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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

A Trotter-Suzuki approximation for Lie groups with applications to Hamiltonian simulation

We present a product formula to approximate the exponential of a skew-Hermitian operator that is a sum of generators of a Lie algebra. The number of terms in the product depends on the structure factors. When the generators have large norm with respect to the dimension of the Lie algebra, or when the norm of the effective operator resulting from nested commutators is less than the product of the norms, the number of terms in the product is significantly less than that obtained from well-known results. We apply our results to construct product formulas useful for the quantum simulation of some continuous-variable and bosonic physical systems, including systems whose potential is not quadratic. For many of these systems, we show that the number of terms in the product can be sublinear or even subpolynomial in the dimension of the relevant local Hilbert spaces, where such a dimension is usually determined by the energy scale of the problem. Our results emphasize the power of quantum computers for the simulation of various quantum systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Temperature dependent simulation of diamond depleted Schottky PIN diodes

Diamond is considered as an ideal material for high field and high power devices due to its high breakdown field, high lightly doped carrier mobility, and high thermal conductivity. The modeling and simulation of diamond devices are therefore important to predict the performances of diamond based devices. In this context, we use Silvaco{sup ®} Atlas, a drift-diffusion based commercial software, to model diamond based power devices. The models used in Atlas were modified to account for both variable range and nearest neighbor hopping transport in the impurity bands associated with high activation energies for boron doped and phosphorus doped diamond. The models were fit to experimentally reported resistivity data over a wide range of doping concentrations and temperatures. We compare to recent data on depleted diamond Schottky PIN diodes demonstrating low turn-on voltages and high reverse breakdown voltages, which could be useful for high power rectifying applications due to the low turn-on voltage enabling high forward current densities. Three dimensional simulations of the depleted Schottky PIN diamond devices were performed and the results are verified with experimental data at different operating temperatures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Plasma electron hole kinematics. II. Hole tracking Particle-In-Cell simulation

The kinematics of a 1-D electron hole is studied using a novel Particle-In-Cell simulation code. A hole tracking technique enables us to follow the trajectory of a fast-moving solitary hole and study quantitatively hole acceleration and coupling to ions. We observe a transient at the initial stage of hole formation when the hole accelerates to several times the cold-ion sound speed. Artificially imposing slow ion speed changes on a fully formed hole causes its velocity to change even when the ion stream speed in the hole frame greatly exceeds the ion thermal speed, so there are no reflected ions. The behavior that we observe in numerical simulations agrees very well with our analytic theory of hole momentum conservation and the effects of “jetting.”.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Computational simulations of hydrogen circular migration in protonated acetylene induced by circularly polarized light

The hydrogens in protonated acetylene are very mobile and can easily migrate around the C 2 core by moving between classical and non-classical structures of the cation. The lowest energy structure is the T-shaped, non-classical cation with a hydrogen bridging the two carbons. Conversion to the classical H 2 CCH + ion requires only 4 kcal/mol. The effect of circularly polarized light on the migration of hydrogens in oriented C 2 H 3 + has been simulated by Born-Oppenheimer molecular dynamics. Classical trajectory calculations were carried out with the M062X/6-311+G(3df,2pd) level of theory using linearly and circularly polarized 32 cycle 7 μm cosine squared pulses with peak intensity of 5.6 × 10 13 W/cm 2 and 3.15 × 10 13 W/cm 2 , respectively. These linearly and circularly polarized pulses transfer similar amounts of energy and total angular momentum to C 2 H3 + . The average angular momentum vectors of the three hydrogens show opposite directions of rotation for right and left circularly polarized light, but no directional preference for linearly polarized light. This difference results in an appreciable amount of angular displacement of the three hydrogens relative to the C 2 core for circularly polarized light, but only an insignificant amount for linearly polarized light. In conclusion, over the course of the simulation with circularly polarized light, this corresponds to a propeller-like motion of the three hydrogens around the C 2 core of protonated acetylene.

08 HYDROGEN↗
DOE OSTI2014

Cosmic reionization on computers. I. Design and calibration of simulations

Cosmic Reionization On Computers is a long-term program of numerical simulations of cosmic reionization. Its goal is to model fully self-consistently (albeit not necessarily from the first principles) all relevant physics, from radiative transfer to gas dynamics and star formation, in simulation volumes of up to 100 comoving Mpc, and with spatial resolution approaching 100 pc in physical units. In this method paper, we describe our numerical method, the design of simulations, and the calibration of numerical parameters. Using several sets (ensembles) of simulations in 20 h {sup –1} Mpc and 40 h {sup –1} Mpc boxes with spatial resolution reaching 125 pc at z = 6, we are able to match the observed galaxy UV luminosity functions at all redshifts between 6 and 10, as well as obtain reasonable agreement with the observational measurements of the Gunn-Peterson optical depth at z < 6.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Fully coupled simulation of cosmic reionization. I. numerical methods and tests

Here, we describe an extension of the Enzo code to enable fully coupled radiation hydrodynamical simulation of inhomogeneous reionization in large similar to(100 Mpc)(3) cosmological volumes with thousands to millions of point sources. We solve all dynamical, radiative transfer, thermal, and ionization processes self-consistently on the same mesh, as opposed to a postprocessing approach which coarse-grains the radiative transfer. But, we employ a simple subgrid model for star formation which we calibrate to observations. The numerical method presented is a modification of an earlier method presented in Reynolds et al. differing principally in the operator splitting algorithm we use to advance the system of equations. Radiation transport is done in the gray flux-limited diffusion (FLD) approximation, which is solved by implicit time integration split off from the gas energy and ionization equations, which are solved separately. This results in a faster and more robust scheme for cosmological applications compared to the earlier method. The FLD equation is solved using the hypre optimally scalable geometric multigrid solver from LLNL. By treating the ionizing radiation as a grid field as opposed to rays, our method is scalable with respect to the number of ionizing sources, limited only by the parallel scaling properties of the radiation solver. We test the speed and accuracy of our approach on a number of standard verification and validation tests. We show by direct comparison with Enzo's adaptive ray tracing method Moray that the well-known inability of FLD to cast a shadow behind opaque clouds has a minor effect on the evolution of ionized volume and mass fractions in a reionization simulation validation test. Finally, we illustrate an application of our method to the problem of inhomogeneous reionization in a 80 Mpc comoving box resolved with 3200(3) Eulerian grid cells and dark matter particles.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Large-Eddy Simulations of Idealized Atmospheric Boundary Layers Using Nalu-Wind

Accurate prediction of wind-plant performance relies, in part, on properly characterizing the turbulent atmospheric boundary layer (ABL) flow in which wind turbines operate. Large-eddy simulation (LES) is a powerful tool for simulating ABLs because it resolves the largest, most energetic scales of three-dimensional turbulent motions. Yet LES predictions are well known to depend on modeling choices such as grid resolution, numerical discretization schemes, and closures for unresolved scales of turbulence. Here, we evaluate how these choices influence predictions of ABL winds using Nalu-Wind, a wind-specific fork of the open-source, generalized, unstructured, massively parallel flow solver NaluCFD/Nalu.

17 WIND ENERGY↗
DOE OSTI2014

Guidelines for volume force distributions within actuator line modeling of wind turbines on large-eddy simulation-type grids

The objective of this work is to develop and test a set of general guidelines for choosing parameters to be used in the state-of-the-art actuator line method (ALM) for modeling wind turbine blades in computational fluid dynamics (CFD). The actuator line method is being increasingly used for the computation of wake interactions in large wind farms in which fully blade-resolving simulations are expensive and require complicated rotating meshes. The focus is on actuator line behavior using fairly isotropic grids of low aspect ratio typically used for large-eddy simulation (LES). Forces predicted along the actuator lines need to be projected onto the flow field as body forces, and this is commonly accomplished using a volumetric projection. In this study, particular attention is given to the spanwise distribution of the radius of this projection. A new method is proposed where the projection radius varies along the blade span following an elliptic distribution. The proposed guidelines for actuator line parameters are applied to the National Renewable Energy Laboratory's (NREL's) Phase VI rotor and the NREL 5-MW turbine. Results obtained are compared with available data and the blade-element code XTurb-PSU. As a result, it is found that the new criterion for the projection radius leads to improved prediction of blade tip loads for both blade designs.

17 WIND ENERGY↗
DOE OSTI2021

Describing the Mechanism of Instability Suppression Using a Central Pilot Flame With Coupled Experiments and Simulations

Pilot flames are commonly used to extend combustor operability limits and suppress combustion oscillations in low-emissions gas turbines. Combustion oscillations, a coupling between heat release rate oscillations and combustor acoustics, can arise at the operability limits of low-emissions combustors where the flame is more susceptible to perturbations. While the use of pilot flames is common in land-based gas turbine combustors, the mechanism by which they suppress instability is still unclear. In this study, we consider the impact of a central jet pilot on the stability of a swirl-stabilized flame in a variable-length, single-nozzle combustor. Previously, the pilot flame was found to suppress the instability for a range of equivalence ratios and combustor lengths. We hypothesize that combustion oscillation suppression by the pilot occurs because the pilot provides hot gases to the vortex breakdown region of the flow that recirculate and improve the static, and hence dynamic, stability of the main flame. This hypothesis is based on a series of experimental results that show that pilot efficacy is a strong function of pilot equivalence ratio but not pilot flow rate, which would indicate that the temperature of the pilot products as well as the combustion intensity of the pilot flame play more of a role in oscillation stabilization than the length of the pilot flame relative to the main flame. Further, the pilot-flame efficacy increases with pilot-flame equivalence ratio until it matches the main-flame equivalence ratio; at pilot equivalence ratios greater than the main equivalence ratio, the pilot-flame efficacy does not change significantly with pilot equivalence ratio. To understand these results, we use large-eddy simulation (LES) to provide a detailed analysis of the flow in the region of the pilot flame and the transport of radical species in the region between the main flame and pilot flame. Furthermore, the simulation, using a flamelet/progress variable-based chemistry tabulation approach and standard eddy viscosity/diffusivity turbulence closure models, provides detailed information that is inaccessible through experimental measurements.

42 ENGINEERING↗
DOE OSTI2015

FEM design and simulation of a short, 10 MV, S-band Linac with Monte Carlo dose simulations

Purpose: Current commercial 10 MV Linac waveguides are 1.5 m. The authors’ current 6 MV linear accelerator–magnetic resonance imager (Linac–MR) system fits in typical radiotherapy vaults. To allow 10 MV treatments with the Linac–MR and still fit within typical vaults, the authors design a 10 MV Linac with an accelerator waveguide of the same length (27.5 cm) as current 6 MV Linacs. Methods: The first design stage is to design a cavity such that a specific experimental measurement for breakdown is applicable to the cavity. This is accomplished through the use of finite element method (FEM) simulations to match published shunt impedance, Q factor, and ratio of peak to mean-axial electric field strength from an electric breakdown study. A full waveguide is then designed and tuned in FEM simulations based on this cavity design. Electron trajectories are computed through the resulting radio frequency fields, and the waveguide geometry is modified by shifting the first coupling cavity in order to optimize the electron beam properties until the energy spread and mean energy closely match values published for an emulated 10 MV Linac. Finally, Monte Carlo dose simulations are used to compare the resulting photon beam depth dose profile and penumbra with that produced by the emulated 10 MV Linac. Results: The shunt impedance, Q factor, and ratio of peak to mean-axial electric field strength are all matched to within 0.1%. A first coupling cavity shift of 1.45 mm produces an energy spectrum width of 0.347 MeV, very close to the published value for the emulated 10 MV of 0.315 MeV, and a mean energy of 10.53 MeV, nearly identical to the published 10.5 MeV for the emulated 10 MV Linac. The depth dose profile produced by their new Linac is within 1% of that produced by the emulated 10 MV spectrum for all depths greater than 1.5 cm. The penumbra produced is 11% narrower, as measured from 80% to 20% of the central axis dose. Conclusions: The authors have successfully designed and simulated an S-band waveguide of length of 27.5 cm capable of producing a 10 MV photon beam. This waveguide operates well within the breakdown threshold determined for the cavity geometry used. The designed Linac produces depth dose profiles similar to those of the emulated 10 MV Linac (waveguide-length of 1.5 m) but yields a narrower penumbra.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

Improvements in simulation of multiple scattering effects in ATLAS fast simulation

Fast ATLAS Tracking Simulation (Fatras) package was verified on single layer geometry with respect to full simulation with GEANT4. Fatras hadronic interactions and multiple scattering simulation were studied in comparison with GEANT4. Disagreement was found in multiple scattering distributions of primary charged particles (μ, π, e). A new model for multiple scattering simulation was implemented in Fatras. The model was based on R. Frühwirth’s mixture models. New model was tested on single layer geometry and a good agreement with GEANT4 was achieved. Also a comparison of reconstructed tracks’ parameters was performed for Inner Detector geometry, and Fatras with new multiple scattering model proved to have better agreement with GEANT4. New model of multiple scattering was added as a part of Fatras package in the development release of ATLAS software—ATHENA.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Large-Eddy Simulation of Shallow Cumulus over Land: A Composite Case Based on ARM Long-Term Observations at Its Southern Great Plains Site

Based on long-term observations by the Atmospheric Radiation Measurement program at its Southern Great Plains site, a new composite case of continental shallow cumulus (ShCu) convection is constructed for large-eddy simulations (LES) and single-column models. The case represents a typical daytime nonprecipitating ShCu whose formation and dissipation are driven by the local atmospheric conditions and land surface forcing and are not influenced by synoptic weather events. The case includes early morning initial profiles of temperature and moisture with a residual layer; diurnally varying sensible and latent heat fluxes, which represent a domain average over different land surface types; simplified large-scale horizontal advective tendencies and subsidence; and horizontal winds with prevailing direction and average speed. Observed composite cloud statistics are provided for model evaluation. The observed diurnal cycle is well reproduced by LES; however, the cloud amount, liquid water path, and shortwave radiative effect are generally underestimated. LES are compared between simulations with an all-or-nothing bulk microphysics and a spectral bin microphysics. The latter shows improved agreement with observations in the total cloud cover and the amount of clouds with depths greater than 300 m. When compared with radar retrievals of in-cloud air motion, LES produce comparable downdraft vertical velocities, but a larger updraft area, velocity, and updraft mass flux. Both observations and LES show a significantly larger in-cloud downdraft fraction and downdraft mass flux than marine ShCu.

58 GEOSCIENCES↗
DOE OSTI2020

EQSIM—A multidisciplinary framework for fault-to-structure earthquake simulations on exascale computers, part II: Regional simulations of building response

The existing observational database of the regional-scale distribution of strong ground motions and measured building response for major earthquakes continues to be quite sparse. As a result, details of the regional variability and spatial distribution of ground motions, and the corresponding distribution of risk to buildings and other infrastructure, are not comprehensively understood. Utilizing high-performance computing platforms, emerging high-resolution, physics-based ground motion simulations can now resolve frequencies of engineering interest and provide detailed synthetic ground motions at high spatial density. This provides an opportunity for new insight into the distribution of infrastructure seismic demands and risk. In the work presented herein, the EQSIM fault-to-structure computational framework described in a companion paper, McCallen et al., is employed to investigate the regional-scale response of buildings to large earthquakes. A representative M = 7.0 strike-slip event is used to explore the distribution and amplitude of building demand, and comparisons are made between building response computed with fault-to-structure simulations and building response computed with existing measured near-fault earthquake records. New information on the distribution and variability of building response from high-performance parallel simulations is described and analyzed, and favorable first comparisons between building response predicted with both fault-to-structure simulations and real ground motions records are presented.

58 GEOSCIENCES↗
DOE OSTI2022

Determination of the spent fuel decay heat with the VERA core simulator

VERA core simulator capabilities to predict spent fuel decay heat have been explored. The comparison with the Serpent2 and NEWT/TRITON sequence from the SCALE package, performed on the NPP Krško fuel test cases, has enabled independent verification of the successful implementation of the VERA depletion/decay calculation sequence applied on the extended nuclide set. Since the VERA is a 3-D core simulator, the focus in the rest of the paper was on the investigation of the 3-D effects and non-linearity of the soluble boron concentration averaging process, which are difficult to assess with most of available computational tools. A difference in the decay heat prediction between the 3-D and 2-D model approaches was analyzed. In addition, the impact of the Inconel grids on the decay heat was determined. Averaging the concentration of soluble boron over the fuel irradiation period has been found to be a viable approach, since it results in slight decay heat overprediction, which is considered conservative for most applications. Finally, demonstration on the Watts Bar Unit 1 cycle 1 depletion has shown formidable VERA capabilities to accurately predict spent fuel decay heat.

Kromar, Marjan↗
DOE OSTI2023

LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems

We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

PICS: SIMULATIONS OF STRONG GRAVITATIONAL LENSING IN GALAXY CLUSTERS

Gravitational lensing has become one of the most powerful tools available for investigating the “dark side” of the universe. Cosmological strong gravitational lensing, in particular, probes the properties of the dense cores of dark matter halos over decades in mass and offers the opportunity to study the distant universe at flux levels and spatial resolutions otherwise unavailable. Studies of strongly lensed variable sources offer even further scientific opportunities. One of the challenges in realizing the potential of strong lensing is to understand the statistical context of both the individual systems that receive extensive follow-up study, as well as that of the larger samples of strong lenses that are now emerging from survey efforts. Motivated by these challenges, we have developed an image simulation pipeline, Pipeline for Images of Cosmological Strong lensing (PICS), to generate realistic strong gravitational lensing signals from group- and cluster-scale lenses. PICS uses a low-noise and unbiased density estimator based on (resampled) Delaunay Tessellations to calculate the density field; lensed images are produced by ray-tracing images of actual galaxies from deep Hubble Space Telescope observations. Other galaxies, similarly sampled, are added to fill in the light cone. The pipeline further adds cluster member galaxies and foreground stars into the lensed images. The entire image ensemble is then observed using a realistic point-spread function that includes appropriate detector artifacts for bright stars. Noise is further added, including such non-Gaussian elements as noise window-paning from mosaiced observations, residual bad pixels, and cosmic rays. The aim is to produce simulated images that appear identical—to the eye (expert or otherwise)—to real observations in various imaging surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

SHOULD ONE USE THE RAY-BY-RAY APPROXIMATION IN CORE-COLLAPSE SUPERNOVA SIMULATIONS?

We perform the first self-consistent, time-dependent, multi-group calculations in two dimensions (2D) to address the consequences of using the ray-by-ray+ transport simplification in core-collapse supernova simulations. Such a dimensional reduction is employed by many researchers to facilitate their resource-intensive calculations. Our new code (Fornax) implements multi-D transport, and can, by zeroing out transverse flux terms, emulate the ray-by-ray+ scheme. Using the same microphysics, initial models, resolution, and code, we compare the results of simulating 12, 15, 20, and 25 M {sub ⊙} progenitor models using these two transport methods. Our findings call into question the wisdom of the pervasive use of the ray-by-ray+ approach. Employing it leads to maximum post-bounce/pre-explosion shock radii that are almost universally larger by tens of kilometers than those derived using the more accurate scheme, typically leaving the post-bounce matter less bound and artificially more “explodable.” In fact, for our 25 M {sub ⊙} progenitor, the ray-by-ray+ model explodes, while the corresponding multi-D transport model does not. Therefore, in two dimensions, the combination of ray-by-ray+ with the axial sloshing hydrodynamics that is a feature of 2D supernova dynamics can result in quantitatively, and perhaps qualitatively, incorrect results.

79 ASTRONOMY AND ASTROPHYSICS↗