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Results for “Classical molecular dynamic simulations”

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 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Potentials of mean force fail to describe chemical bond-breaking in solution

Many liquid phase studies assume that the potential energy surfaces of reacting molecules are the same as in the gas phase, neglecting complex solvent dynamics that can completely alter the nature of chemical reactivity. Even studies that include solvent effects typically only consider them in an average, equilibrium way as part of a potential of mean force (PMF). In this work, we use mixed quantum/classical simulations to compare how equilibrium and non-equilibrium solvent motions affect the photodissociation of a simple diatomic molecule, NaK + , in liquid tetrahydrofuran. A PMF analysis shows that as the excited-state molecule dissociates with the solvent at equilibrium, the bonding electron remains associated with K + at short bond distances but eventually localizes on Na + at the end of dissociation. When we examine non-equilibrium dynamical photodissociation trajectories, however, we find that they fall into three distinct categories: about a quarter of them have the bonding electron mainly associated with Na + , another quarter stay mainly associated with K + , and about half have the bonding electron shared roughly equally between the two ions. The results show that equilibrium PMFs cannot accurately describe the dynamics of bond-breaking chemical reactions in solution because there is insufficient time for the solvent to reach equilibrium on the time scale over which bond dissociation occurs. Furthermore, our analysis shows that the solvent coupling between the electronic energy surfaces is similar at and away from equilibrium, suggesting that other factors, such as solute velocity-driven solvent memory effects, play a more important role in explaining the failure of the equilibrium PMF to predict the non-equilibrium dynamics.

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

Capturing electronic decoherence in quantum-classical dynamics using the ring-polymer-surface-hopping–density-matrix approach

Simulations of coupled electronic and nuclear dynamics in molecules can be quite challenging due to the involved interplay of the many degrees of freedom. Because a full quantum treatment of both electrons and nuclei is computationally very demanding, it is generally restricted to model systems or rather small molecules and short timescales. Mixed quantum-classical dynamics methods such as Tully's fewest switches surface hopping (FSSH) can be used to overcome this limitation. However, FSSH is known to poorly describe electronic coherences and decoherence phenomena. Here, we present an approach that combines FSSH with ring-polymer molecular dynamics (RPMD) in a specific way that aims to alleviate the coherence problem. Termed the ring-polymer-surface-hopping–density-matrix approach, this method uses an electronic density-matrix formulation to calculate surface hopping rates. Additionally, this incorporates decoherence effects into FSSH in a natural way by taking into account the spatial spreading of the ring polymer that mimics the width of a nuclear wave packet in each RPMD trajectory. By applying our method to Tully's one-dimensional model system, we demonstrate that this method captures a crucial decoherence mechanism that is missing in FSSH. Furthermore, our method turns out to be superior at describing electronic coherences compared with earlier attempts at combining RPMD and FSSH.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Deep learning of accurate force field of ferroelectric HfO 2

The discovery of ferroelectricity in HfO 2 -based thin films opens up new opportunities for using this silicon-compatible ferroelectric to realize low-power logic circuits and high-density nonvolatile memories. The functional performances of ferroelectrics are intimately related to their dynamic responses to external stimuli such as electric fields at finite temperatures. Molecular dynamics is an ideal technique for investigating dynamical processes on large length and time scales, though its applications to new materials are often hindered by the limited availability and accuracy of classical force fields. Here we present a deep neural network–based interatomic force field of HfO 2 learned from ab initio data using a concurrent learning procedure. The model potential is able to predict structural properties such as elastic constants, equation of states, phonon dispersion relationships, and phase transition barriers of various hafnia polymorphs with accuracy comparable with density functional theory calculations. Here, the validity of this model potential is further confirmed by the reproduction of experimental sequences of temperature-driven ferroelectric-paraelectric phase transitions of HfO 2 with isobaric-isothermal ensemble molecular dynamics simulations. We suggest a general approach to extend the model potential of HfO 2 to related material systems including dopants and defects.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

A quantum processor based on coherent transport of entangled atom arrays

The ability to engineer parallel, programmable operations between desired qubits within a quantum processor is key for building scalable quantum information systems. In most state-of-the-art approaches, qubits interact locally, constrained by the connectivity associated with their fixed spatial layout. Here we demonstrate a quantum processor with dynamic, non-local connectivity, in which entangled qubits are coherently transported in a highly parallel manner across two spatial dimensions, between layers of single- and two-qubit operations. Our approach makes use of neutral atom arrays trapped and transported by optical tweezers; hyperfine states are used for robust quantum information storage, and excitation into Rydberg states is used for entanglement generation. We use this architecture to realize programmable generation of entangled graph states, such as cluster states and a seven-qubit Steane code state. Furthermore, we shuttle entangled ancilla arrays to realize a surface code state with thirteen data and six ancillary qubits and a toric code state on a torus with sixteen data and eight ancillary qubits. Finally, we use this architecture to realize a hybrid analogue–digital evolution and use it for measuring entanglement entropy in quantum simulations, experimentally observing non-monotonic entanglement dynamics associated with quantum many-body scars. Realizing a long-standing goal, these results provide a route towards scalable quantum processing and enable applications ranging from simulation to metrology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Characterizing the Mechanisms of Ca and Mg Carbonate Ion-Pair Formation with Multi-Level Molecular Dynamics/Quantum Mechanics Simulations

The carbonate minerals of Ca and Mg are abundant throughout the lithosphere and have recently garnered significant research interest as possible long-term carbon sinks in the sequestration of atmospheric carbon dioxide. Nonetheless, an understanding of the atomic-level processes comprising their mineralization remains limited. Furthermore, we characterize and contrast the mechanisms of contact ion-pair formation in aqueous Ca and Mg carbonate systems, which represents the most fundamental step leading to the formation of their mineral solids. Utilizing multilevel embedded correlated wavefunction-based ab initio molecular dynamics/quantum mechanics simulations, we characterize not only the dynamics of these processes but also factors arising from the electronic structure of the involved species, revealing further details of the fundamentally different mechanisms for the interconversion between the contact ion-pairs and solvent-shared ion-pairs of Ca versus Mg carbonate.

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

Temperature and radiation effects on brittle versus ductile fracture behavior in miscible phase boundaries: insight from atomistic simulations

Temperature- and irradiation-assisted failure mechanisms in miscible phase boundaries are clarified via atomistic calculations. We first establish the temperature-dependent brittle-to-ductile transition in U–Zr miscible phase boundaries. Our results confirm that these boundaries are mostly brittle at low temperatures and ductile at elevated temperatures. We then investigate the changes induced by irradiation on the fracture mechanisms in such phase boundaries. The irradiation-induced defect accumulation follows a multi-stage process that starts with the accumulation of isolated small dislocation loops before transitioning to the saturation and growth of larger dislocation loops and end up with a reorganization into forest dislocations. The accumulation of loops is the primary feature to participate in the delineation between brittle and ductile interfacial fracture in irradiated phase boundaries. At low damage levels, radiation defect interactions with the crack tip are limited and U–Zr miscible boundaries fail through the emission of dislocations ahead of the crack tip followed by brittle cleavage in agreement with the classical Griffith’s criterion for crack stability. At higher damage levels, the failure mode transitions from brittle crack growth to ductile void growth. In this case, the microcrack tip is blunted by the high density of pre-existing, radiation-induced defects in the vicinity of the crack. This interaction leads to the development and growth of a cavity at the interface as opposed to interfacial cleavage.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Thermal transport in defective and disordered materials

With significant recent advancements in thermal sciences—such as the development of new theoretical and experimental techniques, and the discovery of new transport mechanisms—it is helpful to revisit the fundamentals of vibrational heat conduction to formulate an updated and informed physical understanding. The increasing maturity of simulation and modeling methods sparks the desire to leverage these techniques to rapidly improve and develop technology through digital engineering and multi-scale, electro-thermal models. With that vision in mind, this review attempts to build a holistic understanding of thermal transport by focusing on the often unaddressed relationships between subfields, which can be critical for multi-scale modeling approaches. For example, we outline the relationship between mode-specific (computational) and spectral (analytical) models. We relate thermal boundary resistance models based on perturbation approaches and classic transmissivity based models. We discuss the relationship between lattice dynamics and molecular dynamics approaches along with two-channel transport frameworks that have emerged recently and that connect crystal-like and amorphous-like heat conduction. Throughout, we discuss best practices for modeling experimental data and outline how these models can guide material-level and system-level design.

42 ENGINEERING↗
DOE OSTI2023

Real-space inversion and super-resolution of ultrafast scattering

Ultrafast scattering using x-rays or electrons is an emerging method to obtain structure dynamics at the atomic lengthscales and timescales. However, directly resolving in real-space atomic motions is inherently limited by the finite detector range and the probe energy. So, as a result, the time-resolved signal interpretation is mostly done in reciprocal space and relies on modeling and simulations of specific structures and processes. Here, we introduce a model-free approach to directly resolve scattering signals in real space, surpassing the diffraction limit, using scattering kernels and signal priors that naturally arise from the measurement constraints. We demonstrate the approach on simulated and experimental data, recover multiple atomic motions at sub-angstrom resolutions, and discuss the recovery accuracy and resolution limits versus signal fidelity. The approach offers a robust path to obtain high-resolution real-space information of atomic-scale structure dynamics using current time-resolved x-ray or electron scattering sources.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

SULI Intern Final Report: Computationally Investigating Hydrogen Thermo-Diffusion in Yttrium Hydride Using Multiscale Methods

The renaissance of nuclear energy has arrived, heralding an age of abundant inexpensive clean energy, and renewed space exploration. In nuclear-powered spacecraft and microreactors, safety and size are of utmost importance. Yttrium Hydride (YHx) is being researched for its utility as a neutron moderator in nuclear reactors; the hydrogen in YHx slows down neutrons, enabling a continuous nuclear reaction in the reactor. This has the benefit of allowing reactors to be more safe, compact, and efficient. The goal of this effort is to computationally predict the coefficient of temperature-dependent hydrogen diffusion within YHx, the Soret coefficient. This parameter is essential for determining the safe operating modes of YHx moderators. Zirconium Hydride (ZrHx) is used in the Training, Research, Isotopes, General Atomics (TRIGA) reactor, is the reference material for these calculations. In this work, nanoscale atomic modeling in the Vienna Ab initio Simulation Package (VASP) is combined with the mesoscale finite element phase-field module in the Multiphysics Object-Oriented Simulation Environment (MOOSE); this culminates in a new multiscale computational method to simulate Soret diffusion of hydrogen in YHx. This data is useful for predicting experimental outcomes. This workflow involves convergence testing followed by static, Nudged Elastic Band (NEB), Quasi-Harmonic Approximation (QHA), and Molecular Dynamics (MD) calculations - linked with phase field simulation. NEB simulates hydrogen migration, while QHA and MD predict temperature-dependent properties. The static calculations align with literature, and preliminary NEB and QHA calculations yield accurate results. Once the atomic calculations are complete, we will incorporate Electron Backscatter Diffraction (EBSD) images and VASP-generated parameters into the phase field module to simulate intra- and intergranular transport of hydrogen in ZrHx and YHx. Future research will extend our approach to fuel-moderator materials systems such as Uranium-Yttrium Hydride (U-YHx). This work contributes to the development of advanced nuclear energy solutions for space travel.

36 - MATERIALS SCIENCE↗
DOE OSTI2022

Interstitial proton transport through defective MXenes

Proton transport across nanometer-thick membranes in an aqueous medium is important for applications in energy and molecular sieving. Recently, Hu et al. [Nature 516(7530), 227–230 (2014)] experimentally demonstrated proton tunneling through 2D materials like graphene and hexagonal boron nitride, opening up a wide range of applications in hydrogen-based technologies such as fuel cells. Here, we demonstrate proton transport in an aqueous medium across a 2D cubic Ti 2 C membrane, a representative defective MXene, from ab initio molecular dynamics simulations. We observe bidirectional translocation of protons, which occurs through the interstitial vacancies in the surface. We show from our simulations that water dissociates on the membrane and the dissociated proton moves into the interstitial sites in the membrane. The proton hops from interstitial-to-interstitial and transports across the membrane. Here, we also show that this interstitial proton transport is associated with an induced electric field that is modulated with bidirectional transport of protons across the membrane.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Quantum Ornstein-Zernike theory for two-temperature two-component plasmas

Laboratory plasma production almost always preferentially heats either the ions or electrons, leading to a two-temperature state. In this state, density functional theory molecular dynamic simulation is the state of the art for modeling bulk material properties. We construct a statistical mechanics model for the two temperature limit that is theoretically consistent with the molecular dynamics method. We proceed to derive the electron-ion multi-temperature quantum Ornstein-Zernike equations for the first time. This allows the construction of a two-temperature two-component plasma model using the average atom from which we can compute bulk material properties at a fraction of the computation time of the two-temperature density functional theory simulation. The accuracy of the model is benchmarked against ion pair correlation and self-diffusion results from ab initio simulation. Here, we proceed to compute the viscosity and ion thermal conductivity as a function of both ion and electron temperature.

Ab initio molecular dynamics↗
DOE OSTI2024

Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why

A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained (CG) conformational dynamics. Constrained by the fluctuation–dissipation theorem, the approach can build CG models in dynamical consistency (DC) with all-atom molecular dynamics. Here, we also propose practical criteria for AIGLE to enforce long-term DC. Case studies of a toy polymer, with 20 CG sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling CG conformational dynamics in practice.

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

Structural and dynamic mechanisms of GABA A receptor modulators with opposing activities

γ-Aminobutyric acid type A (GABA A ) receptors are pentameric ligand-gated ion channels abundant in the central nervous system and are prolific drug targets for treating anxiety, sleep disorders and epilepsy. Diverse small molecules exert a spectrum of effects on γ-aminobutyric acid type A (GABA A ) receptors by acting at the classical benzodiazepine site. They can potentiate the response to GABA, attenuate channel activity, or counteract modulation by other ligands. Structural mechanisms underlying the actions of these drugs are not fully understood. Here we present two high-resolution structures of GABA A receptors in complex with zolpidem, a positive allosteric modulator and heavily prescribed hypnotic, and DMCM, a negative allosteric modulator with convulsant and anxiogenic properties. These two drugs share the extracellular benzodiazepine site at the α/γ subunit interface and two transmembrane sites at β/α interfaces. Structural analyses reveal a basis for the subtype selectivity of zolpidem that underlies its clinical success. Molecular dynamics simulations provide insight into how DMCM switches from a negative to a positive modulator as a function of binding site occupancy. Together, these findings expand our understanding of how GABA A receptor allosteric modulators acting through a common site can have diverging activities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Impact of solvation on the electronic resonances in uracil

Interactions of low-energy electrons with the DNA and RNA nucleobases are known to form metastable states, known as electronic resonances. In this work, we study electron attachment to solvated uracil, an RNA nucleobase, using the orbital stabilization method at the Equation of Motion-Coupled Cluster for Electron Affinities with Singles and Doubles (EOM-EA-CCSD) level of theory with the Effective Fragment Potential (EFP) solvation method. We benchmarked the approach using multireference methods, as well as by comparing EFP and full quantum calculations. The impact of solvation on the first one particle (1p) shape resonance, formed by electron attachment to the π* LUMO orbital, as well as the first two particle one hole (2p1h) resonance, formed by electron attachment to neutral uracil's π–π* excited state, was investigated. We used molecular dynamics simulations for solvent configurations and applied charge stabilization technique-based biased sampling to procure configurations adequate to cover the entire range of the electron attachment energy distribution. The electron attachment energy in solution is found to be distributed over a wide range of energies, between 4.6 eV to 6.8 eV for the 2p1h resonance, and between −0.1 eV to 2 eV for the 1p resonance. The solvent effects were similar for the two resonances, indicating that the exact electron density of the state is not as important as the solvent configurations. Multireference calculations extended the findings showing that solvation effects are similar for the lowest four resonances, further indicating that the specific solute electron density is not as important, but rather the water configurations play the most important role in solvation effects. Lastly, by comparing bulk solvation to clusters of uracil with a few water molecules around it, we find that the impact of microsolvation is very different from that of bulk solvation.

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

Dynamic embedding of effective harmonic normal mode vibrations in all-atomistic energy gap fluctuations: Case study of light harvesting 2 complex

Environmental effects in excitation energy transfer have mostly been modeled by baths of harmonic oscillators, but to what extent such modeling provides a reliable description of actual interactions between molecular systems and environments remains an open issue. Here, we address this issue by investigating fluctuations in the excitation energies of the light harvesting 2 complex using a realistic all-atomistic simulation of the potential energy surface. Our analyses reveal that molecular motions exhibit significant anharmonic features, even for underdamped intramolecular vibrations. In particular, we find that the anharmonicity contributes to the broadening of spectral densities and substantial overlaps between neighboring peaks, which complicates the meaning of mode frequencies constituting a bath model. Thus, we develop a strategy to construct a minimally underdamped harmonic bath that has a clear connection to all-atomistic dynamics by utilizing actual normal modes of molecules but optimizing their frequencies such that the resulting bath model can best reproduce the all-atomistic simulation results. By subtracting the underdamped contribution from the entire fluctuations, we also show that identifying a residual spectral density representing all other contributions with overdamped behavior is possible. We find that this can be fitted well with a well-established analytic form of a spectral density function or, alternatively, modeled as explicit time dependent fluctuations with muti-exponential or power law type correlation functions. We provide an assessment and the implications of these possibilities. The approach presented here can also serve as a general strategy to construct a simplified bath model that can effectively represent the underlying all-atomistic bath dynamics.

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

Scalable simulation of coupled adsorption and transport of methane in confined complex porous media with density preconditioning

The growing significance of shales and tight formations in the transition to less carbon-intensive and clean energy drives the research endeavor to understand the physics of gas flow within these systems. However, shales are composed of massively heterogeneous physical and chemical features. Most nano-sized pores connect to millimeter-scale fractures, leading to multiscale transport. These nano-scale pore throats demonstrate non-classical flow behavior, such as non-negligible slip velocities and adsorbed gas layers at the boundary. As a result, classical computational fluid dynamics models do not capture the physics. In this work, we develop a coupling scheme for the multiple-relaxation-time (MRT) lattice Boltzmann (LB) method that integrates the Peng-Robinson equation of state into a pseudo-potential interaction model to capture the physics of methane flow in irregular networks of channels that represent nano-scale porous media. We use atomistic simulations to calibrate and validate our model in slit nano-channels. We propose a preconditioning scheme to initialize the coupled transport and adsorption simulation of methane in complex porous media. The results of this implementation of LB agree with Direct Simulation Monte Carlo (DSMC) and Molecular Dynamics (MD) simulations. We then scale up the LB implementation through vectorization and indirect addressing. We parallelize it using Message Passing Interface (MPI) and OpenMP frameworks to simulate transport and adsorption in complex media with a million lattices. Additionally, we analyze the differences between coupled and transport-only simulations in two case studies and show that considering phase behavior, i.e., adsorption, can significantly change the flow behavior. This work constitutes an important step towards bridging the gap between molecular flow and system-scale behavior of complex disordered porous media.

42 ENGINEERING↗
DOE OSTI2021

Entropy Pair Functional Theory: Direct Entropy Evaluation Spanning Phase Transitions

We prove that, within the class of pair potential Hamiltonians, the excess entropy is a universal, temperature-independent functional of the density and pair correlation function. This result extends Henderson’s theorem, which states that the free energy is a temperature dependent functional of the density and pair correlation. The stationarity and concavity of the excess entropy functional are discussed and related to the Gibbs–Bugoliubov inequality and to the free energy. We apply the Kirkwood approximation, which is commonly used for fluids, to both fluids and solids. Approximate excess entropy functionals are developed and compared to results from thermodynamic integration. The pair functional approach gives the absolute entropy and free energy based on simulation output at a single temperature without thermodynamic integration. We argue that a functional of the type, which is strictly applicable to pair potentials, is also suitable for first principles calculation of free energies from Born–Oppenheimer molecular dynamics performed at a single temperature. In conclusion, this advancement has the potential to reduce the evaluation the free energy to a simple modification to any procedure that evaluates the energy and the pair correlation function.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Liquid to crystal Si growth simulation using machine learning force field

Machine learning force field (ML-FF) has emerged as a potential promising approach to simulate various material phenomena for large systems with ab initio accuracy. However, most ML-FFs have been used to study the phenomena relatively close to the equilibrium ground states. In this work, we have studied a far from equilibrium system of liquid to crystal Si growth using ML-FF. Here, we found that our ML-FF based on ab initio decomposed atomic energy can reproduce all the aspects of ab initio simulated growth, from local energy fluctuations to transition temperatures, to diffusion constant, and growth rates. We have also compared the growth simulation with the Stillinger-Weber classical force field and found significant differences. A procedure is also provided to correct a systematic fitting bias in the ML-FF training process, which exists in all training models, otherwise critical results like transition temperature will be wrong.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗