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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia

Abstract The ability to deduce carcinogenic potential from subchronic, repeat dose rodent studies would constitute a major advance in chemical safety assessment and drug development. This study investigated an error-corrected NGS method (CarcSeq) for quantifying cancer driver mutations (CDMs) and deriving a metric of clonal expansion predictive of future neoplastic potential. CarcSeq was designed to interrogate subsets of amplicons encompassing hotspot CDMs applicable to a variety of cancers. Previously, normal human breast DNA was analyzed by CarcSeq and metrics based on mammary-specific CDMs were correlated with tissue donor age, a surrogate of breast cancer risk. Here we report development of parallel methodologies for rat. The utility of the rat CarcSeq method for predicting neoplastic potential was investigated by analyzing mammary tissue of 16-week-old untreated rats with known differences in spontaneous mammary neoplasia (Fischer 344, Wistar Han, and Sprague Dawley). Hundreds of mutants with mutant fractions ≥ 10−4 were quantified in each strain, most were recurrent mutations, and 42.5% of the nonsynonymous mutations have human homologs. Mutants in the mammary-specific target of the most tumor-sensitive strain (Sprague Dawley) showed the greatest nonsynonymous/synonymous mutation ratio, indicative of positive selection consistent with clonal expansion. For the mammary-specific target (Hras, Pik3ca, and Tp53 amplicons), median absolute deviation correlated with percentages of rats that develop spontaneous mammary neoplasia at 104 weeks (Pearson r = 1.0000, 1-tailed p = .0010). Therefore, this study produced evidence CarcSeq analysis of spontaneously occurring CDMs can be used to derive an early metric of clonal expansion relatable to long-term neoplastic outcome.

McKim, Karen L.↗
DOE OSTI2022

Source-to-Source Automatic Differentiation of OpenMP Parallel Loops

This article presents our work toward correct and efficient automatic differentiation of OpenMP parallel worksharing loops in forward and reverse mode. Automatic differentiation is a method to obtain gradients of numerical programs, which are crucial in optimization, uncertainty quantification, and machine learning. The computational cost to compute gradients is a common bottleneck in practice. For applications that are parallelized for multicore CPUs or GPUs using OpenMP, one also wishes to compute the gradients in parallel. Here, we propose a framework to reason about the correctness of the generated derivative code, from which we justify our OpenMP extension to the differentiation model. We implement this model in the automatic differentiation tool Tapenade and present test cases that are differentiated following our extended differentiation procedure. Performance of the generated derivative programs in forward and reverse mode is better than sequential, although our reverse mode often scales worse than the input programs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Energy levels, oscillator strengths, line strengths, and transition probabilities in Si-like ions of La XLIII, Er LIV, Tm LV, and Yb LVI

Detailed calculations using the multi-configuration Dirac–Fock (MCDF) method are carried out for the lowest 64 fine-structure levels of the 3s{sup 2}3p{sup 2}, 3s{sup 2}3p3d, 3s3p{sup 3}, 3s3p{sup 2}3d, 3s{sup 2}3d{sup 2}, and 3p{sup 4} configurations in Si-like ions of La XLIII, Er LIV, Tm LV, and Yb LVI. Energies, oscillator strengths, wavelengths, line strengths, and radiative electric dipole transition rates are given for all ions. A parallel calculation using the many-body perturbation theory (MBPT) method is also carried out to assess the present energy levels accuracy. Comparisons are performed between these two sets of energy levels, as well as with other available results, showing that they are in good agreement with each other within 0.5%. These high accuracy results can be used to the modeling and the interpretation of astrophysical objects and fusion plasmas. - Highlights: • Energy levels and E1 transition rates of Si-like ions are presented. • Breit interaction and Quantum Electrodynamics effects are discussed. • Present results should be useful in the astrophysical application and plasma modeling.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2015

SU-C-304-03: Experimental Investigation On the Accuracy of Plastic Scintillation Dosimeters in Small Fields

Purpose: To investigate the accuracy of the Exradin W1 (SI) and of an “in-house” plastic scintillation dosimeter (CHUQ PSD) in small radiation fields. Methods: Output factor (OF) measurements with the W1 and CHUQ PSD were performed for field sizes of 0.5 x 0.5, 1 x 1 and 2 x 2 cm{sup 2}. Both detectors were placed parallel to the central axis (CAX) in water. The spectrum discrimination calibration method was performed in each set-up to account for the Cerenkov (CRV) signal created in the fiber. The OFs were compared to the expected field factors in water derived using i) Monte Carlo (MC) simulations of an accurate accelerator model and ii) microLion (PTW) and D1V diode (SI) OFs. MC-derived correction factors were applied to both the microLion and D1V OFs. For the CHUQ PSD the calibration was repeated in water (// CAX), solid water (perpendicular to CAX) and under a shielded configuration. The signal was collected using a spectrometer (wavelength range = 185–1100 nm). Spectral analysis was performed to evaluate potential changes of the spectral distributions under the various calibration set-up configurations. Results: The W1 OFs presented an over-response for the 0.5 x 0.5 cm{sup 2} in the range of 3 – 4.1% relative to the expected field factor. The CHUQ PSD presented an under-response in the range of 1.5 – 2.7%, without accounting for volume averaging. The CRV spectra under the various calibration procedures appeared similar to each other and only minor changes were observed to the respective OFs. Conclusion: The W1 and CHUQ PSD can be used in small fields down to a 1 x 1 cm{sup 2} field size. Discrepancies were encountered between the two detectors for the smallest field size of 0.5 x 0.5 cm{sup 2} with the CHUQ PSD exhibiting a closer agreement to the expected field factor. Funding sources: 1) Alexander S. Onassis Public Benefit Foundation in Greece and 2) CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council, Grant number: 432290, RGPIN-2014-06475.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Computing resonant modes of accelerator cavities by solving nonlinear eigenvalue problems via rational approximation

Here, we present an efficient and reliable algorithm for solving a class of nonlinear eigenvalue problems arising from the modeling of particle accelerator cavities. The eigenvalue nonlinearity in these problems results from the use of waveguides to couple external power sources or to allow certain excited electromagnetic modes to exit the cavity. We use a rational approximation to reduce the nonlinear eigenvalue problem first to a rational eigenvalue problem. We then apply a special linearization procedure to turn the rational eigenvalue problem into a larger linear eigenvalue problem with the same eigenvalues, which can be solved by existing iterative methods. By using a compact scheme to represent both the linearized operator and the eigenvectors to be computed, we obtain a numerical method that only involves solving linear systems of equations of the same dimension as the original nonlinear eigenvalue problem. We refer to this method as a compact rational Krylov (CORK) method. We implemented the CORK method in the Omega3P module of the Advanced Computational Electromagnetic 3D Parallel (ACE3P) simulation suite and validated it by comparing the computed cavity resonant frequencies and damping Q factors of a small model problem to those obtained from a fitting procedure that uses frequency responses computed by another ACE3P module called S3P. We also used the CORK method to compute trapped modes damped in an ideal eight 9-cell SRF cavity cryomodule. This was the first time it was possible to compute these modes directly. The damping Q factors of the computed modes match well with those measured in experiments and the difference in resonant frequencies is within the range introduced by cavity imperfection. Therefore, the CORK method is an extremely valuable tool for computational cavity design.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Efficient quadrature rules for finite element discretizations of nonlocal equations

In this paper we design efficient quadrature rules for finite element discretizations of nonlocal diffusion problems with compactly supported kernel functions. Two of the main challenges in nonlocal modeling and simulations are the prohibitive computational cost and the nontrivial implementation of discretization schemes, especially in three-dimensional settings. In this work we circumvent both challenges by introducing a parametrized mollifying function that improves the regularity of the integrand, utilizing an adaptive integration technique, and exploiting parallelization. We first showthat the “mollified” solution converges to the exact one as the mollifying parameter vanishes, then we illustrate the consistency and accuracy of the proposed method on several two- and three-dimensional test cases. Furthermore, we demonstrate the good scaling properties of the parallel implementation of the adaptive algorithm and we compare the proposed method with recently developed techniques for efficient finite element assembly.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Flux tube train model for local turbulence simulation of toroidal plasmas

A new simulation method for local turbulence in toroidal plasmas is developed by extending the conventional idea of the flux tube model. In the new approach, a train of flux tubes is employed, where flux tube simulation boxes are serially connected at each end along a field line so as to preserve a symmetry of the local gyrokinetic equations for image modes in an axisymmetric torus. Validity of the flux tube train model is confirmed against the toroidal ion temperature gradient turbulence for a case with a long parallel correlation of fluctuations, demonstrating numerical advantages over the conventional method in the time step size and the symmetry-preserving property.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Simulation of confined magnetohydrodynamic flows with Dirichlet boundary conditions using a pseudo-spectral method with volume penalization

A volume penalization approach to simulate magnetohydrodynamic (MHD) flows in confined domains is presented. Here the incompressible visco-resistive MHD equations are solved using parallel pseudo-spectral solvers in Cartesian geometries. The volume penalization technique is an immersed boundary method which is characterized by a high flexibility for the geometry of the considered flow. In the present case, it allows to use other than periodic boundary conditions in a Fourier pseudo-spectral approach. The numerical method is validated and its convergence is assessed for two- and three-dimensional hydrodynamic (HD) and MHD flows, by comparing the numerical results with results from literature and analytical solutions. The test cases considered are two-dimensional Taylor–Couette flow, the z-pinch configuration, three dimensional Orszag–Tang flow, Ohmic-decay in a periodic cylinder, three-dimensional Taylor–Couette flow with and without axial magnetic field and three-dimensional Hartmann-instabilities in a cylinder with an imposed helical magnetic field. Finally, we present a magnetohydrodynamic flow simulation in toroidal geometry with non-symmetric cross section and imposing a helical magnetic field to illustrate the potential of the method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Metallization and stringing for back-contact solar cells

Metallization and stringing methods for back-contact solar cells, and resulting solar cells, are described. In an example, in one embodiment, a method involves aligning conductive wires over the back sides of adjacent solar cells, wherein the wires are aligned substantially parallel to P-type and N-type doped diffusion regions of the solar cells. The method involves bonding the wires to the back side of each of the solar cells over the P-type and N-type doped diffusion regions. The method further includes cutting every other one of the wires between each adjacent pair of the solar cells.

Terao, Akira↗
DOE OSTI2025

Robustness of Deep Learning Classification to Adversarial Input on GPUs: Asynchronous Parallel Accumulation Is a Source of Vulnerability

The ability of machine learning (ML) classification models to resist small, targeted input perturbations—known as adversarial attacks—is a key measure of their safety and reliability. We show that floating-point non associativity (FPNA) coupled with asynchronous parallel programming on GPUs is sufficient to result in misclassification, without any perturbation to the input. Additionally, we show that this misclassification is particularly significant for inputs close to the decision boundary and that standard adversarial robustness results may be overestimated up to 4.6 when not considering machine-level details. We first study a linear classifier, before focusing on standard Graph Neural Network (GNN) architectures and datasets used in robustness assessments. We develop a novel black-box attack using Bayesian optimization to discover external workloads that can change the instruction scheduling which bias the output of reductions on GPUs and reliably lead to misclassification. Motivated by these results, we present a new learnable permutation (LP) gradient-based approach to learning floating-point operation orderings that lead to misclassifications. The LP approach provides a worst-case estimate in a computationally efficient manner, avoiding the need to run identical experiments tens of thousands of times over a potentially large set of possible GPU states or architectures. Finally, using instrumentation-based testing, we investigate parallel reduction ordering across different GPU architectures under external background workloads, when utilizing multi-GPU virtualization, and when applying power capping. Our results demonstrate that parallel reduction ordering varies significantly across architectures under the first two conditions, substantially increasing the search space required to fully test the effects of this parallel scheduler-based vulnerability. These results and the methods developed here can help to include machine-level considerations into adversarial robustness assessments, which can make a difference in safety and mission critical applications.

Shanmugavelu, Sanjif [Maxeler Technologies, a Groq↗
DOE OSTI2018

Analysis of Nonclassical Fracture Problems for Prestressed Bodies with Interacting Cracks

We consider two types of nonclassical fracture mechanisms, namely, the fracture of cracked bodies with initial (residual) stresses acting along the crack planes and the fracture of solids under compression along parallel cracks. To investigate nonaxisymmetric and axisymmetric problems for infinite solids containing two parallel coaxial cracks or a periodic set of coaxial parallel cracks, we use a combined analytic-numerical method within the framework of the three-dimensional linearized mechanics of solids. The analysis involves the representation of stresses and displacements in the linearized theory via harmonic potential functions. With the use of the integral Fourier–Hankel transformations, the problems are reduced to the solution of Fredholm integral equations of the second kind. This approach allows us to investigate problems in a unified general form for compressible and noncompressible homogeneous isotropic or transversely isotropic elastic bodies with an arbitrary structure of the elastic potential, and the material specification of the model is carried out only in the stage of numerical analysis of the resolving equations obtained in the general form. The effects of initial stresses on the stress intensity factors are analyzed for highly elastic materials and layered composites (modeled as transversely isotropic elastic bodies). The “resonance-like” effects are revealed when compressive initial stresses reach the values corresponding to the local loss of stability of the material in the vicinity of cracks, which, according to the indicated combined method, allows one to determine the critical (limiting) load parameters under the conditions of compression of the body along the cracks. The conclusions concerning the dependences of the stress intensity factors and critical (limiting) parameters of compression on the geometric parameters of the problems are formulated as well as concerning the dependences on physical and mechanical characteristics of the materials.

42 ENGINEERING↗
DOE OSTI2017

Collidoscope: An Improved Tool for Computing Collisional Cross-Sections with the Trajectory Method

Ion mobility-mass spectrometry (IM-MS) can be a powerful tool for determining structural information about ions in the gas phase, from small covalent analytes to large, native-like or denatured proteins and complexes. For large biomolecular ions, which may have a wide variety of possible gas-phase conformations and multiple charge sites, quantitative, physically explicit modeling of collisional cross sections (CCSs) for comparison to IMS data can be challenging and time-consuming. We present a “trajectory method” (TM) based CCS calculator, named “Collidoscope,” which utilizes parallel processing and optimized trajectory sampling, and implements both He and N{sub 2} as collision gas options. Also included is a charge-placement algorithm for determining probable charge site configurations for protonated protein ions given an input geometry in pdb file format. Results from Collidoscope are compared with those from the current state-of-the-art CCS simulation suite, IMoS. Collidoscope CCSs are within 4% of IMoS values for ions with masses from ~18 Da to ~800 kDa. Collidoscope CCSs using X-ray crystal geometries are typically within a few percent of IM-MS experimental values for ions with mass up to ~3.5 kDa (melittin), and discrepancies for larger ions up to ~800 kDa (GroEL) are attributed in large part to changes in ion structure during and after the electrospray process. Due to its physically explicit modeling of scattering, computational efficiency, and accuracy, Collidoscope can be a valuable tool for IM-MS research, especially for large biomolecular ions. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Crosslinking and Gelation of Polymer Brushes and Free Polymer Chains in a Confined Space during Controlled Radical Polymerization-A Computer Simulation Study

The confinement effect on crosslinking and gelation during controlled/living copolymerization of a monovinyl and a divinyl monomer was studied by Monte Carlo computer simulation using the dynamic lattice liquid method. The simulated reactions took place in plane-parallel slits of various widths for various grafting densities (GDs) and various initial initiator/crosslinker ratios ([X] 0 /[Ini] 0 ). Monomers and crosslinkers were initially randomly distributed in the slit, but initiators were either anchored to one solid plane (polymer brushes) or randomly distributed (free chains). For brushes, the gel point (GP) depended on GD and [X] 0 /[Ini] 0 . The higher these parameters, the lower was the gel point. The gel point was also affected by the slit width. For free, nongrafted chains, the dependence of GP on slit width was negligible. For brushes, a nonuniform density of crosslinks was found, the highest density was close to the wall. This asymmetry was high at the gel point and decreased at higher conversions.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data

Abstract While the advances in synchrotron light sources, together with the development of focusing optics and detectors, allow nanoscale ptychographic imaging of materials and biological specimens, the corresponding experiments can yield terabyte-scale volumes of data that can impose a heavy burden on the computing platform. Although graphics processing units (GPUs) provide high performance for such large-scale ptychography datasets, a single GPU is typically insufficient for analysis and reconstruction. Several works have considered leveraging multiple GPUs to accelerate the ptychographic reconstruction. However, most of these works utilize only the Message Passing Interface to handle the communications between GPUs. This approach poses inefficiency for a hardware configuration that has multiple GPUs in a single node, especially while reconstructing a single large projection, since it provides no optimizations to handle the heterogeneous GPU interconnections containing both low-speed (e.g., PCIe) and high-speed links (e.g., NVLink). In this paper, we provide an optimized intranode multi-GPU implementation that can efficiently solve large-scale ptychographic reconstruction problems. We focus on the maximum likelihood reconstruction problem using a conjugate gradient (CG) method for the solution and propose a novel hybrid parallelization model to address the performance bottlenecks in the CG solver. Accordingly, we have developed a tool, called PtyGer ( Pty chographic G PU(multipl e )-based r econstruction), implementing our hybrid parallelization model design. A comprehensive evaluation verifies that PtyGer can fully preserve the original algorithm’s accuracy while achieving outstanding intranode GPU scalability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Transport induced by ion cyclotron range of frequencies waves

The Vlasov equation, which includes the effect of the ion cyclotron range of frequencies (ICRF) waves, can be written as the Fokker-Planck equation which describes the quasilinear transport in phase space by using the Lie-transform method. The radial transport fluxes of particle, energy and parallel momentum driven by ICRF waves in the slab geometry have been derived. The results show that the ICRF-induced radial redistributions of particle, energy and parallel momentum are driven by the inhomogeneity in energy of the equilibrium distribution function, and related to the correlation between the excursion in the real space and the excursion in energy. For the case with strong asymmetry of k{sub y} spectrum, the ICRF-induced radial transport driven by the energy inhomogeneity dominates the ICRF-induced radial transport driven by the spatial inhomogeneity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Magnetometry of single ferromagnetic nanoparticles using magneto-optical indicator films with spatial amplification

We present a magneto-optical technique to spatially amplify and image fringe fields from single ferromagnetic nanorods. The fringe fields nucleate magnetic domains in a low-coercivity, perpendicularly magnetized indicator film, which are expanded by an applied out-of-plane field from the nanoscale to the microscale for measurement with polar Kerr microscopy. The nucleation location and therefore magnetic orientation of the sample nanorod are detected as spatially dependent field biases in locally measured hysteresis loops of the indicator film. We first discuss our method to fabricate the high-sensitivity indicator film with low energy argon ion irradiation. We then present a map of the amplified signal produced from a single nanorod as measured by the indicator film and compare it with a simultaneously obtained, unamplified fringe field map. The comparison demonstrates the advantage of the amplification mechanism and the capability of the technique to be performed with single-spot magneto-optical Kerr effect magnetometers. Our signal-to-noise ratio determines a minimum measureable particle diameter of tens of nanometers for typical transition metals. We finally use our method to obtain hysteresis loops from multiple nanorods in parallel. Our technique is unperturbed by applied in-plane fields for magnetic manipulation of nanoparticles, is robust against many common noise sources, and is applicable in a variety of test environments. We conclude with a discussion of the future optimization and application of our indicator film technique.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Complex-energy approach to sum rules within nuclear density functional theory

The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish an efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Magnetic phase transition in coupled spin-lattice systems: A replica-exchange Wang-Landau study

Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with a Heisenberg-like spin Hamiltonian, facilitating the treatment of both the atomic coordinates and the spins as explicit phase variables. Using a model parameterized for bcc iron, we study the magnetic phase transition in these complex systems via the recently introduced, massively parallel replica-exchange Wang-Landau Monte Carlo method. Comparison with the results obtained from rigid lattice (spin-only) simulations shows that the transition temperature as well as the amplitude of the peak in the specific heat curve is marginally affected by the lattice vibrations. Moreover, we report the results were found to be sensitive to the particular choice of interatomic potential.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗