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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 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
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 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↗
DOE OSTI2017

Regenerative Carbonate-Based Thermochemical Energy Storage System for Concentrating Solar Power

Southern Research has developed a thermochemical energy storage (TCES) technology that utilizes the endothermic-exothermic reversible carbonation of calcium oxide (lime) to store thermal energy at high-temperatures, such as those achieved by next generation concentrating solar power (CSP) facilities. The major challenges addressed in the development of this system include refining a high capacity, yet durable sorbent material and designing a low thermal resistance low-cost heat exchanger reactor system to move heat between the sorbent and a heat transfer fluid under conditions relevant for CSP operation (e.g., energy density, reaction kinetics, heat flow). The proprietary stabilized sorbent was developed by Precision Combustion, Inc. (PCI). A factorial matrix of sorbent compositions covering the design space was tested using accelerated high throughput screening in a thermo-gravimetric analyzer. Several promising formulations were selected for more thorough evaluation and one formulation with high capacity (0.38 g CO 2 /g sorbent) and durability (>99.7% capacity retention over 100 cycles) was chosen as a basis for further development of the energy storage reactor system. In parallel with this effort, a full range of currently available commercial and developmental heat exchange reactor systems and sorbent loading methods were examined through literature research and contacts with commercial vendors. Process models were developed to examine if a heat exchange reactor system and balance of plant can meet required TCES performance and cost targets, optimizing tradeoffs between thermal performance, exergetic efficiency, and cost. Reactor types evaluated included many forms, from microchannel reactor, to diffusion bonded heat exchanger, to shell and tube heat exchangers. The most viable design for application to a supercritical CO 2 power cycle operating at 200-300 bar pressure and >700°C was determined to be a combination of a diffusion bonded heat exchanger with a shell and tube reactor. A bench scale reactor system was then designed and constructed to test sorbent performance under more commercially relevant conditions. This system utilizes a tube-in tube reactor design containing approximately 250 grams sorbent and is able to operate under a wide range of temperature, pressure and flow conditions as needed to explore system performance under a variety of operating conditions. A variety of sorbent loading methods may be tested using the reactor design. Initial bench test results over 25 cycles showed very high sorbent stability (>99%) and sufficient capacity (>0.28 g CO 2 /g sorbent) for an economical commercial-scale system. Initial technoeconomic evaluation of the proposed storage system show that the sorbent cost should not have a significant impact on overall system cost, and that the largest cost impacts come from the heat exchanger reactor and balance of plant equipment, including compressors and gas storage, due to the high temperatures for sCO 2 cycles. Current estimated system costs are $47/kWhth based on current material and equipment cost estimates.

14 SOLAR ENERGY↗
DOE OSTI2014

Workshop on Modeling and Simulation of Systems and Applications, August 13-14, 2014, University of Washington, Seattle

In our efforts to continue the momentum toward quantitative understanding of the performance, power, and reliability of systems and applications, the modeling and simulation (hereafter ModSim) community gathered for its annual Workshop on Modeling & Simulation of Systems and Applications, held August 13-14, 2014 in Seattle. The 2014 Workshop on Modeling & Simulation of Systems and Applications, or ModSim 2014, focused on three critical technological areas: 1. Integrated Modeling and Simulation of Performance, Power, and Reliability; 2. Standards, Integration, and Interoperability of ModSim Methodologies and Tools; and 3. Advances in Core Modeling and Simulation Methods and Tools. The two-day meeting featured 21 presentations (based on peer-reviewed submissions) delivered over six parallel sessions, and there were six invited talks. Discussions aimed toward consolidating and directing this diverse technical community were especially beneficial as we continue to map out the future and form of ModSim research and development. This report presents a summary of the presentations, discussions, and findings culled from ModSim 2014. Each of the three critical technology areas are presented, structured as major research directions, gaps, cross-pollination, and path forward.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Perpendicular Diffusion Coefficient of Comic Rays: The Presence of Weak Adiabatic Focusing

The influence of adiabatic focusing on particle diffusion is an important topic in astrophysics and plasma physics. In the past, several authors have explored the influence of along-field adiabatic focusing on the parallel diffusion of charged energetic particles. In this paper, using the unified nonlinear transport theory developed by Shalchi and the method of He and Schlickeiser, we derive a new nonlinear perpendicular diffusion coefficient for a non-uniform background magnetic field. This formula demonstrates that the particle perpendicular diffusion coefficient is modified by along-field adiabatic focusing. For isotropic pitch-angle scattering and the weak adiabatic focusing limit, the derived perpendicular diffusion coefficient is independent of the sign of adiabatic focusing characteristic length. For the two-component model, we simplify the perpendicular diffusion coefficient up to the second order of the power series of the adiabatic focusing characteristic quantity. We find that the first-order modifying factor is equal to zero and that the sign of the second order is determined by the energy of the particles.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

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

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 OSTI2013

Nanoscale lamellar photoconductor hybrids and methods of making same

An article of manufacture and methods of making same. In one embodiment, the article of manufacture has a plurality of zinc oxide layers substantially in parallel, wherein each zinc oxide layer has a thickness d.sub.1, and a plurality of organic molecule layers substantially in parallel, wherein each organic molecule layer has a thickness d.sub.2 and a plurality of molecules with a functional group that is bindable to zinc ions, wherein for every pair of neighboring zinc oxide layers, one of the plurality of organic molecule layers is positioned in between the pair of neighboring zinc oxide layers to allow the functional groups of the plurality of organic molecules to bind to zinc ions in the neighboring zinc oxide layers to form a lamellar hybrid structure with a geometric periodicity d.sub.1+d.sub.2, and wherein d.sub.1 and d.sub.2 satisfy the relationship of d.sub.1.ltoreq.d.sub.2.ltoreq.3d.sub.1.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Method for adhering a coating to a substrate structure

A method for adhering a coating to a substrate structure comprises selecting a substrate structure having an outer surface oriented substantially parallel to a direction of radial stress, modifying the outer surface to provide a textured region having steps to adhere a coating thereto, and applying a coating to extend over at least a portion of the textured region, wherein the steps are oriented substantially perpendicular to the direction of radial stress to resist deformation of the coating relative to the substrate structure. A rotating component comprises a substrate structure having an outer surface oriented substantially parallel to a direction of radial stress. The outer surface defines a textured region having steps to adhere a coating thereto, and a coating extends over at least a portion of the textured region. The steps are oriented substantially perpendicular to the direction of radial stress to resist creep.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Scalable smoothing strategies for a geometric multigrid method for the immersed boundary equations

The immersed boundary (IB) method is a widely used approach to simulating fluid-structure interaction (FSI). Although explicit versions of the IB method can suffer from severe time step size restrictions, these methods remain popular because of their simplicity and generality. In prior work (Guy et al., Adv Comput Math, 2015), some of us developed a geometric multigrid preconditioner for a stable semi-implicit IB method under Stokes flow conditions; however, this solver methodology used a Vanka-type smoother that presented limited opportunities for parallelization. This work extends this Stokes-IB solver methodology by developing smoothing techniques that are suitable for parallel implementation. Specifically, we demonstrate that an additive version of the Vanka smoother can yield an effective multigrid preconditioner for the Stokes-IB equations, and we introduce an efficient Schur complement-based smoother that is also shown to be effective for the Stokes-IB equations. We investigate the performance of these solvers for a broad range of material stiffnesses, both for Stokes flows and flows at nonzero Reynolds numbers, and for thick and thin structural models. We show here that linear solver performance degrades with increasing Reynolds number and material stiffness, especially for thin interface cases. Nonetheless, the proposed approaches promise to yield effective solution algorithms, especially at lower Reynolds numbers and at modest-to-high elastic stiffnesses.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

System and method of storing and analyzing information

A system and method of storing and analyzing information is disclosed. The system includes a compiler layer to convert user queries to data parallel executable code. The system further includes a library of multithreaded algorithms, processes, and data structures. The system also includes a multithreaded runtime library for implementing compiled code at runtime. The executable code is dynamically loaded on computing elements and contains calls to the library of multithreaded algorithms, processes, and data structures and the multithreaded runtime library.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

System and method of storing and analyzing information

A system and method of storing and analyzing information is disclosed. The system includes a compiler layer to convert user queries to data parallel executable code. The system further includes a library of multithreaded algorithms, processes, and data structures. The system also includes a multithreaded runtime library for implementing compiled code at runtime. The executable code is dynamically loaded on computing elements and contains calls to the library of multithreaded algorithms, processes, and data structures and the multithreaded runtime library.

Feo, John T.↗