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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Spectral Denoising for Accelerated Analysis of Correlated Ionic Transport

Computation of correlated ionic transport properties from molecular dynamics in the Green-Kubo formalism is expensive, as one cannot rely on the affordable mean square displacement approach. We use spectral decomposition of the short-time ionic displacement covariance to learn a set of diffusion eigenmodes that encode the correlation structure and form a basis for analyzing the ionic trajectories. This allows systematic reduction of the uncertainty and accelerate computations of ionic conductivity in systems with a steady-state correlation structure. We provide mathematical and numerical proofs of the method’s robustness and demonstrate it on realistic electrolyte materials.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRSDate not supplied

Building and Breaking Carbon Composites with REACTER

Carbon composites have become indispensable for aerospace and other high-performance applications, and a detailed picture of their morphology and failure mechanisms remains difficult to obtain through experiment. REACTER is a versatile computational modeling tool for atomistic molecular dynamics designed to model chemical reactions at the speed and length scales of classical force fields.1 In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites, carbon-fiber reinforced polymers (CFRP) and carbon nanotube (CNT) composites. Carbon fiber core morphologies were created by the method of Desai et al.,2 but using the advanced reaction constraints framework of REACTER, their proposed multistep procedure was reduced to a single uninterrupted molecular dynamics simulation. The carbon fiber filler was embedded into a polymer matrix by simulated in situ polymerization of several thermosetting resins, including bismaleimide and polyarylacetylene, to obtain the final CFRP model. To generate the second class of carbon composite, CNT networks were grown dynamically using the new ‘create atoms’ feature of REACTER, and similarly infiltrated with resin to obtain CNT composites. The resulting models were compared directly to experiment using simulated high resolution transmission electron microscopy and x-ray diffraction. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third-order DFT-based tight-binding (DFTB3) simulations, via a reaction constraint on the total potential energy of the involved atoms.

Molecular Dynamics↗
DOE OSTI2021

Molecular Dynamics Driven by the Many-Body Expansion (MBE-MD)

Here, we present a protocol for classical and nuclear quantum dynamics, in which the energies and forces are generated by the many-body expansion (MBE), and apply it to water clusters using the TTM2.1-F and MB-Pol interaction potentials at various temperatures. We carry out MBE-MD classical and nuclear quantum dynamical simulations in which the energies and forces of the full system are approximated by the 2-, 3-, and 4-body terms of the MBE expansion and compare the average potential and the vibrational density of states (VDOS) with the full simulation, i.e., the one for which no MBE is used. Our results indicate that the thermally averaged potential energy from the MBE up to the 4-body term converges with near identical behavior to the one from the full simulation. The 3-body makes a substantial contribution (~20%) to the energy, whereas the 4- body is necessary for obtaining quantitatively accurate energetics and forces, albeit making a small contribution to each (~2%). We further show that the harmonic frequencies are reproduced to within a few wavenumbers (cm -1 ) at the 4-body level, and that the slowest modes to converge with the MBE rank are those involving the strongest hydrogen bonds. Anharmonicity exacerbates this effect, so that a 4-body description of the energies and forces is needed to achieve accurate anharmonic vibrational frequencies in the hydrogen-bonded OH-stretching region. We also discuss the asymptotic scaling of the MBE-MD protocol with respect to the cost of the underlying potential energy evaluation, suggesting that electronic structure methods that scale at least as N 4 ,N being the size of the system, are needed to result in savings over the traditional full MD simulation. We anticipate that MBE-MD protocol can evolve into a powerful and practical method, which will allow for highly accurate ab initio MD simulations on a much broader range of molecular systems than can be currently handled.

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

Understanding Viscoelasticity of an Entangled Silicone Copolymer via Coarse-Grained Molecular Dynamics Simulations

Entangled dynamics is important for understanding rheological properties of long-chain polymers. For entangled homopolymers, the classic tube-reptation model and its refinements have been successfully applied to quantify properties like diffusion coefficient and zero-rate viscosity. However, the application of such models to copolymers has been limited despite scientific and industrial importance. Here, we study the entangled melt dynamics of poly(dimethyl-co-diphenyl)siloxane random copolymer for a range of mean-composition-ratio ϕ of the diphenyl component via long-term molecular dynamics simulation with a recently developed coarse-grained model. We found that the segmental relaxation is heterogeneous at the monomeric level because of compositional fluctuations. However, at the chain-entanglement level and higher length scales, the viscoelastic response is homogeneous with compositional dependence only through the overall diphenyl fraction ϕ. The relaxation modulus of the entangled copolymer melt conforms to the Likhtman–McLeish model, and the viscosity predicted using our current coarse-grained parameters is in good quantitative agreement with experimental data.

Copolymers↗
DOE OSTI2021

Bayesian force fields from active learning for simulation of inter-dimensional transformation of stanene

Abstract We present a way to dramatically accelerate Gaussian process models for interatomic force fields based on many-body kernels by mapping both forces and uncertainties onto functions of low-dimensional features. This allows for automated active learning of models combining near-quantum accuracy, built-in uncertainty, and constant cost of evaluation that is comparable to classical analytical models, capable of simulating millions of atoms. Using this approach, we perform large-scale molecular dynamics simulations of the stability of the stanene monolayer. We discover an unusual phase transformation mechanism of 2D stanene, where ripples lead to nucleation of bilayer defects, densification into a disordered multilayer structure, followed by formation of bulk liquid at high temperature or nucleation and growth of the 3D bcc crystal at low temperature. The presented method opens possibilities for rapid development of fast accurate uncertainty-aware models for simulating long-time large-scale dynamics of complex materials.

Chemistry↗
DOE OSTI2024

Nonadiabatic dynamics with classical trajectories: The problem of an initial coherent superposition of electronic states

Advances in coherent light sources and development of pump–probe techniques in recent decades have opened the way to study electronic motion in its natural time scale. When an ultrashort laser pulse interacts with a molecular target, a coherent superposition of electronic states is created and the triggered electron dynamics is coupled to the nuclear motion. A natural and computationally efficient choice to simulate this correlated dynamics is a trajectory-based method where the quantum-mechanical electronic evolution is coupled to a classical-like nuclear dynamics. These methods must approximate the initial correlated electron–nuclear state by associating an initial electronic wavefunction to each classical trajectory in the ensemble. Different possibilities exist that reproduce the initial populations of the exact molecular wavefunction when represented in a basis. We show that different choices yield different dynamics and explore the effect of this choice in Ehrenfest, surface hopping, and exact-factorization-based coupled-trajectory schemes in a one-dimensional two-electronic-state model system that can be solved numerically exactly. Furthermore, this work aims to clarify the problems that standard trajectory-based techniques might have when a coherent superposition of electronic states is created to initialize the dynamics, to discuss what properties and observables are affected by different choices of electronic initial conditions and to point out the importance of quantum-momentum-induced electronic transitions in coupled-trajectory schemes.

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

Charge regulation effects on colloidal mixture nanoparticles

Changes in pH within a system containing dissociable sites affect the protonation and deprotonation of these groups, thereby influencing their physical properties. In response, the system modifies their surface charge, affecting electrostatic interactions, aggregation, stability, and structural behavior. Although the pH can be tuned in experiments, it is difficult to model this phenomenon using simulations or theoretical approaches. Here, we perform hybrid Monte Carlo-molecular dynamics simulations to model charge regulation effects in an equimolar colloidal charged system. We compare charge regulation effects with those of a system in which the charges of colloidal nanoparticles are not dissociable. The comparison between the two cases modifies the phase diagram, and it changes the volume fraction where a percolation network of nanoparticles is found. Charge regulation is found to destroy network formation, as the charge in the nanoparticles is modified because of the cooperativity dependency of the degree of charge dissociation sites among the nanoparticles favoring cluster formation. Furthermore, our work suggests that the ionic and/or electronic conductivity in functionalized nanoparticles can be modified by changing pH values. It also guides the experimental design of oppositely charged nanoparticles as inks for 3D printing processes.

Classical statistical mechanics↗
DOE OSTI2021

Calculation of self-diffusion coefficients in supercritical carbon dioxide using mean force kinetic theory

This paper presents an application of mean force kinetic theory (MFT) to the calculation of the self-diffusivity of CO 2 in the supercritical fluid regime. Two modifications to the typical application of MFT are employed to allow its application to a system of molecular species. Therefore, the first is the assumption that the inter-particle potential of mean force can be obtained from the molecule center-of-mass pair correlation function, which in the case of CO 2 is the C–C pair correlation function. The second is a new definition of the Enskog factor that describes the effect of correlations at the surface of the collision volume. The new definition retains the physical picture that this quantity represents a local density increase, resulting from particle correlations, relative to that in the zero density homogeneous fluid limit. These calculations are facilitated by the calculation of pair correlation functions from molecular dynamics (MD) simulations using the FEPM2 molecular CO2 model. The self-diffusivity calculated from theory is in good agreement with that from MD simulations up to and slightly beyond the density at the location of the Frenkel line. The calculation is compared with and is found to perform similarly well to other commonly used models but has a greater potential for application to systems of mixed species and to systems of particles with long range interatomic potentials due to electrostatic interactions.

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

AENET–LAMMPS and AENET–TINKER : Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials

Machine-learning potentials (MLPs) trained on data from quantum-mechanics based first-principles methods can approach the accuracy of the reference method at a fraction of the computational cost. To facilitate efficient MLP-based molecular dynamics and Monte Carlo simulations, an integration of the MLPs with sampling software is needed. Here, we develop two interfaces that link the atomic energy network (ænet) MLP package with the popular sampling packages TINKER and LAMMPS. The three packages, ænet, TINKER, and LAMMPS, are free and open-source software that enable, in combination, accurate simulations of large and complex systems with low computational cost that scales linearly with the number of atoms. Scaling tests show that the parallel efficiency of the ænet–TINKER interface is nearly optimal but is limited to shared-memory systems. The ænet–LAMMPS interface achieves excellent parallel efficiency on highly parallel distributed memory systems and benefits from the highly optimized neighbor list implemented in LAMMPS. We demonstrate the utility of the two MLP interfaces for two relevant example applications: the investigation of diffusion phenomena in liquid water and the equilibration of nanostructured amorphous battery materials.

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

Investigations of water/oxide interfaces by molecular dynamics simulations

Water/oxide interfaces are ubiquitous on earth and show significant influence on many chemical processes. For example, understanding water and solute adsorption as well as catalytic water splitting can help build better fuel cells and solar cells to overcome our looming energy crisis; the interaction between biomolecules and water/oxide interfaces is one hypothesis to explain the origin of life. However, knowledge in this area is still limited due to the difficulty of studying water/solid interfaces. As a result, research using increasingly sophisticated experimental techniques and computational simulations has been carried out in recent years. Although it is difficult for experimental techniques to provide detailed microscopic structural information, molecular dynamics (MD) simulations have satisfactory performance. In this report, we discuss classical and ab initio MD simulations of water/oxide interfaces. Generally, we are interested in the following questions: How do solid surfaces perturb interfacial water structure? How do interfacial water molecules and adsorbed solutes affect solid surfaces and how do interfacial environments affect solvent and solute behavior? Finally, we discuss progress in the application of neural network potential based MD simulations, which offer a promising future because this approach has already enabled ab initio level accuracy for very large systems and long trajectories.

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

Rapid cooling of the in-plane motion of two-dimensional ion crystals in a Penning trap to millikelvin temperatures

Here, we propose a highly feasible technique with no experimental overhead to rapidly cool the in-plane degrees of freedom of large two-dimensional ion crystals in Penning traps. Through simulations, we demonstrate that our approach enables the in-plane modes to cool down to a temperature of around 1 mK in less than 10 ms. Our technique relies on near-resonant coupling of the poorly cooled in-plane motions and the efficiently cooled out-of-plane motions, and is achieved without introducing additional potentials. The rapid cooling enabled by our approach is in contrast to typical operating conditions, where our simulations of the laser cooling dynamics suggest that the ion crystal's in-plane motion cools very slowly on a timescale of several hundreds of milliseconds, a rate likely slower than experimental heating rates. Our work sets the stage for sub-Doppler laser cooling of the planar motion, and more robust and versatile quantum simulation and quantum sensing experiments with two-dimensional crystals in Penning traps.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRSDate not supplied

REACTER: A Heuristic Method for Reactive Molecular Dynamics

REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.

polymer simulations, molecular dynamics↗
DOE OSTI2022

Dynamic signatures of electronically nonadiabatic coupling in sodium hydride: a rigorous test for the symmetric quasi-classical model applied to realistic, ab initio electronic states in the adiabatic representation

Sodium hydride (NaH) in the gas phase presents a seemingly simple electronic structure making it a potentially tractable system for the detailed investigation of nonadiabatic molecular dynamics from both computational and experimental standpoints. The single vibrational degree of freedom, as well as the strong nonadiabatic coupling that arises from the excited electronic states taking on considerable ionic character, provides a realistic chemical system to test the accuracy of quasi-classical methods to model population dynamics where the results are directly comparable against quantum mechanical benchmarks. Here, using a simulated pump–probe type experiment, this work presents computational predictions of population transfer through the avoided crossings of NaH via symmetric quasi-classical Meyer–Miller (SQC/MM), Ehrenfest, and exact quantum dynamics on realistic, ab initio potential energy surfaces. The main driving force for population transfer arises from the ground vibrational level of the D 1 Σ + adiabatic state that is embedded in the manifold of near-dissociation C 1 Σ + vibrational states. When coupled through a sharply localized first-order derivative coupling most of the population transfers between t = 15 and t = 30 fs depending on the initially excited vibronic wavepacket. While quantum mechanical effects are expected due to the reduced mass of NaH, predictions of the population dynamics from both the SQC/MM and Ehrenfest models perform remarkably well against the quantum dynamics benchmark. Additionally, an analysis of the vibronic structure in the nonadiabatically coupled regime is presented using a variational eigensolver methodology.

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

Experimental and Computational Studies of Crystal Nucleation in Composition Gradients (Final Report)

The major goals of this project were to develop and validate a predictive nucleation model that incorporates composition gradients and is applicable to a large range of metallic systems which form both stochiometric and non-stochiometric compounds. Computationally we planned to expand the extent of thermodynamics-based theories and lay the groundwork to improve the general understanding and predictive capabilities of the role that gradients play in phase formation, glass formability and stability, and nucleation and growth events. To address these goals, we used Molecular Dynamics (MD) simulations and both isothermal and isochronal nanocalorimetric experiments on amorphous phases with a controlled composition gradient with the hopes of validating and improving the classical nucleation model and its use in solid solutions. While the computations were successful and identified ways to improve the classical nucleation model, the in situ nanocalorimetry studies proved very challenging due to unexpected difficulties in fabricating effective calorimeters and samples. Thus, we could not experimentally validate our predicted influence of composition gradients on nucleation. Nonetheless, important insights were gained and modifications to the classical nucleation theory were suggested.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Decoupling electrode kinetics to elucidate reaction mechanisms in alkaline water electrolysis

Alkaline water electrolysis (AWE) presents key advantages, including reduced material costs, enhanced operational stability, and compatibility with non-precious metal catalysts, positioning it as a scalable route for hydrogen production. In this study, we introduce a minimally invasive single-cell configuration incorporating a reference electrode via diaphragm extension to form an internal ion channel. This setup, combined with an interfaced potentiostat and auxiliary electrometer, enables real-time, independent monitoring of anode and cathode behavior, offering high-resolution electrochemical diagnostics. While it is well established that the hydrogen evolution reaction (HER) exhibits sluggish kinetics in alkaline media, our study reveals that this limitation persists even in practical AWE systems where nickel-based substrates are used as electrodes. This observation is supported by both experimental data and voltage breakdown modeling. Arrhenius-type analysis reveals that localized electric fields induced by catalysts shift the reaction kinetics from classical Butler–Volmer behavior toward a Marcus-like regime, where interfacial molecular dynamics and bimolecular charge transfer dominate. We propose a semi-empirical model and a surficial reaction mechanism to describe these dynamics. This work underscores the critical need for cathode innovation and provides a rational framework for designing advanced catalysts and electrode architectures to optimize AWE performance.

08 HYDROGEN↗