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At least 937 records · Page 52

In-flight simulation with pilot-center of gravity offset and velocity mismatch

Similarity transformations which preserve modal characteristics and pilot's acceleration cues in in-flight simulation are presented. The model transformation for lateral acceleration matching is developed. A velocity-mismatch example, based on a VRA simulation of the Space Shuttle, illustrates that acceleration matching is achieved at the expense of mismatching in cues which are secondary to the simulated piloting task, while primarily cues are preserved. The approach is applicable for both implicit and explicit model-following, and it can easily be extended to the longitudinal case.

Stengel, R. F.↗

General trends of dihedral conformational transitions in a globular protein

In this paper, dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ~3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD-enhanced sampling. Side chains of the same length (particularly Nχ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. In conclusion, these general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Study of Interesting Solidification Phenomena on the Ground and in Space (MEPHISTO)

Real-time Seebeck voltage variations in a Sn-Bi melt during directional solidification in the MEPHISTO spaceflight experiment flown on the USMP-3 mission, can be correlated with well characterized thruster firings and an Orbiter Main System (OMS) burn. The Seebeck voltage measurement is related to the response of the instantaneous average melt composition at the melt-crystal interface. This allowed us to make a direct comparison of numerical simulations with the experimentally obtained Seebeck signals. Based on the results of preflight and real-time computations, several well-defined thruster firing events were programmed to occur at specific times during the experiment. In particular, we simulated the effects of the thruster firings on melt and crystal composition in a directionally solidifying Sn-Bi alloy. The relative accelerations produced by the firings were simulated by impulsive accelerations of the same magnitude, duration and orientation as the requested firings. A comparison of the simulation results with the Seebeck signal indicates that there is a good agreement between the two. This unique opportunity allows us, for the first time, to quantitatively characterize actual g-jitter effects on an actual crystal growth experiment and to properly calibrate our models of g-jitter effects on crystal growth.

Favier, J.-J.↗

Study of Interesting Solidification Phenomena on the Ground and in Space (MEPHISTO)

Real-time Seebeck voltage variations in a Sn-Bi melt during directional solidification in the MEPHISTO spaceflight experiment flown on the USMP-3 mission, have been correlated with well-characterized thruster firings and an Orbiter Main System (OMS) burn. The Seebeck voltage measurement is related to the response of the instantaneous average melt composition at the melt-crystal interface. This allowed us to make a direct comparison of numerical simulations with the experimentally obtained Seebeck signals. Based on the results of preflight and real-time computations, several well-defined thruster firing events were programmed to occur at specific times during the experiment. In particular, we simulated the effects of the thruster firings on melt and crystal composition in a directionally solidifying Sn-Bi alloy. The relative accelerations produced by the firings were simulated by impulsive accelerations of the same magnitude, duration and orientation as the requested firings. A comparison of the simulation results with the Seebeck signal indicates that there is a good agreement between the two. This unique opportunity allows us to make the first quantitative characterization of actual g-jitter effects on an actual crystal growth experiment and to calibrate our models of g-jitter effects on crystal growth.

Alexander, J. Iwan D.↗

Utilizing many-core accelerators for halo and center finding within a cosmology simulation

Efficiently finding and computing statistics about “halos” (regions of high density) are essential analysis steps for N-body cosmology simulations. However, in state-of-the-art simulation codes, these analysis operators do not currently take advantage of the shared-memory data-parallelism available on multi-core and many-core architectures. The Hybrid / Hardware Accelerated Cosmology Code (HACC) is designed as an MPI+X code, but the analysis operators are parallelized only among MPI ranks, because of the difficulty in porting different X implementations (e.g., OpenMP, CUDA) across all architectures on which it is run. In this paper, we present portable data-parallel algorithms for several variations of halo finding and halo center finding algorithms. These are implemented with the PISTON component of the VTK-m framework, which uses Nvidia's Thrust library to construct data-parallel algorithms that allow a single implementation to be compiled to multiple backends to target a variety of multi-core and many-core architectures. Finally, we compare the performance of our halo and center finding algorithms against the original HACC implementations on the Moonlight, Stampede, and Titan supercomputers. The portability of Thrust allowed the same code to run efficiently on each of these architectures. On Titan, the performance improvements using our code have enabled halo analysis to be performed on a very large data set (81923 particles across 16,384 nodes of Titan) for which analysis using only the existing CPU algorithms was not feasible.

Sewell, Christopher↗

2D numerical simulation of unsteady flows for large scale floods prediction in real time

The challenge of finding a compromise between computational time and level of accuracy and robustness has traditionally expanded the use simplified models rather than full two-dimensional (2D) models for flood simulation. This work presents a GPU accelerated 2D shallow water model for the simulation of flood events in real time. In particular, an explicit first-order finite volume scheme is detailed to control the numerical instabilities that are likely to appear when used in complex topography. The model is first validated with the benchmark test case of the Toce River (Italy) and numerical fixes are demonstrated to be necessary. The model is next applied to reproduce real events in a reach of the Ebro River (Spain) in order to compare simulation results with field data. The second case deals with a large domain (744 km 2 ) and long flood duration (up to 20 days) allowing an analysis of the performance and speed-up achieved by different GPU devices. We report the high values of fit between observed and simulated results as well as the computational times achieved are encouraging to propose the use of the model as forecasting system.

54 ENVIRONMENTAL SCIENCES↗

Beam dynamics in independent phased cavities

Linear accelerators containing the sequence of independently phased cavities with constant geometrical velocity along each structure are widely used in practice. The chain of cavities with identical cell lengths is utilized within a certain beam velocity range, with subsequent transformation to the next chain with higher cavity velocity. Design and analysis of beam dynamics in this type of accelerator are usually performed using numerical simulations. A full theoretical description of particle acceleration in an array of independent phased cavities has not been developed. In the present paper, we provide an analytical treatment of beam dynamics in such linacs employing Hamiltonian formalism. We begin our analysis with an examination of beam dynamics in an equivalent traveling wave of a single cavity, propagating within accelerating section with constant phase velocity. We then consider beam dynamics in arrays of cavities, utilizing an effective traveling wave propagating along with the whole accelerator with the velocity of synchronous (reference) particle. The analysis concluded with the determination of the matched beam conditions. Finally, we present a beam dynamics study in 805 MHz Coupled Cavity Linac of the LANSCE accelerator facility.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Ground Motion Models (GMMs) Improvements Using Earthquake Simulations on High Performance Computers

A computationally efficient simulation platform was developed that can provide representative synthetic ground motions from crustal earthquakes in the Stable Continental Regions of Central and Eastern US (CEUS), using 3D modeling and high-performance computing. The main objective was to use synthetic ground motion to provide constrains to refinements of exiting ergodic Ground Motion Models (GMMs), for large magnitude earthquakes and near-fault distances, for which these models are less reliable. Physics-based broadband (0-5Hz) ground motion simulations were used to estimate the near-fault ground motion amplitudes and within event and between-event variabilities associated with fault rupture characteristics. As part of a strategy for selecting a reginal velocity model and validation of developed rupture modeling technique, ground motions from the moment magnitude Mw5.0 November 7, 2016, Cushing Oklahoma, and Mw5.8 September 3, 2016, Pawnee Oklahoma earthquakes were simulated. In our simulations we used a 3D regional velocity model that was based on Saikia’s 1D velocity model. Saikia’s model demonstrated better performance in modelling high frequency regional wave propagation for CEUS region. The proposed 3D model includes lateral variations added to the 1D background model using the stochastic scheme of Pitarka and Mellors. Comparisons of the simulations with recordings of both earthquakes demonstrated the reliability of our deterministic simulation approach while emphasizing the importance of including small-scale variability in the regional velocity model needed to reproduce the observed high-frequency wave scattering effects. As part of validation analysis, comparisons with different GMMs for a Mw6.5 earthquake in the CESUS region resulted in a very good match between the simulated and empirical ground motion models. Initial investigations of within-event and between-event ground motion variabilities for Mw6.5 scenario earthquakes on a strike-slip fault, suggest that they are strongly related to spatial slip and slip rate variations, average rupture velocity, rupture area and rupture initiation location. For certain scenarios we found that the ground motion variability observed at near-fault distances (< 5 km) also persists at longer distances. Regardless of the rupture scenario, the simulated ground motion tends to fully saturate at short distances and for all periods. The near-fault saturation has to do with the attenuation of waves propagating along the fault and local rupture radiation pattern that also contribute to stronger ground motion variation at such distances. Analysis of effects of rupture initiation location suggest that the peak ground motion (PGV) and spectral acceleration (SA) can be quite variable due to rupture directivity effects. Such effects are stronger at periods longer than 1s. The effect of the 1D velocity models and surface topography on simulated ground motion were investigated by comparing three component synthetic seismograms computed at selected sites. Effect of surface topography was considered using the ratio between spectral accelerations simulated for two 1D models with flat surface topography and realistic model with surface topography. Overall, the topography slightly amplifies (by ~30%) the ground motion amplitude in the frequency range 1-3Hz. The effect of topography is more visible in the surface and coda waves portion of the seismograms.

58 GEOSCIENCES↗

Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A 1 Receptor

Despite intense interest in designing positive allosteric modulators (PAMs) as selective drugs of the adenosine A 1 receptor (A 1 AR), structural binding modes of the receptor PAMs remain unknown. Using the first X-ray structure of the A 1 AR, we have performed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) technique to determine binding modes of the A 1 AR allosteric drug leads. Two prototypical PAMs, PD81723 and VCP171, were selected. Each PAM was initially placed at least 20 Å away from the receptor. Extensive GaMD simulations using the AMBER and NAMD simulation packages at different acceleration levels captured spontaneous binding of PAMs to the A 1 AR. The simulations allowed us to identify low-energy binding modes of the PAMs at an allosteric site formed by the receptor extracellular loop 2 (ECL2), which are highly consistent with mutagenesis experimental data. Furthermore, the PAMs stabilized agonist binding in the receptor. In the absence of PAMs at the ECL2 allosteric site, the agonist sampled a significantly larger conformational space and even dissociated from the A 1 AR alone. In summary, the GaMD simulations elucidated structural binding modes of the PAMs and provided important insights into allostery in the A 1 AR, which will greatly facilitate the receptor structure-based drug design.

60 APPLIED LIFE SCIENCES↗

Coupling coarse-mesh CFD with fine-mesh CFD for modeling molten-salt reactors in the Virtual Test Bed (VTB)

The Nuclear Energy Advanced Modeling and Simulation (NEAMS) program aims at developing a simulation tool kit to accelerate the development and deployment of nuclear power technologies. NEAMS multiphysics tools have been designed to provide numerical simulation support for the design and licensing of GEN IV reactors. Pronghorn is NEAMS's coarse-mesh computational fluid dynamics (CFD) tool, which is designed to run 3D core transients in GEN IV reactors at a reduced computational cost. To increase their accuracy, coarse-mesh CFD simulations require calibrated closure coefficients. One way of computing these coefficients is via the Nek5000, NEAMS's high-fidelity CFD tool. This article discusses our current research lines in informing Pronghorn closure coefficients via Nek5000 to enable multiphysics simulations of the core cavity of the molten-salt fast reactor. We present an application in which Pronghorn mixing length turbulent viscosity has been calibrated from Nek5000 simulations. The resulting Pronghorn thermal-hydraulics model is then coupled to Griffin, the NEAMS neutron transport solver, to solve for the steady-state configuration of the molten-salt fast reactor. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Coupling coarse mesh CFD with fine mesh CFD for modeling for Molten Salt Reactors in the Virtual Test Bed VTB

The Nuclear Energy Advanced Modeling and Simulation (NEAMS) program aims at developing a simulation tool kit to accelerate the development and deployment of nuclear power technologies. NEAMS multiphysics tools have been designed to provide numerical simulation support for the design and licensing of GEN IV reactors. Pronghorn is NEAMS’s coarse-mesh computational fluid dynamics (CFD) tool, which is designed to run 3D core transients in GEN IV reactors at a reduced computational cost. To increase their accuracy, coarse-mesh CFD simulations require calibrated closure coefficients. One way of computing these coefficients is via the Nek5000, NEAMS’s high-fidelity CFD tool. This article discusses our current research lines in informing Pronghorn closure coefficients via Nek5000 to enable multiphysics simulations of the core cavity of the molten-salt fast reactor. We present an application in which Pronghorn mixing length turbulent viscosity has been calibrated from Nek5000 simulations. The resulting Pronghorn thermal-hydraulics model is then coupled to Griffin, the NEAMS neutron transport solver, to solve for the steady-state configuration of the molten-salt fast reactor.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Summary of Jefferson Lab LDRD on FFA@CEBAF Beam Dynamics Simulations

As Thomas Jefferson National Accelerator Facility (Jefferson Lab) looks toward the future, we are considering expanding our energy reach by using Fixed-Field Alternating Gradient (FFA) technology. Significant efforts have been made to design a hybrid accelerator which combines conventional recirculating electron LINAC design with permanent magnet-based FFA technology to increase the number of beam recirculations, and thus the energy. In an effort to further this progress, Jefferson Lab awarded a Laboratory Directed Research and Development (LDRD) grant to focus not on the design, but on detailed simulations of the designs created by the larger collaboration. This document will summarize the work performed during this LDRD, and direct the reader to other proceedings which describe elements of the work in greater detail.

Deitrick, K.↗

Machine Learning Approaches for Rare-Earth Silicate Environmental Barrier Coating Thermochemical and Thermomechanical Property Predictions

Environmental barrier coatings (EBCs) are a necessary enabling technology for the transition from superalloys to silicon carbide (SiC) ceramic matrix composites (CMCs) in gas turbine engines for increased efficiency and decreased fuel costs. SiC-based CMCs are prone to oxidation-based degradation in the engine hot section, and rare-earth (RE) silicates are promising candidates for EBCs due to their close thermal expansion match to the composite substrate and oxidation resistance. However, the design of EBCs is hindered by the large chemical space of candidate materials and the difficulty in obtaining material properties for engineering optimization. This is especially difficult as research continues into mixed-cation or “high-entropy” RE silicates. First-principles computational methods such as density functional theory (DFT) are highly effective at calculating material properties to guide coating design but are limited by their computational cost. Atomistic simulations have the potential to both accelerate property calculations and expand the properties able to be calculated due to their lower computational compared to DFT. However, they require interatomic potentials (IAPs) specific to the material system of interest, and, to our knowledge, there are no suitable IAPs for RE silicates. Machine learning (ML) is a promising technique to accelerate material property predictions indirectly by generating IAPs for atomistic simulations or via direct prediction. In this work, we present two ML approaches to accelerate the calculation of RE silicate properties relevant to EBC design: 1) a ML-derived interatomic potential (IAP) for atomistic simulations of yttrium disilicate (Y2Si2O7) from DFT training data, and 2) a neural network (NN) model to directly predict thermochemical properties of RE silicates and oxides directly from easily obtainable unit cell parameters. Classical MD simulations using the IAP yield lattice properties and bond lengths in good agreement with both DFT and experimental results from x-ray diffraction. Thermodynamic properties calculated using the finite-displacement phonon method and quasi-harmonic approximation were orders of magnitude faster than DFT with good agreement to the DFT results. The IAP was also used to calculate properties such as coefficient of thermal expansion (CTE) that require large simulation supercells and are therefore difficult with DFT. The IAP correctly predicted the anisotropic nature of the CTE in three different phases of Y2Si2O7. The NN model predicts constant pressure heat capacity, Cp, orders of magnitude faster than DFT calculations, which can enable its use as a surrogate model for multiscale simulations. The two methods presented in this work demonstrate the utility of ML for accelerating the prediction of RE silicate properties, which can in turn accelerate EBC design and optimization.

machine learning↗

Particle acceleration and plasma dynamics during magnetic reconnection in the magnetically dominated regime

Magnetic reconnection is thought to be the driver for many explosive phenomena in the universe. The energy release and particle acceleration during reconnection have been proposed as a mechanism for producing high-energy emissions and cosmic rays. We carry out two- and three-dimensional (3D) kinetic simulations to investigate relativistic magnetic reconnection and the associated particle acceleration. The simulations focus on electron–positron plasmas starting with a magnetically dominated, force-free current sheet (σ≡B{sup 2}/(4πn{sub e}m{sub e}c{sup 2})≫1). For this limit, we demonstrate that relativistic reconnection is highly efficient at accelerating particles through a first-order Fermi process accomplished by the curvature drift of particles along the electric field induced by the relativistic flows. This mechanism gives rise to the formation of hard power-law spectra f∝(γ−1){sup −p} and approaches p = 1 for sufficiently large σ and system size. Eventually most of the available magnetic free energy is converted into nonthermal particle kinetic energy. An analytic model is presented to explain the key results and predict a general condition for the formation of power-law distributions. The development of reconnection in these regimes leads to relativistic inflow and outflow speeds and enhanced reconnection rates relative to nonrelativistic regimes. In the 3D simulation, the interplay between secondary kink and tearing instabilities leads to strong magnetic turbulence, but does not significantly change the energy conversion, reconnection rate, or particle acceleration. This study suggests that relativistic reconnection sites are strong sources of nonthermal particles, which may have important implications for a variety of high-energy astrophysical problems.

79 ASTRONOMY AND ASTROPHYSICS↗

SU-E-T-635: Quantitative Study On Beam Flatness Variation with Beam Energy Change

Purpose: Beam flatness check has been proposed for beam energy check for photon beams with flattering filters. In this work, beam flatness change with beam energy was investigated quantitatively using the Monte Carlo method and its significance was compared with depth dose curve change. Methods: Monte Carlo simulations for a linear accelerator with flattering filter were performed with different initial electron energies for photon beams of 6MV and 10MV. Dose calculations in a water phantom were then perform with the phase space files obtained from the simulations. The beam flatness was calculated based on the dose profile at 10 cm depth for all the beams with different initial electron energies. The percentage depth dose (PDD) curves were also analyzed. The dose at 10cm depth (D10) and the ratio of the dose at 10cm and 20cm depth (D10/D20) and their change with the beam energy were calculated and compared with the beam flatness variation. Results: It was found that the beam flatness variation with beam energy change was more significant than the change of D10 and the ratio between D10 and D20 for both 6MV and 10MV beams. Half MeV difference on the initial electron beam energy brought in at least 20% variation on the beam flatness but only half percent change on the ratio of D10 and D20. The change of D10 or D20 alone is even less significant. Conclusion: The beam energy impact on PDD is less significant than that on the beam flatness. If the PDD is used for checking the beam energy, uncertainties of the measurement could possibly disguise its change. Beam flatness changes more significantly with beam energy and therefore it can be used for monitoring the energy change for photon beams with flattering filters. However, other factors which may affect the beam flatness should be watched as well.

07 ISOTOPE AND RADIATION SOURCES↗

Simulation study of Type 2 counterstreaming electrons along auroral field lines

The production of counterstreaming electrons associated with parallel fields along auroral field lines is examined through the use of computer simulation. A 2 1/2-dimensional (two spatial and three velocity dimensions) electrostatic particle algorithm and auroral boundary conditions are used to set up a self-consistent V potential structure. The simulation produces signatures of counterstreaming electrons resembling those observed by the Dynamics Explorer 1 satellite. The main signatures are as follows: (1) the phase space contours of the electron distribution function are elongated along the V-parallel axis, and (2) the energy of electrons streaming in the upward direction is comparable to the energy of the accelerated electron beam. The simulation indicates that a portion of the accelerated electron beam is trapped by large amplitude electrostatic waves produced through the two-stream instability. Strong wave-particle interactions then thermalize the trapped electrons to produce suprathermal electrons streaming in the direction opposite to that of the accelerated electron beam. These results suggest a possible mechanism of producing counterstreaming electron fluxes through nonlinear processes of the two-stream instability.

Wagner, J. S.↗

Numerical Simulation of the Anomalous Transport of High-Energy Cosmic Rays in Galactic Superbubble

A continuous-time random-walk (CTRW) model to simulate the transport and acceleration of high-energy cosmic rays in galactic superbubbles has recently been put forward (Barghouty & Schnee 2102). The new model has been developed to simulate and highlight signatures of anomalous transport on particles' evolution and their spectra in a multi-shock, collective acceleration context. The superbubble is idealized as a heterogeneous region of particle sources and sinks bounded by a random surface. This work concentrates on the effects of the bubble's assumed astrophysical characteristics (cf. geometry and roughness) on the particles' spectra.

Barghouty, A. F.↗