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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Electronic structure and dynamics of confined atoms

Confined atomic systems are of great importance owing a multitude of possible applications in various areas of science and technology. Of particular interest are atoms encaged in the C 60 molecule, A@C 60 , since the near-spherical symmetry of C 60 simplifies theoretical studies, and the stability of C 60 renders it amenable to experimental examination. Herein a review of investigations of the electronic structure and dynamics of A@C 60 is presented in this manuscript focusing on developments in the last decade. Addressed mainly are how the confinement affects electronic structure properties such as ionization potentials, localization of atomic electrons, Shannon entropy, correlation effects, relativistic interactions, and others. In the area of dynamics, photoionization and e-A@C 60 scattering are reviewed and summarized, and the major effects of confinement on the dynamical properties, e.g., confinement resonances, hybridization, Wigner time delay, are delineated.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Dynamics of plasma atomic layer etching: Molecular dynamics simulations and optical emission spectroscopy

Atomic layer etching is intrinsically dynamic as it involves sequential and repeated exposures of a surface to be etched with different species at different energies. The composition and structure of the near surface region change in both time and depth. Full understanding of this process requires resolving both temporal and spatial variations. In this work, we consider silicon (Si) atomic layer etching (ALE) by alternating exposure to chlorine gas (Cl 2 ) and argon ions (Ar + ). Molecular dynamics (MD) simulations are compared to experimental measurements with the aim of better understanding the dynamics of ALE and to test the simulation procedure. The simulations help to more fully interpret the experimental measurements. Further, optical emission measured just above the surface being etched can be related to etch products and can, therefore, be directly compared to simulation predictions. The simulations capture the measured initial product distribution leaving the surface and match the measured etch per cycle reasonably well. While simulations demonstrate the importance of ion-induced surface damage and mixing into a layer below the surface, the depth of which depends mainly on ion energy, the experiments suggest there is more Cl mixed into the layer than the MD procedure predicts.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Split-pulse X-ray photon correlation spectroscopy with seeded X-rays from X-ray laser to study atomic-level dynamics

Abstract With their brilliance and temporal structure, X-ray free-electron laser can unveil atomic-scale details of ultrafast phenomena. Recent progress in split-and-delay optics (SDO), which produces two X-ray pulses with time-delays, offers bright prospects for observing dynamics at the atomic-scale. However, their insufficient pulse energy has limited its application either to phenomena with longer correlation length or to measurement with a fixed delay-time. Here we show that the combination of the SDO and self-seeding of X-rays increases the pulse energy and makes it possible to observe the atomic-scale dynamics in a timescale of picoseconds. We show that the speckle contrast in scattering from water depends on the delay-time as expected. Our results demonstrate the capability of measurement using the SDO with seeded X-rays for resolving the dynamics in temporal and spatial scales that are not accessible by other techniques, opening opportunities for studying the atomic-level dynamics.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Atomic Diffusion, Segregation, and Grain Boundary Migration in Nickel-Based Alloys from Molecular Dynamics Simulations

Grain boundary diffusion and metal mobility in alloys control material performance in many applications and yet remain poorly understood at a mechanistic level. With advances in accessible time and length scales for computational molecular simulations, and recent force field developments, we now possess tools to help unravel those mechanisms. Using large-scale molecular dynamics simulations, here we examined vacancy-mediated diffusion processes in Ni-5Cr alloy with low and high-energy grain boundaries. We show that atomic diffusion inside the grain boundary plane is about four times higher than bulk diffusion, at any temperature, and exhibits a typical Arrhenius behavior with a very small energy barrier (0~.8 eV for Cr and 0.7 eV for Ni within 1300-1600 K). Additionally, the fastest diffusing species inverts; Cr diffusion was faster than Ni in the bulk but slower in the grain boundaries. This is attributed to the creation of high cohesive energy clusters of Cr at the grain boundary. Grain boundary migration was also observed to be temperature dependent and appears to be two times higher in the 5% Cr alloy than in pure Ni, highlighting the important role of the alloying element on grain boundary motion.

Simonnin, Pauline GN↗
DOE OSTI2022

Manipulating and Probing Ultrafast Atomic and Molecular Dynamics (Final Report)

This program has focused on the exploration and control of dynamics in atoms, small molecules, clusters, and micro- or nano-structures following ultrafast excitation and/or driven by strong oscillating fields. In our principal experiments, gas phase atoms and molecules were exposed to short pulses of electromagnetic radiation with frequencies ranging from THz into the XUV spectral regions, and with durations from picoseconds to attoseconds. The pulses coherently induce and/or probe dynamics in the electronic, vibrational, and rotational degrees of freedom of the targets. The overarching goal of the various projects has been to exploit strong-field processes and/or implement novel ultrafast techniques for manipulating and probing coherent electronic and nuclear motion. Typically, the relevant system evolution occurs over attosecond to picosecond timescales. In doing so, we have gained a more complete picture of correlated multi-particle dynamics in atoms, molecules, and other complex systems and expanded the toolbox of useful techniques for manipulating and probing those dynamics. Grant funds were primarily used to: (i) pay salaries and fringe benefits for the PI and postdocs and stipends, tuition, and health care costs for graduate students; (ii) cover travel expenses for the PI, postdocs, and students to attend and participate in professional meetings, conferences, and workshops; and (iii) purchase research materials, supplies, and equipment required for experiments. The research resulted in the publication of 24 peer reviewed articles (including 1 in Nature Physics, 2 in Nature Communications, 7 in Physical Review Letters, and 12 in Physical Review A), and 4 PhD dissertations. The specific results from different funding periods are summarized separately in the main report.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Shadow molecular dynamics and atomic cluster expansions for flexible charge models

A shadow molecular dynamics scheme for flexible charge models is presented, where the shadow Born-Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, are modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born-Oppenheimer molecular dynamics (BOMD) [Eur. Phys. J. B 94, 164 (2021)]. XL-BOMD provides a stable dynamics, while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using the atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO2) and a molecular system of liquid water. The combined ACE + XL-QEq dynamics are stable over a wide range of temperatures both for the oxide and the molecular systems, and provide a precise sampling of the Born-Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Shadow Molecular Dynamics and Atomic Cluster Expansions for Flexible Charge Models

Here, a shadow molecular dynamics scheme for flexible charge models is presented where the shadow Born–Oppenheimer potential is derived from a coarse-grained approximation of range-separated density functional theory. The interatomic potential, including the atomic electronegativities and the charge-independent short-range part of the potential and force terms, is modeled by the linear atomic cluster expansion (ACE), which provides a computationally efficient alternative to many machine learning methods. The shadow molecular dynamics scheme is based on extended Lagrangian (XL) Born–Oppenheimer molecular dynamics (BOMD). XL-BOMD provides stable dynamics while avoiding the costly computational overhead associated with solving an all-to-all system of equations, which normally is required to determine the relaxed electronic ground state prior to each force evaluation. To demonstrate the proposed shadow molecular dynamics scheme for flexible charge models using atomic cluster expansion, we emulate the dynamics generated from self-consistent charge density functional tight-binding (SCC-DFTB) theory using a second-order charge equilibration (QEq) model. The charge-independent potentials and electronegativities of the QEq model are trained for a supercell of uranium oxide (UO 2 ) and a molecular system of liquid water. The combined ACE+XL-QEq molecular dynamics simulations are stable over a wide range of temperatures both for the oxide and for the molecular systems and provide a precise sampling of the Born–Oppenheimer potential energy surfaces. Accurate ground Coulomb energies are produced by the ACE-based electronegativity model during an NVE simulation of UO 2 , predicted to be within 1 meV of those from SCC-DFTB on average during comparable simulations.

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

All-atom molecular dynamics simulations of weak polyionic brushes: influence of charge density on the properties of polyelectrolyte chains, brush-supported counterions, and water molecules

All atom molecular dynamics (MD) simulations of planar Na+-counterion-neutralized polyacrylic acid (PAA) brushes are performed for varying degrees of ionization (and thereby varying charge density) and varying grafting density. Variation in the PE charge density (or degree of ionization) and grafting density leads to massive changes of the properties of the PE molecules (quantified by the changes in the height and the mobility of the PE brushes) as well as the local arrangement and distribution of the brush-supported counterions and water molecules within the brushes. The effect on the counterions is manifested by the corresponding variation of the counterion mobility, counterion concentration, extent of counterion binding to the charged site of the PE brushes, water-in-salt-like structure formation, and counterion-water–oxygen radial distribution function within the PE brushes. On the other hand, the effect on water molecules is manifested by the corresponding variation of water–oxygen–water–oxygen RDF, local water density, water–water and water–PE functional group hydrogen bond networks, static dielectric constant of water molecules, orientational tetrahedral order parameter, and water mobility. Enforcing such varying degree of ionization of weak polyelectrolytes is possible by changing the pH of the surrounding medium. Thus, our results provide insights into the changes in microstructure (at the atomistic level) of weak polyionic brushes at varying pH. Finally, we anticipate that this knowledge will prove to be vital for the efficient design of several nano-scale systems employing PE brushes such as nanomechanical gates, current rectifiers, etc.

42 ENGINEERING↗
DOE OSTI2023

Direct Observation of Transient Structural Dynamics of Atomically Thin Halide Perovskite Nanowires

Halide perovskite is a unique dynamical system, whose structural and chemical processes happening across different timescales have significant impact on its physical properties and device-level performance. However, due to its intrinsic instability, real-time investigation of the structure dynamics of halide perovskite is challenging, which hinders the systematic understanding of the chemical processes in the synthesis, phase transition, and degradation of halide perovskite. Here, we show that atomically thin carbon materials can stabilize ultrathin halide perovskite nanostructures against otherwise detrimental conditions. Moreover, the protective carbon shells enable atomic-level visualization of the vibrational, rotational, and translational movement of halide perovskite unit cells. Albeit atomically thin, protected halide perovskite nanostructures can maintain their structural integrity up to an electron dose rate of 10,000 e – /Å 2 ·s while exhibiting unusual dynamical behaviors pertaining to the lattice anharmonicity and nanoscale confinement. Here, our work demonstrates an effective method to protect beam-sensitive materials during in situ observation, unlocking new solutions to study new modes of structure dynamics of nanomaterials.

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

Linear Discriminant Analysis-Based Machine Learning and All-Atom Molecular Dynamics Simulations for Probing Electro-Osmotic Transport in Cationic-Polyelectrolyte-Brush-Grafted Nanochannels

Deciphering the correct mechanisms governing certain phenomena in polyelectrolyte (PE) brush grafted systems, revealed through atomistic simulations, is an extremely challenging problem. In a recent study, our all-atom molecular dynamics (MD) simulations revealed a non-linearly large electroosmotic (EOS) flow (in the presence of an applied electric field) in nanochannels grafted with PMETAC [Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] brushes. Given the lack of any formal procedure that would have directed us to identify the correct factors responsible for such an occurrence, we needed to spend several months and devote significant analyses to unravel the involved mechanisms. In this paper, we propose a Linear Discriminant Analysis (LDA) based Machine Learning (ML) approach to address this gap. At first, we obtain data on certain basic features from the all-atom MD data. These basic features represent the number of atoms of certain species around one atom of another (or same) species. Here, we obtain such data on basic features for a reference case (case of an EOS flow in PMETAC-brush-grafted nanochannels with a smaller electric field) and a perturbed case (case of an EOS flow in PMETAC-brush-grafted nanochannels with a larger electric field) in bins in which the nanochannel half height has been divided into. These datasets are high-dimensional dataset, to which the LDA is applied. This leads to the projection of the data (between the reference and the perturbed states) in a highly separated form on a 1D line. From such LDA calculations, we are able to identify the relative importance of the different basic features in ensuring this separation of the data (between the reference and the perturbed states) on the 1D line. This relative importance of the different basic features is quantified as “importance scores” for the different features, which in turn tell us what to study and where to study. Such knowledge enables us to rapidly identify the key factors responsible for the non-linearly large EOS transport in PMETAC-brush-grafted nanochannels.

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

All-Atom Molecular Dynamics Simulations of Cationic Polyelectrolyte Brushes in the Presence of Halide Counterions

Understanding the response of the charged polyelectrolyte (PE) brushes and brush-supported water and ions to the changes in the nature of screening counterions is significant in developing strategies for utilizing PE brushes in various applications. In this paper, we employ all-atom molecular dynamics (MD) simulations for studying the behavior of cationic [poly(2-(methacryloyloxy)ethyl) trimethylammonium] (PMETA) brushes and brush-supported water and ions in the presence of different halide (X: I – , Br – , Cl – , and F – ) screening counterions. We find that despite the F– ion having the largest charge density, the extent of binding of the counterions on the PMETAX brushes varies as I – > Br – > Cl – > F – , leading to PMETAX brush height being least with I– counterions and greatest with F – counterions. This trend in the binding of the halide ions matches the previous experimental result and can be explained by identifying the chaotropic nature of the I – and Br – ions that promote a disruption of water structure and a more favorable binding of the ions to the polymer chains. Such a binding trend also ensures that the order of the water molecules around the PMETAX chains or the counterions as well as the number of water–water hydrogen bonds inside the brush layer increases in the following order of the counterion-specific PMETAX brushes: F – > Cl – > Br – > I – . Furthermore, halide-ion-PMETAX-chain binding takes place via both interchain and intrachain bridging: intrachain bridging dominates for the case of counterions that show enhanced binding (I – and Br – ), while interchain bridging is more favored for the case of counterions that show weakened binding (F – and Cl – ). Also, a greater degree of intrachain bridging leads to greater compressibility and flexibility of the brush layer. Lastly, we show that the mobility of the halide ions follows a nonmonotonic trend with the charge density: the mobility decreases as I – < Br – < Cl – (as their binding to the PMETAX chains varies as I – > Br – > Cl – ), but the mobility of F – ions is in between that of I – and Br – ions. We argue that the strongly attached hydration layer and the ensuing friction inside the brush layer lead to such a reduced mobility of the F – ions.

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

Atomic-Scale Dynamics of Five-Fold Twin Mediated Coalescence: Pathway-Dependent and Defect-Governed Nonclassical Growth Mechanisms

Defective crystals with distinct properties have been discovered in many systems. However, the growth mechanism of defective crystals is still poorly understood. Here, in this work, using a 5-fold twinned gold (Au) nanocrystal (NC) as a model system, three new coalescence pathways involving detwinning or twinning have been uncovered through atomic-scale dynamic observations in an aberration-corrected transmission electron microscope coupled with atomistic simulations. This demonstrates that beyond crystal size, coalescence growth dynamics involving 5-fold twins (5-FTs) are highly dependent on crystal defect density and the approach pathways of the crystals. When a 5-FT encounters a smaller 5-FT or a smaller NC in a face-to-face way, a new, larger 5-FT is produced at a relatively fast coalescence growth rate; while in a corner-to-corner way, the coalescence dynamics are more retarded and sluggish, which is conducive to the formation of complex multitwined structures rather than 5-FTs. This highlights that the planar defect density and crystal approach pathway influence the coalescence dynamics of crystals containing 5-FT. Moreover, a column-by-column grain boundary (GB) migration mechanism, which results in bent GBs, was also unveiled during the crystal coalescence process. These results enrich the general understanding of the crystal growth theory and provide new insights into the controllable fabrication of 5-FTs by crystal coalescence mechanisms.

crystallization↗
DOE OSTI2022

Machine learning enabled quantification of the hydrogen bonds inside the polyelectrolyte brush layer probed using all-atom molecular dynamics simulations

The configuration of densely grafted charged polyelectrolyte (PE) brushes is strongly dictated by the properties and behavior of the counterions that screen the PE brush charges and the solvent molecules (typically water) that solvate the brush molecules and these screening counterions. Only recently, efforts have been made to study the PE brushes atomistically, thereby shedding light on the properties of brush-supported ions and water molecules. However, even for such efforts, there are limitations associated with using a generic definition to estimate certain properties of water and ions inside the brush layer. For example, water–water hydrogen bonds (HBs) will behave differently for locations outside and inside the brush layer, given the fact that the densely closely grafted PE brush molecules create a soft nanoconfinement where the water connectivity becomes highly disrupted: therefore, using the same definition to quantify the HBs inside and outside the brush layer will be unwise. In this paper, we address this limitation by employing an unsupervised machine learning (ML) approach to predict the water–water hydrogen bonding inside a cationic PE brush layer modeled using all-atom molecular dynamics (MD) simulations. Here, the ML method, which relies on a clustering approach and uses the equilibrium coordinates of the water molecules (obtained from the all-atom MD simulations) as the input, is capable of identifying the structural modification of water–water HBs (revealed through appropriate clustering of the data) inside the PE brush layer induced soft nanoconfinement. Such capabilities would not have been possible by using a generic definition of the HBs. Our calculations lead to four key findings: (1) the clusters formed inside and outside the brush layer are structurally similar; (2) the margin of the cluster is shorter inside the PE brush layer confirming the possible disruption of the HBs inside the PE brush layer; (3) the average “hydrogen–acceptor-oxygen–donor-oxygen” angle that defines the HB is reduced for the HBs formed inside the brush layer; (4) the use of the generic definition (definition usable for characterizing the HBs in brush-free bulk) leads to an overprediction of the number of HBs formed inside the PE brush layer.

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

All-Atom Molecular Dynamics Simulations of the Temperature Response of Densely Grafted Polyelectrolyte Brushes

Water acts a “good” solvent for most polyelectrolyte (PE) systems due to its high dielectric strength. Theoretical and experimental studies have highlighted some remarkably unconventional properties of strongly water-swollen PE brushes such as a reduction in brush height with increase in temperature. However, an understanding of the atomistic-scale response of the grafted PE chains as well as the local arrangement and organization of the brush-supported counterions and water molecules to changes in temperature is missing. Here, we conduct an all-atom molecular dynamics (MD) study to probe the influence of temperature on the “microstructure” of densely grafted, fully ionized polyacrylic acid (PAA) brushes. The atomistic insights obtained from our study shed light on prior experimental observations and elucidate the key role played by changes in hydrogen bonding network in dictating the hydrophilicity of the brushes. In addition to the temperature-mediated reduction in height of the PE brush layer, we study the influence of temperature on several properties of the brush-supported water molecules such as the number distribution and kinetics of water-water and water-PE hydrogen bonds (HBs), mass density, orientational tetrahedral order parameter, and the activation energy associated with the self-diffusion of water. The effect of temperature on the properties of the brush-trapped counterions is also quantified via changes in their solvation structure, counterion-water radial distribution function (RDF), and the translational mobility. Our findings unravel several hitherto unknown phenomena such as the enhanced propensity for attaining PE brush-induced “water-in-salt”-like scenarios at elevated temperatures, and an increase in the activation energy for the self-diffusion of water with increase in the degree of PE brush-induced nanoconfinement (from ‘bulk water’ to ‘sparsely grafted PE brushes’ to ‘densely grafted PE brushes’). Further, we anticipate that this work will be helpful in improving our predictive capabilities of the temperature response of water-swollen PE brushes, which would be instrumental for better design of several PE brush systems used in a multitude of applications.

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

Atomic-Scale Dynamic Interaction of H 2 O Molecules with Cu Surface

Atomic-scale interaction of water vapor with metal surfaces beyond surface adsorption under technologically relevant conditions remains mostly unexplored. Using aberration-corrected environmental transmission electron microscopy, we reveal the dynamic surface activation of Cu by H 2 O at elevated temperature and pressure. In this study, we find a structural transition from flat to corrugated surface for the Cu(011) under low water-vapor pressure. Increasing the water-vapor pressure leads to the surface reaction of Cu with dissociated H 2 O, resulting in the formation of a metastable “bilayer” Cu-O-H phase. Corroborated by density functional theory and ab initio molecular dynamics calculations, the cooperative O and OH interaction with Cu is responsible for the formation and subsurface propagation of this phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗