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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Graeme A. Bird

Few of those who read the 1963 research note by Graeme A. Bird in Physics of Fluids could have imagined that 50 years later the proposed new numerical technique would have become the dominant numerical technique in molecular gas dynamics. The introduction of the Direct Simulation Monte Carlo (DSMC) method not only has altered the field of molecular gas dynamics but also has influenced fields such as physical chemistry, mathematics, computer science, and aerothermodynamics. Further, the DSMC method has been used to probe into previously uninvestigated theoretical aspects of the Boltzmann equation and has also served as a platform for the development of nonequilibrium chemistry models. The DSMC method’s most noteworthy achievement is that molecular gas dynamics became a practical tool in the hands of aerospace engineers in many situations of spacecraft design and mission analysis.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2017

Precancer Atlas to Drive Precision Prevention Trials

Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. Here, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity – basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. In conclusion, accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA – an immense national resource to interrogate, target, and intercept events that drive oncogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Efficient prediction of human protein-protein interactions at a global scale

Background: Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. Results: On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments. Conclusions: The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Experimental Observations of the Topology of Convolutional Neural Network Activations

Topological data analysis (TDA) is a branch of computational mathematics, bridging algebraic topology and data science, that provides compact, noise-robust representations of complex structures. Deep neural networks (DNNs) learn millions of parameters associated with a series of transformations defined by the model architecture resulting in high-dimensional, difficult to interpret internal representations of input data. As DNNs become more ubiquitous across multiple sectors of our society, there is increasing recognition that mathematical methods are needed to aid analysts, researchers, and practitioners in understanding and interpreting how these models' internal representations relate to the final classification. In this paper we apply cutting edge techniques from TDA with the goal of gaining insight towards interpretability of convolutional neural networks used for image classification. We use two common TDA approaches to explore several methods for modeling hidden layer activations as high-dimensional point clouds, and provide experimental evidence that these point clouds capture valuable structural information about the model's process. First, we demonstrate that a distance metric based on persistent homology can be used to quantify meaningful differences between layers and discuss these distances in the broader context of existing representational similarity metrics for neural network interpretability. Second, we show that a mapper graph can provide semantic insight as to how these models organize hierarchical class knowledge at each layer. These observations demonstrate that TDA is a useful tool to help deep learning practitioners unlock the hidden structures of their models.

topological data analysis, deep learning↗
DOE OSTI2019

Frontiers of Materials Research: A Decadal Survey

Modern materials science builds on knowledge from physics, chemistry, biology, mathematics, computer and data science, and engineering sciences to enable us to understand, control, and expand the material world. Although it is anchored in inquiry-based fundamental science, materials research is strongly focused on discovering and producing reliable and economically viable materials, from super alloys to polymer composites, that are used in a vast array of products essential to today’s societies and economies. Frontiers of Materials Research: A Decadal Survey is aimed at documenting the status and promising future directions of materials research in the United States in the context of similar efforts worldwide. This third decadal survey in materials research reviews the progress and achievements in materials research and changes in the materials research landscape over the last decade; research opportunities for investment for the period 2020-2030; impacts that materials research has had and is expected to have on emerging technologies, national needs, and science; and challenges the enterprise may face over the next decade.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models

Single neuron models are fundamental for computational modeling of the brain's neuronal networks, and understanding how ion channel dynamics mediate neural function. A challenge in defining such models is determining biophysically realistic channel distributions. Here, we present an efficient, highly parallel evolutionary algorithm for developing such models, named NeuroGPU-EA. NeuroGPU-EA uses CPUs and GPUs concurrently to simulate and evaluate neuron membrane potentials with respect to multiple stimuli. We demonstrate a logarithmic cost for scaling the stimuli used in the fitting procedure. NeuroGPU-EA outperforms the typically used CPU based evolutionary algorithm by a factor of 10 on a series of scaling benchmarks. We report observed performance bottlenecks and propose mitigation strategies. Finally, we also discuss the potential of this method for efficient simulation and evaluation of electrophysiological waveforms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Expanded Use of ISOCS Characterization Techniques for WIPP Certification at the Idaho Clean-up Project - 19623

The Advanced Mixed Waste Treatment Project (AMWTP) has been retrieving, treating, characterizing, and shipping legacy Transuranic (TRU) waste for disposal since 2003 as part of the overall Idaho Cleanup Project (ICP) in support of the US Department of Energy. As the ICP has progressed, over 700 containers have been identified that cannot be successfully assayed using the current suite of non-destructive assay (NDA) instruments. To meet this challenge, Fluor Idaho, LLC, and Mirion Technologies (formerly Canberra Industries) have teamed to deploy the In-Situ Object Counting System (ISOCS) to supplement the current NDA capabilities. ISOCS has long been used in various radioactive waste management applications, but never has the ISOCS ability to perform intrinsic efficiency modeling of discrete waste containers been employed to characterize and certify TRU waste for disposal at the Waste Isolation Pilot Plant (WIPP), near Carlsbad, New Mexico. Since the primary disposal facility for this waste is the WIPP, the characterization processes for determining the quantity of radioactive material entrained in the waste are subject to WIPP Waste Acceptance Criteria (WAC) quality requirements and associated performance criteria. Until now, the Carlsbad Field Office (CBFO) WIPP-certified NDA equipment has utilized pre-defined efficiency calibrations for fixed geometries. However, due to the radioactive material content, activity levels, waste stream matrix, and/or the geometries of various size drums, boxes and other-odd-shaped containers or container integrity issues, it may not be suitable to characterize these containers with any of the existing WIPP-certified NDA equipment located at the AMWTP. Therefore, advanced technologies are needed to complete characterization of these problematic waste containers. The July 5, 2016 release of the WIPP WAC, DOE/WIPP-02-3122, Revision 8.0, Appendix A, 'Radioassay Requirements for Transuranic Waste,' was expanded to include several newer concepts such as American Society for Testing and Materials (ASTM) approved methods for efficiency-based calibrations and the use of mathematical computer modeling techniques for calibration. This change prompted AMWTP to pursue obtaining WIPP certification authority for expanded ISOCS techniques to deal with the remaining challenging waste containers and the development and implementation of Mirion's Figures of Merit (FOM) evaluations. These vital FOM evaluations enhance the ISOCS's modeling capabilities by optimizing the dynamic efficiency calibration for each object and reducing the assay's Total Measurement Uncertainty (TMU) budget. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2014

Applicability of ICRP 116 dose conversion coefficients to Korean pediatric population exposed to external photons - Paper 25

In the event of a radiological accident or attack, the estimation of organ dose is crucial to determine the possible health effect to general public. To that end, International Commission on Radiological Protection (ICRP) published a comprehensive set of organ dose conversion coefficients derived from the adult stylized (or mathematical) computational phantoms. More recently, ICRP updated the conversion coefficients based on their new reference computational phantoms, adult male and female voxel phantoms, exposed to a variety of radiation types and irradiation geometries. The adult voxel phantoms represent the organ mass and body dimensions of the Caucasian population. It is known that children generally receive greater radiation dose to organs compared to adults for external irradiation due to their smaller body size. that may provide less shielding to internal organs than adults. However, only a few studies investigated if the organ dose conversion coefficients developed for adults can be used for children and how much dose discrepancy needs to be expected. In this study, we adopted a Korean 7-year-old whole body voxel phantom to calculate a comprehensive organ dose conversion coefficients when the phantom is exposed to external photon irradiation geometries. We also compared the results with the data provided in the ICRP Publication 116, which is based on the ICRP adult voxel phantoms. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2014

yStreX: yeast stress expression database

Over the past decade genome-wide expression analyses have been often used to study how expression of genes changes in response to various environmental stresses. Many of these studies (such as effects of oxygen concentration, temperature stress, low pH stress, osmotic stress, depletion or limitation of nutrients, addition of different chemical compounds, etc.) have been conducted in the unicellular Eukaryal model, yeast Saccharomyces cerevisiae. However, the lack of a unifying or integrated, bioinformatics platform that would permit efficient and rapid use of all these existing data remain an important issue. To facilitate research by exploiting existing transcription data in the field of yeast physiology, we have developed the yStreX database. It is an online repository of analyzed gene expression data from curated data sets from different studies that capture genome-wide transcriptional changes in response to diverse environmental transitions. The first aim of this online database is to facilitate comparison of cross-platform and cross-laboratory gene expression data. Additionally, we performed different expression analyses, meta-analyses and gene set enrichment analyses; and the results are also deposited in this database. Lastly, we constructed a user-friendly Web interface with interactive visualization to provide intuitive access and to display the queried data for users with no background in bioinformatics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This ‘GO Phylogenetic Annotation’ approach integrates GO annotations from evolutionarily related genes across 100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true ‘machine-actionable interoperability’, which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources

The ever-increasing metagenomic data necessitate appropriate cataloguing in a way that facilitates the comparison and better contextualization of the underlying investigations. To this extent, information associated with the sequencing data as well as the original sample and the environment where it was obtained from is crucial. To date, there are not any publicly available repositories able to capture environmental metadata pertaining to hydrocarbon-rich environments. As such, contextualization and comparative analysis among sequencing datasets derived from these environments is to a certain degree hindered or cannot be fully evaluated. The metagenomics data management system for hydrocarbon resources (MetaHCRs) enables the capturing of marker gene and whole metagenome sequencing data as well as over 300 contextual attributes associated with samples, organisms, environments and geological properties, among others. Moreover, MetaHCR implements the Minimum Information about any Sequence–hydrocarbon resource specification from the Genomic Standards Consortium; it integrates a user-friendly web interface and relational database model, and it enables the generation of complex custom search. MetaHCR has been tested with 36 publicly available metagenomic studies, and its modular architecture can be easily customized for other types of environmental and metagenomics studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Physiological fidelity or model parsimony? The relative performance of reverse-toxicokinetic modeling approaches

Physiologically-based toxicokinetic (PBTK) models are often developed to facilitate in vitro to in vivo extrapolation (IVIVE) using a top-down, compartmental approach, favoring architectural simplicity over physiological fidelity despite the lack of general guidelines relating model design to dynamical predictions. Here we explore the impact of design choice (high vs. low fidelity) on chemical distribution throughout an animal’s organ system. Results We contrast transient dynamics and steady states of three previously proposed PBTK models of varying complexity in response to chemical exposure. The steady states for each model were determined analytically to predict exposure conditions from tissue measurements. Steady state whole-body concentrations differ between models, despite identical environmental conditions, which originates from varying levels of physiological fidelity captured by the models. These differences affect the relative predictive accuracy of the inverted models used in exposure reconstruction to link effects-based exposure data with whole-organism response thresholds obtained from in vitro assay measurements. Conclusions Our results demonstrate how disregarding physiological fideltiy in favor of simpler models affects the internal dynamics and steady state estimates for chemical accumulation within tissues, which, in turn, poses significant challenges for the exposure reconstruction efforts that underlie many IVIVE methods. Developing standardized systems-level models for ecological organisms would not only ensure predictive consistency among future modeling studies, but also ensure pragmatic extrapolation of in vivo effects from in vitro data or modeling exposure-response relationships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A weighted state redistribution algorithm for embedded boundary grids

State redistribution is an algorithm that stabilizes cut cells for embedded boundary grid methods. This work extends the earlier algorithm in several important ways. First, state redistribution is extended to three spatial dimensions. Second, we discuss several algorithmic changes and improvements motivated by the more complicated cut cell geometries that can occur in higher dimensions. In particular, we introduce a weighted version with less dissipation in an easily generalizable framework. Third, we demonstrate that state redistribution can also stabilize a solution update that includes both advective and diffusive contributions. Notably, the stabilization algorithm is shown to be effective for incompressible as well as compressible reacting flows. Finally, we discuss the implementation of the algorithm for several exascale-ready simulation codes based on AMReX, demonstrating ease of use in combination with domain decomposition, hybrid parallelism and complex physics.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Scalability of high-performance PDE solvers

Performance tests and analyses are critical to effective high-performance computing software development and are central components in the design and implementation of computational algorithms for achieving faster simulations on existing and future computing architectures for large-scale application problems. In this article, we explore performance and space-time trade-offs for important compute-intensive kernels of large-scale numerical solvers for partial differential equations (PDEs) that govern a wide range of physical applications. We consider a sequence of PDE-motivated bake-off problems designed to establish best practices for efficient high-order simulations across a variety of codes and platforms. We measure peak performance (degrees of freedom per second) on a fixed number of nodes and identify effective code optimization strategies for each architecture. In addition to peak performance, we identify the minimum time to solution at 80% parallel efficiency. The performance analysis is based on spectral and p-type finite elements but is equally applicable to a broad spectrum of numerical PDE discretizations, including finite difference, finite volume, and h-type finite elements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Ensemble‐Based, Large‐Eddy Reconstruction of Wind Turbine Inflow in a Near‐Stationary Atmospheric Boundary Layer Through Generative Artificial Intelligence

ABSTRACT To validate the second‐by‐second dynamics of turbines in field experiments, it is necessary to accurately reconstruct the winds going into the turbine. Current time‐resolved inflow reconstruction techniques estimate wind behavior in unobserved regions using relatively simple spectral‐based models of the atmosphere. Here, we develop a technique for time‐resolved inflow reconstruction that is rooted in a large‐eddy simulation model of the atmosphere. Our “large‐eddy reconstruction” technique blends observations and atmospheric model information through a diffusion model machine learning algorithm, allowing us to generate probabilistic ensembles of reconstructions for a single 10‐min observational period. Our generated inflows can be used directly by aeroelastic codes or as inflow boundary conditions in a large‐eddy simulation. We verify the second‐by‐second reconstruction capability of our technique in three synthetic field campaigns, finding positive Pearson correlation coefficient values () between ground‐truth and reconstructed streamwise velocity, as well as smaller positive correlation coefficient values for unobserved fields (spanwise velocity, vertical velocity, and temperature). We validate our technique in three real‐world case studies by driving large‐eddy simulations with reconstructed inflows and comparing to independent inflow measurements. The reconstructions are visually similar to measurements, follow desired power spectra properties, and track second‐by‐second behavior ().

17 WIND ENERGY↗
DOE OSTI2025

Benchmark study of the DTU OWC chamber with both two-way and one-way absorption

This paper reports on a benchmark study based on small-scale (1:50) measurements of a single, oscillating water column chamber mounted sideways in a long flume. The geometry of the OWC chamber is extracted from a barge-like, attenuator-type floating concept “KNSwing” with 40 chambers targeted for deployment in the Danish part of the North Sea. In addition to traditional two-way energy extraction we also consider one-way energy extraction with passive venting and compare chamber response, pressures and total absorbed energy between the two methods. A blind study was established for the numerical modeling, with participants applying several implementations of weakly nonlinear potential flow theory and commercial Navier–Stokes solvers (CFD). Both compressible and incompressible models were used for the air phase. Potential flow calculations predict more energy absorption near the chamber resonance for one-way absorption than for two-way absorption, but the opposite is found from the experimental measurements. This outcome is mainly attributed to energy losses in the experimental passive valve system, but this conclusion must be confirmed by better experimental measurements. Modeling the one-way valve in CFD proved to be very challenging and only one team was able to provide results which were generally closer to the experiments. The study illustrates the challenges associated with both numerical and experimental analysis of OWC chambers. Air compressibility effects were not found to be important at this scale, even with the large volume of additional air used for the one-way case.

16 TIDAL AND WAVE POWER↗