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A phase boundary for H-Pd(100) was calculated using the Metropolis (1953) algorithm and the embedded atom method (EAM) described by Daw and Foiles (1987). The calculated phase boundary agreed with an experimentally determined phase boundary in its curvature and the coverage at which maximum Tc appeared, but was about 125 K lower than the experimental phase boundary.
The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H 2 O/D 2 O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.
Large-scale river models are being refined over coastal regions to improve the scientific understanding of coastal processes, hazards and responses to climate change. However, coarse mesh resolutions and approximations in physical representations of tidal rivers limit the performance of such models at resolving the complex flow dynamics near the river-ocean interface, resulting in inaccurate simulations of flood inundation. In this research, we propose a machine learning (ML) framework based on the state-of-the-art physics-informed neural network (PINN) to simulate the downscaled flow at the subgrid scale. First, we demonstrate that PINN is able to assimilate observations of various types and solve the one-dimensional (1-D) Saint-Venant equations (SVE) directly. We perform the flow simulations over a floodplain and along an open channel in several synthetic case studies. The PINN performance is evaluated against analytical solutions and numerical models. Our results indicate that the PINN solutions of water depth have satisfactory accuracy with limited observations assimilated. In the case of flood wave propagation induced by storm surge and tide, a new neural network architecture is proposed based on Fourier feature embeddings that seamlessly encodes the periodic tidal boundary condition in the PINN's formulation. Furthermore, we show that the PINN-based downscaling can produce more reasonable subgrid solutions of the along-channel water depth by assimilating observational data. The PINN solution outperforms the simple linear interpolation in resolving the topography and dynamic flow regimes at the subgrid scale. This study provides a promising path towards improving emulation capabilities in large-scale models to characterize fine-scale coastal processes.
Astrophysical jets are collimated high-speed outflows emerging from spinning and accreting matter around celestial objects and may spontaneously result from self-organized processes. Magnetic self-organization is commonly observed in laboratory plasma physics experiments; however, they require close-fitting flux conservers to constrain and stabilize the toroidal or cylindrical structures. Here we report the first observations of a long, stable, free-boundary plasma jet far from chamber walls, embedding a double-helix magnetic structure resembling a force-free plectonemic Taylor state. The jets arise from an experimental setup that mimics an accretion disk and has no close-fitting solid flux conserver. The results support the hypothesis that self-organization could be a universal, intrinsic explanation for jet formation, collimation, and stability and may help explain double-helix features in celestial observations.
The diurnal variation of precipitation processes over the tropics is a well-known phenomenon and has been studied using surface rainfall data, radar reflectivity data, and satellite-derived cloudiness and precipitation. Recently, analyzed observations from Tropical Oceans and Global Atmosphere Coupled Ocean-Atmosphere Response Experiment (TOGA COARE) in the tropical western Pacific ocean to study the relevant mechanisms producing diurnal variation of precipitation. They found that the diurnal Sea surface temperature (SST) cycle is important for afternoon showers in the undisturbed periods and diurnal radiative processes for nocturnal rainfall. Cloud resolving models (CRMS) have been used to determine the mechanisms associated with diurnal variation of precipitating processes. CRMs allow explicit cloud-radiation and air-sea interactive processes. However, CRMs can be only used for idealized simulations (i.e., no feedback between clouds and their embedded large-scale environments; cyclic lateral boundary conditions and idealized initial conditions). In this study, the Penn State/NCAR Mesoscale Model (MM5) with improved physics (i.e., cloud microphysics, radiation, land-soil-vegetation-surface processes, and TOGA COARE flux scheme) and a multiple level nesting technique (covers the TOGA COARE LSA/IFA with a 54 km grid and can nest down to 18, 6 and possibly even 2 km) will be adopted for studying the diurnal variations of rainfall. We will examine precipitation processes over open ocean and over land. We will also perform sensitivity tests to determine how the radiative forcing and diurnal SST cycle affects the development of convection.
Solution of the steady 2-D Euler equations using mesh embedding, or local grid refinement, with a cell-centered finite volume scheme is investigated. Embedded regions which are topologically similar to the global grid are considered. An isoenergetic model for the governing equations is used in Jameson's finite volume multistage scheme with modifications to the boundary conditions and smoothing. A detailed study of the embedding interface flux and smoothing formulations is conducted. Taylor expansion analysis reveals that local second order spatial accuracy is not possible if a conservative interface flux formulation is used. The analysis also gives constraints for local first order accuracy. An energy stability analysis indicates that downwind weighting of interface fluxes causes local instabilities. Analysis shows that conservative interface smoothing formulations must have a locally convective component, but that correct interface formulations allow globally dissipative smoothing. Embedded mesh solutions obtained with this scheme are presented for a transonic airfoil. They show that if embedding interfaces are close to the shocks, then small modifications in the interface location can have large effects on converge and solution accuracy.
Grain boundaries in metallic materials can exist in a wide range of stable and metastable structures. In addition, the properties of a grain boundary may be altered through solute segregation. In this work, we present a formulation that combines the spectrum of embrittling potencies associated with solute segregation with site-occupancy statistics. As a prototype problem, we illustrate the relation between segregation and embrittlement in the case of S segregation to grain boundaries in Ni. To obtain a population of site segregation energies, we perform molecular statics calculations on 378 different symmetric-tilt grain boundaries and their free surface equivalents, using an embedded-atom method interatomic potential developed specifically for studying embrittlement. Our results show that it is important to consider both the energies associated with embrittlement and the probability of occupancy to describe the general embrittling nature of a grain boundary. When analyzed in isolation, certain grain boundaries show large embrittling potencies; however, that effect is diminished when the probability of S segregation to that grain boundary is considered within a polycrystal. We propose a new quantity, the embrittling estimator, which not only categorizes grain boundaries as embrittling or strengthening, but also considers site occupancy probabilities, so that the embrittlement behavior of grain boundaries within a network of grain boundaries can be compared. Finally, we examine the relationship between embrittlement behavior and innate grain boundary properties, such as the free volume, and find statistical evidence that the complex nature of embrittlement cannot be explained by linear correlations with excess volumes or energies. Ultimately, this combined approach provides a theoretical tool to assist grain boundary engineering of metastable alloys.
The extension of computational fluid dynamics techniques to artificial heart flow simulations is illustrated. Unsteady incompressible Navier-Stokes equations written in 3-D generalized curvilinear coordinates are solved iteratively at each physical time step until the incompressibility condition is satisfied. The solution method is based on the pseudo compressibility approach and uses an implicit upwind differencing scheme together with the Gauss-Seidel line relaxation method. The efficiency and robustness of the time accurate formulation of the algorithm are tested by computing the flow through model geometries. A channel flow with a moving indentation is computed and validated with experimental measurements and other numerical solutions. In order to handle the geometric complexity and the moving boundary problems, a zonal method and an overlapping grid embedding scheme are used, respectively. Steady state solutions for the flow through a tilting disk heart valve was compared against experimental measurements. Good agreement was obtained. The flow computation during the valve opening and closing is carried out to illustrate the moving boundary capability.
In this article, proton radiography is a central diagnostic technique for measuring electromagnetic (EM) fields in high-energy-density, laser-produced plasmas. In this technique, protons traverse the plasma where they accumulate small EM deflections which lead to variations in the proton fluence pattern on a detector. Path-integrated EM fields can then be extracted from the fluence image through an inversion process. In this work, experiments of laser-driven foils were conducted on the OMEGA laser and magnetic field reconstructions were performed using both “fluence-based” techniques and high-fidelity “mesh-based” methods. We implement nonzero boundary conditions into the inversion and show their importance by comparing against mesh measurements. Good agreement between the methods is found only when nonzero boundary conditions are used. We also introduce an approach to determine the unperturbed proton source profile, which is a required input in fluence reconstruction algorithms. In this approach, a fluence inversion is embedded inside of a mesh region, which provides overconstrained magnetic boundary conditions. A source profile is then iteratively optimized to satisfy the boundary information. This method substantially enhances the accuracy in recovering EM fields. Lastly, we propose a scheme to quantify uncertainty in the final inversion that is introduced through errors in the source retrieval.
A body-fitted grid embedment technique applicable to inviscid transonic airfoil flow field analysis was developed and verified through a series of tests. Test cases used to verify the technique show that the accuracy of the solution was increased by grid embedding. This enhancement of the solution is especially true when small supercritical zones occur which cannot be adequately described using the main grid only. Results obtained with the SKANFP full potential program are considered with regard to the massive separated flow and high lift and the undesirable unrealistic 'bump' in the vicinity of the separation point due to a mismatch between the unseparated and separated pressure distributions. Techniques used to eliminate this feature are discussed.
The two-dimensional (2-D) finite-difference time domain (FDTD) method is applied to calculate light scattering and absorption by an arbitrarily shaped infinite column embedded in an absorbing dielectric medium. A uniaxial perfectly matched layer (UPML) absorbing boundary condition (ABC) is used to truncate the computational domain. The single-scattering properties of the infinite column embedded in the absorbing medium, including scattering phase functions, extinction and absorption efficiencies, are derived using an area integration of the internal field. An exact solution for light scattering and absorption by a circular cylinder in an absorbing medium is used to examine the accuracy of the 2-D UPML FDTD code. With use of a cell size of 1/120 incident wavelength in the FDTD calculations, the errors in the extinction and absorption efficiencies and asymmetry factors from the 2-D UPML FDTD are generally smaller than approx .1%. The errors in the scattering phase functions are typically smaller than approx .4%. Using the 2-D UPML FDTD technique, light scattering and absorption by long noncircular columns embedded in absorbing media can be accurately solved.
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The precipitates play a significant role in not only enhancing the strength, but also maintaining the high toughness in alloys. However, the interactions of the nanoscale precipitates with dislocations in the high entropy alloys (HEAs) are difficult to observe directly by in-situ TEM experiments due to the limits of the resolution and time. Here, using atomic simulations we report the synergistic strengthening of the coherent precipitate and atomic-scale lattice distortion in the HEAs at cryogenic/elevated temperatures. The effects of temperature, chemical disorder, precipitate spacing, precipitate size, elemental segregation, and dislocation-cutting number on the critical stress for the dislocation to overcome a row of precipitates are studied. A random stacking fault energy landscape along the slip plane, the lattice distortion at different temperatures, and the interface/surface energy at various crystallographic orientations are obtained. Compared with the traditional metals and alloys, HEAs have the severe atomic-scale lattice distortions to generate the local high tensile/compressive stress fields. This complex stress causes the dislocation line to bend, and thus improves the dislocation slip resistance, resulting in the strong solid-solution strengthening. The stacking fault strengthening induced by the obvious difference of the stacking fault energies between the HEA matrix and precipitate (within the inner of the HEA matrix), and the formation of the antiphase domain boundary contribute to the high strength. The precipitate embedded by the solute atoms produces the strong lattice distortion to enhance the dislocation slip resistance at high temperatures. Hence, the current results provide the mechanistic insight into the phenomenon that the coherent precipitate combined with the severe atomic-scale lattice distortion can enhance the strength at cryogenic/elevated temperatures to further broaden the scope of applications of advanced HEAs.
Here, we present a new method for two-material Lagrangian hydrodynamics, which combines the Shifted Interface Method (SIM) with a high-order Finite Element Method. Our approach relies on an exact (or sharp) material interface representation, that is, it uses the precise location of the material interface. The interface is represented by the zero level-set of a continuous high-order finite element function that moves with the material velocity. This strategy allows to evolve curved material interfaces inside curved elements. By reformulating the original interface problem over a surrogate (approximate) interface, located in proximity of the true interface, the SIM avoids cut cells and the associated problematic issues regarding implementation, numerical stability, and matrix conditioning. Accuracy is maintained by modifying the original interface conditions using Taylor expansions. We demonstrate the performance of the proposed algorithms on established numerical benchmarks in one, two and three dimensions.
The manner in which a giant gaseous protoplanet becomes embedded in the primitive solar nebula determines surface boundary conditions which must be used in studying the evolution of such objects. On the one hand, if the system resembles a contact binary system, then the envelope of the protoplanet should approach the entropy of the surrounding nebula. On the other hand angular momentum transfer by resonance and tidal effects between the nebula and the protoplanet may cause the nebula to exhibit a zone of avoidance near the protoplanet, thus inhibiting exchange of material. This problem has been studied with a computer program developed by D. N. C. Lin which simulates disk hydrodynamics by particle motions with dissipation. These studies suggest that for expected values of the protoplanet/protosun mass ratios, significant inhibition of mass exchange is likely, so that it is a reasonable next step to undertake protoplanet evolution studies with the imposition of minimum protoplanet surface temperatures.
The interactive phenomena that occur in supersonic jet mixing flowfields, and numerical modeling techniques developed to analyze such phenomena are discussed. A spatial marching procedure based on solving the parabolized Navier-Stokes jet mixing equations is presented. This procedure combines shock-capturing methodology for the analysis of supersonic mixing regions with pressure-split methodology for the analysis of subsonic mixing regions. The two regions are coupled at viscous sonic lines utilizing a viscous-characteristic coupling procedure. Specialized techniques for the treatment of jet boundary growth, strong discontinuties (Mach disks), and small embedded subsonic zones (behind Mach disks) are presented. Turbulent processes are represented by two-equation turbulence model formulations. In Part II of this article, numerical studies are presented for a variety of supersonic jet interactive phenomena.
Results of a detailed analysis of short large-amplitude magnetic structures (SLAMS) observed at an encounter of the quasi-parallel blow shock by the AMPTE UKS and IRM satellites are presented. Isolated SLAMS, surrounded by solar wind conditions, and embedded SLAMS, which lie within or form the boundary with regions of significant heating and deceleration, are identified. The duration, polarization, and other characteristics of SLAMS are all consistent with their growth directly out of the ULF wave field, including the common occurrence of an attached whistler as found in ULF shocklets. The plasma rest frame propagation speeds and two-spacecraft time delays for all cases show that the SLAMS attempt to propagate upstream against the oncoming flow, but are convected back downstream. The speeds and delays vary systematically with SLAMS amplitude in the way anticipated from nonlinear wave theory, as do their polarization features. Inter-SLAMS regions and boundary regions with solar wind contain hot deflected ions of lesser density than within the SLAMS.
Using two-dimensional particle-in-cell (PIC) together with magnetohydrodynamic (MHD) Q1 simulations of magnetotail dynamics, we investigate the evolution toward onset of reconnection and the subsequent energy transfer and conversion. In either case, reconnection onset is preceded by a driven phase, during which magnetic flux is added to the tail at the high-latitude boundaries, followed by a relaxation phase, during which the configuration continues to respond to the driving. The boundary deformation leads to the formation of thin embedded current sheets, which are bifurcated in the near tail, converging to a single sheet farther out in the MHD simulations. The thin current sheets in the PIC simulation are carried by electrons and are associated with a strong perpendicular electrostatic field, which may provide a connection to parallel potentials and auroral arcs and an ionospheric signal even prior to the onset of reconnection. The PIC simulation very well satisfies integral entropy conservation (intrinsic to ideal MHD) during this phase, supporting ideal ballooning stability. Eventually, the current intensification leads to the onset of reconnection, the formation and ejection of a plasmoid, and a collapse of the inner tail. The earthward flow shows the characteristics of a dipolarization front: enhancement of Bz, associated with a thin vertical electron current sheet in the PIC simulation. Both MHD and PIC simulations show a dominance of energy conversion from incoming Poynting flux to outgoing enthalpy flux, resulting in heating of the inner tail. Localized Joule dissipation plays only a minor role.