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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 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Polymers in Deep Eutectic Solvents

The project investigated the behavior of polymers in ionic liquids such as deep eutectic solvents using an array of techniques. These included the development of atomistic force fields, coarse graining these force fields to the united atom level, large scale molecular dynamics (MD) simulations using new thermostat algorithms, and machine learning (ML) methods for the phase behavior. The project demonstrated the feasibility and accuracy of first principles force fields for ionic liquids, deep-eutectic solvents, and urea-water mixtures. A novel hierarchical coarse graining method was then used to develop accurate and efficient united-atom models, using which microsecond simulations were performed for polymers in ionic liquids. These simulations were in quantitative agreement with experiment, thus resolving previous controversies. Methods were also developed to obtain the potential of mean force between complex ions in solution. Finally, supervised ML methods were developed for the phase behavior of polymers in ionic liquids.

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

Machine learning Frenkel Hamiltonian parameters to accelerate simulations of exciton dynamics

In this manuscript, we develop multiple machine learning (ML) models to accelerate a scheme for parameterizing site-based models of exciton dynamics from all-atom configurations of condensed phase sexithiophene systems. This scheme encodes the details of a system’s specific molecular morphology in the correlated distributions of model parameters through the analysis of many single-molecule excited-state electronic-structure calculations. These calculations yield excitation energies for each molecule in the system and the network of pair-wise intermolecular electronic couplings. In this work, we demonstrate that the excitation energies can be accurately predicted using a kernel ridge regression (KRR) model with Coulomb matrix featurization. We present two ML models for predicting intermolecular couplings. The first one utilizes a deep neural network and bi-molecular featurization to predict the coupling directly, which we find to perform poorly. The second one utilizes a KRR model to predict unimolecular transition densities, which can subsequently be analyzed to compute the coupling. We find that the latter approach performs excellently, indicating that an effective, generalizable strategy for predicting simple bimolecular properties is through the indirect application of ML to predict higher-order unimolecular properties. Such an approach necessitates a much smaller feature space and can incorporate the insight of well-established molecular physics.

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

State predictive information bottleneck

We report the ability to make sense of the massive amounts of high-dimensional data generated from molecular dynamics simulations is heavily dependent on the knowledge of a low-dimensional manifold (parameterized by a reaction coordinate or RC) that typically distinguishes between relevant metastable states, and which captures the relevant slow dynamics of interest. Methods based on machine learning and artificial intelligence have been proposed over the years to deal with learning such low-dimensional manifolds, but they are often criticized for a disconnect from more traditional and physically interpretable approaches. To deal with such concerns, in this work we propose a deep learning based state predictive information bottleneck approach to learn the RC from high-dimensional molecular simulation trajectories. We demonstrate analytically and numerically how the RC learnt in this approach is connected to the committor in chemical physics and can be used to accurately identify transition states. A crucial hyperparameter in this approach is the time delay or how far into the future the algorithm should make predictions about. Through careful comparisons for benchmark systems, we demonstrate that this hyperparameter choice gives useful control over how coarse-grained we want the metastable state classification of the system to be. We thus believe that this work represents a step forward in systematic application of deep learning based ideas to molecular simulations.

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

Data-Driven Approach for Controlled Icosahedral Boron- Rich Compound Growth

This final technical report summarizes the research accomplishments and research highlights at the end of the funding period. This project aimed to leverage existing and new computational data produced from first-principles and molecular dynamics simulations to understand the thermodynamic, mechanical, and electronic properties of icosahedral boron compounds. The goal is to achieve targeted material properties by controlling the synthesis routes of these boron-rich compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2025

Multiscale Machine-Learned Modeling Infrastructure

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

Di Natale, Francesco [Lawrence Livermore National ↗
DOE OSTI2021

Bayesian optimization for chemical products and functional materials

The design of chemical-based products and functional materials is vital to modern technologies, yet remains expensive and slow. Artificial intelligence and machine learning offer new approaches to leverage data to overcome these challenges. Herein this review focuses on recent applications of Bayesian optimization (BO) to chemical products and materials including molecular design, drug discovery, molecular modeling, electrolyte design, and additive manufacturing. Numerous examples show how BO often requires an order of magnitude fewer experiments than Edisonian search. The essential equations for BO are introduced in a self-contained primer specifically written for chemical engineers and others new to the area. Finally, the review discusses four current research directions for BO and their relevance to product and materials design.

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

X-ray and molecular dynamics study of the temperature-dependent structure of molten NaF-Zr⁢F 4

The local atomic structure of NaF-Zr⁢F 4 (53–47 mol%) molten system and its evolution with temperature are examined with x-ray scattering measurements which are then used to validate the quality of ab initio and neural network-based molecular dynamics (NNMD) calculations in the temperature range 515–700°⁢C. The machine-learning enhanced NNMD calculations offer improved efficiency while maintaining accuracy at higher distances compared to ab initio calculations. Looking at the evolution of the pair distribution function with increasing temperature, a fundamental change in the liquid structure within the selected temperature range, accompanied by a slight decrease in overall correlation is revealed. NNMD calculations indicate the coexistence of three different fluorozirconate complexes: [Zr⁢F 6 ] 2– , [Zr⁢F 7 ] 3– , and [Zr⁢F 8 ] 4– , with a shift in the dominant coordination state from the 7-coordinated Zr cation toward a 6-coordinated cation with increasing temperature. The study also highlights the metastability of different local coordination structures, with frequent interconversions between the 6- and 7-coordinate states. Analysis of the Zr-F-Zr angular distribution function reveals the presence of both “edge-sharing” and “corner-sharing” fluorozirconate complexes with specific bond angles and distances in accord with previous studies, while the next-nearest-neighbor cation-cation correlations demonstrate a clear preference for unlike cations as nearest-neighbor pairs, emphasizing nonrandom arrangement. Finally, these findings contribute to a comprehensive understanding of the complex local structure of the molten salt, providing insights into temperature-dependent preferences and correlations within the molten system.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Neural network potential from bispectrum components: A case study on crystalline silicon

In this article, we present a systematic study on developing machine learning force fields (MLFFs) for crystalline silicon. While the main-stream approach of fitting a MLFF is to use a small and localized training set from molecular dynamics simulations, it is unlikely to cover the global features of the potential energy surface. Additionally, to remedy this issue, we used randomly generated symmetrical crystal structures to train a more general Si-MLFF. Furthermore, we performed substantial benchmarks among different choices of material descriptors and regression techniques on two different sets of silicon data. Our results show that neural network potential fitting with bispectrum coefficients as descriptors is a feasible method for obtaining accurate and transferable MLFFs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Liquid–Vapor Phase Equilibrium in Molten Aluminum Chloride (AlCl 3 ) Enabled by Machine Learning Interatomic Potentials

Molten salts are promising candidates in numerous clean energy applications, where knowledge of thermophysical properties and vapor pressure across their operating temperature ranges is critical for safe operations. Due to challenges in evaluating these properties using experimental methods, fast and scalable molecular simulations are essential to complement the experimental data. In this study, we developed machine learning interatomic potentials (MLIP) to study the AlCl 3 molten salt across varied thermodynamic conditions (T = 473–613 K and P = 2.7–23.4 bar), which allowed us to predict temperature-surface tension correlations and liquid–vapor phase diagram from direct simulations of two-phase coexistence in this molten salt. Two MLIP architectures, a Kernel-based potential and neural network interatomic potential (NNIP), were considered to benchmark their performance for AlCl 3 molten salt using experimental structure and density values. The NNIP potential employed in two-phase equilibrium simulations yields the critical temperature and critical density of AlCl 3 that are within 10 K (∼3%) and 0.03 g/cm 3 (∼7%) of the reported experimental values. An accurate correlation between temperature and viscosities is obtained as well. In doing so, we report that the inclusion of low-density configurations in their training is critical to more accurately represent the AlCl 3 system across a wide phase-space. The MLIP trained using PBE-D3 functional in the ab initio molecular dynamics (AIMD) simulations (120 atoms) also showed close agreement with experimentally determined molten salt structure comprising Al 2 Cl 6 dimers, as validated using Raman spectra and neutron structure factor. Furthermore, the PBE-D3 as well as its trained MLIP showed better liquid density and temperature correlation for AlCl 3 system when compared to several other density functionals explored in this work. Overall, the demonstrated approach to predict temperature correlations for liquid and vapor densities in this study can be employed to screen nuclear reactors-relevant compositions, helping to mitigate safety concerns.

Ab initio molecular dynamics↗
DOE OSTI2021

Application of machine learning in the determination of impact parameter in the 132 Sn+ 124 Sn system

Here, 132 Sn + 124 Sn collisions at a beam energy of 270 MeV/nucleon were performed at the Radioactive Isotope Beam Factory (RIBF) in RIKEN to investigate the nuclear equation of state. Reconstructing the impact parameter is one of the important tasks in the experiment as it relates to many observable. In this work, we employ three commonly used algorithms in machine learning, the artificial neural network (ANN), the convolutional neural network (CNN), and the light gradient boosting machine (LightGBM), to determine the impact parameter by analyzing either the charged particle spectra or several features simulated with events from the ultrarelativistic quantum molecular dynamics (UrQMD) model. To closely imitate experimental data and investigate the generalizability of the trained machine learning algorithms, incompressibility of nuclear equation of state and the in-medium nucleon-nucleon cross sections are varied in the UrQMD model to generate the training data. The mean absolute error Δb between the true and the predicted impact parameter is smaller than 0.45 fm if training and testing sets are sampled from the UrQMD model with the same parameter set. However, if training and testing sets are sampled with different parameter sets, Δb would increase to 0.8 fm. The generalizability of the trained machine learning algorithms suggests that these machine learning algorithms can be used reliably to reconstruct the impact parameter in experiment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Quantum-Chemically Informed Machine Learning: Prediction of Energies of Organic Molecules with 10 to 14 Non-hydrogen Atoms

High-fidelity quantum-chemical calculations can provide accurate predictions of molecular energies, but their high computational costs limit their utility, especially for larger molecules. We have shown in previous work that machine learning models trained on high-level quantum-chemical calculations (G4MP2) for organic molecules with one to nine non-hydrogen atoms can provide accurate predictions for other molecules of comparable size at much lower costs. Here we demonstrate that such models can also be used to effectively predict energies of molecules larger than those in the training set. To implement this strategy, we first established a set of 191 molecules with 10–14 non-hydrogen atoms having reliable experimental enthalpies of formation. We then assessed the accuracy of computed G4MP2 enthalpies of formation for these 191 molecules. The error in the G4MP2 results was somewhat larger than that for smaller molecules, and the reason for this increase is discussed. Two density functional methods, B3LYP and ωB97X-D, were also used on this set of molecules, with ωB97X-D found to perform better than B3LYP at predicting energies. The G4MP2 energies for the 191 molecules were then predicted using these two functionals with two machine learning methods, the FCHL-Δ and SchNet-Δ models, with the learning done on calculated energies of the one to nine non-hydrogen atom molecules. The better-performing model, FCHL-Δ, gave atomization energies of the 191 organic molecules with 10–14 non-hydrogen atoms within 0.4 kcal/mol of their G4MP2 energies. Thus, this work demonstrates that quantum-chemically informed machine learning can be used to successfully predict the energies of large organic molecules whose size is beyond that in the training set.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A theoretical study of solid solution strengthening in the refractory medium entropy alloy Nb 45 Ta 25 Ti 15 Hf 15

The refractory medium-entropy alloy (RMEA) Nb 45 Ta 25 Ti 15 Hf 15 exhibits exceptional tensile ductility and fracture toughness at ambient temperature, but its engineering applications are limited by a lack of high temperature strength. Using a machine-learning interatomic potential (MLIP) with near-density functional theory (DFT) accuracy, we conducted molecular dynamics (MD) and statics simulations of the behavior of dislocations with both screw and edge characters. We also analyze experimentally measured yield strengths using the Rao-Suzuki model and the Maresca-Curtin model modified to include a temperature-dependent shear modulus and a bulk modulus-dependent misfit volume, thereby uncovering the mechanisms underlying the yielding of this RMEA. Compared with the published experimental yield strength, the models parameterized by the MLIP effectively reproduce the experimental results over a wide temperature range. The models and MD simulations indicate that yielding is governed by screw dislocations, with dipole dragging as the dominant mechanism. In MD simulations, we observed a potential softening mechanism not considered by the Rao-Suzuki screw model: slow migration of interstitial jogs along the dislocation core, which could lead to the annihilation of vacancy and interstitial jog pairs by their combination.

BCC complex concentrated alloys↗
DOE OSTI2021

Enhancing the formation of ionic defects to study the ice Ih/XI transition with molecular dynamics simulations

Ice Ih, the common form of ice in the biosphere, contains proton disorder. Its proton-ordered counterpart, ice XI, is thermodynamically stable below 72 K. However, the formation of ice XI is kinetically hindered, and experimentally it is obtained by doping with KOH. Doping creates ionic defects that promote the migration of protons and the associated change in proton configuration. In this article, we mimic the effect of doping with a bias potential that enhances the formation of ionic defects in molecular dynamics simulations. The recombination of the ions thus formed proceeds through fast migration of the hydroxide along hydrogen bond loops, providing a physical and expedite way to change the proton configuration. Here, a key ingredient of this approach is a machine learning potential trained with density functional theory data and capable of modelling molecular dissociation. We exemplify the usefulness of this idea by studying the order-disorder transition using an appropriate order parameter that distinguishes the proton environments in ice Ih and XI. We calculate the changes in free energy, enthalpy, and entropy associated with the transition. Our estimated entropy agrees with experiment within the error bars of the calculation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Artificial Intelligence for Autonomous Molecular Design: A Perspective

Domain-aware artificial intelligence has been increasingly adopted in recent years to expedite molecular design in various applications, including drug design and discovery. Recent advances in areas such as physics-informed machine learning and reasoning, software engineering, high-end hardware development, and computing infrastructures are providing opportunities to build scalable and explainable AI molecular discovery systems. This could improve a design hypothesis through feedback analysis, data integration that can provide a basis for the introduction of end-to-end automation for compound discovery and optimization, and enable more intelligent searches of chemical space. Several state-of-the-art ML architectures are predominantly and independently used for predicting the properties of small molecules, their high throughput synthesis, and screening, iteratively identifying and optimizing lead therapeutic candidates. However, such deep learning and ML approaches also raise considerable conceptual, technical, scalability, and end-to-end error quantification challenges, as well as skepticism about the current AI hype to build automated tools. To this end, synergistically and intelligently using these individual components along with robust quantum physics-based molecular representation and data generation tools in a closed-loop holds enormous promise for accelerated therapeutic design to critically analyze the opportunities and challenges for their more widespread application. This article aims to identify the most recent technology and breakthrough achieved by each of the components and discusses how such autonomous AI and ML workflows can be integrated to radically accelerate the protein target or disease model-based probe design that can be iteratively validated experimentally. Taken together, this could significantly reduce the timeline for end-to-end therapeutic discovery and optimization upon the arrival of any novel zoonotic transmission event. Our article serves as a guide for medicinal, computational chemistry and biology, analytical chemistry, and the ML community to practice autonomous molecular design in precision medicine and drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanism of Antiferroelectricity in Polycrystalline ZrO 2

The size and electric field dependent induction of polarization in antiferroelectric ZrO 2 is the key to several technological applications that are unimaginable a decade ago. However, the lack of a deeper understanding of the mechanism hinders progress. Molecular dynamics simulations of polycrystalline ZrO 2 , based on machine-learned interatomic forces with near ab initio quality, shed light on the fundamental mechanism of the size effect on the transition fields. Stress in the oxygen sublattice is the most important factor. The so constructed interatomic forces allow the calculation of the transition fields as a function of the ZrO 2 film thickness and predict the ferroelectricity at large thickness. The simulation results are validated with electrical and piezo response force microscopy measurements. The results allow a clear interpretation of the properties of the double-hysteresis loops as well as the construction of the free energy landscape of ZrO 2 grains.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Davis Computational Spectroscopy Workflow—From Structure to Spectra

Here, we describe an automated workflow that connects a series of atomic simulation tools to investigate the relationship between atomic structure, lattice dynamics, materials properties, and inelastic neutron scattering (INS) spectra. Starting from the atomic simulation environment (ASE) as an interface, we demonstrate the use of a selection of calculators, including density functional theory (DFT) and density functional tight binding (DFTB), to optimize the structures and calculate interatomic force constants. We present the use of our workflow to compute the phonon frequencies and eigenvectors, which are required to accurately simulate the INS spectra in crystalline solids like diamond and graphite as well as molecular solids like rubrene. We have also implemented a machine-learning force field based on Chebyshev polynomials called the Chebyshev interaction model for efficient simulation (ChIMES) to improve the accuracy of the DFTB simulations. We then explore the transferability of our DFTB/ChIMES models by comparing simulations derived from different training sets. We show that DFTB/ChIMES demonstrates ~100× reduction in computational expense while retaining most of the accuracy of DFT as well as yielding high accuracy for different materials outside of our training sets. The DFTB/ChIMES method within the workflow expands the possibilities to use simulations to accurately predict materials properties of increasingly complex structures that would be unfeasible with ab initio methods.

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

The Power of Many: An Ensemble Approach to Spectral Similarity

Quantifying the similarity between two mass spectra─a known reference mass spectrum and an unidentified sample mass spectrum─is at the heart of compound identification workflows in gas chromatography–mass spectrometry (GC-MS). The reference spectrum most like the sample is assigned as its identification (provided some quantitative similarity threshold is met, e.g., 80%) and thus accurately measuring similarity is essential. Significant research has gone toward developing metrics for this purpose, each of which has attempted to improve upon existing methods by incorporating GC-MS-specific information (e.g., peak ratios or retention times) or adopting various statistical and algorithmic frameworks. While this active development has led to a plethora of similarity metrics with demonstrated value across different contexts, the unfortunate consequence has been confusion surrounding which metric should be used as a global standard. No such metric is currently accepted as the standard method because different metrics have demonstrated optimal performance in different contexts. In this work, we propose an ensemble approach to spectral similarity scoring that combines the collective information from across existing similarity metrics to form an improved, globally representative similarity metric as a step toward establishing a global standard method. In conclusion, the resulting ensemble metrics are evaluated on over 88,000 spectra of varying complexity and demonstrate improved abilities to accurately rank the correct reference spectrum as the top-matching candidate for a sample relative to the rankings generated by individual similarity scores.

Carbohydrates↗