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At least 1,567 records · Page 87

SSAGES: Software Suite for Advanced General Ensemble Simulations

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this study, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.

97 MATHEMATICS AND COMPUTING↗

An MHD Code for the Study of Magnetic Structures in the Solar Wind

We have developed a 2.5D MHD code designed to study how the solar wind influences the evolution of transient events in the solar corona and inner heliosphere. The code includes thermal conduction, coronal heating and radiative cooling. Thermal conduction is assumed to be magnetic field-aligned in the inner corona and transitions to a collisionless formulation in the outer corona. We have developed a stable method to handle field-aligned conduction around magnetic null points. The inner boundary is placed in the upper transition region, and the mass flux across the boundary is determined from 1D field-aligned characteristics and a 'radiative energy balance' condition. The 2.5D nature of this code makes it ideal for parameter studies not yet possible with 3D codes. We have made this code publicly available as a tool for the community. To this end we have developed a graphical interface to aid in the selection of appropriate options and a graphical interface that can process and visualize the data produced by the simulation. As an example, we show a simulation of a dipole field stretched into a helmet streamer by the solar wind. Plasmoids periodically erupt from the streamer, and we perform a parameter study of how the frequency and location of these eruptions changed in response to different levels of coronal heating. As a further example, we show the solar wind stretching a compact multi-polar flux system. This flux system will be used to study breakout coronal mass ejections in the presence of the solar wind.

corona↗

Transition probabilities of the low-lying levels of Kr XXIV

Energy levels, radiative rates, and wavelengths are calculated for all levels of 3s{sup 2}3p, 3s3p{sup 2}, 3s{sup 2}3d, 3p{sup 3}, 3s3p3d, 3p{sup 2}3d and 3s3d{sup 2} configurations of Al-like krypton ion (Kr XXIV). Multiconfigurational Dirac–Hartree–Fock (MCDHF) method is adopted for calculating energy levels and radiative rates. Transition probabilities are reported for E1 and M2 transitions from the ground level. The valence–valence and core–valence correlation effects are accounted for in a systematic way. Breit interactions and quantum electrodynamics effects are estimated in subsequent relativistic configuration interaction calculations. Comparisons are made with the available data in the literature and good agreement has been found which confirms the reliability of our results.

74 ATOMIC AND MOLECULAR PHYSICS↗

Environmental dynamics at orbital altitudes

The work reported involved the improvement of aerodynamic theory for free molecular and transition flow regimes. The improved theory was applied to interpretation of the dynamic response of objects traveling through the atmosphere. Satellite drag analysis includes analysis methods, atmospheric super rotation effects, and satellite lift effects on orbital dynamics. Transition flow regimes were studied with falling sphere data and errors resulting in inferred atmospheric parameters from falling sphere techniques. Improved drag coefficients reveal considerable error in previous falling sphere data. The drag coefficient has been studied for the entire spectrum of Knudsen Number and speed ratio, with particular emphasis on the theory of the very low-speed ratio regime.

Karr, G. R.↗

Kinetics and dynamics of the C( 3 P) + H 2 O reaction on a full-dimensional accurate triplet state potential energy surface

A full dimensional accurate potential energy surface (PES) for the C( 3 P) and H 2 O reaction is developed based on ~34 000 data points calculated at the level of the explicitly correlated unrestricted coupled cluster method with single, double, and perturbative triple excitations with the augmented correlation-consistent polarized triple zeta basis set (CCSD(T)-F12a/AVTZ). The PES is invariant with respect to the permutation of the two hydrogen atoms and the total root mean square error (RMSE) of the fit is only 0.31 kcal mol -1 . The PES features two barriers in the entrance channel and several potential minima, as well as multiple product channels. The rate coefficients of this reaction calculated using a transition-state theory and quasi-classical trajectory (QCT) method are small near room temperature, consistent with experiments. The reaction dynamics is also investigated with QCT on the new PES, which found that the reactivity is constrained by the entrance barriers and the final product branching is not statistical.

Li, Jun↗

Mixing and Transition Control Studied

Considerable progress in understanding nonlinear phenomena in both unbounded and wallbounded shear flow transition has been made through the use of a combination of high- Reynolds-number asymptotic and numerical methods. The objective of this continuing work is to fully understand the nonlinear dynamics so that ultimately (1) an effective means of mixing and transition control can be developed and (2) the source terms in the aeroacoustic noise problem can be modeled more accurately. Two important aspects of the work are that (1) the disturbances evolve from strictly linear instability waves on weakly nonparallel mean flows so that the proper upstream conditions are applied in the nonlinear or wave-interaction streamwise region and (2) the asymptotic formulations lead to parabolic problems so that the question of proper out-flow boundary conditions--still a research issue for direct numerical simulations of convectively unstable shear flows--does not arise. Composite expansion techniques are used to obtain solutions that account for both mean-flow-evolution and nonlinear effects. A previously derived theory for the amplitude evolution of a two-dimensional instability wave in an incompressible mixing layer (which is in quantitative agreement with available experimental data for the first nonlinear saturation stage for a plane-jet shear layer, a circular-jet shear layer, and a mixing layer behind a splitter plate) have been extended to include a wave-interaction stage with a three-dimensional subharmonic. The ultimate wave interaction effects can either give rise to explosive growth or an equilibrium solution, both of which are intimately associated with the nonlinear self-interaction of the three dimensional component. The extended theory is being evaluated numerically. In contrast to the mixing-layer situation, earlier comparisons of theoretical predictions based on asymptotic methods and experiments in wall-bounded shear-flow transition have been somewhat lacking in one aspect or another. The current work strongly suggests that the main weakness is the underlying asymptotic representation of the linear "part" of the problem and not the explicit modeling of the nonlinear/wave-interaction effects. Consequently, the long-wave-length/high-Reynolds-number asymptotic limit for the Blasius boundary-layer stability problem was reexamined, and a new dispersion relationship for the instability waves that is uniformly valid for both the upper- and lower branch regions to the required order of approximation was obtained. A comparison with numerical results, obtained by solving the Orr-Sommerfeld stability problem, shows that the asymptotic formula provides surprisingly good results, even for values of the frequency parameter usually encountered in experimental investigations. This is particularly evident in the dynamically important upper-branch region, where much of the nonlinear interactions in transition experiments are believed to take place. The result is important in that it can be used to greatly improve the accuracy of weakly nonlinear critical-layer-based theories, and a consistent nonlinear theory is currently under evaluation.

Source record↗

A strain-driven thermotropic phase boundary in BaTiO 3 at room temperature by cycling compression

In BaTiO 3 single crystals, we observed a strain-driven phase transition from the tetragonal phase to the tetragonal-orthorhombic phase boundary which can be introduced by slow cycling compressions (a loading of up to 0.5 GPa, strain rate of 10 -4 s -1 , and 100 cycles) at room temperature. Different from the well-known tetragonal to cubic phase transition under stress (~2 GPa), it only takes place locally around bent 90° domain walls. The inhomogeneous local stress and electrical fields as well as the mobile point defect pinning effect contribute to the phase re-entrance. Through comparison experiments by in situ synchrotron x-ray diffraction, Raman scattering, and (scanning) transmission electron microscopy, we explored the phase transition mechanism. Based on that, we developed a mechanical method to obtain well-stabilized high-density thermotropic phase boundary structures (with tetragonal, orthorhombic, and bridging monoclinic phases) in BaTiO 3 for potential applications.

36 MATERIALS SCIENCE↗

Radiochromic film based transit dosimetry for verification of dose delivery with intensity modulated radiotherapy

Purpose: To evaluate the transit dose based patient specific quality assurance (QA) of intensity modulated radiation therapy (IMRT) for verification of the accuracy of dose delivered to the patient. Methods: Five IMRT plans were selected and utilized to irradiate a homogeneous plastic water phantom and an inhomogeneous anthropomorphic phantom. The transit dose distribution was measured with radiochromic film and was compared with the computed dose map on the same plane using a gamma index with a 3% dose and a 3 mm distance-to-dose agreement tolerance limit. Results: While the average gamma index for comparisons of dose distributions was less than one for 98.9% of all pixels from the transit dose with the homogeneous phantom, the passing rate was reduced to 95.0% for the transit dose with the inhomogeneous phantom. Transit doses due to a 5 mm setup error may cause up to a 50% failure rate of the gamma index. Conclusions: Transit dose based IMRT QA may be superior to the traditional QA method since the former can show whether the inhomogeneity correction algorithm from TPS is accurate. In addition, transit dose based IMRT QA can be used to verify the accuracy of the dose delivered to the patient during treatment by revealing significant increases in the failure rate of the gamma index resulting from errors in patient positioning during treatment.

60 APPLIED LIFE SCIENCES↗

Nanomechanics of Ferroelectric Thin Films and Heterostructures

The focus of this chapter is to provide basic concepts of how external strains/stresses altering ferroelectric property of a material and how to evaluate quantitatively the effect of strains/stresses on phase stability, domain structure, and material ferroelectric properties using the phase-field method. The chapter starts from a brief introduction of ferroelectrics and the Landau-Devinshire description of ferroelectric transitions and ferroelectric phases in a homogeneous ferroelectric single crystal. Due to the fact that ferroelectric transitions involve crystal structure change and domain formation, strains and stresses can be produced inside of the material if a ferroelectric transition occurs and it is confined. These strains and stresses affect in turn the domain structure and material ferroelectric properties. Therefore, ferroelectrics and strains/stresses are coupled to each other. The ferroelectric-mechanical coupling can be used to engineer the material ferroelectric properties by designing the phase and structure. The followed section elucidates calculations of the strains/stresses and elastic energy in a thin film containing a single domain, twinned domains to complicated multidomains constrained by its underlying substrate. Furthermore, a phase field model for predicting ferroelectric stable phases and domain structure in a thin film is presented. Examples of using substrate constraint and temperature to obtain interested ferroelectric domain structures in BaTiO3 films are demonstrated b phase field simulations.

Ferroelectrics↗

A Search for Planetary Transits of the Star HD 187123 by Spot Filter CCD Differential Photometry

A novel method for performing high precision, time series CCD differential photometry of bright stars using a spot filter, is demonstrated. Results for several nights of observing of the 51 Pegasi b-type planet bearing star HD 187123 are presented. Photometric precision of 0.0015 - 0.0023 magnitudes is achieved. No transits are observed at the epochs predicted from the radial velocity observation. If the planet orbiting HD 187123 at 0.0415 AU is an inflated Jupiter similar in radius to HD 209458b it would have been detected at the greater than 6(sigma), level if the orbital inclination is near 90 degrees and at the greater than 3(sigma), level if the orbital inclination is as small as 82.7 degrees.

Castellano, T.↗

Modeling Multi-Step Organic Reactions: Can Density Functional Theory Deliver Misleading Chemistry?

Many organic reactions are characterized by a complex mechanism with a variety of transition states and intermediates of different chemical natures. Their correct and accurate theoretical characterization critically depends on the accuracy of the computational method used. In this work, we study a complex ambimodal cycloaddition with five transition states, two intermediates, and three products, and we ask whether density functional theory (DFT) can provide a correct description of this type of complex and multifaceted reaction. Our work fills a gap in that most systematic benchmarks of DFT for chemical reactions have considered much simpler reactions. Our results show that many density functionals not only lead to seriously large errors but also differ from one another in predicting whether the reaction is ambimodal. Only a few of the available functionals provide a balanced description of the complex and multifaceted reactions. The parameters varied in the tested functionals are the ingredients, the treatment of medium-range and nonlocal correlation energy, and the inclusion of Hartree–Fock exchange. Furthermore, these results show a clear need for more benchmarks on the mechanisms of large molecules in complex reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Topological Phase Transition and Phonon-Space Dirac Topology Surfaces in ZrTe5

We use first-principles methods to demonstrate that, in ZrTe 5 , a layered van der Waals material like graphite, atomic displacements corresponding to five of the six zone-center A g (symmetry-preserving) phonon modes can drive a topological transition from a strong to a weak topological insulator with a Dirac semimetal state emerging at the transition, giving rise to a Dirac topology surface in the multidimensional space formed by the A g phonon modes. This implies that the topological transition in ZrTe 5 , can be realized with many different settings of external stimuli capable of penetrating through the phonon-space Dirac surface without breaking the crystallographic symmetry. Furthermore, we predict that domains with effective mass of opposite signs can be created by laser pumping and will host Weyl modes of opposite chirality propagating along the domain boundaries. Studying phonon-space topology surfaces provides a new route to understanding and utilizing the exotic physical properties of ZrTe 5 , and related quantum materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Targeted synthesis, characterization, and electrochemical analysis of transition-metal-oxide catalysts for the oxygen evolution reaction

Hydrogen fuel can be produced through the electrochemical splitting of water, an energy-intensive process that requires the use of electrocatalysts to be more efficient. Whereas current precious-metal-based electrocatalysts might be costly on a larger scale, transition-metal-oxide catalysts are more earth abundant and have shown promising activity. Here, the development and improvement of highly active transition-metal-oxide electrocatalysts is thus an important area of study where different catalyst enhancement strategies are used to drive the field forward. Additionally, transition-metal-oxide catalysts come in various different structures with their own advantages; thus, this review is focused on investigating the continuing field of transition-metal-oxide electrocatalysts of different structures and innovative methods of improving activity. By the end, new and promising paths forward in this field will be highlighted, particularly in the development of rock-salt oxides for the water-splitting system.

08 HYDROGEN↗

Temperature dependent photoexcited carrier dynamics in multiferroic BiFeO{sub 3} film: A hidden phase transition

The ultrafast carrier dynamics of the multiferroic BiFeO{sub 3} film in a broad temperature range is investigated using optical pump-probe spectroscopy. The photoexcited electrons release their energy with optical phonons emission through electron-phonon coupling in about 1 ps. The following intermediate process is identified as dynamical spin-lattice coupling in several picoseconds. Furthermore, the peak values of the optical reflectivity and the time constants of carrier relaxation channels show significant changes while the temperature varies from 137.5 K to around 195 K, this aligns with the previously reported hidden phase transition. Our study demonstrates that ultrafast spectroscopy is a sensitive method to look into the dynamical interactions among the on-site high-energy electrons accumulated in the p conduction band of Bi, coherent optical phonon, as well as the spin degree of freedom. These features play crucial roles in the characterization of phase transitions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Machine learning for impurity charge-state transition levels in semiconductors from elemental properties using multi-fidelity datasets

Quantifying charge-state transition energy levels of impurities in semiconductors is critical to understanding and engineering their optoelectronic properties for applications ranging from solar photovoltaics to infrared lasers. While these transition levels can be measured and calculated accurately, such efforts are time-consuming and more rapid prediction methods would be beneficial. Here, we significantly reduce the time typically required to predict impurity transition levels using multi-fidelity datasets and a machine learning approach employing features based on elemental properties and impurity positions. We use transition levels obtained from low-fidelity (i.e., local-density approximation or generalized gradient approximation) density functional theory (DFT) calculations, corrected using a recently proposed modified band alignment scheme, which well-approximates transition levels from high-fidelity DFT (i.e., hybrid HSE06). Further, the model fit to the large multi-fidelity database shows improved accuracy compared to the models trained on the more limited high-fidelity values. Crucially, in our approach, when using the multi-fidelity data, high-fidelity values are not required for model training, significantly reducing the computational cost required for training the model. Our machine learning model of transition levels has a root mean squared (mean absolute) error of 0.36 (0.27) eV vs high-fidelity hybrid functional values when averaged over 14 semiconductor systems from the II–VI and III–V families. As a guide for use on other systems, we assessed the model on simulated data to show the expected accuracy level as a function of bandgap for new materials of interest. Finally, we use the model to predict a complete space of impurity charge-state transition levels in all zinc blende III–V and II–VI systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tensor train continuous time solver for quantum impurity models

The simulation of strongly correlated quantum impurity models is a significant challenge in modern condensed matter physics that has multiple important applications. Thus far, the most successful methods for approaching this challenge involve Monte Carlo techniques that accurately and reliably sample perturbative expansions to any order. However, the cost of obtaining high precision through these methods is high. Recently, tensor train decomposition techniques have been developed as an alternative to Monte Carlo integration. In this study, we apply these techniques to the single-impurity Anderson model at equilibrium by calculating the systematic expansion in power of the hybridization of the impurity with the bath. Furthermore, we demonstrate the performance of the method in a paradigmatic application, examining the first-order phase transition on the infinite-dimensional Bethe lattice, which can be mapped to an impurity model through dynamical mean field theory. Our results indicate that using tensor train decomposition schemes allows the calculation of finite-temperature Green's functions and thermodynamic observables with unprecedented accuracy. The methodology holds promise for future applications to frustrated multiorbital systems, using a combination of partially summed series with other techniques pioneered in diagrammatic and continuous time quantum Monte Carlo.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Analysis of Instabilities in Non-Axisymmetric Hypersonic Boundary Layers Over Cones

Hypersonic flows over circular cones constitute one of the most important generic configurations for fundamental aerodynamic and aerothermodynamic studies. In this paper, numerical computations are carried out for Mach 6 flows over a 7-degree half-angle cone with two different flow incidence angles and a compression cone with a large concave curvature. Instability wave and transition-related flow physics are investigated using a series of advanced stability methods ranging from conventional linear stability theory (LST) and a higher-fidelity linear and nonlinear parabolized stability equations (PSE), to the 2D eigenvalue analysis based on partial differential equations. Computed N factor distribution pertinent to various instability mechanisms over the cone surface provides initial assessments of possible transition fronts and a guide to corresponding disturbance characteristics such as frequency and azimuthal wave numbers. It is also shown that strong secondary instability that eventually leads to transition to turbulence can be simulated very efficiently using a combination of advanced stability methods described above.

Li, Fei↗