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At least 109 records · Page 6

Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer

Background: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3). Results: Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy. Conclusions: Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection.

59 BASIC BIOLOGICAL SCIENCES↗

A high-precision finite element method for shock-tube calculations

A two-pass explicit scheme is developed in order to exploit some of the capabilities of finite difference modeling (FDM) for finite element modeling (FEM), which offers the opportunity to account for any type of geometry in fluid flow modeling. Features of the first-order upwind and the Lax-Wendroff high precision explicit finite difference algorithms are reviewed. A flux limiter is developed for FEM to serve as an analog for the single limiter function which has been defined for the various FDMs. It is shown that an antidiffusive limiter must be introduced into the weighting function which normally multiplies the time-derivative term in the variational equation. The two-pass scheme which results is demonstrated to be the equivalent of FDMs with five-point support. However, the present scheme is valid only for one-dimensional calculations and linear shape functions for shock tube flow phenomena. Further work is required for its use with nonlinear hyperbolic systems.

Hughes, T. J. R.↗

Application of numerical optimization to the design of supercritical airfoils without drag-creep

Recent applications of numerical optimization to the design of advanced airfoils for transonic aircraft have shown that low-drag sections can be developed for a given design Mach number without an accompanying drag increase at lower Mach numbers. This is achieved by imposing a constraint on the drag coefficient at an off-design Mach number while the drag at the design Mach number is the objective function. Such a procedure doubles the computation time over that for single design-point problems, but the final result is worth the increased cost of computation. The ability to treat such multiple design-point problems by numerical optimization has been enhanced by the development of improved airfoil shape functions. Such functions permit a considerable increase in the range of profiles attainable during the optimization process.

Hicks, R. M.↗

Analysis of the EMCCD point-source response using x-rays

Electron Multiplying Charge Coupled Devices, EMCCD are used as x-ray detectors. The NSLS-II Soft Inelastic x-ray Scattering (SIX) beam line has two EMCCDs for x-ray detection in the spectrometer arm. The spectrometer with high resolving power disperses x-rays vertically. The x-ray vertical position on the sensor plane is related to its energy. This allows for very accurate x-ray energy measurements through x-ray coordinates. X-rays interact with silicon and create a number of electron-hole pairs proportional to the x-ray energy. Electrons drift and diffuse toward pixel gates and are collected there. The diffused electrons form a charge cloud distributed over several neighboring pixels. This charge sharing enables coordinate measurements with accuracy better than the pixel pitch. The charge distribution shape has to be taken into account to achieve ultimate accuracy in coordinate measurements. In this paper, we present a method of the charge distribution shape analysis and demonstrate its applications. The drift and diffusion of electrons ftom the point of generation to pixel gates results in the bell-shaped electron cloud usually approximated by Gaussian shape. The number of electrons collected under a pixel is proportional to the shape function integral. These electron packets get transferred to the sense node of the output amplifier. The transfer process could introduce distortions to the original charge distribution. For example, during transfers, electrons in the packet could be exposed to traps if they are present in the sensor. The trapping and later the release processes distort the apparent shape of the charge distribution. Therefore, deviations of the charge distribution shape ftom the originally symmetrical form can indicate the presence of trap centers in the sensor and can be used for sensor diagnostics.

47 OTHER INSTRUMENTATION↗

Quantum control of exciton wave functions in 2D semiconductors

Excitons—bound electron-hole pairs—play a central role in light-matter interaction phenomena and are crucial for wide-ranging applications from light harvesting and generation to quantum information processing. A long-standing challenge in solid-state optics has been to achieve precise and scalable control over excitonic motion. We present a technique using nanostructured gate electrodes to create tailored potential landscapes for excitons in 2D semiconductors, enabling in situ wave function shaping at the nanoscale. Our approach forms electrostatic traps for excitons in various geometries, such as quantum dots, rings, and arrays thereof. We show independent spectral tuning of spatially separated quantum dots, achieving degeneracy despite material disorder. Owing to the strong light-matter coupling of excitons in 2D semiconductors, we observe unambiguous signatures of confined exciton wave functions in optical reflection and photoluminescence measurements. This work unlocks possibilities for engineering exciton dynamics and interactions at the nanometer scale, with implications for optoelectronic devices, topological photonics, and quantum nonlinear optics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Mirror-centered representation of a focusing hyperbolic mirror for X-ray beamlines

Conic sections are commonly used in reflective X-ray optics. Hyperbolic mirrors can focus a converging light source and are frequently paired with elliptical or parabolic mirrors in Wolter type configurations. This paper derives the closed-form expression for a mirror-centered hyperbolic shape, with zero-slope at the origin. Combined with the slope and curvature, such an expression facilitates metrology, manufacturing and mirror-bending calculations. Previous works consider ellipses, parabolas, magnifying hyperbolas or employ lengthy approximations. Here, the exact shape function is given in terms of the mirror incidence angle and the source and image distances.

47 OTHER INSTRUMENTATION↗

Analytic and numerical vibronic spectra from quasi-classical trajectory ensembles

The truncated Wigner approximation to quantum dynamics in phase space is explored in the context of computing vibronic line shapes for monomer linear optical spectra. We consider multiple model potential forms including a shifted harmonic oscillator with both equal and unequal frequencies on the ground and excited state potentials as well as a shifted Morse potential model. For the equal-frequency shifted harmonic oscillator model, we derive an analytic expression for the exact vibronic line shape that emphasizes the importance of using a quantum mechanical distribution of phase space initial conditions. For the unequal-frequency shifted harmonic oscillator model, we are no longer able to obtain an exact expression for the vibronic line shape in terms of independent deterministic classical trajectories. We show how one can rigorously account for corrections to the truncated Wigner approximation through nonlinear responses of the line shape function to momentum fluctuations along a classical trajectory and demonstrate the qualitative improvement in the resulting spectrum when the leading-order quantum correction is included. Finally, we numerically simulate absorption spectra of a highly anharmonic shifted Morse potential model. We find that, while finite quantization and the dissociation limit are captured with reasonable accuracy, there is a qualitative breakdown of the quasi-classical trajectory ensemble’s ability to describe the vibronic line shape when the relative shift in Morse potentials becomes large. The work presented here provides clarity on the origin of unphysical negative features known to contaminate absorption spectra computed with quasi-classical trajectory ensembles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An adaptive space-time phase field formulation for dynamic fracture of brittle shells based on LR NURBS

Here, we present an adaptive space-time phase field formulation for dynamic fracture of brittle shells. Their deformation is characterized by the Kirchhoff–Love thin shell theory using a curvilinear surface description. All kinematical objects are defined on the shell’s mid-plane. The evolution equation for the phase field is determined by the minimization of an energy functional based on Griffith’s theory of brittle fracture. Membrane and bending contributions to the fracture process are modeled separately and a thickness integration is established for the latter. The coupled system consists of two nonlinear fourth-order PDEs and all quantities are defined on an evolving two-dimensional manifold. Since the weak form requires C 1 -continuity, isogeometric shape functions are used. The mesh is adaptively refined based on the phase field using Locally Refinable (LR) NURBS. Time is discretized based on a generalized-α method using adaptive time-stepping, and the discretized coupled system is solved with a monolithic Newton–Raphson scheme. Finally, the interaction between surface deformation and crack evolution is demonstrated by several numerical examples showing dynamic crack propagation and branching.

42 ENGINEERING↗

Three-dimensional canard-wing shape optimization in aircraft cruise and maneuver environments

This paper demonstrates a numerical technique for canard-wing shape optimization at two operating conditions. For purposes of simplicity, a mean surface wing paneling code is employed for the aerodynamic calculations. The optimization procedures are based on the method of feasible directions. The shape functions for describing the thickness, camber, and twist are based on polynomial representations. The primary design requirements imposed restrictions on the canard and wing volumes and on the lift coefficients at the operating conditions. Results indicate that significant improvements in minimum drag and lift-to-drag ratio are possible with reasonable aircraft geometries. Calculations were done for supersonic speeds with Mach numbers ranging from 1 to 6. Planforms were mainly of a delta shape with aspect ratio of 1.

De Silva, B. M. E.↗

Driving mode analysis—How uncertain functional inputs propagate to an output

Abstract Driving mode analysis elucidates how correlated features of uncertain functional inputs jointly propagate to produce uncertainty in the output of a computation. Uncertain input functions are decomposed into three terms: the mean functions, a zero‐mean driving mode, and zero‐mean residual. The random driving mode varies along a single direction, having fixed functional shape and random scale. It is uncorrelated with the residual, and under linear error propagation, it produces an output variance equal to that of the full input uncertainty. Finally, the driving mode best represents how input uncertainties propagate to the output because it minimizes expected squared Mahalanobis distance amongst competitors. These characteristics recommend interpretation of the driving mode as the single‐degree‐of‐freedom component of input uncertainty that drives output uncertainty. We derive the functional driving mode, show its superiority to other seemingly sensible definitions, and demonstrate the utility of driving mode analysis in an application. The application is the simulation of neutron transport in criticality experiments. The uncertain input functions are nuclear data that describe how Pu reacts to bombardment by neutrons. Visualization of the driving mode helps scientists understand what aspects of correlated functional uncertainty have effects that either reinforce or cancel one another in propagating to the output of the simulation.

97 MATHEMATICS AND COMPUTING↗

First-and Second-Order Displacement Transfer Functions for Structural Shape Calculations Using Analytically Predicted Surface Strains

New first- and second-order displacement transfer functions have been developed for deformed shape calculations of nonuniform cross-sectional beam structures such as aircraft wings. The displacement transfer functions are expressed explicitly in terms of beam geometrical parameters and surface strains (uniaxial bending strains) obtained at equally spaced strain stations along the surface of the beam structure. By inputting the measured or analytically calculated surface strains into the displacement transfer functions, one could calculate local slopes, deflections, and cross-sectional twist angles of the nonuniform beam structure for mapping the overall structural deformed shapes for visual display. The accuracy of deformed shape calculations by the first- and second-order displacement transfer functions are determined by comparing these values to the analytically predicted values obtained from finite element analyses. This comparison shows that the new displacement transfer functions could quite accurately calculate the deformed shapes of tapered cantilever tubular beams with different tapered angles. The accuracy of the present displacement transfer functions also are compared to those of the previously developed displacement transfer functions.

Ko, William L.↗

Multibody dynamics: Modeling component flexibility with fixed, free, loaded, constraint, and residual modes

The assumed-modes method in multibody dynamics allows the elastic deformation of each component in the system to be approximated by a sum of products of spatial and temporal functions commonly known as modes and modal coordinates respectively. The choice of component modes used to model articulating and non-articulating flexible multibody systems is examined. Attention is directed toward three classical Component Mode Synthesis (CMS) methods whereby component normal modes are generated by treating the component interface (I/F) as either fixed, free, or loaded with mass and stiffness contributions from the remaining components. The fixed and free I/F normal modes are augmented by static shape functions termed constraint and residual modes respectively. A mode selection procedure is outlined whereby component modes are selected from the Craig-Bampton (fixed I/F plus constraint), MacNeal-Rubin (free I/F plus residual), or Benfield-Hruda (loaded I/F) mode sets in accordance with a modal ordering scheme derived from balance realization theory. The success of the approach is judged by comparing the actuator-to-sensor frequency response of the reduced order system with that of the full order system over the frequency range of interest. A finite element model of the Galileo spacecraft serves as an example in demonstrating the effectiveness of the proposed mode selection method.

Spanos, John T.↗

Functionally Graded Adhesives for Composite Joints

Adhesives with functionally graded material properties are being considered for use in adhesively bonded joints to reduce the peel stress concentrations located near adherend discontinuities. Several practical concerns impede the actual use of such adhesives. These include increased manufacturing complications, alterations to the grading due to adhesive flow during manufacturing, and whether changing the loading conditions significantly impact the effectiveness of the grading. An analytical study is conducted to address these three concerns. An enhanced joint finite element, which uses an analytical formulation to obtain exact shape functions, is used to model the joint. Furthermore, proof of concept testing is conducted to show the potential advantages of functionally graded adhesives. In this study, grading is achieved by strategically placing glass beads within the adhesive layer at different densities along the joint.

Stapleton, Scott E.↗

PROFILE: Airfoil Geometry Manipulation and Display

This report provides user information for program PROFILE, an aerodynamics design utility for plotting, tabulating, and manipulating airfoil profiles. A dozen main functions are available. The theory and implementation details for two of the more complex options are also presented. These are the REFINE option, for smoothing curvature in selected regions while retaining or seeking some specified thickness ratio, and the OPTIMIZE option, which seeks a specified curvature distribution. Use of programs QPLOT and BPLOT is also described, since all of the plots provided by PROFILE (airfoil coordinates, curvature distributions, pressure distributions)) are achieved via the general-purpose QPLOT utility. BPLOT illustrates (again, via QPLOT) the shape functions used by two of PROFILE's options. These three utilities should be distributed as one package. They were designed and implemented for the Applied Aerodynamics Branch at NASA Ames Research Center, Moffett Field, California. They are all written in FORTRAN 77 and run on DEC and SGI systems under OpenVMS and IRIX.

Collins, Leslie↗

Modified Displacement Transfer Functions for Deformed Shape Predictions of Slender Curved Structures with Varying Curvatives

To eliminate the need to use finite-element modeling for structure shape predictions, a new method was invented. This method is to use the Displacement Transfer Functions to transform the measured surface strains into deflections for mapping out overall structural deformed shapes. The Displacement Transfer Functions are expressed in terms of rectilinearly distributed surface strains, and contain no material properties. This report is to apply the patented method to the shape predictions of non-symmetrically loaded slender curved structures with different curvatures up to a full circle. Because the measured surface strains are not available, finite-element analysis had to be used to analytically generate the surface strains. Previously formulated straight-beam Displacement Transfer Functions were modified by introducing the curvature-effect correction terms. Through single-point or dual-point collocations with finite-elementgenerated deflection curves, functional forms of the curvature-effect correction terms were empirically established. The resulting modified Displacement Transfer Functions can then provide quite accurate shape predictions. Also, the uniform straight-beam Displacement Transfer Function was applied to the shape predictions of a section-cut of a generic capsule (GC) outer curved sandwich wall. The resulting GC shape predictions are quite accurate in partial regions where the radius of curvature does not change sharply.

displacement transfer functions↗

Image Correlation Pattern Optimization for Micro-Scale In-Situ Strain Measurements

The accuracy and precision of digital image correlation (DIC) is a function of three primary ingredients: image acquisition, image analysis, and the subject of the image. Development of the first two (i.e. image acquisition techniques and image correlation algorithms) has led to widespread use of DIC; however, fewer developments have been focused on the third ingredient. Typically, subjects of DIC images are mechanical specimens with either a natural surface pattern or a pattern applied to the surface. Research in the area of DIC patterns has primarily been aimed at identifying which surface patterns are best suited for DIC, by comparing patterns to each other. Because the easiest and most widespread methods of applying patterns have a high degree of randomness associated with them (e.g., airbrush, spray paint, particle decoration, etc.), less effort has been spent on exact construction of ideal patterns. With the development of patterning techniques such as microstamping and lithography, patterns can be applied to a specimen pixel by pixel from a patterned image. In these cases, especially because the patterns are reused many times, an optimal pattern is sought such that error introduced into DIC from the pattern is minimized. DIC consists of tracking the motion of an array of nodes from a reference image to a deformed image. Every pixel in the images has an associated intensity (grayscale) value, with discretization depending on the bit depth of the image. Because individual pixel matching by intensity value yields a non-unique scale-dependent problem, subsets around each node are used for identification. A correlation criteria is used to find the best match of a particular subset of a reference image within a deformed image. The reader is referred to references for enumerations of typical correlation criteria. As illustrated by Schreier and Sutton and Lu and Cary systematic errors can be introduced by representing the underlying deformation with under-matched shape functions. An important implication, as discussed by Sutton et al., is that in the presence of highly localized deformations (e.g., crack fronts), error can be reduced by minimizing the subset size. In other words, smaller subsets allow the more accurate resolution of localized deformations. Contrarily, the choice of optimal subset size has been widely studied and a general consensus is that larger subsets with more information content are less prone to random error. Thus, an optimal subset size balances the systematic error from under matched deformations with random error from measurement noise. The alternative approach pursued in the current work is to choose a small subset size and optimize the information content within (i.e., optimizing an applied DIC pattern), rather than finding an optimal subset size. In the literature, many pattern quality metrics have been proposed, e.g., sum of square intensity gradient (SSSIG), mean subset fluctuation, gray level co-occurrence, autocorrelation-based metrics, and speckle-based metrics. The majority of these metrics were developed to quantify the quality of common pseudo-random patterns after they have been applied, and were not created with the intent of pattern generation. As such, it is found that none of the metrics examined in this study are fit to be the objective function of a pattern generation optimization. In some cases, such as with speckle-based metrics, application to pixel by pixel patterns is ill-conditioned and requires somewhat arbitrary extensions. In other cases, such as with the SSSIG, it is shown that trivial solutions exist for the optimum of the metric which are ill-suited for DIC (such as a checkerboard pattern). In the current work, a multi-metric optimization method is proposed whereby quality is viewed as a combination of individual quality metrics. Specifically, SSSIG and two auto-correlation metrics are used which have generally competitive objectives. Thus, each metric could be viewed as a constraint imposed upon the others, thereby precluding the achievement of their trivial solutions. In this way, optimization produces a pattern which balances the benefits of multiple quality metrics. The resulting pattern, along with randomly generated patterns, is subjected to numerical deformations and analyzed with DIC software. The optimal pattern is shown to outperform randomly generated patterns.

Bomarito, G. F.↗

A duality-based coupling of Cosserat crystal plasticity and phase field theories for modeling grain refinement

High-rate deformation processes of metals entail intense grain refinement and special attention needs to be paid to capture the evolution of microstructure. In this article, a new formulation for coupling Cosserat crystal plasticity and phase field is developed. A common approach is to penalize kinematic incompatibility between lattice orientation and displacement-based elastic rotation. However, this can lead to significant solution sensitivity to the penalty parameter, resulting in low accuracy and convergence rates. To address these issues, a duality-based formulation is developed which directly imposes the rotational kinematic compatibility. A weak inf-sup-based skew-symmetric stress projection is introduced to suppress instabilities present in the dual formulation. An additional least squares stabilization is introduced to suppress the spurious lattice rotation with a suitable parameter range derived analytically and validated numerically. The required high-order continuity is attained by the reproducing kernel approximation. It is observed that equal order displacement-rotation-phase field approximations are stable, which allows efficient employment of the same set of shape functions for all independent variables. The proposed formulation is shown to yield superior accuracy and convergence with marginal parameter sensitivity compared to the penalty-based approach and successfully captures the dominant rotational recrystallization mechanism including block dislocation structures and grain boundary migration.

42 ENGINEERING↗

Extended isogeometric analysis of multi-material and multi-physics problems using hierarchical B-splines

Here, this paper presents an immersed, isogeometric finite element framework to predict the response of multi-material, multi-physics problems with complex geometries using locally refined discretizations. To circumvent the need to generate conformal meshes, this work uses an extended finite element method (XFEM) to discretize the governing equations on non-conforming, embedding meshes. A flexible approach to create truncated hierarchical B-splines discretizations is presented. This approach enables the refinement of each state variable field individually to meet field-specific accuracy requirements. To obtain an immersed geometry representation that is consistent across all hierarchically refined B-spline discretizations, the geometry is immersed into a single mesh, the XFEM background mesh, which is constructed from the union of all hierarchical B-spline meshes. An extraction operator is introduced to represent the truncated hierarchical B-spline bases in terms of Lagrange shape functions on the XFEM background mesh without loss of accuracy. The truncated hierarchical B-spline bases are enriched using a generalized Heaviside enrichment strategy to accommodate small geometric features and multi-material problems. The governing equations are augmented by a formulation of the face-oriented ghost stabilization enhanced for locally refined B-spline bases. We present examples for two- and three-dimensional linear elastic and thermo-elastic problems. The numerical results validate the accuracy of our framework. The results also demonstrate the applicability of the proposed framework to large, geometrically complex problems.

42 ENGINEERING↗