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NASA NTRS1974

A smoothing algorithm using cubic spline functions

Two algorithms are presented for smoothing arbitrary sets of data. They are the explicit variable algorithm and the parametric variable algorithm. The former would be used where large gradients are not encountered because of the smaller amount of calculation required. The latter would be used if the data being smoothed were double valued or experienced large gradients. Both algorithms use a least-squares technique to obtain a cubic spline fit to the data. The advantage of the spline fit is that the first and second derivatives are continuous. This method is best used in an interactive graphics environment so that the junction values for the spline curve can be manipulated to improve the fit.

Smith, R. E., Jr.↗

NASA NTRS2003

Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

NASA Discipline Life Sciences Technologies↗

DOE OSTI2022

Ab initio investigation of elastic properties of dilute Cu alloys for high-gradient accelerating structures

The elastic properties and solid solution strengthening of several Cu alloys that may be promising for high gradient applications were studied using ab initio calculations based on density functional theory. Specifically, the temperature and solute concentration dependence of elastic properties including bulk and shear moduli, thermal expansion coefficient, and heat capacity of these alloys were calculated. We found that the bulk and shear moduli are linearly dependent on the solute concentration in the dilute regime and change significantly for different Cu alloys. The thermal expansion coefficient and heat capacity are comparatively less sensitive to solute concentrations. Solid solution strengthening is observed to be linearly correlated with the change of lattice parameter of Cu. This work provides an in-depth understanding of the elastic properties of Cu alloys, which is key for predicting their performance at high gradient in normal conducting accelerating structures.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Extreme stress gradient effects on microstructural fatigue crack propagation rates in Ni microbeams

The fatigue crack propagation behavior of microstructurally small cracks growing under extreme stress gradients was investigated in Ni microbeams under fully reversed cyclic loading. A technique to calculate the crack growth rates in microbeams with two different normalized stress gradients (17% and 50% μm{sup −1}) is developed and validated. Decreasing crack propagation rates are observed over the first 2 μm, and the rates are more than 1 order of magnitude slower for the devices with 50% μm{sup −1} stress gradients. This fundamental knowledge is critical to predict the fatigue reliability of advanced metallic microcomponents under bending such as in microelectromechanical systems or flexible/stretchable electronics.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Methods, software and datasets to verify DVH calculations against analytical values: Twenty years late(r)

Purpose: The authors designed data, methods, and metrics that can serve as a standard, independent of any software package, to evaluate dose-volume histogram (DVH) calculation accuracy and detect limitations. The authors use simple geometrical objects at different orientations combined with dose grids of varying spatial resolution with linear 1D dose gradients; when combined, ground truth DVH curves can be calculated analytically in closed form to serve as the absolute standards. Methods: DICOM RT structure sets containing a small sphere, cylinder, and cone were created programmatically with axial plane spacing varying from 0.2 to 3 mm. Cylinders and cones were modeled in two different orientations with respect to the IEC 1217 Y axis. The contours were designed to stringently but methodically test voxelation methods required for DVH. Synthetic RT dose files were generated with 1D linear dose gradient and with grid resolution varying from 0.4 to 3 mm. Two commercial DVH algorithms—PINNACLE (Philips Radiation Oncology Systems) and PlanIQ (Sun Nuclear Corp.)—were tested against analytical values using custom, noncommercial analysis software. In Test 1, axial contour spacing was constant at 0.2 mm while dose grid resolution varied. In Tests 2 and 3, the dose grid resolution was matched to varying subsampled axial contours with spacing of 1, 2, and 3 mm, and difference analysis and metrics were employed: (1) histograms of the accuracy of various DVH parameters (total volume, D{sub max}, D{sub min}, and doses to % volume: D99, D95, D5, D1, D0.03 cm{sup 3}) and (2) volume errors extracted along the DVH curves were generated and summarized in tabular and graphical forms. Results: In Test 1, PINNACLE produced 52 deviations (15%) while PlanIQ produced 5 (1.5%). In Test 2, PINNACLE and PlanIQ differed from analytical by >3% in 93 (36%) and 18 (7%) times, respectively. Excluding D{sub min} and D{sub max} as least clinically relevant would result in 32 (15%) vs 5 (2%) scored deviations for PINNACLE vs PlanIQ in Test 1, while Test 2 would yield 53 (25%) vs 17 (8%). In Test 3, statistical analyses of volume errors extracted continuously along the curves show PINNACLE to have more errors and higher variability (relative to PlanIQ), primarily due to PINNACLE’s lack of sufficient 3D grid supersampling. Another major driver for PINNACLE errors is an inconsistency in implementation of the “end-capping”; the additional volume resulting from expanding superior and inferior contours halfway to the next slice is included in the total volume calculation, but dose voxels in this expanded volume are excluded from the DVH. PlanIQ had fewer deviations, and most were associated with a rotated cylinder modeled by rectangular axial contours; for coarser axial spacing, the limited number of cross-sectional rectangles hinders the ability to render the true structure volume. Conclusions: The method is applicable to any DVH-calculating software capable of importing DICOM RT structure set and dose objects (the authors’ examples are available for download). It includes a collection of tests that probe the design of the DVH algorithm, measure its accuracy, and identify failure modes. Merits and applicability of each test are discussed.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Development of grain-scale slip activity and lattice rotation fields in Inconel 718

Using a combination of in-situ high-resolution digital image correlation (HR-DIC), Heaviside-DIC method (H-DIC), and crystal plasticity finite element (CPFE), we investigate the evolution of intragranular lattice rotations and slip activity during monotonic and cyclic loading in a high performance, polycrystalline face centered cubic material. The CPFE employs a quasi-3D model microstructure, which is a highly resolved mirror representation of the experimental in-situ test sample. In agreement, the measurements and calculations reveal that most grains, regardless of their size and lattice orientation, develop intragranular lattice rotation gradients that span the grain. For a small cluster of grains on the deformed material, we perform HR-DIC analysis of slip lines to demonstrate agreement in the active slip systems and changes in this local slip activity across the individual grains. The combined analysis reveals that deforming grains are divided into sub-granular regions of uniform lattice rotation and these regions are most often associated with only one or two active slip systems. The gradient lines that divide them correspond to changes in the predominant slip system. The model is used to examine the evolution of intragranular lattice rotation in a single fully reversed tension-compression cycle. The calculations indicate that intragranular gradients intensify during the reverse loading path as nearest neighboring regions appear to shed lattice rotation, increasing the lattice rotation in some regions, while shutting down rotation in neighboring regions. So these findings provide insight into the irreversible changes that develop within deforming grains at the scale of the grain, particularly the heterogeneous development of intragranular lattice rotation in early stages of deformation, which could serve as precursors to localization.

36 MATERIALS SCIENCE↗

NASA NTRS2003

Numerical Calculation of the Morphology of a Solid/Liquid Interface Near an Insoluble Particle

A numerical mathematical model capable of accurately describing the evolution of the shape of the solid/liquid interface in the proximity of a foreign particle is presented in this paper. The model accounts for the influence of the temperature gradient and the Gibbs-Thomson and disjoining pressure effects. It shows that for the systems characterized by k(sub P) < k(sub L) the disjoining pressure causes the interface curvature to change its sign in the close-contact particle/interface region. It also shows that the increase of the temperature gradient diminishes the effect of the disjoining pressure. Calculated critical solidification velocities for the pushing/engulfment transition are compared with experimental measurements performed in microgravity conditions.

Catalina, Adrian V.↗

NASA NTRS1983

Advanced methods for preparation and characterization of infrared detector materials

Crystals were prepared by the Bridgman-Stockbarger method with a wide range of crystal growth rates and temperature gradients adequate to prevent constitutional supercooling under diffusion-limited, steady-state, growth conditions. The longitudinal compositional gradients for different growth conditions and alloy compositions were calculated and compared with experimental data to develop a quantitative model of solute redistribution during the crystal growth of the alloys. Measurements were performed to ascertain the effect of growth conditions on radial compositional gradients. The pseudobinary HgTe-CdTe constitutional phase diagram was determined by precision differential-thermal-analysis measurements and used to calculate the segregation coefficient of Cd as a function of x and interface temperature. Experiments were conducted to determine the ternary phase equilibria in selected regions of the Hg-Cd-Te constitutional phase diagram. Electron and hole mobilities as functions of temperature were analyzed to establish charge-carrier scattering probabilities. Computer algorithms specific to Hg(1-x)CdxTe were developed for calculations of the charge-carrier concentration, charge-carrier mobilities, Hall coefficient, and Dermi Fermi energy as functions of x, temperature, ionized donor and acceptor concentrations, and neutral defect concentrations.

Broerman, J. G.↗

DOE OSTI2015

Dirac cones in transition metal doped boron nitride

The transition metal (TM) doped zinc blende boron nitride (c-BN) is studied by using the first principle calculation. TM atoms fill in the interstitials in c-BN and form two-dimensional honeycomb lattice. The generalized gradient approximation and projector augmented wave method are used. The calculated density of states and band structures show that d electrons of TM atoms form impurity bands in the gap of c-BN. When the TM-BN system is in ferromagnetic or non-magnetic state, Dirac cones emerge at the K point in Brillouin zone. When TM is Ti and Co, the Dirac cones are spin polarized and very close to the Fermi level, which makes them promising candidates of Dirac half-metal [H. Ishizuka and Y. Motome, Phys. Rev. Lett. 109, 237207 (2012)]. While TM is Ni and Cu, the system is non-magnetic and Dirac cones located above the Fermi level.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Electron cyclotron heating can drastically alter reversed shear Alfvén eigenmode activity in DIII-D through finite pressure effects

Here, a recent DIII-D experiment investigating the impact of electron cyclotron heating (ECH) on neutral beam driven reversed shear Alfvén eigenmode (RSAE) activity is presented. The experiment includes variations of ECH injection location and timing, current ramp rate, beam injection geometry (on/off-axis), and neutral beam power. Essentially all variations carried out in this experiment were observed to change the impact of ECH on AE activity significantly. In some cases, RSAEs were observed to be enhanced with ECH near the off-axis minimum in magnetic safety factor (${{q}_{\min}}$ ), in contrast to the original DIII-D experiments where the modes were absent when ECH was deposited near ${{q}_{\min}}$ . It is found that during intervals when the geodesic acoustic mode (GAM) frequency at ${{q}_{\min}}$ is elevated and the calculated RSAE minimum frequency, including contributions from thermal plasma gradients, is very near or above the nominal TAE frequency (f TAE ), RSAE activity is not observed or RSAEs with a much reduced frequency sweep range are found. This condition is primarily brought about by ECH modification of the local electron temperature (T e ) which can raise both the local T e at ${{q}_{\min}}$ as well as its gradient. A q-evolution model that incorporates this reduction in RSAE frequency sweep range is in agreement with the observed spectra and appears to capture the relative balance of TAE or RSAE-like modes throughout the current ramp phase of over 38 DIII-D discharges. Detailed ideal MHD calculations using the NOVA code show both modification of plasma pressure and pressure gradient at ${{q}_{\min}}$ play an important role in modifying the RSAE activity. Analysis of the ECH injection near the ${{q}_{\min}}$ case where no frequency sweeping RSAEs are observed shows the typical RSAE is no longer an eigenmode of the system. What remains is an eigenmode with poloidal harmonic content reminiscent of the standard RSAE, but absent of the typical frequency sweeping behavior. The remaining eigenmode is also often strongly coupled to gap TAEs. Analysis with the non-perturbative gyro fluid code TAEFL confirms this change in RSAE activity and also shows a large drop in the resultant mode growth rates.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1980

Advanced methods for preparation and characterization of infrared detector materials

Mercury cadmium telluride crystals were prepared by the Bridgman method with a wide range of crystal growth rates and temperature gradients adequate to prevent constitutional supercooling under diffusion-limited, steady state, growth conditions. The longitudinal compositional gradients for different growth conditions and alloy compositions were calculated and compared with experimental data to develop a quantitative model of the crystal growth kinetics for the Hg(i-x)CdxTe alloys, and measurements were performed to ascertain the effect of growth conditions on radial compositional gradients. The pseudobinary HgTe-CdTe constitutional phase diagram was determined by precision differential thermal analysis measurements and used to calculate the segregation coefficient of Cd as a function of x and interface temperature. Computer algorithms specific to Hg(1-x)CdxTe were developed for calculations of the charge carrier concentrations, charge carrier mobilities, Hall coefficient, optical absorptance, and Fermi energy as functions of x, temperature, ionized donor and acceptor concentrations, and neutral defect concentrations.

Lehoczky, S. L.↗

NASA NTRS1987

Low Reynolds number modeling of turbulent flows with and without wall transpiration

A full Reynolds-stress closure that is capable of describing the flow all the way to the wall is formulated. The closure is based on the conventional high Reynolds number form of the redistribution model, the inclusion of molecular diffusion, and a modified dissipation model to account for viscous effects near a wall. Two dissipation models are investigated along with two gradient diffusion and two redistribution models. Their respective effects on the calculated flow properties are assessed by comparing them with the data of fully developed turbulent flows and a developing pipe flow with wall transpiration. The near-wall behavior is very well predicted; however, the wall correction to the redistribution modeling is found to have little effect on the calculated results. The overall behavior of the fully developed turbulent flows is best described by a nonisotropic gradient diffusion model, a return-to-isotropy redistribution model, and a dissipation model that accounts for viscous behavior near a wall. This same closure also gives the best prediction of the axial pressure drop behavior along a pipe with a uniform wall suction. Furthermore, the near-wall behavior of such a flow is very well predicted by this closure.

So, Ronald M. C.↗

DOE OSTI2021

The dependence of the gradients of oxygen and nitrogen-to-oxygen on stellar age in MaNGA galaxies

For this work, we derived the oxygen abundance (O/H), the nitrogen-to-oxygen (N/O) abundance ratio, and their corresponding radial gradients for a sample of 1431 galaxies from the MaNGA DR15 survey using two different realisations of the strong line method: empirical R calibration and the Bayesian model-based HII-CHI-MISTRY (HCM) code. We find that both abundance calculation methods reveal a correlation between the O/H gradient and the stellar mass of a galaxy. This relation is non-linear, with the steepest average gradients in the intermediate mass range and flatter average gradients for high- and low-mass galaxies. The relation between the N/O gradient and the stellar mass is, on average, non-linear with the steepest gradients in the intermediate mass range (log(M/M ⊙ )~10), flatter gradients for high-mass galaxies, and the flattest gradients for low-mass galaxies. However, the general trend of steepening N/O gradients for higher masses, as reported in previous studies, remains evident. We find a dependence between the O/H and N/O gradients and the galaxy mean stellar age traced by the D(4000) index. For galaxies of lower masses, both gradients are, generally, steeper for intermediate values of D(4000) and flatter for low and high values of D(4000). Only the most massive galaxies do not show this correlation. We interpret this behaviour as an evolution of the metallicity gradients with the age of stellar population. Though the galaxies with a positive slope of the D(4000) radial gradient tend to have flatter O/H and N/O gradients, as compared to those with a negative D(4000) gradient.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2016

Surface-Plasmon-Mediated Gradient Force Enhancement and Mechanical State Transitions of Graphene Sheets

Graphene, a two-dimensional material possessing extraordinary properties in electronics as well as mechanics, provides a great platform for various optoelectronic and opto-mechanical devices. Here in this article, we theoretically study the optical gradient force arising from the coupling of surface plasmon modes on parallel graphene sheets, which can be several orders stronger than that between regular dielectric waveguides. Furthermore, with an energy functional optimization model, possible force-induced deformation of graphene sheets is calculated. We show that the significantly enhanced optical gradient force may lead to mechanical state transitions of graphene sheets, which are accompanied by abrupt changes in reflection and transmission spectra of the system. Our demonstrations illustrate the potential for a broader graphene-related applications such as force sensors and actuators.

36 MATERIALS SCIENCE↗

NASA NTRS1991

Thermal calibration and analysis of a Bridgman flight furnace

A combination of computer modeling and experimental measurements is proposed which permits the calibration of the temperature profile for a spacecraft flight furnace. The Fluent code based on the finite difference method uses the furnace set-point temperatures as boundary conditions to model a Bridgman directional solidification furnace. Experimental measurements are employed as a comparison for the numerical analysis, and the radial gradients and wall temperatures are selected when the calculated values are sufficiently close to those from measurements. The calculations are found to agree with experimental data, and some results of the modeling are given which relate to specific furnace parameters. The CFD approach facilitates the transposition of furnace calibration to microgravitational operation in addition to providing precise initial radial temperature gradients and furnace-wall temperatures.

Knuteson, D. J.↗

DOE OSTI2021

Skyrme pseudopotentials at next-to-next-to-leading order: Construction of local densities and first symmetry-breaking calculations

There is an ongoing quest to improve on the spectroscopic quality of nuclear energy density functionals (EDFs) of the Skyrme type through extensions of its traditional form. One direction for such activities is the inclusion of terms of higher order in gradients in the EDF. We report on exploratory symmetry-breaking calculations performed for an extension of the Skyrme EDF that includes central terms with four gradients at next-to-next-to-leading order (N2LO) and for which the high-quality parametrization SN2LO1 has been constructed recently. Up to now, the investigation of such functionals with higher-order terms was limited to infinite matter and spherically symmetric configurations of singly and doubly magic nuclei. We address here nuclei and phenomena that require us to consider axial and nonaxial deformation, both for reflection-symmetric and also reflection-asymmetric shapes, as well as the breaking of time-reversal invariance. Achieving these calculations demanded a number of formal developments. These all resulted from the formulation of the N2LO EDF requiring the introduction of new local densities with additional gradients that are not present in the EDF at NLO. Their choice is not unique, but can differ in the way the gradients are coupled. While designing a numerical implementation of N2LO EDFs in Cartesian three-dimensional coordinate-space representation, we have developed a novel definition and a new unifying notation for normal and pair densities that contain gradients at arbitrary order. Besides having mnemonic advantages, the new notation allows for the easy identification of redundancies and reducibilities in a given set of local densities, and the new definition makes it straightforward to construct densities that automatically adopt the symmetries of the many-body state they are constructed from. The resulting scheme resolves several issues with some of the choices that have been made for local densities in the past, in particular when breaking time-reversal symmetry. Guided by general practical considerations, we propose an alternative form of the N2LO contribution to the Skyrme EDF that is built from a different set of densities. It has exactly the same physics content, but is much more efficient to handle in formal discussions and, compared to the original formulation, leads to a substantial reduction of computational cost and memory requirements in deformed codes. As representative examples for the performance of SN2LO1, we have chosen the ground states of even-even Kr and Nd isotopes, the fission barrier of 240 Pu as well as the superdeformed rotational band of 194 Hg. Overall, for the nuclei and phenomena studied here, the SN2LO1 parametrization does not yet present a systematic improvement over standard NLO parametrizations. This finding calls for improved fit protocols that better discriminate between NLO and N2LO terms and better exploit the unique features of the additional degrees of freedom offered by the latter.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2000

The Sensitivity of Model Ozone to Advective and Photochemical Processes in the High Latitude Winter Lower Stratosphere

Three dimensional chemistry and transport models (CTMs) contain a set of coupled continuity equations which describe the evolution of constituents such as ozone and other minor species which affect ozone. Both advection and photochemical processes contribute to constituent evolution, and a CTM provides a means to evaluate these contributions separately. Such evaluation is particularly useful when both terms are important to the modeled tendency. An example is the ozone tendency in the high latitude winter lower stratosphere, where advection tends to increase ozone, and catalytic processes involving chlorine radicals tend to decrease ozone. The Goddard three dimensional chemistry and transport model uses meteorological fields from the Goddard Earth Observing System Data Assimilation System, thus the modeled ozone evolution may reproduce the observed evolution and provide a test of the model representation of photochemical processes if the transport is shown to be modeled appropriately. We have investigated the model advection further using diabatic trajectory calculations. For long lived constituents such as N2O, the model field for a particular time on a potential temperature surface is compared with a field produced by calculating 15 day back trajectories for a fixed latitude longitude grid, and mapping model N2O at the terminus of the back trajectories onto the initial grid. This provides a quantitative means to evaluate two aspects of the CTM transport: one, the model horizontal gradient between middle latitudes and the polar vortex is compared with the gradient produced using the non-diffusive trajectory calculation; two, the model vertical advection, which is produced by the divergence of the horizontal winds, is compared with the vertical transport expected from diabatic cooling.

Douglass, A.↗

DOE OSTI2019

Improved unconstrained energy functional method for eigensolvers in electronic structure calculations

This paper reports on the performance of a preconditioned conjugate gradient based iterative eigensolver using an unconstrained energy functional minimization scheme. In contrast to standard implementations, this scheme avoids an explicit reorthogonalization of the trial eigenvectors and becomes an attractive alternative for the solution of very large problems. The unconstrained formulation is implemented in the first-principles materials and chemistry CP2K code, which performs electronic structure calculations based on a density functional theory approximation to the solution of the many-body Schrödinger equation. We study the convergence of the unconstrained formulation, as well as its parallel scaling, on a Cray XC40 at the National Energy Research Scientific Computing Center (NERSC). The systems we use in our studies are bulk liquid water, a supramolecular catalyst gold(III)-complex, a bilayer of MoS2-WSe2 and a divacancy point defect in silicon, with the number of atoms ranging from 2,247 to 12,288. We show that the unconstrained formulation with an appropriate preconditioner has good convergence properties and scales well to 230k cores, roughly 38% of the full machine.

Del Ben, M↗