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Thermodynamic properties of interstitial solid solutions with fcc metals from atomically discrete model by computer simulation
Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) assists in understanding of the mechanisms involved. Thus the reliability of predicting in-space durability of materials based on ground laboratory testing should be improved. A computational model which simulates atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of an assumed mechanistic behavior of atomic oxygen interaction based on in-space atomic oxygen erosion of unprotected polymers and ground laboratory atomic oxygen interaction with protected polymers, prediction of atomic oxygen interaction with protected polymers on LDEF was accomplished. However, the results of these predictions are not consistent with the observed LDEF results at defect sites in protected polymers. Improved agreement between observed LDEF results and predicted Monte Carlo modeling can be achieved by modifying of the atomic oxygen interactive assumptions used in the model. LDEF atomic oxygen undercutting results, modeling assumptions, and implications are presented.
The calculation of open shell ionization level and radiative properties of materials in Non-Local Thermal Equilibrium (NLTE) is currently still a major challenge for any atomic model. The predictions of various NLTE atomic codes at these conditions still differ significantly. In recent years, a new buried layer platform was developed at the Lawrence Livermore National Laboratory and the Laboratory for Laser Energetics. This platform is used to measure ionization distribution and emission of open L-shell, mid-Z ions and open M-shell, high-Z ions at NLTE conditions that are relevant in many laser plasma applications. These experiments offer a unique chance for benchmarking the atomic models. In order to perform these experiments, a uniform well characterized plasma source is required. In this work, we present one-dimensional (1D) and two-dimensional simulations of the experimental platform. These simulations were used for both the design and the analysis of the experiments. The simulations demonstrate the different phases of hydrodynamic evolution of the target and identify the time windows in which uniform conditions can be achieved. A 1D expansion of the target was found to be adequate to describe the target's evolution for most of the experiment duration. The fast 1D simulations were compared with recent experimental results from the Omega laser facility. The sensitivity of the results to several modeling parameters such as the electron flux limiter and laser resonant absorption is reported.
Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.
Confinement breaks the translational symmetry of materials, making all thermodynamic and kinetic quantities functions of position. Such symmetry breaking can be used to obtain configurations that are not otherwise accessible in the bulk. Here, we use computer simulations to explore the effect of substrate-liquid interactions on thermodynamic and kinetic anisotropies induced by a solid substrate. We consider n-octane nano-films that are in contact with substrates with varying degrees of attraction, parameterized by an interaction parameter ϵ{sub S}. Complete freezing of octane nano-films is observed at low temperatures, irrespective of ϵ{sub S}, while at intermediate temperatures, a frozen monolayer emerges at solid-liquid and vapor-liquid interfaces. By carefully inspecting the profiles of translational and orientational relaxation times, we confirm that the translational and orientational degrees of freedom are decoupled at these frozen monolayers. At sufficiently high temperatures, however, free interfaces and solid-liquid interfaces close to loose (low-ϵ{sub S}) substrates undergo “pre-freezing,” characterized by mild peaks in several thermodynamic quantities. Two distinct dynamic regimes are observed at solid-liquid interfaces. The dynamics is accelerated in the vicinity of loose substrates, while sticky (high-ϵ{sub S}) substrates decelerate dynamics, sometimes by as much as two orders of magnitude. These two distinct dynamical regimes have been previously reported by Haji-Akbari and Debenedetti [J. Chem. Phys. 141, 024506 (2014)] for a model atomic glass-forming liquid. We also confirm the existence of two correlations—proposed in the above-mentioned work—in solid-liquid subsurface regions of octane thin films, i.e., a correlation between atomic density and normal stress, and between atomic translational relaxation time and lateral stress. Finally, we inspect the ability of different regions of an octane film to explore the potential energy landscape by performing inherent structure calculations, and observe no noticeable difference between the free surface and the bulk in efficiently exploring the potential energy landscape. This is unlike the films of model atomic glass formers that tend to sample their respective landscape more efficiently at free surfaces. We discuss the implications of this finding to the ability of octane—and other n-alkanes—to form ultrastable glasses.
Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in hardware and software. Flexible fitting of atomic models to three-dimensional (3D) cryo-EM reconstructions by molecular dynamics (MD) simulation is a popular technique but often requires technical expertise in computer simulation. This work introduces cryo_fit, a package for the automatic flexible fitting of atomic models in cryo-EM maps using MD simulation. Additionally, the package is integrated with the Phenix software suite. The module was designed to automate the multiple steps of MD simulation in a reproducible manner, as well as facilitate refinement and validation through Phenix. Through the use of cryo_fit, scientists with little experience in MD simulation can produce high quality atomic models automatically and better exploit the potential of cryo-EM.
A theoretical model has been suggested that makes it possible to predict the profile of a film deposited on the walls of a high aspect ratio structure (trench) by atomic layer deposition versus the deposition parameters. In addition, the model allows one to calculate the optimal time of precursor doping that provides the conformal coating of the trench walls. The deposition of films with different thicknesses has been described by an approximant that includes two asymptotical deposition conditions with different relationships between the precursor molecule sticking coefficient and aspect ratio of the trench.
Here, in this tutorial review, we report the state-of-the-art of the modeling approaches of Single Atom Catalysts (SAC) for water splitting and fuel cells reactions. The discussion applies for Hydrogen Evolution Reaction (HER), Oxygen Reduction Reaction (OER), Hydrogen Oxidation Reaction (HOR), and Oxygen Reduction Reaction (ORR). The main scope of this work is to underline the relevant aspects of SACs modelling. On the one hand, the review could help computational chemists aiming to start the study of SACs. On the other hand, experimentalists could find the critical analysis of DFT results of interest to understand better the strengths and weaknesses of simulations, and how to interpret computational results. After an introductory section of SACs, we start by briefly presenting the state-of-the-art methodologies. Then, we analyze the critical aspects for a reliable prediction of the electronic properties, and we discuss the robustness of the structural models and ways to validate them. Furthermore, we discuss the main approaches to predict catalytic activity and selectivity, which is the final goal of the computational catalysis. We conclude this review with a critical analysis of the current challenges in the field, and the main limitations of the modeling approaches that are described.
Minimum variance estimation requires that the statistics of random observation errors be modeled properly. If measurements are derived through the use of atomic frequency standards, then one source of error affecting the observable is random fluctuation in frequency. This is the case, for example, with range and integrated Doppler measurements from satellites of the Global Positioning and baseline determination for geodynamic applications. An analytic method is presented which approximates the statistics of this random process. The procedure starts with a model of the Allan variance for a particular oscillator and develops the statistics of range and integrated Doppler measurements. A series of five first order Markov processes is used to approximate the power spectral density obtained from the Allan variance.
We describe an integrated modelling approach to accelerate the search for novel, single-phase, multicomponent materials with high magnetocrystalline anisotropy (MCA). For a given system we predict the nature of atomic ordering, its dependence on the magnetic state, and then proceed to describe the consequent MCA, magnetisation, and magnetic critical temperature (Curie temperature). Crucially, within our modelling framework, the same ab initio description of a material’s electronic structure determines all aspects. We demonstrate this holistic method by studying the effects of alloying additions in FeNi, examining systems with the general stoichiometries Fe 4 Ni 3 X and Fe 3 Ni 4 X, for additives including X = Pt, Pd, Al, and Co. The atomic ordering behaviour predicted on adding these elements, fundamental for determining a material’s MCA, is rich and varied. Equiatomic FeNi has been reported to require ferromagnetic order to establish the tetragonal L1 0 order suited for significant MCA. Our results show that when alloying additions are included in this material, annealing in an applied magnetic field and/or below a material’s Curie temperature may also promote tetragonal order, along with an appreciable effect on the predicted hard magnetic properties.
An analytical formula is developed to accurately represent the photoabsorption cross section of atomic Oxygen for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects, that accurately predict the absorption oscillator strengths below threshold and merge consistently and continuously to the above-threshold cross section. Further, minor adjustments are made to the threshold energies in order to reliably align the atomic Rydberg resonances after consideration of both experimental and observed line positions. At energies far below or above the K-edge region, the formulation is based on both outer- and inner-shell direct photoionization, including significant shake-up and shake-off processes that result in photoionization-excitation and double-photoionization contributions to the total cross section. The ultimate purpose for developing a definitive model for oxygen absorption is to resolve standing discrepancies between the astronomically observed and laboratory-measured line positions, and between the inferred atomic and molecular oxygen abundances in the interstellar medium from XSTAR and SPEX spectral models.
Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) will assist in understanding the mechanisms involved, and will lead to improved reliability in predicting in-space durability of materials based on ground laboratory testing. A computational simulation of atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of assumed mechanistic behavior of atomic oxygen and results of both ground laboratory and LDEF data, a predictive Monte Carlo model was developed which simulates the oxidation processes that occur on polymers with applied protective coatings that have defects. The use of high atomic oxygen fluence-directed ram LDEF results has enabled mechanistic implications to be made by adjusting Monte Carlo modeling assumptions to match observed results based on scanning electron microscopy. Modeling assumptions, implications, and predictions are presented, along with comparison of observed ground laboratory and LDEF results.
We report on the development of a model framework to simulate spray flames from direct injection of liquid fuel into an automotive cylinder engine. The approach to this challenging problem was twofold. On one hand, the interface-capturing multiphase computer code CLSVOF was used to resolve the rapidly evolving, topologically convoluted interfaces that separate the liquid fuel from the gas at injection: the main challenges to address were the treatment of the high-pressure flow inside the injector, which required the inclusion of compressibility effects; and the computational framework necessary to achieve a Direct Numerical Simulation (DNS) level of accuracy. On the other hand, the scales of turbulent fuel mixing and combustion in the cylinder engine were ad- dressed by the high-performance computer code RAPTOR within the Large Eddy Simulation (LES) framework. To couple the two computational methods, a novel methodology was developed to describe the dense spray dynamics in Raptor from the assigned spray size distribution and dispersion angle derived from CLSVOF. This new, independent Eulerian Multi-Fluid (EMF) spray module was developed based on the kinetic description of a system of droplets as a pressure-less gas; as we will show, it was demonstrated to efficiently render the near-nozzle coupling in mass, momentum, and energy with the carrier gas phase.
We report on the development of a model framework to simulate spray flames from direct injection of liquid fuel into an automotive cylinder engine. The approach to this challenging problem was twofold. On one hand, the interface-capturing multiphase computer code CLSVOF was used to resolve the rapidly evolving, topologically convoluted interfaces that separate the liquid fuel from the gas at injection: the main challenges to address were the treatment of the high-pressure flow inside the injector, which required the inclusion of compressibility effects; and the computational framework necessary to achieve a Direct Numerical Simulation (DNS) level of accuracy. On the other hand, the scales of turbulent fuel mixing and combustion in the cylinder engine were addressed by the high-performance computer code RAPTOR within the Large Eddy Simulation (LES) framework. To couple the two computational methods, a novel methodology was developed to de- scribe the dense spray dynamics in Raptor from the assigned spray size distribution and dispersion angle derived from CLSVOF. This new, independent Eulerian Multi-Fluid (EMF) spray module was developed based on the kinetic description of a system of droplets as a pressure-less gas; as we will show, it was demonstrated to efficiently render the near-nozzle coupling in mass, momentum, and energy with the carrier gas phase.
Refractory complex concentrated alloys (RCCA) offer exceptionally high-temperature strength compared to pure metals and dilute alloys, but predictive theory for RCCA design is lacking. We present large-scale molecular Dynamics (MD) simulations of crystal plasticity to explore alloy compositions for maximum mechanical strength, focusing on Fe-Ta-W and Nb-Ta-Mo-W alloy families modeled with Embedded Atom Model (EAM) and Spectral Neighbor Analysis Potentials (SNAP). To efficiently guide the search for strong alloy compositions, we employ iterative optimization using Gaussian process regression. Many simulated RCCA compositions exhibit pronounced cocktail strengthening, with strengths surpassing their strongest constituent metal, tungsten. Contrary to expectations, the highest strength is found on binary edges of the RCCA composition space. Detailed analyses of atomistic simulations reveal that, similar to pure BCC metals, plastic response in RCCA is primarily governed by screw dislocations. However, at large strains, dislocation multiplication and interactions (Taylor hardening) become the dominant mechanisms contributing to RCCA strength.
The central purpose of this project is the improvement of liquid-fueled rocket motor design technology in order to assist the establishment of economical commercial access to space through the development of engines with enhanced performance and reliability. Specific research effort is focused on spray physics and associated combustion instability phenomena. Results concerning high pressure droplet gasification model, droplet turbulent dispersion model, and spray atomization model will contribute to the development of new computational tools for design of stable liquid propellant rocket engines.
We describe an integrated modelling approach to accelerate the search for novel, single-phase, multicomponent materials with high magnetocrystalline anisotropy (MCA). For a given system we predict the nature of atomic ordering, its dependence on the magnetic state, and then proceed to describe the consequent MCA, magnetisation, and magnetic critical temperature (Curie temperature). Crucially, within our modelling framework, the same ab initio description of a material’s electronic structure determines all aspects. We demonstrate this holistic method by studying the effects of alloying additions in FeNi, examining systems with the general stoichiometries Fe 4 Ni 3 X and Fe 3 Ni 4 X, for additives including X = Pt, Pd, Al, and Co. The atomic ordering behaviour predicted on adding these elements, fundamental for determining a material’s MCA, is rich and varied. Equiatomic FeNi has been reported to require ferromagnetic order to establish the tetragonal L1 0 order suited for significant MCA. Our results show that when alloying additions are included in this material, annealing in an applied magnetic field and/or below a material’s Curie temperature may also promote tetragonal order, along with an appreciable effect on the predicted hard magnetic properties.
A computer model for microenvironment atomic oxygen exposure has been developed to extend atomic oxygen modeling capability to include shadowing and reflections. The model uses average exposure conditions established by the direct exposure model and extends the application of these conditions to treat surfaces of arbitrary shape and orientation.