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Results for “Molecular dynamics computer simulation”

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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Gas Phase Synthesis of Benzene via the Propargyl Radical Self-Reaction

Polycyclic Aromatic Hydrocarbons (PAHs) have been invoked in fundamental molecular mass growth processes in our galaxy. We provide compelling evidence of the formation of the very first ringed aromatic and building block of PAHs - benzene - via the self-recombination of two resonantly stabilized propargyl (C 3 H 3 ) radicals in dilute environments using isomer selective synchrotron-based mass spectrometry coupled to theoretical calculations. Along with benzene, three other structural isomers (1,5-hexadiyne, fulvene, 2-ethynyl-1,3-butadiene) and o-benzyne are detected and their branching ratios quantified experimentally and verified with the aid of computational fluid dynamics and kinetic simulations. Furthermore, these results uncover molecular growth pathways not only in interstellar, circumstellar, and solar systems environments, but also in combustion systems gaining us a better understanding of the hydrocarbon chemistry of our universe.

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

Modeling Equilibrium Solid–Liquid Interfaces under Effective Constant Chemical Potential Using Machine Learning Interatomic Potentials

The chemical potential (μ) of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot maintain constant chemical potential with reference to a targeted concentration or chemical potential under nonequilibrium or dynamic conditions, as solute species can migrate to the interface and deplete (or enrich) the bulk due to solute-interface interactions. In this study, we introduce a simple and computationally efficient approach named iterative quasi-constant chemical potential molecular dynamics (iqCμMD) simulation, which helps simulate targeted molar concentrations of species in solution. iqCμMD overcomes the limitations of conventional MD by adjusting the number of species in the solution to reach a target bulk concentration (chemical potential), which allows simulation of the interface under the bulk conditions comparable to experiment. We demonstrate our approach using machine learning interatomic potential (MLIP)-based MD simulations of the Na 2 SO 4,aq –graphene interface, and to show the transferability of our approach, we also perform classical force field-based MD simulations of NaCl aq –air and NaCl aq –graphite interfaces, which produce comparable results to previous CμMD simulations. Our results also show that the iqCμMD approach efficiently achieves the desired bulk ion concentration within two iterations, and by utilizing MLIPs, we can achieve converged results using relatively small-scale simulations compared to previous CμMD simulations. By combining iqCμMD with MLIP-driven simulations, solid–liquid interfaces can be modeled under an effective constant chemical potential with DFT-level accuracy. Here, we show that iqCμMD offers a robust and simple computational framework for constant chemical potential simulations, as its only requirement is to be able to converge interfacial simulations with a measurable bulk region.

Chemical structure↗
DOE OSTI2024

Shock Hugoniot calculations using on-the-fly machine learned force fields with ab initio accuracy

We present a framework for computing the shock Hugoniot using on-the-fly machine learned force field (MLFF) molecular dynamics simulations. In particular, we employ an MLFF model based on the kernel method and Bayesian linear regression to compute the free energy, atomic forces, and pressure, in conjunction with a linear regression model between the internal and free energies to compute the internal energy, with all training data generated from Kohn–Sham density functional theory (DFT). We verify the accuracy of the formalism by comparing the Hugoniot for carbon with recent Kohn–Sham DFT results in the literature. In so doing, we demonstrate that Kohn–Sham calculations for the Hugoniot can be accelerated by up to two orders of magnitude, while retaining ab initio accuracy. We apply this framework to calculate the Hugoniots of 14 materials in the FPEOS database, comprising 9 single elements and 5 compounds, between temperatures of 10 kK and 2 MK. We find good agreement with first principles results in the literature while providing tighter error bars. In addition, we confirm that the inter-element interaction in compounds decreases with temperature.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

High-throughput screening of tribological properties of monolayer films using molecular dynamics and machine learning

Monolayer films have shown promise as a lubricating layer to reduce friction and wear of mechanical devices with separations on the nanoscale. These films have a vast design space with many tunable properties that can affect their tribological effectiveness. For example, terminal group chemistry, film composition, and backbone chemistry can all lead to films with significantly different tribological properties. This design space, however, is very difficult to explore without a combinatorial approach and an automatable, reproducible, and extensible workflow to screen for promising candidate films. Here, using the Molecular Simulation Design Framework (MoSDeF), a combinatorial screening study was performed to explore 9747 unique monolayer films (116 964 total simulations) and a machine learning (ML) model using a random forest regressor, an ensemble learning technique, to explore the role of terminal group chemistry and its effect on tribological effectiveness. The most promising films were found to contain small terminal groups such as cyano and ethylene. The ML model was subsequently applied to screen terminal group candidates identified from the ChEMBL small molecule library. Approximately 193 131 unique film candidates were screened with approximately a five order of magnitude speed-up in analysis compared to simulation alone. The ML model was thus able to be used as a predictive tool to greatly speed up the initial screening of promising candidate films for future simulation studies, suggesting that computational screening in combination with ML can greatly increase the throughput in combinatorial approaches to generate in silico data and then train ML models in a controlled, self-consistent fashion.

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

Fundamental microscopic properties as predictors of large-scale quantities of interest: Validation through grain boundary energy trends

Correlations between fundamental microscopic properties computable from first principles, which we term canonical properties, and complex large-scale quantities of interest (QoIs) provide an avenue to predictive materials discovery. Here, we propose that such correlations can be efficiently discovered through simulations utilizing approximate interatomic potentials (IPs), which serve as an ensemble of “synthetic materials”. As a proof of principle we build a regression model relating canonical properties to the symmetric tilt grain boundary (GB) energy curves in face-centered cubic crystals, characterized by the scaling factor in the universal lattice matching model of Runnels et al. (2016), which we take to be our QoI. Our analysis recovers known correlations of GB energy to other properties and discovers new ones. We also demonstrate, using available density functional theory (DFT) GB energy data, that the regression model constructed from IP data is consistent with DFT results, confirming the assumption that the IPs and DFT belong to same statistical pool and thereby validating the approach. Regression models constructed in this fashion can be used to predict large-scale QoIs based on first-principles data and provide a general method for training IPs for QoIs beyond the scope of first-principles calculations.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Cross-scale covariance for material property prediction

A simulation can stand its ground against an experiment only if its prediction uncertainty is known. The unknown accuracy of interatomic potentials (IPs) is a major source of prediction uncertainty, severely limiting the use of large-scale classical atomistic simulations in a wide range of scientific and engineering applications. Here we explore covariance between predictions of metal plasticity, from 178 large-scale (~10 8 atoms) molecular dynamics (MD) simulations, and a variety of indicator properties computed at small-scales (≤10 2 atoms). All simulations use the same 178 IPs. In a manner similar to statistical studies in public health, we analyze correlations of strength with indicators, identify the best predictor properties, and build a cross-scale “strength-on-predictors” regression model. This model is then used to estimate regression error over the statistical pool of IPs. Small-scale predictors found to be highly covariant with strength are computed using expensive quantum-accurate calculations and used to predict flow strength, within the statistical error bounds established in our study.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.

Biochemistry & Molecular Biology↗
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 OSTI2020

Equation of state of hot, dense magnesium derived with first-principles computer simulations

Using two first-principles computer simulation techniques, path integral Monte Carlo and density functional theory molecular dynamics, we derive the equation of state of magnesium in the regime of warm dense matter, with densities ranging from 0.43 to 86.11 g cm –3 and temperatures from 20,000 K to 5×10 8 K. These conditions are relevant for the interiors of giant planets and stars as well as for shock compression measurements and inertial confinement fusion experiments. Here, we study ionization mechanisms and the electronic structure of magnesium as a function of density and temperature. We show that the L shell electrons, 2s and 2p energy bands, merge at high densities. This results in gradual ionization of the L-shell with increasing density and temperature. In this regard, Mg differs from MgO, which is also reflected in the shape of its principal shock Hugoniot curve. For Mg, we predict a single broad pressure-temperature region, where the shock compression ratio is approximately 4.9. Mg thus differs from Si and Al plasmas that exhibit two well-separated compression maxima on the Hugoniot curve for L and K shell ionizations. Finally, we study multiple shocks and effects of preheat and precompression.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Next-Generation Materials Design: Quantum Mechanics and Data-Driven Modeling

The future of materials design is rapidly advancing through the combination of quantum mechanics and data-driven modeling. These approaches integrate quantum principles with advanced data analysis, enabling precise insights into material behavior. This talk will highlight recent progress in using these methods for computational design, particularly in high-entropy alloy catalysts, emphasizing the role of hierarchical machine-learning architectures for accurate predictions. Additionally, I will discuss our work on developing machine learning interatomic potentials (MLPs) for single-element metals, metal oxides, and alloys under extreme conditions, focusing on melting behavior and phase properties at high temperatures and pressures. We have also refined our MLP models to capture dynamic surface interactions, such as CO2 and CO adsorption on MgO, using both static and molecular dynamics simulations. These models maintain high accuracy while significantly reducing computational costs compared to first-principles calculations. By enabling efficient and accurate simulations, this work supports broader community adoption, optimizes datasets for materials discovery, and extends the accessible time, size, and environmental conditions beyond the limits of experiments and traditional simulations.

machine learning↗
DOE OSTI2023

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Chemistry↗
DOE OSTI2025

Quantum Simulation of Molecular Dynamics Processes─A Benchmark Study Using a Classical Simulator and Present-Day Quantum Hardware

Here, we explore how the fundamental problems in quantum molecular dynamics can be modeled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes propagation of a free wave packet, vibration of a harmonic oscillator, and tunneling through a barrier. Each of these problems starts with the initial wave packet setup. Although Qiskit provides a general method for initializing wave functions, in most cases it generates deep quantum circuits. While these circuits perform well on noiseless simulators, they suffer from excessive noise on quantum hardware. To overcome this issue, we designed a shallower quantum circuit for preparing a Gaussian-like initial wave packet, which improves the performance of real hardware. Next, quantum circuits are implemented to apply the kinetic and potential energy operators for the evolution of a wave function over time. The results of our modeling on classical emulators of quantum hardware agree perfectly with the results obtained using the traditional (classical) methods. This serves as a benchmark and demonstrates that the quantum algorithms and Qiskit codes we developed are accurate. However, the results obtained on the actual quantum hardware available today, such as IBM’s superconducting qubits and IonQ’s trapped ions, indicate large discrepancies due to hardware limitations. This work highlights both the potential and challenges of using quantum computers to solve fundamental quantum molecular dynamics problems.

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

Nonideal mixing effects in warm dense matter studied with first-principles computer simulations

Here, we study nonideal mixing effects in the regime of warm dense matter (WDM) by computing the shock Hugoniot curves of BN, MgO, and MgSiO 3 . First, we derive these curves from the equations of state (EOS) of the fully interacting systems, which were obtained using a combination of path integral Monte Carlo calculations at high temperature and density functional molecular dynamics simulations at lower temperatures. We then use the ideal mixing approximation at constant pressure and temperature to rederive these Hugoniot curves from the EOS tables of the individual elements. We find that the linear mixing approximation works remarkably well at temperatures above ~2 × 10 5 K, where the shock compression ratio exceeds ~3.2. The shape of the Hugoniot curve of each compound is well reproduced. Regions of increased shock compression, which emerge because of the ionization of L and K shell electrons, are well represented, and the maximum compression ratio of the Hugoniot curves is reproduced with high precision. Some deviations are seen near the onset of the L shell ionization regime, where ionization equilibrium in the fully interacting system cannot be well reproduced by the ideal mixing approximation. This approximation also breaks down at lower temperatures, where chemical bonds play an increasingly important role. However, the results imply that the equilibrium properties of binary and ternary mixtures in the regime of WDM can be derived from the EOS tables of the individual elements. This significantly simplifies the characterization of binary and ternary mixtures in the WDM and plasma phases, which otherwise requires large numbers of more computationally expensive first-principles computer simulations.

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

CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling

Large-scale simulations with complex electron interactions remain one of the greatest challenges for atomistic modelling. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study technologically relevant phenomena. Here we present the Crystal Hamiltonian Graph Neural Network (CHGNet), a graph neural network-based machine-learning interatomic potential (MLIP) that models the universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory calculations of more than 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li x MnO 2 , the finite temperature phase diagram for Li x FePO 4 and Li diffusion in garnet conductors. We highlight the significance of charge information for capturing appropriate chemistry and provide insights into ionic systems with additional electronic degrees of freedom that cannot be observed by previous MLIPs.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Quantum-Based Molecular Dynamics Simulations Using Tensor Cores

Tensor cores, along with tensor processing units, represent a new form of hardware acceleration specifically designed for deep neural network calculations in artificial intelligence applications. Tensor cores provide extraordinary computational speed and energy efficiency but with the caveat that they were designed for tensor contractions (matrix–matrix multiplications) using only low-precision floating-point operations. Despite this perceived limitation, we demonstrate how tensor cores can be applied with high efficiency to the challenging and numerically sensitive problem of quantum-based Born–Oppenheimer molecular dynamics, which requires highly accurate electronic structure optimizations and conservative force evaluations. The interatomic forces are calculated on-the-fly from an electronic structure that is obtained from a generalized deep neural network, where the computational structure naturally takes advantage of the exceptional processing power of the tensor cores and allows for high performance in excess of 100 Tflops on a single Nvidia A100 GPU. Stable molecular dynamics trajectories are generated using the framework of extended Lagrangian Born–Oppenheimer molecular dynamics, which combines computational efficiency with long-term stability, even when using approximate charge relaxations and force evaluations that are limited in accuracy by the numerically noisy conditions caused by the low-precision tensor core floating-point operations. A canonical ensemble simulation scheme is also presented, where the additional numerical noise in the calculated forces is absorbed into a Langevin-like dynamics.

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

Accuracy, transferability, and computational efficiency of interatomic potentials for simulations of carbon under extreme conditions

Large-scale atomistic molecular dynamics (MD) simulations provide an exceptional opportunity to advance the fundamental understanding of carbon under extreme conditions of high pressures and temperatures. However, the fidelity of these simulations depends heavily on the accuracy of classical interatomic potentials governing the dynamics of many-atom systems. Here, this study critically assesses several popular empirical potentials for carbon, as well as machine learning interatomic potentials (MLIPs), in their ability to simulate a range of physical properties at high pressures and temperatures, including the diamond equation of state, its melting line, shock Hugoniot, uniaxial compressions, and the structure of liquid carbon. Empirical potentials fail to accurately predict the behavior of carbon under high pressure–temperature conditions. In contrast, MLIPs demonstrate quantum accuracy, with Spectral Neighbor Analysis Potential (SNAP) and atomic cluster expansion (ACE) being the most accurate in reproducing the density functional theory results. ACE displays remarkable transferability despite not being specifically trained for extreme conditions. Furthermore, ACE and SNAP exhibit superior computational performance on graphics processing unit-based systems in billion atom MD simulations, with SNAP emerging as the fastest. In addition to offering practical guidance in selecting an interatomic potential with a fine balance of accuracy, transferability, and computational efficiency, this work also highlights transformative opportunities for groundbreaking scientific discoveries facilitated by quantum-accurate MD simulations with MLIPs on emerging exascale supercomputers.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Geometrically necessary dislocation fingerprints of dislocation loop absorption at grain boundaries

Here we present a numerical methodology to compute the Nye-tensor fingerprints of dislocation loop absorption at grain boundaries (GBs) for comparison with TEM observations of irradiated polycrystals. Our approach links atomistic simulations of self-interstitial atom (SIA) prismatic loops gliding toward and interacting with GBs in body-centered cubic iron with experimentally extracted geometrically necessary dislocation (GND) maps to facilitate the interpretation of damage processes. The Nye-tensor analysis is strongly mesh-size dependent—corresponding to resolution-dependent TEM observations. The method computes GND fingerprints from discretized dislocation line segments extracted from molecular dynamics simulations of dislocation loops being absorbed at a GB. Specifically, we perform MD simulation of prismatic loops of two diameters and monitor the three stages of the absorption process: loop glide, the partial, and full absorption of the loops at a [1 0 0] symmetric tilt GB. These methods provide a framework for future investigations of the nature of defect absorption by grain boundaries under irradiation conditions.

36 MATERIALS SCIENCE↗