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At least 253 records · Page 14

Disordered crystal structure of 20H-AlON, Al{sub 10}O{sub 3}N{sub 8}

The disordered crystal structure of 20H-AlON (Al{sub 10}O{sub 3}N{sub 8}) was determined by combined use of X-ray powder diffraction and transmission electron microscopy. The title compound is hexagonal with space group P6{sub 3}/mmc (Z=2) and the unit-cell dimensions are a=0.307082(5) nm, c=5.29447(8) nm and V=0.432376(12) nm{sup 3}. The structural model showed the positional disordering of three of the six Al sites in the unit cell. The reliability indices calculated from the Rietveld method were R{sub wp}=6.97%, S (=R{sub wp}/R{sub e})=1.68, R{sub p}=5.45%, R{sub B}=5.13% and R{sub F}=4.56%. We interpreted the disordered structure of 20H-AlON as a statistical average of six different types of ordered structural configurations, which are composed of an octahedral [Al(O, N){sub 6}] layer and tetrahedral [Al(O, N){sub 4}] layers. We demonstrated the high correlations between the hexagonal unit-cell dimensions and the octahedral layer concentrations for AlON and SiAlON polytypoids. - Graphical abstract: Variations of a and c/(n{sub O}+n{sub T}) with n{sub O}/(n{sub O}+n{sub T}). The a and c are the hexagonal unit-cell dimensions of AlON, SiAlON and AlN. The n{sub O} and n{sub T} are, respectively, the numbers of octahedral and tetrahedral layers in the unit cells. The unit-cell dimensions in literature are plotted in black plus for AlON and black cross for SiAlON. The unit-cell dimensions of AlN are a=0.3110 nm and c=0.4980 nm. - Highlights: • Crystal structure of Al10O3N8 is determined by laboratory X-ray powder diffraction. • The atom arrangements are represented by the split-atom model. • Six types of ordered atom arrangements are derived from the disordered structure. • Hexagonal unit-cell dimensions changed systematically for AlON and SiAlON compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sesame-style decomposition of KS-DFT molecular dynamics for direct interrogation of nuclear models

A common paradigm used in the construction of equations of state is to decompose the thermodynamics into a superposition of three terms: a static-lattice cold curve, a contribution from the thermal motion of the nuclei, and a contribution from the thermal excitation of the electrons. While statistical mechanical models for crystals provide tractable framework for the nuclear contribution in the solid phase, much less is understood about the nuclear contribution above the % melt temperature $(C^{(nuc)}_ν≈3R)$ and how it should transition to the high-temperature limit $(C^{(nuc)}_ν\sim\frac{3}{2}R)$. Here, we describe an algorithm for extracting both the thermal nuclear and thermal electronic contributions from quantum molecular dynamics (QMD) simulations. We then use the VASP QMD package to probe thermal nuclear behavior of liquid aluminum at normal density to compare the results to semi-empirical models – the Johnson generic model, the Chisolm high-temperature liquid model, and the CRIS model. The thermal electronic energy is also calculated from the VASP results and compared to the Kohn-Sham calculations from QE-DFT simulations, Green’s function average atom calculations, and the Thomas-Fermi atomic model.

74 ATOMIC AND MOLECULAR PHYSICS↗

Soft x-ray spectrum unfold of K-edge filtered x-ray diode arrays using cubic splines

Cubic spline interpolation is able to recover temporally and spectrally resolved soft x-ray flux from an array of K-edge filtered x-ray diodes without the need for a priori assumptions about the spectrum or the geometry of the emitting volume. The mathematics of the cubic spline interpolation is discussed in detail. The analytic nature of the cubic spline solution allows for analytical error propagation, and the method of calculating the error for radiation temperature, spectral power, and confidence intervals of the unfolded spectrally resolved flux is explained. An unfold of a blackbody model demonstrates the accuracy of the cubic spline unfold. Tests of cubic spline performance using spectrally convolved detailed atomic model simulation results have been performed to measure the method's ability to conserve spectral power to within a factor of 2 or better in line-dominated regimes. The unfold is also demonstrated to work when information from the x-ray diode array is limited due to high signal-to-noise ratios or lack of signal due to over-attenuation or over-filtration of the x-ray diode signal. Here, the robustness of the unfold with respect to background subtraction and raw signal processing, signal alignment between diode traces, limited signal information, and initial conditions is discussed. Results from an example analysis of a halfraum drive are presented to demonstrate the capabilities of the unfold in comparison with previously established methods.

47 OTHER INSTRUMENTATION↗

Adaptive four-level modeling of laser cooling of solids

Laser cooling of rare-earth doped solids has been demonstrated across a wide range of material platforms, inspiring the development of simple phenomenological models such as the four-level model to elucidate the universal properties of laser cooling under various operating conditions. However, these models usually require the input of full absorption spectra that must be provided experimentally or by additional complicated atomic modeling. In this Letter, we propose that a four-level model, when extended to admit effective energy levels adaptive to the pumping photon energy, can accurately predict the cooling efficiency as a function of temperature and pumping frequency using only few inputs such as the absorption coefficient measured at a single frequency and temperature. Our model exploits the quasi-equilibrium properties of the excitation of rare-earth ions for the determination of the effective four energy levels. The model is validated against published experimental results for a span of materials including ytterbium/thulium-doped glass and crystals. With the verified model, we derive explicit expressions for the optimal frequency and the operating bandwidth of pumping lasers. Our model significantly simplifies the modeling process of laser cooling and is expected to stimulate further development of optical refrigeration.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Stellar model chromospheres. VIII - 70 Ophiuchi A /K0 V/ and Epsilon Eridani /K2 V/

Model atmospheres for the late-type active-chromosphere dwarf stars 70 Oph A and Epsilon Eri are computed from high-resolution Ca II K line profiles as well as Mg II h and k line fluxes. A method is used which determines a plane-parallel homogeneous hydrostatic-equilibrium model of the upper photosphere and chromosphere which differs from theoretical models by lacking the constraint of radiative equilibrium (RE). The determinations of surface gravities, metallicities, and effective temperatures are discussed, and the computational methods, model atoms, atomic data, and observations are described. Temperature distributions for the two stars are plotted and compared with RE models for the adopted effective temperatures and gravities. The previously investigated T min/T eff vs. T eff relation is extended to Epsilon Eri and 70 Oph A, observed and computed Ca II K and Mg II h and k integrated emission fluxes are compared, and full tabulations are given for the proposed models. It is suggested that if less than half the observed Mg II flux for the two stars is lost in noise, the difference between an active-chromosphere star and a quiet-chromosphere star lies in the lower-chromospheric temperature gradient.

Kelch, W. L.↗

Low-Temperature Oxidation of Methanol to Formaldehyde on a Model Single-Atom Catalyst: Pd Atoms on Fe 3 O 4 (001)

Single atom catalysis has been a topic of increasing interest due to the potential for improved selectivity, reactivity, and catalyst cost. However, single atom catalysts are still difficult to characterize under realistic reaction conditions, leading to controversy regarding the capabilities of single atoms and a need for model studies. Herein, we examine the reaction of methanol on single Pd atoms supported on Fe 3 O 4 (001) under ultra-high vacuum conditions. On clean Fe 3 O 4 (001) a small fraction of methanol is converted to formaldehyde through a methoxy intermediate at 516 K. The addition of single Pd atoms lowers the barrier to C-H bond cleavage by a factor of two, resulting in formaldehyde desorption by 290 K. Furthermore, Pd atoms sinter by 300 K in the presence of methanol, and Pd clusters do not exhibit the same chemistry. Single atom sites significantly lower the barrier to the oxidation of methanol, although their stability remains an issue.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Wide ranging equation of state with Tartarus: A hybrid Green’s function/orbital based average atom code

Average atom models are widely used to make equation of state tables and for calculating other properties of materials over a wide range of conditions, from zero temperature isolated atom to fully ionized free electron gases. The numerical challenge of making these density functional theory based models work for any temperature, density or nuclear species is formidable. Here we present in detail a hybrid Green’s function/orbital based approach that has proved to be stable and accurate for wide ranging conditions. Algorithmic strategies are discussed. In particular the decomposition of the electron density into numerically advantageous parts is presented and a robust and rapid self consistent field method based on a quasi-Newton algorithm is given. Example application to the equation of state of lutetium (Z = 71) is explored in detail, including the effect of relativity, finite temperature exchange and correlation, and a comparison to a less approximate method. Furthermore, the hybrid scheme is found to be numerically stable and accurate for lutetium over at least 6 orders of magnitude in density and 5 orders of magnitude in temperature.

74 ATOMIC AND MOLECULAR PHYSICS↗

Development of Ion Stopping Models for HED Plasmas Using Unified Self-Consistent Field Models and Self-Consistent Electron Distributions

We have implemented several corrections to the electronic stopping power model combining the RPA dielectric response formalism and local density approximation with electronic density distribution calculated in an average atom model. These modifications include strong collision correction, local field correction, electron binding energy correction, and the Barkas effect. The combined results bring the RPA-LDA stopping power in cold targets to closer agreements with experiments for a wide range of materials. The same method is then applied to the stopping of ions in warm dense plasmas. The computational framework developed during this project is publicly available on GitHub (https://github.com/dedx-erpa/dedx). Tabulated data for protons in cold target for common materials are located in the data/ subdirectory of the repository.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Configurational-Bias Monte Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures into Atomistic Models

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when contrasted with the existing simpler back-mapping methods. The error in the RDFs of backmapped relative to reference configuration for the CCBMC, MD, and MC were found to be 6.9, 8.7, and 12.9 respectively for the hexagonal system. For the cubic system the relative error of the RDFs for the CCBMC, MD, and MC were found to be 18.2, 34.6, and 39.0 respectively. Finally, our results demonstrate the efficiency and efficacy of our new back-mapping approach, especially for crystalline systems where simple force-field based relaxations have a tendency to get trapped in local minima.

74 ATOMIC AND MOLECULAR PHYSICS↗

Surface tension and long range corrections of cylindrical interfaces

The calculation of the surface tension of curved interfaces has been deeply investigated from molecular simulation during this last past decade. Recently, the thermodynamic Test-Area (TA) approach has been extended to the calculation of surface tension of curved interfaces. In the case of the cylindrical vapour-liquid interfaces of water and Lennard-Jones fluids, it was shown that the surface tension was independent of the curvature of the interface. In addition, the surface tension of the cylindrical interface is higher than that of the planar interface. Molecular simulations of cylindrical interfaces have been so far performed (i) by using a shifted potential, (ii) by means of large cutoff without periodic boundary conditions, or (iii) by ignoring the long range corrections to the surface tension due to the difficulty to estimate them. Indeed, unlike the planar interfaces there are no available operational expressions to consider the tail corrections to the surface tension of cylindrical interfaces. We propose here to develop the long range corrections of the surface tension for cylindrical interfaces by using the non-exponential TA (TA2) method. We also extend the formulation of the Mecke-Winkelmann corrections initially developed for planar surfaces to cylindrical interfaces. We complete this study by the calculation of the surface tension of cylindrical surfaces of liquid tin and copper using the embedded atom model potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cloud Impacts on Photochemistry: Building a Climatology of Photolysis Rates from the Atmospheric Tomography Mission

Measurements from actinic flux spectroradiometers on board the NASA DC-8 during the Atmospheric Tomography (ATom) mission provide an extensive set of statistics on how clouds alter photolysis rates (J values) throughout the remote Pacific and Atlantic Ocean basins. J values control tropospheric ozone and methane abundances, and thus clouds have been included for more than three decades in tropospheric chemistry modeling. ATom made four profiling circumnavigations of the troposphere capturing each of the seasons during 2016–2018. This work examines J values from the Pacific Ocean flights of the first deployment, but publishes the complete Atom-1 data set (29 July to 23 August 2016). We compare the observed J values (every 3 s along flight track) with those calculated by nine global chemistry– climate/transport models (globally gridded, hourly, for a mid-August day). To compare these disparate data sets, we build a commensurate statistical picture of the impact of clouds on J values using the ratio of J -cloudy (standard, sometimes cloudy conditions) to J -clear (artificially cleared of clouds). The range of modeled cloud effects is inconsistently large but they fall into two distinct classes: (1) models with large cloud effects showing mostly enhanced J values aloft and or diminished at the surface and (2) models with small effects having nearly clear-sky J values much of the time. The ATom-1 measurements generally favor large cloud effects but are not precise or robust enough to point out the best cloud-modeling approach. The models here have resolutions of 50–200 km and thus reduce the occurrence of clear sky when averaging over grid cells. In situ measurements also average scattered sunlight over a mixed cloud field, but only out to scales of tens of kilometers. A primary uncertainty remains in the role of clouds in chemistry, in particular, how models average over cloud fields, and how such averages can simulate measurements.

actinic flux spectroradiometers↗

Imaging Unstained Synthetic Polymer Crystals and Defects on Atomic Length Scales Using Cryogenic Electron Microscopy

Properties of soft crystalline materials such as synthetic polymers are governed by locations of constituent atoms. Determining atomic-scale structures in these materials is difficult because they degrade rapidly when studied by electron microscopy, and techniques such as x-ray scattering average over volumes much larger than coherent blocks of the unit cells. We obtained cryo-electron microscopy images of self-assembled nanosheets of a peptoid polymer, made by solid-phase synthesis, in which we see a variety of crystalline motifs. A combination of crystallographic and single particle methods, developed for cryo-electron microscopy of biological macromolecules, was used to obtain high resolution images of the crystals. Individual crystals contain grains that are mirror images of each other with concomitant grain boundaries. We have used molecular dynamic simulations to build an atomic model of the crystal structure to facilitate the interpretation of electron micrographs. Direct visualization of crystalline grains and grain boundaries on atomic length scales represents a new level of information for the polymer field.

36 MATERIALS SCIENCE↗

Mechanosensitive Ion Channels in Bacteria: Functional Domains and Mechanisms of Gating

The past funding period was productive for the group. The progress in the mechanosensitive channel field was critically affected in the end of 1998 by the solution of the crystal structure of the mycobacterial homolog of MscL by our colleagues from Caltech. Having the structure of TbMscL in the closed state, we developed a detailed homology model of EcoMscL, and related the structural model with the wealth of functional phenomenology available for the E. coli version of the channel (EcoMscL). The biophysical properties of the open MscL helped to model the open conformation and infer the pathway for the entire gating transition. The following experiments provided strong support to the atomic model of the gating process, and allowed to make further predictions. The work has advanced our understanding of tension-driven conformational transitions in membrane-embedded mechanosensory proteins, determine major energetic contributions and set the stage for further exploration of the whole family of mechanosensitive channels. The results have been published in seven experimental and theoretical papers, with three other papers currently in press or in preparation.

Sukharev, Sergei↗

Reinforcement learning based hybrid bond-order coarse-grained interatomic potentials for exploring mesoscale aggregation in liquid–liquid mixtures

Exploring mesoscopic physical phenomena has always been a challenge for brute-force all-atom molecular dynamics simulations. Although recent advances in computing hardware have improved the accessible length scales, reaching mesoscopic timescales is still a significant bottleneck. Coarse-graining of all-atom models allows robust investigation of mesoscale physics with a reduced spatial and temporal resolution but preserves desired structural features of molecules, unlike continuum-based methods. Here, we present a hybrid bond-order coarse-grained forcefield (HyCG) for modeling mesoscale aggregation phenomena in liquid–liquid mixtures. The intuitive hybrid functional form of the potential offers interpretability to our model, unlike many machine learning based interatomic potentials. We parameterize the potential with the continuous action Monte Carlo Tree Search (cMCTS) algorithm, a reinforcement learning (RL) based global optimizing scheme, using training data from all-atom simulations. The resulting RL-HyCG correctly describes mesoscale critical fluctuations in binary liquid–liquid extraction systems. cMCTS, the RL algorithm, accurately captures the mean behavior of various geometrical properties of the molecule of interest, which were excluded from the training set. The developed potential model along with the RL-based training workflow could be applied to explore a variety of other mesoscale physical phenomena that are typically inaccessible to all-atom molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unveiling the Finite Temperature Physics of Hydrogen Chains via Auxiliary Field Quantum Monte Carlo

The ability to accurately predict the finite temperature properties and phase diagrams of realistic quantum solids is central to uncovering new phases and engineering materials with novel properties ripe for device applications. Nonetheless, there remain comparatively few many-body techniques capable of elucidating the finite temperature physics of solids from first principles. Here, we take a significant step toward developing such a technique by generalizing our previous, exact fully ab initio finite temperature Auxiliary Field Quantum Monte Carlo (FT-AFQMC) method to model periodic solids and employing it to uncover the finite temperature physics of periodic hydrogen chains. Our chains’ unit cells consist of 10 hydrogen atoms modeled in a minimal basis, and we sample 5 k-points from the first Brillouin zone to arrive at a supercell consisting of 50 orbitals and 50 electrons. Based upon our calculations of these chains’ many-body energies, free energies, entropies, heat capacities, double and natural occupancies, and charge and spin correlation functions, we outline their metal–insulator and magnetic ordering as a function of both H–H bond distance and temperature. At low temperatures approaching the ground state, we observe both metal–insulator and ferromagnetic–antiferromagnetic crossovers at bond lengths between 0.5 and 0.75 Å. We then demonstrate how this low-temperature ordering evolves into a metallic phase with decreasing magnetic order at higher temperatures. In order to contextualize our results, we compare the features we observe to those previously seen in one-dimensional, half-filled Hubbard models at finite temperature and in ground state hydrogen chains. Interestingly, we identify signatures of the Pomeranchuk effect in hydrogen chains for the first time and show that spin and charge excitations that typically arise at distinct temperatures in the Hubbard model are indistinguishably coupled in these systems. Beyond qualitatively revealing the many-body phase behavior of hydrogen chains in a numerically exact manner without invoking the phaseless approximation, our efforts shed light on the further theoretical developments that will be required to construct the phase diagrams of the more complex transition metal, lanthanide, and actinide solids of longstanding interest to physicists.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic simulation of cracks under mixed mode loading

A discrete atomic model of a crack tip in iron under mixed mode loads is examined. The results indicate that the behavior of the crack at the atomic scale as a function of the ratio of mode I to mode II component of load is quite complex. In general, crack tip plasticity appears to increase as the mode II component of load increases.

Mullins, M.↗

Colloidal Disorder-Order Transition Experiment Probes Particle Interactions in Microgravity

Everything in the universe is made up of the same basic building blocks - atoms. All physical properties of matter such as weight, hardness, and color are determined by the kind of atoms present and the way they interact with each other. The Colloidal Disorder-Order Transition (CDOT) shuttle flight experiment tested fundamental theories that model atomic interactions. The experiment was part of the Second United States Microgravity Laboratory (USML-2) aboard the Space Shuttle Columbia, which flew from October 20 to November 5, 1995.

Source record↗

On the atomic line profiles in high pressure plasmas

In a previous contribution to this journal [H. P. Stormberg, J. Appl. Phys. 51(4), 1963 (1980)], Stormberg presented an analytical expression for the convolution of Lorentz and Levy line profiles, which models atomic radiative transitions in high pressure plasmas. Unfortunately, the derivations are flawed with errors and the final expression, while correct, is accompanied by misguiding comments about the meaning of the symbols used therein, in particular the “complex error function.” In this paper, we discuss the broadening mechanisms that give rise to Stormberg's model and present a correct derivation of his final result. We will also provide an alternative expression, based on the Faddeeva function, which has decisive computational advantages and emphasizes the real-valuedness of the result. The MATLAB/Octave scripts of our implementation have been made available on the publisher's website for future reference.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗