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At least 937 records · Page 52

Insights from Computational Studies on the Anisotropic Volume Change of Li x NiO 2 at High States of Charge (x < 0.25)

The need for high-capacity Li-ion battery cathodes has favored the increase of Ni content in commercial battery cells. However, at high states of charge (SOCs), Ni-rich materials undergo a phase transition and volume collapse with deleterious effects on battery performance. It is uncertain whether this drastic volume change is caused by the phase transition or not. To provide more insight into the volume-phase transition relationship in the high Ni cathode LixNiO 2 , we performed density functional theory calculations, along with molecular dynamics simulations using machine learning potentials to calculate the temperature- and composition-dependent free energy differences between the suspected phases at high SOCs (x < 0.25). Herein, we find that the calculated free energy difference between the suspected phases containing different oxygen stacking sequences is small at room temperature. Furthermore, we find that the collapse of the layered LiNiO 2 c-lattice parameter at high SOCs is mainly due to the electronic depletion of the oxygen sublattice and the lack of screening from positive Li ions. The interactions between adjacent oxygen ions across an empty Li layer (NiO 2 ) are largely controlled by van der Waals interactions and are in fact similar regardless of the oxygen stacking, which explains the negligible free energy differences between O1 and O3 stacking in NiO 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing the Effect of Explicit Polarizability on Models of Carbon Dioxide Solvation in Ionic Liquids

Ionic liquids are an important possible carbon capture material because of their anomalously high sorption selectivity for carbon dioxide over other gases common in air. Many research groups have investigated the molecular origins of this property and provided important insights, including using 1D and 2D-IR spectroscopy. Molecular dynamics simulations have been indispensable to the interpretation of these experiments. In prior molecular dynamics simulation work, charge-scaled force fields have typically been used to provide a mean-field treatment of effects vital to ionic liquid systems such as charge transfer and polarization. Here, we compare models of carbon dioxide solvated in ionic liquids with explicit polarization to models of the same with implicit polarizability through charge-scaling. We calculate structural, dynamical, and spectroscopic properties, and make comparisons to the same items measured in experiment. In this study, we focus on two ionic liquids: 1-butyl-3- methylimidazolium (BMIM + ) paired with bis(trifluoromethane sulfonyl imide) (Tf 2 N − ) and 1-butyl-3-methylimidazolium (BMIM+) paired with hexafluorophosphate (PF 6 − ). We find that many structural, dynamical, and spectroscopic properties are changed when polarization is modeled explicitly. We also find that explicit polarizability softens local ion cages around the carbon dioxide and that the long-time diffusion of the carbon dioxide is gated by the reorganization of the ionic liquid molecules. Comparisons to experiment show modest improvement of many observables compared with experiment for the explicitly polarizable model over the charge-scaled model. Overall, our results show that charge-scaled force fields are likely sufficient to compute spectroscopic properties of carbon dioxide in ionic liquids and suggest some interpretive rules for understanding their structural and dynamical properties. Those using charge-scaled force fields should generally assume that the ion cages around solutes such as carbon dioxide are too stiff and cation-rich in their models and adjust their interpretations and predictions accordingly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Anomalous size effect on yield strength enabled by compositional heterogeneity in high-entropy alloy nanoparticles

High-entropy alloys (HEAs), although often presumed to be random solid solutions, have recently been shown to display nanometer-scale variations in the arrangements of their multiple chemical elements. Here, we study the effects of this compositional heterogeneity in HEAs on their mechanical properties using in situ compression testing in the transmission electron microscope (TEM), combined with molecular dynamics simulations. We report an anomalous size effect on the yield strength in HEAs, arising from such compositional heterogeneity. By progressively reducing the sample size, HEAs initially display the classical “smaller-is-stronger” phenomenon, similar to pure metals and conventional alloys. However, as the sample size is decreased below a critical characteristic length (~180 nm), influenced by the size-scale of compositional heterogeneity, a transition from homogeneous deformation to a heterogeneous distribution of planar slip is observed, coupled with an anomalous “smaller-is-weaker” size effect. Atomic-scale computational modeling shows these observations arise due to compositional fluctuations over a few nanometers. These results demonstrate the efficacy of influencing mechanical properties in HEAs through control of local compositional variations at the nanoscale.

36 MATERIALS SCIENCE↗

Symmetrized Drude Oscillator Force Fields Improve Numerical Performance of Polarizable Molecular Dynamics

Drude oscillator potentials are a popular and computationally efficient class of polarizable models that represent each polarizable atom as a positively charged Drude core harmonically bound to a negatively charged Drude shell. Here we show that existing force fields that place all non-Coulomb forces on the Drude core and none on the shell inadvertently couple the dipole to non-Coulombic forces. This introduces errors where interactions with neutral particles can erroneously induce atomic polarization, leading to spurious polarizations in the absence of an electric field, exacerbating violations of equipartition in the employed Carr–Parinello scheme. A suitable symmetrization of the interaction potential that correctly splits the force between the Drude core and shell can correct this shortcoming, improving the stability and numerical performance of Drude oscillator-based simulations. The symmetrization procedure is straightforward and only requires the rescaling of a few force field parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering the fracture resistance of 2H-transition metal dichalcogenides using vacancies: An in-silico investigation based on HRTEM images

Vacancy engineering of 2H-transition metal dichalcogenides (2H-TMDs) has recently attracted great attention due to its potential to fine-tune the phonon and opto-electric properties of these materials. From a mechanical perspective, this symmetry-breaking process typically reduces the overall crack resistance of the material and adversely affects its reliability. However, vacancies can trigger the formation of heterogeneous phases that synergistically improve fracture properties. In this study, using MoSe2 as an example, we characterize the types and density of vacancies that can emerge under electron irradiation and quantify their effect on fracture. Molecular dynamic (MD) simulations, employing a re-parameterized Tersoff potential capable of accurately capturing bond dissociation and structural phase changes, reveal that isolated transition metal monovacancies or chalcogenide divacancies tend to arrest the crack tip and hence enhance the monolayer toughness. In contrast, isolated chalcogenide monovacancies do not significantly affect toughness. The investigation further reveals that selenium vacancy lines, formed by high electron dose rates, alter the crack propagating direction and lead to multiple crack kinking. Using atomic displacements and virial stresses together with a continuum mapping, displacement, strain, and stress fields are computed to extract mechanistic information, e.g., conditions for crack kinking and size effects in fracture events. The study also reveals the potential of specific defect patterns, “vacancy engineering,” to improve the toughness of 2H-TMDs materials.

36 MATERIALS SCIENCE↗

Nanotwinned alloys under high pressure

Nanotwinned alloys are of interest due to their high strength and ductility, but twin boundaries may not be stable under shear. Computational studies indicate that high hydrostatic pressure may suppress detwinning mechanisms. Here, in this study, we investigate the microstructural changes of nanotwinned-nanocrystalline copper-nickel and Inconel 725 alloys under quasi-hydrostatic pressures up to 50 gigapascals (GPa). The alloys are compressed in a diamond anvil cell. In-situ x-ray diffraction (XRD) and ex-situ transmission electron microscopy (TEM) were employed to monitor microstructural changes. Twin boundary deformation and grain growth occur at 11.4 GPa quasi-hydrostatic pressure in the copper-nickel alloy. Molecular dynamics (MD) simulations reveal that hydrostatic pressure causes elevated local shear stress at grain boundaries, which leads to atomic rearrangements. A superposition of hydrostatic and deviatoric pressures lead to partial dislocation mediated twin boundary migration. In contrast, the Inconel 725 alloy showed stable twin and grain boundaries up to a quasi-hydrostatic pressure of 12.7 GPa. Texture, high solid solution strengthening, and low stacking fault energy are hypothesized to the enhanced microstructural stability in Inconel 725.

36 MATERIALS SCIENCE↗

Rational Enzyme Design for Controlled Functionalization of Acetylated Xylan for Cell-Free Polymer Biosynthesis

Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.

93 SC - Biological and Environmental Research (BER↗

Ab initio molecular dynamics with enhanced sampling in heterogeneous catalysis

Ab initio molecular dynamics simulations combined with enhanced sampling techniques are becoming widespread methods to investigate chemical phenomena in catalytic systems. These techniques automatically include finite temperature effects, anharmonicity, and collective dynamics in their robust description of enthalpic and entropic contributions, which can have significant impact on reaction free energy landscapes. This contrasts with standard ab initio static approaches that are based on assessing reaction free energies from various coarse-grained descriptions of the reaction potential energy surface. Enhanced sampling ab initio molecular dynamics opens the way to first principles simulations of systems of increasing complexity like solid/liquid catalytic interfaces. Here, we aim at guiding the reader through the basis of these techniques, summarizing their fundamental theoretical and practical aspects, and reviewing the relevant literature in the field. After a brief introduction to the problem, we will illustrate the advantage of using molecular simulations to include finite temperature effects, examine the most common ab initio techniques currently in use, describe their application to solid state heterogeneous catalysts, and finally critically review the most popular enhanced sampling techniques used in computational catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of Soret effect on hydrogen and helium retention in PFC tungsten under ELM-like conditions

Abstract In our previous work, we have demonstrated using nonequilibrium molecular-dynamics simulations that the fluxes of helium and self-interstitial atoms in the presence of a thermal gradient in tungsten are directed opposite to the heat flux, indicating that species transport is governed by a Soret effect, namely, thermal-gradient-driven diffusion, characterized by a negative heat of transport that drives species transport uphill, i.e. from the cooler to the hot regions of the tungsten sample. In this work, the findings of our thermal and species transport analysis have been implemented in our cluster-dynamics code, Xolotl, which has been used to compute temperature and species profiles over spatiotemporal scales representative of plasma-facing component (PFC) tungsten under typical reactor operating conditions, including extreme heat loads at the plasma-facing surface characteristic of plasma instabilities that induce edge localized modes (ELMs). We demonstrate that the steady-state species profiles, when properly accounting for the Soret effect, vary significantly from those where temperature-gradient-driven transport is not accounted for and discuss the implications of such a Soret effect on the response to plasma exposure of plasma-facing tungsten. Although our cluster-dynamics simulations do not yet include self-clustering of helium or hydrogen blister formation, our simulation results show that the Soret effect substantially reduces helium and hydrogenic species retention inside PFC tungsten.

36 MATERIALS SCIENCE↗

Time-dependent computational studies of flames in microgravity

The research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of the NASA Microgravity Science and Applications Program is described. The primary focus was on investigating fundamental questions concerning the propagation and extinction of premixed flames in Earth gravity and in microgravity environments. The approach was to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. A combination of one-dimensional and two-dimensional simulations was used to investigate the effects of curvature and dilution on ignition and propagation of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the mechanism leading to cellular instability, and to study the effects of gravity on the transition to cellular structure. A flame in a microgravity environment can be extinguished without external losses, and the mechanism leading to cellular structure is not preferential diffusion but a thermo-diffusive instability. The simulations have also lead to a better understanding of the interactions between buoyancy forces and the processes leading to thermo-diffusive instability.

Oran, Elaine S.↗

Time-dependent Computational Studies of Premixed Flames in Microgravity

This report describes the research performed at the Center for Reactive Flow and Dynamical Systems in the Laboratory for Computational Physics and Fluid Dynamics, at the Naval Research Laboratory, in support of NASA Microgravity Science and Applications Program. The primary focus of this research is on investigating fundamental questions concerning the propagation and extinction of premixed flames in earth gravity and in microgravity environments. Our approach is to use detailed time-dependent, multispecies, numerical models as tools to simulate flames in different gravity environments. The models include a detailed chemical kinetics mechanism consisting of elementary reactions among the eight reactive species involved in hydrogen combustion, coupled to algorithms for convection, thermal conduction, viscosity, molecular and thermal diffusion, and external forces. The external force, gravity, can be put in any direction relative to flame propagation and can have a range of values. Recently more advanced wall boundary conditions such as isothermal and no-slip have been added to the model. This enables the simulation of flames propagating in more practical systems than before. We have used the numerical simulations to investigate the effects of heat losses and buoyancy forces on the structure and stability of flames, to help resolve fundamental questions on the existence of flammability limits when there are no external losses or buoyancy forces in the system, to understand the interaction between the various processes leading to flame instabilities and extinguishment, and to study the dynamics of cell formation and splitting. Our studies have been able to bring out the differences between upward- and downward-propagating flames and predict the zero-gravity behavior of these flames. The simulations have also highlighted the dominant role of wall heat losses in the case of downward-propagating flames. The simulations have been able to qualitatively predict the formation of multiple cells and the cessation of cell-splitting. Our studies have also shown that some flames in a microgravity environment can be extinguished due to a chemical instability and without any external losses. However, further simulations are needed to more completely understand upward-propagating and zero-gravity flames as well as to understand the potential effect of radiative heat losses.

Kailasanath, K.↗

Machine Phase Fullerene Nanotechnology: 1996

NASA has used exotic materials for spacecraft and experimental aircraft to good effect for many decades. In spite of many advances, transportation to space still costs about $10,000 per pound. Drexler has proposed a hypothetical nanotechnology based on diamond and investigated the properties of such molecular systems. These studies and others suggest enormous potential for aerospace systems. Unfortunately, methods to realize diamonoid nanotechnology are at best highly speculative. Recent computational efforts at NASA Ames Research Center and computation and experiment elsewhere suggest that a nanotechnology of machine phase functionalized fullerenes may be synthetically relatively accessible and of great aerospace interest. Machine phase materials are (hypothetical) materials consisting entirely or in large part of microscopic machines. In a sense, most living matter fits this definition. To begin investigation of fullerene nanotechnology, we used molecular dynamics to study the properties of carbon nanotube based gears and gear/shaft configurations. Experiments on C60 and quantum calculations suggest that benzyne may react with carbon nanotubes to form gear teeth. Han has computationally demonstrated that molecular gears fashioned from (14,0) single-walled carbon nanotubes and benzyne teeth should operate well at 50-100 gigahertz. Results suggest that rotation can be converted to rotating or linear motion, and linear motion may be converted into rotation. Preliminary results suggest that these mechanical systems can be cooled by a helium atmosphere. Furthermore, Deepak has successfully simulated using helical electric fields generated by a laser to power fullerene gears once a positive and negative charge have been added to form a dipole. Even with mechanical motion, cooling, and power; creating a viable nanotechnology requires support structures, computer control, a system architecture, a variety of components, and some approach to manufacture. Additional information is contained within the original extended abstract.

Globus, Al↗

Computer Simulation of the Forces Acting on a Submerged Polystyrene Probe as it Approaches the Succinonitrile Melt-Solid Interface

A Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. A mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. Ultimately, the goal is to measure the forces between a particle and the crystal-melt interface. Two modes of AFM operation are considered in this paper - a stationary and a "tapping" one. The continuous mechanics approach to model tip-surface interaction is presented. At microscopic levels, tip contamination and details of tip-surface interaction are modeled using a molecular dynamics approach for the case of polystyrene - succinonitrile contact. Integration of the mesoscale model with a molecular dynamic model is discussed.

Bune, Andris V.↗

TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics

TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Here, electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Theory and Simulation of Ultrafast Multidimensional Nonlinear X-ray Spectroscopy of Molecules (Final Report)

Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.

74 ATOMIC AND MOLECULAR PHYSICS↗

An Efficient Reactive Force Field without Explicit Coordination Dependence for Studying Caustic Aluminum Chemistry

Reactive force fields (RFFs) are an expedient approach to sample chemical reaction paths in complex systems, relative to density functional theory. However, there is continued need to improve efficiencies, specifically in systems that have slow transverse degrees of freedom, as in highly viscous and superconcentrated solutions. Here, we present an RFF that is differentiated from current models (e.g., ReaxFF) by omitting explicit dependence on the atom coordination and employing a small parameter set based on Lennard-Jones, Gaussian, and Stillinger–Weber potentials. In this study, the model was parametrized from AIMD simulation data and is used to model aluminate reactivity in sodium hydroxide solutions with extensive validation against experimental radial distribution functions, computed free energy profiles for oligomerization, and formation energies. In conclusion, the model enables simulation of early stage Al(OH) 3 nucleation which has significant relevance to industrial processing of aluminum and has a computational cost that is reduced by 1 order of magnitude relative to ReaxFF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of a Reactive Force Field for Simulating Photoinitiated Acrylate Polymerization

Light-driven and photo-curable polymer based additive manufacturing (AM) has enormous potential due to its excellent resolution and precision. Acrylated radical chain-growth polymerized resins are widely used in photopolymer AM due to their fast kinetics, and often serve as a departure point for developing other resin materials for photopolymer-based AM technologies. For successful control of the photopolymer resins, the molecular basis of the acrylate free-radical polymerization has to be understood in detail. We present an optimized reactive force field (ReaxFF) for molecular dynamics (MD) simulations of acrylate polymer resins that captures radical polymerization thermodynamics and kinetics. The force field is trained against an extensive training set including density functional theory (DFT) calculations of reaction pathways along the radical polymerization from methyl acrylate to methyl butyrate, bond dissociation energies, and structures and partial charges of several molecules and radicals. We also found that it was critical to train the force field against an incorrect, nonphysical reaction pathway observed in simulations that used parameters not optimized for acrylate polymerization. As a result, the parameterization process utilizes a parallelized search algorithm, and the resulting model can describe polymer resin formation, crosslinking density, conversion rate, and residual monomers of the complex acrylate mixtures.

36 MATERIALS SCIENCE↗

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↗