and Emulation of X-Ray Diffraction from Dynamic Compression Experiments

Many important aspects of the dynamic thermo-mechanical response of materials occur at the mesoscale, i.e. a physical scale of interactions smaller than what can be adequately described by homogenous behaviors, yet larger than the scale of the atomic lattice. Concurrent advancements in computational power, continuum theory, and experimental diagnostics are enabling unprecedented understanding of such interactions. However, we cannot develop a sufficient level of confidence in such mesoscale capability until the constitutive description of the underlying constituents is reliably representative of their actual physical behavior. Therefore, there is a strong need to combine experimental, modeling, and data-science techniques to validate models of the thermomechanical response of individual single crystals. One experimental diagnostic with high potential impact to shock physics and materials science is in-situ x-ray diffraction. This paper is primarily focused on simulation of x-ray diffraction in shock physics, but with an aim toward quantifying parametric uncertainty of simulation models. Here, we develop and demonstrate a data-science and model-driven approach to constrain the parameterization of continuum models of crystal lattice deformation associated with the shock response of crystalline materials. The framework is built around the connection between continuum hydrodynamic simulations of lattice deformation and a new Bragg diffraction simulation code, BarberShop. The dynamic deformation of a crystal lattice is modeled using the DiscoFlux model within an arbitrary Lagrangian-Eulerian hydrodynamic code, FLAG. These detailed continuum simulations of lattice deformation can be computationally slow, thus a statistical model is used to emulate the evolution of lattice deformation fields in time and across the considered model parameter space. Emulated lattice deformation fields can then be generated rapidly for any combination of physics model parameters. In turn, these fields can be fed into BarberShop to realize a rapid prediction of Bragg diffraction patterns associated with particular values of physics model parameters. The framework enables parameterization of the single crystal model to obtain Bragg diffraction patterns that most closely resemble a corresponding measurement. Furthermore, the framework naturally provides sensitivities of the lattice deformation to the physics parameters. We highlight the utility of this framework through the application to a synthetic closed-loop inverse problem leading to the parameterization of a single crystal material model. As a model problem, we consider the dynamic response of the energetic molecular crystal, cyclotrimethylenetrinitramine (or RDX), under dynamic compression induced by simulated flyer plate impact experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Liquid-liquid phase transition of hydrogen and its critical point: Analysis from ab initio simulation and a machine-learned potential

We simulate high-pressure hydrogen in its liquid phase close to molecular dissociation using a machine-learned interatomic potential. The model is trained with density functional theory (DFT) forces and energies, with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional. We show that an accurate NequIP model, an E(3)-equivariant neural network potential, accurately reproduces the phase transition present in PBE. Moreover, the computational efficiency of this model allows for substantially longer molecular dynamics trajectories, enabling us to perform a finite-size scaling (FSS) analysis to distinguish between a crossover and a true first-order phase transition. Here, we locate the critical point of this transition, the liquid-liquid phase transition (LLPT), at 1200-1300 K and 155-160 GPa, a temperature lower than most previous estimates and close to the melting transition.

08 HYDROGEN↗
DOE OSTI2022

Atomistic Materials Modeling of High-Pressure Hydrogen Interactions in Ethylene Propylene Diene Monomer (EPDM) Rubber

Elastomeric rubbers serve a vital role as sealing materials in the hydrogen storage and transport infrastructure. With applications including O-rings and hose-liners, these components are exposed to pressurized hydrogen at a range of temperatures, cycling rates, and pressure extremes. Cyclic (de)pressurization is known to degrade these materials through the process of cavitation. This readily visible failure mode occurs as a fracture or rupture of the material and is due to the oversaturated gas localizing to form gas bubbles. Computational modeling in the Hydrogen Materials Compatibility Program (H-Mat), co-led by Sandia National Laboratories and Pacific Northwest National Laboratory, employs multi-scale simulation efforts to build a predictive understanding of hydrogen-induced damage in materials. Modeling efforts within the project aim to provide insight into how to formulate materials that are less sensitive to high-pressure hydrogen-induced failure. In this document, we summarize results from atomistic molecular dynamics simulations, which make predictive assessments of the effects of compositional variations in the commonly used elastomer, ethylene propylene diene monomer (EPDM).

08 HYDROGEN↗
DOE OSTI2021

Assessment of mechanical, thermal properties and crystal shapes of monoclinic tricalcium silicate from atomistic simulations

The two most common polymorphs in industrial alite, M1 and M3, were characterized at the molecular scale. Different methods were employed and discussed to assess mechanical properties and specific heat of both polymorphs. The calculated homogenized elastic moduli and specific heat were found in good agreement with experimental measurements. A comparative analysis of spacial Youngs modulus reveal isotropic and anisotropic spacial distribution for M{sub 1} and M{sub 3} respectively. A more isotropic compressive strength is also reported for M{sub 1} when compared to M{sub 3} polymorph. Cleavage energies computation allowed to proposed equilibrium shapes for both polymorph, with significant differences. While the lowest cleavage energies were found along (100) and (001) for both polymorphs, the constructed M1 crystal possesses 3 independent facets, against seven for the M3 polymorph.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Biochemical Process Modeling and Simulation (BPMS)

The Biochemical Process Modeling and Simulation project aims to reduce the cost and time of research by applying theory, modeling, and simulation to the most relevant bottlenecks in the biochemical process. We use molecular modeling, quantum mechanics, metabolic modeling, fluid dynamics, and reaction-diffusion methods in close collaboration with pretreatment, hydrolysis, upgrading, and TEA. The project's outcomes are increased yields and efficiency of the biochemical process, added value to products, and reduced price of fuels by specifically targeting catalytic efficiency, reactor design, enzyme efficiency, and microbial design. We work closely with experimental projects to identify problems and iterate with experiments to find and refine solutions. By working with experimentalists, we decide on problems that can be solved with simulation that could otherwise not be solved or would take too long with experiment alone to reach BETO's targets. Over the years, we have produced solutions that have resulted in determining the most likely fatty-acid derivative for passive transport out of bacteria that upgrade biomass, and we have also designed enzyme mutations for enhanced lignin upgrading. Metabolic models have been developed to tune the activity of 2,3 butanediol production for the 2030 target. A computational method to deliver understanding of how complex omics data can be interpreted in the metabolic pathways of organisms used in the Agile Biofoundry. We have found methods to overcome specific barriers and continue to develop those methods. Our reactor studies have guided the design of both the microbes and reactors for aerobic and micro-aerobic production at all scales and have been instrumental in improving the accuracy of techno-economic analysis models. This project is essential in the process of selecting the final processes for 2030 SAF production targets. More specifically, recently, we have: 1) Predicted the strength of the basic structural interactions in commodity plastics to provide guidance for plastics upcycling strategies. 2) Developed computational tool to improve the characterization of lignin-derived compounds 3) Developed new methodologies to enable Machine Learning-based Directed Evolution for protein engineering. 4) Developed Machine Learning methods to predict protein promiscuity and mutations to further improve microbial and enzymatic driven processes and demonstrated the utility of ML approaches to engineering proteins from sparse experimental datasets. 5) Developed new methods to enable high-fidelity simulation of aerobic fermentation at industrial scale and resolving mismatch of time scales through subcycling/operator splitting 7) Identified the difficulty in preventing local high-oxygen conditions in industrial bubble columns, which leads to less-desirable acetoin production, suggesting future research directions in alternative reactor configurations (e.g loop reactors, shallow-channel reactors).

BIOMASS FUELS↗
DOE OSTI2023

Recent progress on in-medium properties of heavy mesons from finite-temperature EFTs

Mesons with heavy flavor content are an exceptional probe of the hot QCD medium produced in heavy-ion collisions. In the past few years, significant progress has been made toward describing the modification of the properties of heavy mesons in the hadronic phase at finite temperature. Ground-state and excited-state thermal spectral properties can be computed within a self-consistent many-body approach that employs appropriate hadron-hadron effective interactions, providing a unique opportunity to confront hadronic Effective Field Theory predictions with recent and forthcoming lattice QCD simulations and experimental data. In this article, we revisit the application of the imaginary-time formalism to extend the calculation of unitarized scattering amplitudes from the vacuum to finite temperature. These methods allow us to obtain the ground-state thermal spectral functions. The thermal properties of the excited states that are dynamically generated within the molecular picture are also directly accessible. We present here the results of this approach for the open-charm and open-bottom sectors. We also analyze how the heavy-flavor transport properties, which are strongly correlated to experimental observables in heavy-ion collisions, are modified in hot matter. In particular, transport coefficients can be computed using an off-shell kinetic theory that is fully consistent with the effective theory describing the scattering processes. The results of this procedure for both charm and bottom transport coefficients are briefly discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Machine learning interatomic potential for predicting the thermal properties of uranium nitride

We present a combined computational and experimental investigation of the thermal properties of uranium nitride (UN), focusing on the development of a machine learning interatomic potential (MLIP) using the moment tensor potential framework. The MLIP was trained on density functional theory (DFT) data and validated against various quantities including energies, forces, elastic constants, phonon dispersion, and defect formation energies, achieving excellent agreement with DFT calculations, prior experimental results, and our thermal conductivity measurement. The potential was then employed in molecular dynamics simulations to predict key thermal properties such as melting point, thermal expansion, specific heat, and lattice thermal conductivity. To further assess model accuracy, we fabricated a UN sample and performed new thermal conductivity measurements representative of single-crystal properties, which showed strong agreement with the MLIP predictions. This work confirms the reliability and predictive capability of the developed potential for determining the thermal properties of UN.

36 - MATERIALS SCIENCE↗
DOE OSTI2024

Multiparticle cumulant mapping for Coulomb explosion imaging: Calculations and algorithm

We present a versatile cumulant mapping algorithm for analyzing correlated particle emission, offering insights into complex electronic and nuclear dynamics. Recently, we have demonstrated the use of cumulant mapping to extract information-rich correlations between the momenta of multiple fragments produced in Coulomb explosion imaging experiments [C. Cheng et al., Phys. Rev. Lett. 130, 093001 (2023)]. We define cumulant mapping in terms of histograms, enabling fast computation of linear (additive) observables. However, applying the same algorithm to nonlinear (nonadditive) observables poses challenges, as the computation time of conventional estimators scales nonlinearly with data size. To overcome this, we develop estimators and an accompanying algorithm to enable computationally efficient estimation of the cumulant of interest. Comparisons of computation times and signal-to-noise ratios reveal the superior performance of our approach. This method is demonstrated on the (D+, D+, C+, O+) dissociation channel of CD 2 ⁢O 4+ produced in a strong-field ionization experiment. Additionally, Poisson statistics are used to simulate the two methods and provide insights into the efficiency of our algorithm. The proposed methodology unlocks efficient computation of cumulant mapping for a broader range of complex systems and observables, such as the laser pulse dependence of ionization dynamics.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Exploring Li-Ion Transport Properties of Li 3 TiCl 6 : A Machine Learning Molecular Dynamics Study

We performed large-scale molecular dynamics simulations based on a machine-learning force field (MLFF) to investigate the Li-ion transport mechanism in cation-disordered Li 3 TiCl 6 cathode at six different temperatures, ranging from 25°C to 100°C. In this work, deep neural network method and data generated by ab − initio molecular dynamics (AIMD) simulations were deployed to build a high-fidelity MLFF. Radial distribution functions, Li-ion mean square displacements (MSD), diffusion coefficients, ionic conductivity, activation energy, and crystallographic direction-dependent migration barriers were calculated and compared with corresponding AIMD and experimental data to benchmark the accuracy of the MLFF. From MSD analysis, we captured both the self and distinct parts of Li-ion dynamics. The latter reveals that the Li-ions are involved in anti-correlation motion that was rarely reported for solid-state materials. Similarly, the self and distinct parts of Li-ion dynamics were used to determine Haven’s ratio to describe the Li-ion transport mechanism in Li 3 TiCl 6 . Obtained trajectory from molecular dynamics infers that the Li-ion transportation is mainly through interstitial hopping which was confirmed by intra- and inter-layer Li-ion displacement with respect to simulation time. Ionic conductivity (1.06 mS/cm) and activation energy (0.29eV) calculated by our simulation are highly comparable with that of experimental values. Overall, the combination of machine-learning methods and AIMD simulations explains the intricate electrochemical properties of the Li 3 TiCl 6 cathode with remarkably reduced computational time. Thus, our work strongly suggests that the deep neural network-based MLFF could be a promising method for large-scale complex materials.

Selvaraj, Selva Chandrasekaran (ORCID:000000029023↗
DOE OSTI2023

COWALKER:EFFECTIVE TRANSPORT PROPERTIES OF COMPOSITE MATERIALS

SF-23-026 This software computes effective transport properties of composite materials involving fibers and nanoparticles using a random-walk algorithm that efficiently scales to an arbitrary number of processes and cores. Effective transport properties (thermal, electrical) are key to bridge the microstructure of complex materials with its macroscopic behavior. Traditional approaches either use effective medium approximations (closed mathematical expressions that are approximation for certain conditions) or continuum simulation models such as finite element or finite volume, which require the generation of a mesh for each configuration explored. cowalker leverages the equivalence between laplacian or heat equation-based models and random walks to compute the asymptotic transport properties from an ensemble of first sojourn times of a random walker moving through the composite material. This allows us to directly define a composite material as a collection of particles and use algorithms developed for molecular dynamics to quickly compute the intersection of the walker with the different interfaces in the material. cowalker is developed in C++, and it relies on the GNU Scientific Library for random generation. cowalker is currently delivered as source code, so the GSL library is not included in cowalker's distribution. A more userfriendly version, cowalker.jl is currently in development and will be released as part of cowalker.

YANGUAS-GIL, ANGEL↗
DOE OSTI2025

Tunable Topological Phonon for Next-generation Quantum Transduction

This project aims to understand the critical factors that determine transduction performance of topological phonons across an oxide perovskite/tungsten diselenide heterojunction. We will investigate mechanisms of their propagation and interfacial coupling using modeling and machine learning approaches. Methods include density functional theory, molecular dynamics, numerical transport simulations, and active learning for building up a training dataset for force field development.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Data-driven modeling of dislocation mobility from atomistics using physics-informed machine learning

Dislocation mobility, which dictates the response of dislocations to an applied stress, is a fundamental property of crystalline materials that governs the evolution of plastic deformation. Traditional approaches for deriving mobility laws rely on phenomenological models of the underlying physics, whose free parameters are in turn fitted to a small number of intuition-driven atomic scale simulations under varying conditions of temperature and stress. This tedious and time-consuming approach becomes particularly cumbersome for materials with complex dependencies on stress, temperature, and local environment, such as body-centered cubic crystals (BCC) metals and alloys. In this paper, we present a novel, uncertainty quantification-driven active learning paradigm for learning dislocation mobility laws from automated high-throughput large-scale molecular dynamics simulations, using Graph Neural Networks (GNN) with a physics-informed architecture. We demonstrate that this Physics-informed Graph Neural Network (PI-GNN) framework captures the underlying physics more accurately compared to existing phenomenological mobility laws in BCC metals.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARSCoV. The key to understanding SARS-CoV-2's higher infectivity lies partly in its host receptor recognition mechanism. Experiments show that the human angiotensin converting enzyme 2 (ACE2) protein, which serves as the primary receptor for both CoVs, binds to the receptor binding domain (RBD) of CoV-2's spike protein stronger than SARS-CoV's spike RBD. The molecular basis for this difference in binding affinity, however, remains unexplained from X-ray structures. To go beyond insights gained from X-ray structures and investigate the role of thermal fluctuations in structure, we employ all-atom molecular dynamics simulations. Microseconds-long simulations reveal that while CoV and CoV-2 spike-ACE2 interfaces have similar conformational binding modes, CoV-2 spike interacts with ACE2 via a larger combinatorics of polar contacts, and on average, makes 45% more polar contacts. Correlation analysis and thermodynamic calculations indicate that these differences in the density and dynamics of polar contacts arise from differences in spatial arrangements of interfacial residues, and dynamical coupling between interfacial and non-interfacial residues. Furthermore, these results recommend that ongoing efforts to design spike-ACE2 peptide blockers will benefit from incorporating dynamical information as well as allosteric coupling effects.

59 BASIC BIOLOGICAL SCIENCES↗