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Results for “Machine learning molecular dynamics”

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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

On-the-fly active learning of interpretable Bayesian force fields for atomistic rare events

Abstract Machine learned force fields typically require manual construction of training sets consisting of thousands of first principles calculations, which can result in low training efficiency and unpredictable errors when applied to structures not represented in the training set of the model. This severely limits the practical application of these models in systems with dynamics governed by important rare events, such as chemical reactions and diffusion. We present an adaptive Bayesian inference method for automating the training of interpretable, low-dimensional, and multi-element interatomic force fields using structures drawn on the fly from molecular dynamics simulations. Within an active learning framework, the internal uncertainty of a Gaussian process regression model is used to decide whether to accept the model prediction or to perform a first principles calculation to augment the training set of the model. The method is applied to a range of single- and multi-element systems and shown to achieve a favorable balance of accuracy and computational efficiency, while requiring a minimal amount of ab initio training data. We provide a fully open-source implementation of our method, as well as a procedure to map trained models to computationally efficient tabulated force fields.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Accurate Hellmann–Feynman forces from density functional calculations with augmented Gaussian basis sets

The Hellmann–Feynman (HF) theorem provides a way to compute forces directly from the electron density, enabling efficient force calculations for large systems through machine learning (ML) models for the electron density. The main issue holding back the general acceptance of the HF approach for atom-centered basis sets is the well-known Pulay force which, if naively discarded, typically constitutes an error upward of 10 eV/Å in forces. In this work, we demonstrate that if a suitably augmented Gaussian basis set is used for density functional calculations, the Pulay force can be suppressed, and HF forces can be computed as accurately as analytical forces with state-of-the-art basis sets, allowing geometry optimization and molecular dynamics to be reliably performed with HF forces. Our results pave a clear path forward for the accurate and efficient simulation of large systems using ML densities and the HF theorem.

Pathak, Shivesh (ORCID:0000000172798195)↗
DOE OSTI2023

Attosecond probing and control of charge migration in carbon-chain molecule

In quantum mechanics, when an electron is quickly ripped off from a molecule, a superposition of new eigenstates of the cation creates an electron wave packet that governs the charge flow inside, which has been called charge migration (CM). Experimentally, extracting such dynamics at its natural (attosecond) timescale is quite difficult. We report the first such experiment in a linear carbon-chain molecule, butadiyne (C 4 H 2 ), via high-harmonic spectroscopy (HHS). By employing advanced theoretical and computational tools, we showed that the wave packet and the CM of a single molecule are reconstructed from the harmonic spectra for each fixed-in-space angle of the molecule. For this one-dimensional molecule, we calculate the center of charge $\langle$ x $\rangle$ ( t ) to obtain v cm , to quantify the migration speed and how it depends on the orientation angle. The findings also uncover how the electron dynamics at the first few tens to hundreds of attoseconds depends on molecular structure. The method can be extended to other molecules where the HHS technique can be employed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
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 OSTI2023

Uncertainty-driven dynamics for active learning of interatomic potentials

Machine learning (ML) models, if trained to data sets of high-fidelity quantum simulations, produce accurate and efficient interatomic potentials. Active learning (AL) is a powerful tool to iteratively generate diverse data sets. In this approach, the ML model provides an uncertainty estimate along with its prediction for each new atomic configuration. If the uncertainty estimate passes a certain threshold, then the configuration is included in the data set. Here we develop a strategy to more rapidly discover configurations that meaningfully augment the training data set. The approach, uncertainty-driven dynamics for active learning (UDD-AL), modifies the potential energy surface used in molecular dynamics simulations to favor regions of configuration space for which there is large model uncertainty. The performance of UDD-AL is demonstrated for two AL tasks: sampling the conformational space of glycine and sampling the promotion of proton transfer in acetylacetone. The method is shown to efficiently explore the chemically relevant configuration space, which may be inaccessible using regular dynamical sampling at target temperature conditions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Machine learning interatomic potential for silicon-nitride (Si 3 N 4 ) by active learning

Silicon nitride (Si 3 N 4 ) is an extensively used material in the automotive, aerospace, and semiconductor industries. However, its widespread use is in contrast to the scarce availability of reliable interatomic potentials that can be employed to study various aspects of this material on an atomistic scale, particularly its amorphous phase. In this work, we developed a machine learning interatomic potential, using an efficient active learning technique, combined with the Gaussian approximation potential (GAP) method. Our strategy is based on using an inexpensive empirical potential to generate an initial dataset of atomic configurations, for which energies and forces were recalculated with density functional theory (DFT); thereafter, a GAP was trained on these data and an iterative re-training algorithm was used to improve it by learning on-the-fly. When compared to DFT, our potential yielded a mean absolute error of 8 meV/atom in energy calculations for a variety of liquid and amorphous structures and a speed-up of molecular dynamics simulations by 3–4 orders of magnitude, while achieving a first-rate agreement with experimental results. Our potential is publicly available in an open-access repository.

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

Active Learning Framework

Machine learning (ML) of interatomic potentials show great promise to accelerate scientific simulation, e.g., by emulating expensive computations at a high accuracy but much reduced computational cost. Training datasets are calculated from computationally expensive ab initio quantum mechanics methods, density functional theory (DFT). Trained on this data, an ML model can be very successful in predicting energy and forces for new atomic configurations. A critical factor is the quality and diversity of the training dataset. Thus, a highly automated approach to dataset construction based on active learning framework is designed suitable for material physics. The active learning scheme begins with fully randomized atomic configurations. Then, many Molecular Dynamics (MD) trajectories are simulated using current ML potentials, where each MD trajectory is initialized to a random disordered configuration. The temperature is varied in order to diversify the sampled configuration during these simulations. The variance of predictions for eight neural networks within an ensemble is analyzed to determine whether the model is operating as expected. This helps in determining whether collecting more data would be helpful to the model by checking the ensemble variance is greater than the threshold. In this case, the MD trajectory is terminated and the final atomic configuration is placed on a queue (SQL database) for DFT calculations and added to training dataset. Periodically, ML model is retrained to the updated training model. This Active Learning loop is iterated until the cost of MD simulations becomes prohibitively expensive. The MD simulations will hopefully be sufficiently robust to support nucleation after many active learning iterations. In this sense, active learning scheme must automatically discover the important low energy and nonequilibrium physics.

Nebgen, Benjamin↗
DOE OSTI2022

Utilizing CellBox to Describe Varied Dynamical Systems

CellBox is a hybrid modeling framework that integrates machine-learning approaches with explicit mathematical modeling to determine the behavior of dynamical systems, intended for determining the complex interactions of molecule and phenotype within a cellular environment using perturbation/response-based data. The original work utilized analysis of a melanoma cell line, SK-Mel-133, which we sought to expand to and evaluate effectiveness in describing other nonlinear systems both within and outside of biology. We evaluated with two models. One model is based upon the free-fall of an object under a velocity-dependent drag force; this produced inherent perturbation/response data. The other model is based upon a form of mass-action molecular kinetics; for this, we ran the simulation to steady state in each species for each perturbation and select the steady state as input for CellBox. We determined that CellBox, outside of its original use case, can still strongly predict even non-biological dynamical systems in the small-perturbation regime, with r = 0.99977 to 0.85123, p < 0.05 for freefall. However, CellBox cannot accurately predict behavior within large-perturbation regimes, p >> 0.05 for freefall. In addition, we performed a naïve comparison of CellBox network structure to known network structure in the mass-action model to assess accuracy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Diamond under extremes

Diamond is, by virtue of the covalent bonding between atoms and the very strong carbon to carbon bonds, the hardest natural material. It has been a fascinating material since its discovery, first as a decorative gem and more recently, for its numerous industrial uses because of its extreme hardness, elastic modulus, and optical transparency. In recent years, it has become a preferred ablator for laser shock experiments, and this has led to its choice as the capsule material for fusion experiments at the National Ignition Facility. Further, this review covers both experimental and computational (including machine learning) advancements in research on diamond subjected extreme conditions of temperature and pressure. The synergy between shock and ramp loading experiments and atomic level simulations is proving to be powerful in advancing our understanding of diamond under extremes.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Machine learning enables interpretable discovery of innovative polymers for gas separation membranes

Polymer membranes perform innumerable separations with far-reaching environmental implications. Despite decades of research, design of new membrane materials remains a largely Edisonian process. To address this shortcoming, we demonstrate a generalizable, accurate machine learning (ML) implementation for the discovery of innovative polymers with ideal performance. Specifically, multitask ML models are trained on experimental data to link polymer chemistry to gas permeabilities of He, H 2 , O 2 , N 2 , CO 2 , and CH 4 . We interpret the ML models and extract valuable insights into the contributions of different chemical moieties to permeability and selectivity. We then screen over 9 million hypothetical polymers and identify thousands that lie well above current performance upper bounds, including hundreds of never-before-seen ultrapermeable polymer membranes with O 2 and CO 2 permeability greater than 10 4 and 10 5 Barrers, respectively. High-fidelity molecular dynamics simulations confirm the ML-predicted gas permeabilities of the promising candidates, which suggests that many can be translated to reality.

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

Machine Learned Hückel Theory: Interfacing Physics and Deep Neural Networks

The Hückel Hamiltonian is an incredibly simple tight-binding model known for its ability to capture qualitative physics phenomena arising from electron interactions in molecules and materials. Part of its simplicity arises from using only two types of empirically fit physics-motivated parameters: the first describes the orbital energies on each atom and the second describes electronic interactions and bonding between atoms. By replacing these empirical parameters with machine-learned dynamic values, we vastly increase the accuracy of the extended Hückel model. The dynamic values are generated with a deep neural network, which is trained to reproduce orbital energies and densities derived from density functional theory. The resulting model retains interpretability, while the deep neural network parameterization is smooth and accurate and reproduces insightful features of the original empirical parameterization. Altogether, this work shows the promise of utilizing machine learning to formulate simple, accurate, and dynamically parameterized physics models.

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

Periodic GFN1-xTB Tight Binding: A Generalized Ewald Partitioning Scheme for the Klopman–Ohno Function

A novel formulation is presented for the treatment of electrostatics in the periodic GFN1-xTB tight-binding model. Periodic GFN1-xTB is hindered by the functional form of the second-order electrostatics, which only recovers Coulombic behavior at large interatomic distances and lacks a closed-form solution for its Fourier transform. We address this by introducing a binomial expansion of the Klopman–Ohno function to partition short- and long-range interactions, enabling the use of a generalized Ewald summation for the solution of the electrostatic energy. This approach is general and is applicable to any damped potential of the form |R n + c| –m . Benchmarks on the X23 molecular crystal dataset and a range of prototypical bulk semiconductors demonstrate that this systematic treatment of the electrostatics eliminates unphysical behavior in the equation of state curves. In the bulk systems studied, we observe a mean absolute error in total energy of 35 meV/atom, comparable to the machine-learned universal force field, M3GNet, and sufficiently precise for structure relaxation. These results highlight the promising potential of GFN1-xTB as a universal tight-binding parametrization.

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

De novo design of programmable inducible promoters

Abstract Ligand-responsive allosteric transcription factors (aTF) play a vital role in genetic circuits and high-throughput screening because they transduce biochemical signals into gene expression changes. Programmable control of gene expression from aTF-regulated promoter is important because different downstream effector genes function optimally at different expression levels. However, tuning gene expression of native promoters is difficult due to complex layers of homeostatic regulation encoded within them. We engineered synthetic promoters de novo by embedding operator sites with varying affinities and radically reshaped binding preferences within a minimal, constitutive Escherichia coli promoter. Multiplexed cell-based screening of promoters for three TetR-like aTFs generated with this approach gave rich diversity of gene expression levels, dynamic ranges and ligand sensitivities and were 50- to 100-fold more active over their respective native promoters. Machine learning on our dataset revealed that relative position of the core motif and bases flanking the core motif play an important role in modulating induction response. Our generalized approach yields customizable and programmable aTF-regulated promoters for engineering cellular pathways and enables the discovery of new small molecule biosensors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Computational modeling of grain boundary segregation: A review

Nearly all metals, alloys, ceramics, and their associated composites are polycrystalline in nature, with grain boundaries that separate well-defined crystalline regions that influence materials properties. In all but the most pure elemental systems, intentional solutes or impurities are present and can segregate to, or less commonly away from, the grain boundaries, in turn influencing boundary behavior, their stability, and associated materials properties. In some cases, grain-boundary segregation can also trigger “phase-like” structural transitions that dramatically alter the essential nature of the boundary. With the development of advanced electron microscopy techniques, researchers can directly observe grain-boundary structures and segregation with atomic precision. Despite such spatial resolution, the underlying mechanisms governing grain-boundary segregation remain difficult to characterize. As a result, computational modeling techniques such as density functional theory, molecular dynamics, mesoscale phase-field, continuum defect theory, and others are important complementary tools to experimental observations for studying grain-boundary segregation behavior. In conclusion, these computational methods offer the ability to explore the underlying formation mechanisms of grain-boundary segregation, elucidate complex segregation behavior, and provide insights into solutions to effectively controlling microstructure.

36 MATERIALS SCIENCE↗
DOE OSTI2021

On the quenching of star formation in observed and simulated central galaxies: evidence for the role of integrated AGN feedback

ABSTRACT In this paper, we investigate how massive central galaxies cease their star formation by comparing theoretical predictions from cosmological simulations: EAGLE, Illustris, and IllustrisTNG with observations of the local Universe from the Sloan Digital Sky Survey (SDSS). Our machine learning (ML) classification reveals supermassive black hole mass (MBH) as the most predictive parameter in determining whether a galaxy is star forming or quenched at redshift z = 0 in all three simulations. This predicted consequence of active galactic nucleus (AGN) quenching is reflected in the observations, where it is true for a range of indirect estimates of MBH via proxies as well as its dynamical measurements. Our partial correlation analysis shows that other galactic parameters lose their strong association with quiescence, once their correlations with MBH are accounted for. In simulations, we demonstrate that it is the integrated power output of the AGN, rather than its instantaneous activity, which causes galaxies to quench. Finally, we analyse the change in molecular gas content of galaxies from star-forming to passive populations. We find that both gas fractions (fgas) and star formation efficiencies (SFEs) decrease upon transition to quiescence in the observations but SFE is more predictive than fgas in the ML passive/star-forming classification. These trends in the SDSS are most closely recovered in IllustrisTNG and are in direct contrast with the predictions made by Illustris. We conclude that a viable AGN feedback prescription can be achieved by a combination of preventative feedback and turbulence injection which together quench star formation in central galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Robust training of machine learning interatomic potentials with dimensionality reduction and stratified sampling

Abstract Machine learning interatomic potentials (MLIPs) enable accurate simulations of materials at scales beyond that accessible by ab initio methods and play an increasingly important role in the study and design of materials. However, MLIPs are only as accurate and robust as the data on which they are trained. Here, we present DImensionality-Reduced Encoded Clusters with sTratified (DIRECT) sampling as an approach to select a robust training set of structures from a large and complex configuration space. By applying DIRECT sampling on the Materials Project relaxation trajectories dataset with over one million structures and 89 elements, we develop an improved materials 3-body graph network (M3GNet) universal potential that extrapolates more reliably to unseen structures. We further show that molecular dynamics (MD) simulations with the M3GNet universal potential can be used instead of expensive ab initio MD to rapidly create a large configuration space for target systems. We combined this scheme with DIRECT sampling to develop a reliable moment tensor potential for titanium hydrides without the need for iterative augmentation of training structures. This work paves the way for robust high-throughput development of MLIPs across any compositional complexity.

Qi, Ji (ORCID:0000000158089931)↗
DOE OSTI2025

Inverse mapping of properties to composition through generative modeling for designing molten salts

Generative modeling (GM) has been increasingly used for the inverse design and optimization of materials, yet its application to molten salt mixtures remains unexplored despite how a successful approach to the inverse design of molten salts would contribute to efficiently exploiting their customizability and unlocking their advantages in applications, such as energy production and energy storage. This work presents a workflow for the inverse design of molten salts with targeted density values, addressing the challenge of representing these complex mixtures in GM. A dataset of critically evaluated molten salt densities is used to train a variational autoencoder coupled with a predictive deep neural network, which then can be used to generate new molten salt compositions with desired density values. The effectiveness of the approach is demonstrated by designing mixtures with distinct densities and validating the predicted values using ab initio molecular dynamics simulations.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

A reactive molecular dynamics model for uranium/hydrogen containing systems

Uranium-based materials are valuable assets in the energy, medical, and military industries. However, understanding their sensitivity to hydrogen embrittlement is particularly challenging due to the toxicity of uranium and the computationally expensive nature of quantum-based methods generally required to study such processes. In this regard, we have developed a Chebyshev Interaction Model for Efficient Simulation (ChIMES) that can be employed to compute energies and forces of U and UH3 bulk structures with vacancies and hydrogen interstitials with accuracy similar to that of Density Functional Theory (DFT) while yielding linear scaling and orders of magnitude improvement in computational efficiency. Here, we show that the bulk structural parameters, uranium and hydrogen vacancy formation energies, and diffusion barriers predicted by the ChIMES potential are in strong agreement with the reference DFT data. We then use ChIMES to conduct molecular dynamics simulations of the temperature-dependent diffusion of a hydrogen interstitial and determine the corresponding diffusion activation energy. Our model has particular significance in studies of actinides and other high-Z materials, where there is a strong need for computationally efficient methods to bridge length and time scales between experiments and quantum theory.

36 MATERIALS SCIENCE↗