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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 1,585 records · Page 88
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Application of an Evolutionary Algorithm for Parameter Optimization in a Gully Erosion Model

Herein we demonstrate how to use model optimization to determine a set of best-fit parameters for a landform model simulating gully incision and headcut retreat. To achieve this result we employed the Covariance Matrix Adaptation Evolution Strategy (CMA-ES), an iterative process in which samples are created based on a distribution of parameter values that evolve over time to better fit an objective function. CMA-ES efficiently finds optimal parameters, even with high-dimensional objective functions that are non-convex, multimodal, and non-separable. We ran model instances in parallel on a high-performance cluster, and from hundreds of model runs we obtained the best parameter choices. This method is far superior to brute-force search algorithms, and has great potential for many applications in earth science modeling. We found that parameters representing boundary conditions tended to converge toward an optimal single value, whereas parameters controlling geomorphic processes are defined by a range of optimal values.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Dissecting protein tyrosine phosphatase signaling by engineered chemogenetic control of its activity

Protein tyrosine phosphatases (PTPases) are critical mediators of dynamic cell signaling. A tool capable of identifying transient signaling events downstream of PTPases is essential to understand phosphatase function on a physiological time scale. We report a broadly applicable protein engineering method for allosteric regulation of PTPases. This method enables dissection of transient events and reconstruction of individual signaling pathways. Implementation of this approach for Shp2 phosphatase revealed parallel MAPK and ROCK II dependent pathways downstream of Shp2, mediating transient cell spreading and migration. Furthermore, we show that the N-SH2 domain of Shp2 regulates MAPK-independent, ROCK II-dependent cell migration. Engineered targeting of Shp2 activity to different protein complexes revealed that Shp2-FAK signaling induces cell spreading whereas Shp2-Gab1 or Shp2-Gab2 mediates cell migration. We identified specific transient morphodynamic processes induced by Shp2 and determined the role of individual signaling pathways downstream of Shp2 in regulating these events. Broad application of this approach is demonstrated by regulating PTP1B and PTP-PEST phosphatases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

COLA with scale-dependent growth: applications to screened modified gravity models

We present a general parallelized and easy-to-use code to perform numerical simulations of structure formation using the COLA (COmoving Lagrangian Acceleration) method for cosmological models that exhibit scale-dependent growth at the level of first and second order Lagrangian perturbation theory. For modified gravity theories we also include screening using a fast approximate method that covers all the main examples of screening mechanisms in the literature. We test the code by comparing it to full simulations of two popular modified gravity models, namely f ( R ) gravity and nDGP, and find good agreement in the modified gravity boost-factors relative to ΛCDM even when using a fairly small number of COLA time steps.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Genetic-algorithm retrieval of the molecular alignment distribution with high-order harmonics generated from transiently aligned CO 2 molecules

Using genetic algorithm, we propose a method to retrieve the alignment distribution of transiently aligned CO 2 molecules from the high-order harmonic generation (HHG) spectra. The retrieval method is based on the quantitative rescattering (QRS) model where averaged photorecombination transition dipole can be factored out from the parallel (or perpendicular) harmonic spectra after the propagation of the harmonic fields in the gas medium. We examine how the retrieved alignment distributions are affected by uncertainty in alignment dependent ionization probability and on multiple orbital contribution to the HHG. We further confirm that alignment distribution is more accurately retrieved by using the minima in the HHG spectra driven by a long-wavelength laser. In addition, we show that earlier experimental data on the ratios between the perpendicular and the parallel HHG components of aligned CO 2 molecules are in better agreement with the QRS model if the macroscopic propagation and multiple orbital interference are included in the theoretical calculation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Investigation of HTS Twisted Stacked-Tape Cable (TSTC) Conductor for High-Field, High-Current Fusion Magnets

Here, the critical currents of a twisted single-tape were measured at 4.2 K in fields up to 17 T. It was confirmed that the critical current of a twisted-tape was similar to that of a flat tape in c-axis fields. Based on the single-tape critical-currents, a 40-tape (4-mm width) twisted stacked-tape cable (TSTC) conductor was experimentally evaluated at fields up to 17 T at 4.2 K. It was found that the Lorentz load degradation of the TSTC conductor was negligible at the end of a cyclic test. The TSTC cabling method has been considered to be suitable for developing a high-field high-current REBCO conductor for magnet applications as well as power transmission cables. A method to fabricate the inner legs of a D-shape toroidal field coil using a TSTC conductor has been discussed. This method allows the conductor to properly resist the transverse Lorentz load and mitigate ac loss issues by adopting a parallel-HTS-tape flat cable configuration where necessary.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Instability Issue of Paralleled Dies in an SiC Power Module in Solid-State Circuit Breaker Applications

Paralleled dies in a power module could have instability issues during high current switching transients. Here, the instability is caused by the differential-mode oscillation among paralleled MOSFETs. Conventional analyses of paralleled MOSFETs’ stability are normally limited to a single operating point, which ignores the influences of the switching trajectory and nonlinear device parameters on stability. This article reveals that the switching trajectory can significantly influence parallel stability. The analysis is improved by solving eigenvalues of state-space modeling system matrices of all operating points that the switching trajectory goes through considering nonlinear device parameters. Higher voltage and current stresses result in greater real parts of complex eigenvalues, which explains why the paralleled MOSFETs are more unstable with higher voltage and current stresses. To improve stability in solid-state circuit breaker applications, we propose a method to manipulate the switching trajectory to avoid the unstable region where the conventional hard switching trajectory normally goes through. Experimental results show that the turn- off current capability can be increased from ~five times of rated current with the gate oscillation using the conventional turn- off trajectory to ~ten times of rated current without the gate oscillation using the optimal turn- off trajectory.

42 ENGINEERING↗
DOE OSTI2014

Properties of HfLaO MOS capacitor deposited on SOI with plasma enhanced atomic layer deposition

Amorphous HfLaO dielectric film was successfully deposited on a silicon-on-insulator (SOI) substrate by plasma enhanced atomic layer deposition with in situ plasma treatment. The HfLaO film retained its insulating characteristics and is thermally stable even after annealing at 800 °C. The film has a dielectric constant of 27.3 and leakage of only 0.03 mA/cm{sup 2} at a gate bias of |Vg − V{sub fb}| = 1 V. The capacitance equivalent oxide thickness is 0.7 nm. A new parallel electrode testing structure was applied to measure C–V and J–V characteristics for the SOI samples. This testing method for metal–oxide–semiconductor capacitors has potential uses for measuring other layered substrates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

On the feasibility of optical-CT imaging in media of different refractive index

Purpose: Achieving accurate optical-CT 3D dosimetry without the use of viscous refractive index (RI) matching fluids would greatly increase convenience. Methods: Software has been developed to simulate optical-CT 3D dosimetry for a range of scanning configurations including parallel-beam, point, and converging light sources. For each configuration the efficacy of three refractive media was investigated: air, water, a fluid closely matched to PRESAGE{sup Registered-Sign }, and perfect matching (RI = 1.00, 1.33, 1.49, and 1.501 respectively). Reconstructions were performed using both filtered backprojection (FBP) and algebraic reconstruction technique (ART). The efficacy of the three configurations and the two algorithms was evaluated by calculating the usable radius (i.e., the outermost radius where data were accurate to within 2%), and gamma ({Gamma}) analysis. This definition recognizes that for optical-CT imaging, errors are greatest near the edge of the dosimeter, where refraction can be most pronounced. Simulations were performed on three types of dose distribution: uniform, volumetric modulated arc therapy (VMAT), and brachytherapy (Cs-137). Results: For a uniformly irradiated dosimeter the usable radius achieved with filtered backprojection was 68% for water-matching and 31% for dry-scanning in air. Algebraic reconstruction gave usable radii of 99% for both water and air (dry-scanning), indicating greater recovery of useful data for the uniform distribution. FBP and ART performed equally well for a VMAT dose distribution where less dose is delivered near the edge of the dosimeter. In this case, the usable radius was 86% and 53% for scanning in water and air, respectively. For brachytherapy, the usable radius was 99% and 98% for scanning in water and air, respectively using FBP, and a major decrease was seen with ART. Point source geometry provided 1%-2% larger usable radii than parallel geometry. Converging geometry recovered less usable dosimetry data (up to 10% reduced usable radii) than point and parallel geometries. A further disadvantage of converging geometry was an increased requirement on detector size by up to 18 Degree-Sign . Conclusions: For applications where dose information is not required in the periphery of the dosimeter, some dry and low-viscous matching configurations may be feasible. For all three dose distributions (uniform, VMAT, brachytherapy) the point source geometry produced slightly more favorable results (an extra 1%-2% usable radii) than parallel and converging. When dosimetry is required on the periphery, best results were obtained using close refractive matching and ART. A concern for water or dry-scanning is the increase in required detector size, introducing potential cost penalties for manufacturing.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Low-frequency quantitative ultrasound imaging of cell death in vivo

Purpose: Currently, no clinical imaging modality is used routinely to assess tumor response to cancer therapies within hours to days of the delivery of treatment. Here, the authors demonstrate the efficacy of ultrasound at a clinically relevant frequency to quantitatively detect changes in tumors in response to cancer therapies using preclinical mouse models.Methods: Conventional low-frequency and corresponding high-frequency ultrasound (ranging from 4 to 28 MHz) were used along with quantitative spectroscopic and signal envelope statistical analyses on data obtained from xenograft tumors treated with chemotherapy, x-ray radiation, as well as a novel vascular targeting microbubble therapy.Results: Ultrasound-based spectroscopic biomarkers indicated significant changes in cell-death associated parameters in responsive tumors. Specifically changes in the midband fit, spectral slope, and 0-MHz intercept biomarkers were investigated for different types of treatment and demonstrated cell-death related changes. The midband fit and 0-MHz intercept biomarker derived from low-frequency data demonstrated increases ranging approximately from 0 to 6 dBr and 0 to 8 dBr, respectively, depending on treatments administrated. These data paralleled results observed for high-frequency ultrasound data. Statistical analysis of ultrasound signal envelope was performed as an alternative method to obtain histogram-based biomarkers and provided confirmatory results. Histological analysis of tumor specimens indicated up to 61% cell death present in the tumors depending on treatments administered, consistent with quantitative ultrasound findings indicating cell death. Ultrasound-based spectroscopic biomarkers demonstrated a good correlation with histological morphological findings indicative of cell death (r{sup 2}= 0.71, 0.82; p < 0.001).Conclusions: In summary, the results provide preclinical evidence, for the first time, that quantitative ultrasound used at a clinically relevant frequency, in addition to high-frequency ultrasound, can detect tissue changes associated with cell death in vivo in response to cancer treatments.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

SU-E-T-33: A Feasibility-Seeking Algorithm Applied to Planning of Intensity Modulated Proton Therapy: A Proof of Principle Study

Purpose: To investigate the applicability of feasibility-seeking cyclic orthogonal projections to the field of intensity modulated proton therapy (IMPT) inverse planning. Feasibility of constraints only, as opposed to optimization of a merit function, is less demanding algorithmically and holds a promise of parallel computations capability with non-cyclic orthogonal projections algorithms such as string-averaging or block-iterative strategies. Methods: A virtual 2D geometry was designed containing a C-shaped planning target volume (PTV) surrounding an organ at risk (OAR). The geometry was pixelized into 1 mm pixels. Four beams containing a subset of proton pencil beams were simulated in Geant4 to provide the system matrix A whose elements a-ij correspond to the dose delivered to pixel i by a unit intensity pencil beam j. A cyclic orthogonal projections algorithm was applied with the goal of finding a pencil beam intensity distribution that would meet the following dose requirements: D-OAR < 54 Gy and 57 Gy < D-PTV < 64.2 Gy. The cyclic algorithm was based on the concept of orthogonal projections onto half-spaces according to the Agmon-Motzkin-Schoenberg algorithm, also known as ‘ART for inequalities’. Results: The cyclic orthogonal projections algorithm resulted in less than 5% of the PTV pixels and less than 1% of OAR pixels violating their dose constraints, respectively. Because of the abutting OAR-PTV geometry and the realistic modelling of the pencil beam penumbra, complete satisfaction of the dose objectives was not achieved, although this would be a clinically acceptable plan for a meningioma abutting the brainstem, for example. Conclusion: The cyclic orthogonal projections algorithm was demonstrated to be an effective tool for inverse IMPT planning in the 2D test geometry described. We plan to further develop this linear algorithm to be capable of incorporating dose-volume constraints into the feasibility-seeking algorithm.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-JeP2-11: Polymer Gels as 3D QA Devices in Magnetic Resonance-Guided Radiation Therapy

Purpose: To demonstrate the potential of polymer gels to serve as 3D QA devices in MR-guided radiotherapy. Methods: Custom-designed polymer gel dosimeters (MGS Research, Madison, CT) were centered on the penumbras of a radiation field, parallel to the magnetic field lines inside a 1.5 T MR scanner integrated with a 7 MV linac (MR-Linac). 15 Gy were delivered perpendicular to the magnetic field. Coronal MR images were acquired with a 2D balanced-Fast Field Echo (b-FFE) sequence in real-time during irradiation and with a 2D spin echo sequence at different times after irradiation. Signal intensities (SI) were measured inside and outside the radiation field on b-FFE images obtained during irradiation. Spin-spin relaxation rate (R2) maps were calculated from images after irradiation and penumbra widths were calculated from these maps. Results: A difference in SI between areas of the dosimeter inside and outside of the radiation field could be measured immediately after the beam was turned on. The difference in SI increased throughout the duration of the exposure. R2 values from immediately after irradiation were 83% of those measured 24h post-irradiation. At 1h after irradiation, the R2 values were 87% of those at 24h indicating that polymerization of the gel was still ongoing. At 24h postirradiation the width of the 80/20 penumbra on the left field edge measured 6.5 mm and on the right 5.6 mm. Conclusion: The MR-Linac allows for MR imaging during treatment and measurements of 3D dose distributions with steep dose gradients without having to transfer dosimeters for read-out. The results showed promise for polymer gels as relative 3D QA devices to verify radiation treatment plans delivered by an MR-Linac. To our knowledge, this was the first time that polymer gels were used for real-time image acquisition. Further investigations into the application of polymer gel dosimetry on MR-Linac are ongoing.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Reducing Parallel Communication in Algebraic Multigrid through Sparsification

Algebraic multigrid (AMG) is an $\mathcal{O}(n)$ solution process for many large sparse linear systems. A hierarchy of progressively coarser grids which utilize complementary relaxation and interpolation operators is constructed. High-energy error is reduced by relaxation, while low-energy error is mapped to coarse-grid matrices and reduced there. However, large parallel communication costs often limit parallel scalability. Furthermore, as the multigrid hierarchy is formed, each coarse matrix is formed through a triple matrix product. The resulting coarse grids often have significantly more nonzeros per row than the original fine-grid operator, thereby generating high parallel communication costs associated with sparse matrix-vector multiplication (SpMV) on coarse levels. In this paper, we introduce a method that systematically removes entries in coarse-grid matrices after the hierarchy is formed, leading to improved communication costs. We sparsify by removing weakly connected or unimportant entries in the matrix, leading to improved solve time. The main trade-off is that if the heuristic identifying unimportant entries is used too aggressively, then AMG convergence can suffer. To counteract this, the original hierarchy is retained, allowing entries to be reintroduced into the solver hierarchy if convergence is too slow. This enables a balance between communication cost and convergence, as necessary. In this paper we present new algorithms for reducing communication and present a number of computational experiments in support.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks

Abstract Background Due to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and experimental results from parallel sequencing provide available information about the affinity and accessibility of genome and are commonly used features in binding sites prediction. The attention mechanism in deep learning has shown its capability to learn long-range dependencies from sequential data, such as sentences and voices. Until now, no study has applied this approach in binding site inference from massively parallel sequencing data. The successful applications of attention mechanism in similar input contexts motivate us to build and test new methods that can accurately determine the binding sites of transcription factors. Results In this study, we propose a novel tool (named DeepGRN) for transcription factors binding site prediction based on the combination of two components: single attention module and pairwise attention module. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets. The results show that DeepGRN achieves higher unified scores in 6 of 13 targets than any of the top four methods in the DREAM challenge. We also demonstrate that the attention weights learned by the model are correlated with potential informative inputs, such as DNase-Seq coverage and motifs, which provide possible explanations for the predictive improvements in DeepGRN. Conclusions DeepGRN can automatically and effectively predict transcription factor binding sites from DNA sequences and DNase-Seq coverage. Furthermore, the visualization techniques we developed for the attention modules help to interpret how critical patterns from different types of input features are recognized by our model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Adaptive multiple super fast simulated annealing for stochastic microstructure reconstruction

Fast image reconstruction from statistical information is critical in image fusion from multimodality chemical imaging instrumentation to create high resolution image with large domain. Stochastic methods have been used widely in image reconstruction from two point correlation function. The main challenge is to increase the efficiency of reconstruction. A novel simulated annealing method is proposed for fast solution of image reconstruction. Combining the advantage of very fast cooling schedules, dynamic adaption and parallelization, the new simulation annealing algorithm increases the efficiencies by several orders of magnitude, making the large domain image fusion feasible.

adaptive multiple super fast simulated annealing↗
DOE OSTI2017

Long-time molecular dynamics simulations on massively parallel platforms: A comparison of parallel replica dynamics and parallel trajectory splicing

Molecular dynamics (MD) is one of the most widely used techniques in computational materials science. By providing fully resolved trajectories, it allows for a natural description of static, thermodynamic, and kinetic properties. A major hurdle that has hampered the use of MD is the fact that the timescales that can be directly simulated are very limited, even when using massively parallel computers. We compare two time-parallelization approaches, parallel replica dynamics (ParRep) and parallel trajectory splicing (ParSplice), that were specifically designed to address this issue for rare event systems by leveraging parallel computing resources. Using simulations of the relaxation of small disordered platinum nanoparticles, a comparative performance analysis of the two methods is presented. Finally, the results show that ParSplice can significantly outperform ParRep in the common case where the trajectory remains trapped for a long time within a region of configuration space but makes rapid structural transitions within this region.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Factors Controlling Redox Speciation of Plutonium and Neptunium in Extraction Separation Processes

The objective of the project was to examine the factors controlling redox speciation of plutonium and neptunium in UREX+ extraction in terms of redox potentials, redox mechanism, kinetics and thermodynamics. Researchers employed redox-speciation extractions schemes in parallel to the spectroscopic experiments. The resulting distribution of redox species w studied using spectroscopic, electrochemical, and spectro-electrochemical methods. This work resulted in collection of data on redox stability and distribution of redox couples in the nitric acid/nitrate electrolyte and the development of redox buffers to stabilize the desired oxidation state of separated radionuclides. The effects of temperature and concentrations on the redox behavior of neptunium were evaluated.

Paulenova, Alena↗
DOE OSTI2014

Load Balancing Scientific Applications

The largest supercomputers have millions of independent processors, and concurrency levels are rapidly increasing. For ideal efficiency, developers of the simulations that run on these machines must ensure that computational work is evenly balanced among processors. Assigning work evenly is challenging because many large modern parallel codes simulate behavior of physical systems that evolve over time, and their workloads change over time. Furthermore, the cost of imbalanced load increases with scale because most large-scale scientific simulations today use a Single Program Multiple Data (SPMD) parallel programming model, and an increasing number of processors will wait for the slowest one at the synchronization points. To address load imbalance, many large-scale parallel applications use dynamic load balance algorithms to redistribute work evenly. The research objective of this dissertation is to develop methods to decide when and how to load balance the application, and to balance it effectively and affordably. We measure and evaluate the computational load of the application, and develop strategies to decide when and how to correct the imbalance. Depending on the simulation, a fast, local load balance algorithm may be suitable, or a more sophisticated and expensive algorithm may be required. We developed a model for comparison of load balance algorithms for a specific state of the simulation that enables the selection of a balancing algorithm that will minimize overall runtime.

97 MATHEMATICS AND COMPUTING↗