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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Parallel Radioisotope Collection and Analysis in Response to the Fukushima Release

Two independent air samplers were operated at Pacific Northwest National Laboratory in parallel during the collection of samples from the Fukushima reactor releases. One system is an automated aerosol collection and analysis unit, while the other was a manual sampler of higher daily air volume. The samples collected each day showed excellent correlation in radionuclide activity, although some variations were seen. These variations illustrate the reproducibility of the air sample radionuclide measurements made by the Comprehensive Nuclear-Test-Ban Treaty International Monitoring System (IMS) and show a simple way to acquire useful parallel samples for scientific purposes. In particular, a party wishing to have a “copy” of a sample acquired by the verification regime of the treaty could employ this method and have results similar to the IMS station at low cost and even higher sensitivity.

Atmospheric Aerosol Sampling↗
DOE OSTI2026

Commuting embeddings for parallel strategies in non-local games

Non-local games provide a versatile framework for probing quantum correlations and for benchmarking the power of entanglement. In finite dimensions, the standard method for playing several games in parallel requires a tensor product of the local Hilbert spaces, which scales additively in the number of qubits. In this work, we show that this additive cost can be reduced by exploiting algebraic embeddings. We introduce two forms of compressions. First, when a referee selects one game from a finite collection of games at random, the game quantum strategy can be implemented using a maximally entangled state of dimension equal to the largest individual game, thereby eliminating the need for repeated state preparations. Second, we establish conditions under which several games can be played simultaneously in parallel on fewer qubits than the tensor product baseline. These conditions are expressed in terms of commuting embeddings of the game algebras. Moreover, we provide a constructive framework for building such embeddings. Using tools from Lie theory, we show that aligning the various game algebras into a common Cartan decomposition enables such a qubit reduction. Beyond the theoretical contribution, our framework casts NLGs as algebraic primitives for distributed and resource-constrained quantum computations and suggested NLGs as a comparable device-independent dimension witness.

Commuting embeddings↗
DOE OSTI2016

Parallel and interacting stochastic approximation annealing algorithms for global optimisation

We present the parallel and interacting stochastic approximation annealing (PISAA) algorithm, a stochastic simulation procedure for global optimisation, that extends and improves the stochastic approximation annealing (SAA) by using population Monte Carlo ideas. The efficiency of standard SAA algorithm crucially depends on its selfadjusting mechanism which presents stability issues in high dimensional or rugged optimisation problems. The proposed algorithm involves simulating a population of SAA chains that interact each other in a manner that significantly improves the stability of the self-adjusting mechanism and the search for the global optimum in the sampling space, as well as it inherits SAA desired convergence properties when a square-root cooling schedule is used. It can be implemented in parallel computing environments in order to mitigate the computational overhead. As a result, PISAA can address complex optimisation problems that it would be difficult for SAA to satisfactory address. We demonstrate the good performance of the proposed algorithm on challenging applications including Bayesian network learning and protein folding. Our numerical comparisons suggest that PISAA outperforms the simulated annealing, stochastic approximation annealing, and annealing evolutionary stochastic approximation Monte Carlo.

Local trap↗
DOE OSTI2017

Parallel Spectral Acquisition with Orthogonal ICR Cells

FT-based high performance mass analyzers yield increased resolving power and mass measurement accuracy, yet require increased duration of signal acquisition that can limit many applications. The implementation of stronger magnetic fields, multiple detection electrodes for harmonic signal detection, and an array of multiple mass analyzers arranged along the magnetic field axis have been used to decrease required acquisition time. The results presented here show that multiple ion cyclotron resonance (ICR) mass analyzers can also be implemented orthogonal to the central magnetic field axis. The orthogonal ICR cell system presented here consisting of two cells (master and slave cells) was constructed with printed circuit boards and installed within a single superconducting magnet and vacuum system. A master cell was positioned, as is normally done with ICR cells, on the central magnetic field axis and a slave cell was located off this central axis, but directly adjacent and alongside the master cell. To achieve ion transfer between cells, ions that were initially trapped in the master cell were drifted across the magnetic field into the slave cell with application of a small DC field applied perpendicularly to the magnetic field axis. A subsequent population of ions was injected and accumulated in the master cell. Simultaneous excitation of cyclotron motion of ions in both cells was carried out; ICR signals from each cell were independently amplified and recorded in parallel. Presented here are the initial results of successful parallel spectral acquisition with this orthogonal dual ICR cell array. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

A new method approximating offset curve by Bézier curve using parallel derivative curves

In this paper, we present a new method for the offset approximation of an n-th degree Bézier curve by an n+1-th degree Bézier curve using parallel derivative curves. Our method is based on the Gauss map approximation of the n-th degree Bézier curve by the n+1-th degree Bézier curve whose derivative curve is parallel to that of the n-th degree Bézier curve. Thus, the convolution of the Gauss map approximation curve and n-th Bézier curve is a polynomial of degree n+1, which is our offset approximation of the n-th degree Bézier curve. Our approximation method has two advantages. One is that the offset approximation method yields a non-rational (polynomial) curve which is obtained by the simple sum of two Bézier curves. The other is that the offset approximation curve satisfying the endpoint interpolation of the given offset curve automatically has the same tangent lines as the offset curve at both endpoints. We illustrate our offset approximation method with some numerical examples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Parallelized hybrid optimization methods for nonsmooth problems using NOMAD and linesearch

Two parallelized hybrid methods are presented for single-function optimization problems with side constraints. The optimization problems are difficult not only due to possible existence of local minima and nonsmoothness of functions, but also due to the fact that objective function and constraint values for a solution vector can only be obtained by querying a black box whose execution requires considerable computational effort. Examples are optimization problems in Engineering where objective function and constraint values are computed via complex simulation programs, and where local minima exist and smoothness of functions is not assured. The hybrid methods consist of the well-known method NOMAD and two new methods called DENCON and DENPAR that are based on the linesearch scheme CS-DFN. The hybrid methods compute for each query a set of solution vectors that are evaluated in parallel. The hybrid methods have been tested on a set of difficult optimization problems produced by a certain seeding scheme for multiobjective optimization. We compare computational results with solution by NOMAD, DENCON, and DENPAR as stand-alone methods. It turns out that among the stand-alone methods, NOMAD is significantly better than DENCON and DENPAR. However, the hybrid methods are definitely better than NOMAD.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Extending TOUGH + HYDRATE with a parallel particle transport simulator: numerical investigation of sand production during gas production from hydrate deposits

A new parallel code for simulating particle transport in porous media is integrated with the TOUGH + HYDRATE simulator to investigate sand production associated with gas production from unconsolidated gas hydrate-bearing sediments (HBS). Here, the parallel coupled simulator is named THMPT and uses the integral finite difference method to describe the Darcian and non-Darcian flow of fluids and heat transport, the finite element method to describe the associated geomechanical changes, and the discrete element method to track the trajectory of individual sand particles within the HBS. The THMPT simulator is written in Fortran, incorporates multiple optimized algorithms, and can comprehensively address the coupled flow, thermal, chemical, geomechanical, and particle transport processes that characterize the system behaviors during gas production from HBS. The simulator can capture all processes involved in sand particle transport in porous media, including sand detachment, collision, clogging (i.e., bridging), and migration. A benchmark case study of sand production in the course of depressurization-induced gas production from a representative HBS reveals various distinct microscopic particle migration mechanisms and the adverse impact of sand particle detachment, transport, and clogging. The numerical investigation also examines the effect of bottomhole pressure on mitigating sand production. The simulation results indicate that sand clogging near the wellbore significantly reduces permeability, decreasing gas production by at least 50%. Lastly, the efficiency of gravel packing in mitigating sand production is numerically evaluated, revealing that the structure of the porous media appears to profoundly influence the macroscopic motion behavior of sand particles and sand clogging characteristics.

discrete element method↗
DOE OSTI2021

Asynchronous distributed-memory task-parallel algorithm for compressible flows on unstructured 3D Eulerian grids

Here, we discuss the implementation of a finite element method, used to numerically solve the Euler equations of compressible flows, using an asynchronous runtime system (RTS). The algorithm is implemented for distributed-memory machines, using stationary unstructured 3D meshes, combining data-, and task-parallelism on top of the Charm++ RTS. Charm++’s execution model is asynchronous by default, allowing arbitrary overlap of computation and communication. Task-parallelism allows scheduling parts of an algorithm independently of, or dependent on, each other. Built-in automatic load balancing enables continuous redistribution of computational load by migration of work units based on real-time CPU load measurement. The RTS also features automatic checkpointing, fault tolerance, resilience against hardware failure, and supports power-, and energy-aware computation. We demonstrate scalability up to 25 x 10 9 cells at $\mathscr{O}$10 4 compute cores and the benefits of automatic load balancing for irregular workloads. The full source code with documentation is available at https://quinoacomputing.org.

42 ENGINEERING↗
DOE OSTI2013

The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification

Highlights: •The parallel reaction monitoring method was applied to ubiquitin quantification. •The ubiquitin PRM method is highly sensitive even in biological samples. •Using the method, we revealed that Ufd4 assembles the K29-linked ubiquitin chain. -- Abstract: Ubiquitylation is an essential posttranslational protein modification that is implicated in a diverse array of cellular functions. Although cells contain eight structurally distinct types of polyubiquitin chains, detailed function of several chain types including K29-linked chains has remained largely unclear. Current mass spectrometry (MS)-based quantification methods are highly inefficient for low abundant atypical chains, such as K29- and M1-linked chains, in complex mixtures that typically contain highly abundant proteins. In this study, we applied parallel reaction monitoring (PRM), a quantitative, high-resolution MS method, to quantify ubiquitin chains. The ubiquitin PRM method allows us to quantify 100 attomole amounts of all possible ubiquitin chains in cell extracts. Furthermore, we quantified ubiquitylation levels of ubiquitin-proline-β-galactosidase (Ub-P-βgal), a historically known model substrate of the ubiquitin fusion degradation (UFD) pathway. In wild-type cells, Ub-P-βgal is modified with ubiquitin chains consisting of 21% K29- and 78% K48-linked chains. In contrast, K29-linked chains are not detected in UFD4 knockout cells, suggesting that Ufd4 assembles the K29-linked ubiquitin chain(s) on Ub-P-βgal in vivo. Thus, the ubiquitin PRM is a novel, useful, quantitative method for analyzing the highly complicated ubiquitin system.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Structural basis for cargo binding and autoinhibition of Bicaudal-D1 by a parallel coiled-coil with homotypic registry

Bicaudal-D1 (BICD1) is an α-helical coiled-coil protein mediating the attachment of specific cargo to cytoplasmic dynein. It plays an essential role in minus end-directed intracellular transport along microtubules. The third C-terminal coiled-coil region of BICD1 (BICD1 CC3) has an important role in cargo sorting, including intracellular vesicles associating with the small GTPase Rab6 and the nuclear pore complex Ran binding protein 2 (RanBP2), and inhibiting the association with cytoplasmic dynein by binding to the first N-terminal coiled-coil region (CC1). The crystal structure of BICD1 CC3 revealed a parallel homodimeric coiled-coil with asymmetry and complementary knobs-into-holes interactions, differing from Drosophila BicD CC3. Furthermore, our binding study indicated that BICD1 CC3 possesses a binding surface for two distinct cargos, Rab6 and RanBP2, and that the CC1-binding site overlaps with the Rab6-binding site. These findings suggest a molecular basis for cargo recognition and autoinhibition of BICD proteins during dynein-dependent intracellular retrograde transport. - Highlights: • BICD1 CC3 is a parallel homodimeric coiled-coil with axial asymmetry. • The coiled-coil packing of BICD1 CC3 is adapted to the equivalent heptad position. • BICD1 CC3 has distinct binding sites for two classes of cargo, Rab6 and RanBP2. • The CC1-binding site of BICD1 CC3 overlaps with the Rab6-binding site.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

A fast parallel 3D Poisson solver with longitudinal periodic and transverse open boundary conditions for space-charge simulations

A three-dimensional (3D) Poisson solver with longitudinal periodic and transverse open boundary conditions can have important applications in beam physics of particle accelerators. Here, we present a fast efficient method to solve the Poisson equation using a spectral finite-difference method. This method uses a computational domain that contains the charged particle beam only and has a computational complexity of $O(N_u (logN_{mode}))$, where $N_u$ is the total number of unknowns and $N_{mode}$ is the maximum number of longitudinal or azimuthal modes. This saves both the computational time and the memory usage of using an artificial boundary condition in a large extended computational domain. The new 3D Poisson solver is parallelized using a message passing interface (MPI) on multi-processor computers and shows a reasonable parallel performance up to hundreds of processor cores.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

SQDFT: Spectral Quadrature method for large-scale parallel O ( N ) Kohn–Sham calculations at high temperature

We present SQDFT: a large-scale parallel implementation of the Spectral Quadrature (SQ) method for $\mathscr{O}(N)$ Kohn–Sham Density Functional Theory (DFT) calculations at high temperature. Specifically, we develop an efficient and scalable finite-difference implementation of the infinite-cell Clenshaw–Curtis SQ approach, in which results for the infinite crystal are obtained by expressing quantities of interest as bilinear forms or sums of bilinear forms, that are then approximated by spatially localized Clenshaw–Curtis quadrature rules. We demonstrate the accuracy of SQDFT by showing systematic convergence of energies and atomic forces with respect to SQ parameters to reference diagonalization results, and convergence with discretization to established planewave results, for both metallic and insulating systems. Here, we further demonstrate that SQDFT achieves excellent strong and weak parallel scaling on computer systems consisting of tens of thousands of processors, with near perfect $\mathscr{O}(N)$ scaling with system size and wall times as low as a few seconds per self-consistent field iteration. Finally, we verify the accuracy of SQDFT in large-scale quantum molecular dynamics simulations of aluminum at high temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

DFT-FE – A massively parallel adaptive finite-element code for large-scale density functional theory calculations

We present an accurate, efficient and massively parallel finite-element code, DFT-FE, for large-scale ab-initio calculations (reaching ~100,000 electrons) using Kohn-Sham density functional theory (DFT). DFT-FE is based on a local real-space variational formulation of the Kohn-Sham DFT energy functional that is discretized using a higher-order adaptive spectral finite-element (FE) basis, and treats pseudopotential and all-electron calculations in the same framework, while accommodating non-periodic, semi-periodic and periodic boundary conditions. We discuss the main aspects of the code, which include, the various strategies of adaptive FE basis generation, and the different approaches employed in the numerical implementation of the solution of the discrete Kohn-Sham problem that are focused on significantly reducing the floating point operations, communication costs and latency. We demonstrate the accuracy of DFT-FE by comparing the energies, ionic forces and periodic cell stresses on a wide range of problems with popularly used DFT codes. Further, we demonstrate that DFT-FE significantly outperforms widely used plane-wave codes---both in CPU-times and wall-times, and on both non-periodic and periodic systems---at systems sizes beyond a few thousand electrons, with over 5-10 fold speedups in systems with more than 10,000 electrons. In conclusion, the benchmark studies also highlight the excellent parallel scalability of DFT-FE, with strong scaling demonstrated on up to 192,000 MPI tasks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

RF-transpond: A 1D coupled cold plasma wave and plasma transport model for ponderomotive force driven density modification parallel to B

The RF-Transpond code couples a fluid plasma transport solver with a frequency domain cold plasma RF wave solver in a 1D domain parallel to a strong background magnetic field. A ponderomotive force term proportional to parallel gradients in the electric field strength is included in the transport model in order to describe ponderomotive effects in the scrape-off layer (SOL) of fusion plasmas. The transport and wave codes are verified independently and a coupled case corresponding to experimental parameters from the LArge Plasma Device (LAPD) is presented. The density perturbation ratio R n , calculated to describe ponderomotive force driven modifications, is up to 20% for the simulation inputs used.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

SPACE: 3D parallel solvers for Vlasov-Maxwell and Vlasov-Poisson equations for relativistic plasmas with atomic transformations

A parallel, relativistic, three-dimensional particle-in-cell code SPACE has been developed for the simulation of electromagnetic fields, relativistic particle beams, and plasmas. In addition to the standard second-order Particle-in-Cell (PIC) algorithm, SPACE includes efficient novel algorithms to resolve atomic physics processes such as multi-level ionization of plasma atoms, recombination, and electron attachment to dopants in dense neutral gases. SPACE also contains a highly adaptive particle-based method, called Adaptive Particle-in-Cloud (AP-Cloud), for solving the Vlasov-Poisson problems. It eliminates the traditional Cartesian mesh of PIC and replaces it with an adaptive octree data structure. The code's algorithms, structure, capabilities, parallelization strategy, and performance have been discussed. Additionally, typical examples of SPACE applications to accelerator science and engineering problems are described.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Parallel diffusion operator for magnetized plasmas with improved spectral fidelity

Diffusive transport processes in magnetized plasmas are highly anisotropic, with fast parallel transport along the magnetic field lines sometimes faster than perpendicular transport by orders of magnitude. This constitutes a major challenge for describing non-grid-aligned magnetic structures in Eulerian (grid-based) simulations. Here, the present paper describes and validates a new method for parallel diffusion in magnetized plasmas based on the anti-symmetry representation [Halpern and Waltz, Phys. Plasmas 25, 060703 (2018)]. In the anti-symmetry formalism, diffusion manifests as a flow operator involving the logarithmic derivative of the transported quantity. Qualitative plane wave analysis shows that the new operator naturally yields better discrete spectral resolution compared to its conventional counterpart. Numerical simulations comparing the new method against existing finite difference methods are carried out, showing significant improvement. In particular, we find that combining anti-symmetry with finite differences in diagonally staggered grids essentially eliminates the so-called “artificial numerical diffusion” that affects conventional finite difference and finite volume methods.

Anisotropic diffusion↗
DOE OSTI2018

Computing the ankle-brachial index with parallel computational fluid dynamics

The ankle-brachial index (ABI), a ratio of arterial blood pressure in the ankles and upper arms, is used to diagnose and monitor circulatory conditions such as coarctation of the aorta and peripheral artery disease. Computational simulations of the ABI can potentially determine the parameters that produce an ABI indicative of ischemia or other abnormalities in blood flow. However, 0- and 1-D computational methods are limited in describing a 3-D patient-derived geometry. Thus, we present a massively parallel framework for computational fluid dynamics (CFD) simulations in the full arterial system. Additionally, using the lattice Boltzmann method to solve the Navier–Stokes equations, we employ highly parallelized and scalable methods to generate the simulation domain and efficiently distribute the computational load among processors. For the first time, we compute an ABI with 3-D CFD. In this proof-of-concept study, we investigate the dependence of ABI on the presence of stenoses, or narrowed regions of the arteries, by directly modifying the arterial geometry. As a result, our framework enables the computation a hemodynamic factor characterizing flow at the scale of the full arterial system, in a manner that is extensible to patient-specific imaging data and holds potential for treatment planning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Parallel multiscale simulations of a brain aneurysm

Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in future work.

60 APPLIED LIFE SCIENCES↗