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At least 415 records · Page 23

Dislocation dynamics in polycrystalline materials

An extension of the dislocation dynamics method to polycrystalline materials is presented with emphasis on handling interactions between dislocations and grain boundaries. The key new features of the method include: (1) a grain boundary detection algorithm, (2) new dislocation emission criteria based on power dissipation and area growth, (3) mobility of dislocations at grain boundaries, and (4) extension of topological operations e.g. mesh adaption, collision, and dissociation to handle dislocations interacting with grain boundaries. Furthermore, verification and validation examples are executed to compare our calculations with existing analytic methods, molecular dynamics simulations, and experimental observations.

36 MATERIALS SCIENCE↗

First-Principles Simulation of Beam-Induced Processes Underlying Atomic Manipulation in Electron Microscopes

The development of experimental methods and apparatuses capable of promoting atomically precise material manipulations holds great promise for realizing the ultimate limit of feature miniaturization in materials and devices. The ability to modify materials atom by atom is anticipated to usher in new technologies in areas as diverse as separation science, medicine, and quantum information science. Historically, scanning probe-based techniques have been the most prominent approaches in this space. However, these methods are best suited for the manipulation of surface-exposed regions of materials, as the strong perturbations required for bond scission are delivered most effectively to atoms in the near-proximity to the scanning probe. In contrast, convergent electron beams with energies tuned slightly below the threshold for inducing irreversible knock-on damage have recently been employed (within scanning transmission electron microscopy) to promote atomic-scale bond rearrangements in various beam-stable solids. Currently, however, the efficiency and selectivity of beam-induced atomic manipulation processes with focused electron beams are such that long irradiation times are required to induce a desired atomic rearrangement. With a better understanding of the underlying physics dictating the outcome of a given irradiation event, methods can be devised to improve the efficiency of these techniques so that their promise can be fully realized through widespread adoption.To this end, this Account details our recent efforts to develop and apply tractable first-principles simulation approaches for studying the response of materials to electric beam-like external electric potentials applied in real space. We briefly review the concepts and capabilities in the area of atomically precise materials manipulation and review the early demonstrations of accomplishments in this area, focusing on studies using scanned convergent electron beam probes in particular. We expound upon the depth of the challenge and identify critical shortcomings of theoretical methods that have previously been employed in the simulation of beam-induced processes. We then describe the computational methods that we have generalized from the concepts and tools most commonly applied to the study of molecular photochemistry and how our adaptations of these methods can be employed to capture the relevant dynamical phenomena for beam-induced processes ranging from the initial electron scattering to the ensuing multistate reactions. Here, we contextualize these methods within the current state of the art in this area, which has historically focused primarily on the simulation of inelastic image formation in the electron microscope for the purpose of interpreting the results of quantitative electron microscopy experiments. We demonstrate that the spatial distribution of state-specific excitation rates due to the presence of an external (probe) electric charge is inhomogeneous, such that irradiation at particular locations in materials can favor specific electronic transitions (and disallow others). In addition to the potential for excited-state reaction pathways to be accessed through the initial inelastic scattering of the tightly focused electron beam from the targeted atoms, we also identify favorable conditions for the electronically nonadiabatic evolution of the highly vibrationally excited system to open complex multistate reaction pathways. Implications of the early results for understanding the mechanisms and potential routes to improved efficiency and selectivity in beam-induced reactions are discussed. We conclude with a summary of the current state of theory and modeling capabilities in this area and provide our perspective on future directions for theoretical and experimental developments that we view as crucial to advancing the use of convergent electron beams in mode-specific, atomically precise platforms for direct-write materials modifications.

36 MATERIALS SCIENCE↗

Understanding Adsorption and Reactions at Aqueous Oxide Interfaces with Neural Network Potential Molecular Dynamics

Chemical processes at metal oxide−water interfaces are of central importance in geochemistry, biology, and energy technologies. A better understanding of these processes would allow us to make a significant step toward optimizing and controlling them, which could in turn lead to broader impacts. Computational modeling is indispensable to accomplishing this task because complexity and disorder often make it difficult to extract atomistic information from experiments. Balancing computational cost and accuracy, simulation schemes based on efficient machine learning representations of the potential energy surface (PES) predicted by ab initio calculations have become increasingly popular over the past decade. In particular, several studies have demonstrated the ability of machine learning models to accurately reproduce the complex ab initio PESs of aqueous oxide interfaces, allowing simulations of systems and processes that are not accessible with ab initio methods. In this Account, we review our recent efforts to understand adsorption processes and reactions at aqueous oxide interfaces using deep potential molecular dynamics (DPMD), a simulation scheme employing deep neural networks (DNNs), which has proven to be quite successful in accurately describing many different systems in the condensed phase. After summarizing the DPMD methodology, we first review our work on the acid−base chemistry of oxide surfaces in contact with water, a fundamental characteristic that controls proton transfer and surface charge at the interface. We focus on the aqueous interface of rutile IrO 2 , an oxide material thus far considered the best catalyst for the oxygen evolution reaction (OER). We show that this interface is characterized by a large fraction of dissociated water and a strong Brønsted acidity of the surface sites, in good agreement with the experimentally measured value of the point of zero proton charge. In our second example, we investigate how the adsorption of organic species from ambient air or water affects the structure and wettability of the aqueous interfaces of TiO 2 , a prototypical photocatalytic material. This is a question that is relevant to understanding the UV-induced hydrophilicity of TiO 2 surfaces, a property at the basis of self-cleaning windows and related applications. Specifically focusing on formic and acetic acids, the two most common atmospheric organic acids, our simulations reveal that these acids control the wettability of TiO 2 largely through acid−base chemistry at the interface rather than chemisorption on the oxide surface, a finding that could help improve the design of self-cleaning surfaces and photocatalytic devices. Finally, we review our recent study of methanol at TiO 2 −water interfaces, a system whose interest is largely motivated by the role of methanol in enhancing photocatalytic hydrogen evolution on TiO 2 . Our simulations provide mechanistic insights into the coupled roles of the organic adsorbate and water at the TiO 2 interface, with implications for how methanol enhances the activity of H 2 evolution.

adsorption↗

Nature of molybdenum carbide surfaces for catalytic hydrogen dissociation using machine-learned potentials: an ensemble-averaged perspective

Molybdenum carbides with an electronic structure similar to noble metals have gained attention as a promising low-cost catalyst for biomass valorization and the hydrogen evolution reaction. However, our fundamental understanding of the catalyst surface and how different phases of these catalysts behave at varying reaction conditions is limited to ground state density functional theory calculations as ab initio molecular dynamics (AIMD) is computationally prohibitive at relevant length and time scales. Here, in this work, we train a multi-atomic cluster expansion (MACE) machine-learned interatomic potentials (MLIP) to study hydrogen dissociation and dynamics over Mo, δ-MoC, α-Mo 2 C, and β-Mo 2 C surfaces at varying temperatures and hydrogen partial pressures. Our simulations identify unique and different molecular and atomic hydrogen adsorption sites on different surfaces that do not depend on the temperature. At low hydrogen pressures, the surface coverage is monolayer, which transitions to two-layer adsorption at higher pressures. We find that atomic hydrogen diffusion and recombinations are preferred over molybdenum atom hollow sites, while the diffusion over carbon-terminated facets was negligible, signifying particularly strong C–H interactions. In contrast, molecular hydrogen adsorption occurs mostly atop Mo or the bridging sites. At a comparable hydrogen loading, β-Mo 2 C (001) is the most active surface for hydrogen dissociation reaction. This work provides insights into the dynamic nature of the hydrogen dissociation chemistry and the diversity of hydrogen adsorption sites on molybdenum carbides.

08 HYDROGEN↗

Simplifying computational workflows with the Multiscale Atomic Zeolite Simulation Environment (MAZE)

Zeolites, an important class of 3-dimensional nanoporous materials, have been widely explored for a variety of applications including gas storage, separations, and catalysis. As the properties of these aluminosilicate materials depend on a number of factors (e.g., framework topology, Si/Al ratio, extra-framework cations etc.), detailed experiments (e.g., catalytic properties, adsorption capacities etc.) are often limited to only a handful of materials. Computational methods have played an important role in (1) providing molecular level insights to rationalize experimental observations, and (2) screening large libraries of zeolites to identify promising candidates for experimental synthesis and validation. Different levels of theory and computational chemistry codes are necessary to describe the range of relevant phenomena such as adsorption (e.g., grand canonical Monte Carlo), diffusion (e.g., molecular dynamics), and chemical reactions (e.g., density functional theory). Manipulation of atomic structures, handling of input files, and developing robust workflows becomes quite cumbersome. To mitigate these challenges, we describe the development of the Multiscale Atomic Zeolite Simulation Environment (MAZE) – a Python package that simplifies zeolite-specific calculation workflows by providing a user-friendly interface for systematically manipulating zeolite structures

97 MATHEMATICS AND COMPUTING↗

Effects of MOF linker rotation and functionalization on methane uptake and diffusion

The flexible degrees of freedom in metal–organic frameworks (MOFs) can have significant effects on guest molecule behavior. However, in the majority of studies applying molecular simulations to MOFs, the framework is assumed to be rigid in order to minimize computational cost. Here, in this work, we assess the significance of this assumption on a representative example of methane uptake and diffusion in UiO-66. We introduce an open-source code to modify MOFs through functionalization and linker rotation and we perform Grand Canonical Monte Carlo and molecular dynamics simulations of methane in each of the functionalized and linker-rotated derivatives of UiO-66. We find that linker rotation moderately influences methane uptake and significantly influences methane diffusion. Our assessment provides ranges of property values that serve as measures of uncertainty of these two properties associated with linker rotation. We further determine that void volume fraction and minimum pore size are the features that govern methane uptake and diffusion, respectively. These findings illustrate the impact of linker rotation on MOFs and provide design principles to guide future investigations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Constant-potential molecular dynamics simulations of molten salt double layers for FLiBe and FLiNaK

We report the results of constant-potential molecular dynamics simulations of the double layer interface between molten 2LiF–BeF 2 (FLiBe) and 23LiF–6NaF–21KF (FLiNaK) fluoride mixtures and idealized solid electrodes. Employing methods similar to those used in studies of chloride double layers, we compute the structure and differential capacitance of molten fluoride electric double layers as a function of applied voltage. The role of molten salt structure is probed through comparisons between FLiBe and FLiNaK, which serve as models for strong and weak associate-forming salts, respectively. In FLiBe, screening involves changes in Be–F–Be angles and alignment of the oligomers parallel to the electrode, while in FLiNaK, the electric field is screened mainly by rearrangement of individual ions, predominantly the polarizable potassium cation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Site Disorder Drives Cyanide Dynamics and Fast Ion Transport in Li 6 PS 5 CN

Halide argyrodite solid-state electrolytes of the general formula Li 6 PS 5 X exhibit complex static and dynamic disorder that plays a crucial role in ion transport processes. Here, we unravel the rich interplay between site disorder and dynamics in the plastic crystal argyrodite Li 6 PS 5 CN and the impact on ion diffusion processes through a suite of experimental and computational methodologies, including temperature-dependent synchrotron powder X-ray diffraction, AC electrochemical impedance spectroscopy, 7 Li solid-state NMR, and machine learning-assisted molecular dynamics simulations. Sulfide and (pseudo)halide site disorder between the two anion sublattices unilaterally improves long-range lithium diffusion irrespective of the (pseudo)halide identity, which demonstrates the importance of site disorder in dictating bulk ionic conductivity in the argyrodite family. Furthermore, we find that anion site disorder modulates the presence and time scales of cyanide rotational dynamics. Ordered configurations of anions enable fast, quasi-free rotations of cyanides that occur on time scales of 10 11 Hz at T = 300 K. In contrast, we find that cyanide dynamics are slow or frozen in Li 6 PS 5 CN when site disorder between the cyanide and sulfide sublattices is present at T = 300 K. We rationalize the observed differences in cyanide dynamics in the context of elastic dipole interactions between neighboring cyanide anions and local strain induced by the configurations of site disorder that may impact the energetic landscape for cyanide rotational dynamics. Through this study, we find that anion disorder plays a decisive role in dictating the extent and time scales of both lithium ion and cyanide dynamics in Li 6 PS 5 CN.

36 MATERIALS SCIENCE↗

Coarse-grained molecular dynamics integrated with convolutional neural network for comparing shapes of temperature sensitive bottlebrushes

Quantification of shape changes in nature-inspired soft material architectures of stimuli-sensitive polymers is critical for controlling their properties but is challenging due to their softness and flexibility. Here, we have computationally designed uniquely shaped bottlebrushes of a thermosensitive polymer, poly(N-isopropylacrylamide) (PNIPAM), by controlling the length of side chains along the backbone. Coarse-grained molecular dynamics simulations of solvated bottlebrushes were performed below and above the lower critical solution temperature of PNIPAM. Conventional analyses (free volume, asphericity, etc.) show that lengths of side chains and their immediate environments dictate the compactness and bending in these architectures. We further developed 100 unique convolutional neural network models that captured molecular-level features and generated a statistically significant quantification of the similarity between different shapes. Thus, our study provides insights into the shapes of complex architectures as well as a general method to analyze them. The shapes presented here may inspire the synthesis of new bottlebrushes.

36 MATERIALS SCIENCE↗

The impact of stacking and phonon environment on energy transfer in organic chromophores: computational insights

Energy transfer in organic materials is extensively studied due to many applications in optoelectronics. The electronic and vibrational relaxations within molecular assemblies can be influenced by stacking arrangements or additions of a backbone that unites them. Here, we present the computational study of the photoexcitation dynamics of a perylene diimide monomer, and face-to-face stacked dimer and trimer. By using non-Energy transfer in organic materials is extensively studied due to many applications in optoelectronics. The electronic and vibrational relaxations within molecular assemblies can be influenced by stacking arrangements or additions of a backbone that unites them. In this work, we present the computational study of the photoexcitation dynamics of a perylene diimide monomer, and face-to-face stacked dimer and trimer. By using non-adiabatic excited-state molecular dynamics simulations, we show that the non-radiative relaxation is accelerated with the number of stacked molecules. This effect is explained by differences in the energy splitting between states that impacts their corresponding nonadiabatic couplings. Additionally, our analysis of the vibronic dynamics reveals that the passage through the different conical intersections that participate in the relaxation of the stacked systems, activate a positive feedback mechanism. This effect involves a narrow set of vibrational normal modes that accelerate the process by increasing the efficiency of its vibronic dynamics. In contrast, an addition of a biologically inspired backbone slows down the relaxation rate due to its participation in the vibronic dynamics of the molecular stacking arrangements. Our results suggest the stacking arrangements and common backbones as strategies to modulate the efficiency of electronic and vibrational relaxation of diimide-based systems and other molecular aggregates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scaling of silicon nanoparticle growth in low temperature flowing plasmas

Low temperature plasmas are an emerging method to synthesize high quality nanoparticles (NPs). An established and successful technique to produce NPs is using a capacitively coupled plasma (CCP) in cylindrical geometry. Although a robust synthesis technique, optimizing or specifying NP properties using CCPs, is challenging. In this paper, results from a computational investigation for the growth of silicon NPs in flowing inductively coupled plasmas (ICPs) using Ar/SiH 4 gas mixtures of up to a few Torr are discussed. ICPs produce more locally constrained and quiescent plasma potentials. These positive plasma potentials produce an electrostatic trap for negatively charged NPs, which can significantly extend the residence time of NPs in the plasma, which in turn provides a controllable period for particle growth. The computational platforms used in this study consist of a two-dimensional plasma hydrodynamics model, a three-dimensional nanoparticle growth and trajectory tracking model, and a molecular dynamics simulation for deriving reactive sticking coefficients of silane radicals on Si NPs. Trends for the nanoparticle growth as a function of SiH 4 inlet fraction, gas residence time, energy deposition per particle, pressure, and reactor diameter are discussed. The general path for particle synthesis is the trapping of small NPs in the positive electrostatic potential, followed by entrainment in the gas flow upon reaching a critical particle size. Optimizing or controlling NP synthesis then depends on the spatial distribution of plasma potential, the density of growth species, and the relative time that particles spend in the electrostatic trap and flowing through higher densities of growth species upon leaving the trap.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Molecular dynamics simulations of a dicationic ionic liquid for CO 2 capture

A dicationic ionic liquid ([DBU-PEG][Tf 2 N] 2 ) was studied using classical molecular dynamics simulations to examine its structural and gas separation properties. The dication was designed in an attempt to improve CO 2 solubility by means of tuning the cation-anion interactions of the ionic liquid (IL). The computational model was compared to experimentally obtained density, viscosity, and powder X-ray diffraction spectra. The structure of the IL was further investigated with radial distribution functions and free volume analysis through cavity distributions. It was found that the shape and charge distribution of the dication enhances CO 2 interaction: the CO 2 molecule is hugged by the dication along the PEG linker and close to one of the cationic ends. Here, the geminal design of the dication allows for strong interaction with CO 2 , showing promise as a means of carbon capture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A lightweight method for evaluating in situ workflow efficiency

Performance evaluation is crucial to understanding the behavior of scientific workflows. In this study, we target an emerging type of workflow, called in situ workflows. These workflows tightly couple components such as simulation and analysis to improve overall workflow performance. To understand the tradeoffs of various configurable parameters for coupling these heterogeneous tasks, namely simulation stride, and component placement, separately monitoring each component is insufficient to gain insights into the entire workflow behavior. Through an analysis of the state-of-the-art research, we propose a lightweight metric, derived from a defined in situ step, for assessing resource usage efficiency of an in situ workflow execution. By applying this metric to a synthetic workflow, which is parameterized to emulate behaviors of a molecular dynamics simulation, we explore two possible scenarios (Idle Simulation and Idle Analyzer) for the characterization of in situ workflow execution. In addition to preliminary results from a recently published study [11], we further exploit the proposed metric to evaluate a practical in situ workflow with a real molecular dynamics application, i.e., GROMACS. Here, experimental results show that the in transit placement (analytics on dedicated nodes) sustains a higher frequency for performing in situ analysis compared to the helper-core configuration (analytics co-allocated with simulation).

97 MATHEMATICS AND COMPUTING↗

Field-Dependent Ionic Conductivities from Generalized Fluctuation-Dissipation Relations

We derive a relationship for the electric field dependent ionic conductivity in terms of fluctuations of time integrated microscopic variables. We demonstrate this formalism with molecular dynamics simulations of solutions of differing ionic strength with implicit solvent conditions and molten salts. These calculations are aided by a novel nonequilibrium statistical reweighting scheme that allows for the conductivity to be computed as a continuous function of the applied field. In strong electrolytes, we find the fluctuations of the ionic current are Gaussian, and subsequently, the conductivity is constant with applied field. In weaker electrolytes and molten salts, we find the fluctuations of the ionic current are strongly non-Gaussian, and the conductivity increases with applied field. Furthermore, this nonlinear behavior, known phenomenologically for dilute electrolytes as the Onsager-Wien effect, is general and results from the suppression of ionic correlations at large applied fields, as we elucidate through both dynamic and static correlations within nonequilibrium steady states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Minimization of Disorder as a Key Design Principle for Natural Sizes of Light Harvesting 2 Complexes

The light harvesting 2 (LH2) complex of purple bacteria has excellent energy conversion efficiency. Clarifying the design principle behind such efficiency at the atomistic level is crucial for understanding its structure–function relationship and can be utilized for the design of artificial light harvesting systems. To this end, we conducted comprehensive computational investigation of the dynamical and statistical nature of electronic excited states of pigment molecules in a natural LH2 complex with 9-fold symmetry and its two non-natural in silico analogues with 6- and 12-fold symmetries. To ensure reliable and efficient all-atomistic molecular dynamics simulations, we combined a well established interpolation approach for the construction of the potential energy surface with a neural network machine learning approach. Outcomes of these calculations clarify that non-natural forms of LH2-type complexes have significantly larger quasistatic disorder than those for the natural one. In addition, non-natural systems have more disruptions of the hydrogen bonding, underscoring its crucial role for reducing the disorder. On the other hand, local environmental dynamics are relatively insensitive to the structural changes although there is moderate enhancement in the anharmonic or interatomic components for the synthetic ones. These findings based on all-atomistic simulations provide direct computational evidence that the structure and sizes of natural LH2 complexes are designed to minimize the energetic disorder. We analyze quantitative implications of these for the energy transferring capability of the LH2 complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Uncharacteristic second order martensitic transformation in metals via epitaxial stress fields

While most phase transformations, e.g., ferroelectric or ferromagnetic, can be first or second order depending on external applied fields, martensitic transformations in metallic alloys are nearly universally first order. We demonstrate that epitaxial stress originating from the incorporation of a tailored second phase can modify the free energy landscape that governs the phase transition and change its order from first to second. High-fidelity molecular dynamics simulations show a remarkable change in the character of the martensitic transformation in Ni–Al alloys near the critical point. We observe the continuous evolution of the transformation order parameter and scaling with power-law exponents comparable to those in other ferroic transitions exhibiting critical behavior. Our theoretical work provides a foundation for recent experimental and computational results on martensites near critical points.

36 MATERIALS SCIENCE↗

Onsager Transport Coefficients and Transference Numbers in Polyelectrolyte Solutions and Polymerized Ionic Liquids

Electrolytes featuring negatively charged polymers, such as nonaqueous polyelectrolyte solutions and polymerized ionic liquids, are currently under investigation as potential high cation transference number (t+) electrolytes for lithium-ion batteries. Herein, we use coarse-grained molecular dynamics simulations to characterize the Onsager transport coefficients of polyelectrolyte solutions as a function of chain length and concentration. For all the systems studied, we find that the rigorously computed transference number is substantially lower than that approximated by the ideal solution (Nernst-Einstein) equations typically used to characterize these systems due to the presence of strong anion-anion and cation-anion correlations. None of the polyelectrolyte solutions achieve t+ greater than that of the conventional binary salt electrolyte, with some solutions having negative t+. Overall, this work demonstrates that the Nernst-Einstein assumption does not provide a physically meaningful estimate of the transference number in these solutions and calls into question the expectation of polyelectrolytes to exhibit a high cation transference number.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymer Tacticity Effects in Polymer–Lanthanide Chelation Thermodynamics

Metal-chelating polymers are critical components in numerous applications. However, despite the known influence of polymer tacticity on both bulk and solution properties, most materials used in metal-chelation applications are atactic. Here, we investigate the relationship between polymer tacticity and polymer–lanthanide interactions in aqueous solution. We synthesized a series of five poly(methacrylic acid)s with systematic variations in tacticity (20–99% m diads) and used isothermal titration calorimetry to measure the thermodynamics of lanthanide binding to each material (ΔH, ΔG, ΔS, K a , and stoichiometry). We observed enthalpy–entropy compensation across this tacticity series, finding that both |ΔH| and |ΔS| decreased with decreasing m diad content while ΔG remained similar. Molecular dynamics simulations of the polymer–metal interactions revealed that the observed differences in binding thermodynamics may be largely ascribed to differences in polymer flexibility. Furthermore, these combined experimental and computational results demonstrate that metal binding can be influenced by altering the polymer stereochemistry, ultimately influencing the design of more efficient metal-chelating materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗