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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

The art and power of data imaging

Data imaging and visual data assessment are veritable gold mines in the scientist's quest to understand and accurately interpret numerical data. Graphical displays of various aspects of a dataset offer the analyst insight to the data that no mathematical computation or statistic can provide. It is difficult, at best, for even a skilled and observant statistician to understand the underlying structure of a dataset. Often, there is either too little data to get a good 'picture' of the structure that might be present or there is so much data that one cannot readily assimilate it. Of course, the latter problem (too much data) is, in reality, no problem at all given the abilities of modern computers and software systems to manage large amounts of data. Advances in computer technology and the advent of the global positioning satellite system have enabled scientists from many fields of endeavor to collect and view data in its spatial context. Visual images constructed from spatially referenced data reveal the inherent richness and structure in the data and lead to more informed conclusions. So powerful is data collected with spatial context that a relatively new branch of mathematical statistics, geo-spatial statistics, has emerged. Geo-spatial statistics seek to exploit this context rich data form to better understand the spatial and co-relationships that might exist, but would be otherwise hidden in tabular data or obscured with classic statistical approaches. This paper (and accompanying presentation) will show the power that visual data assessment possesses to understand radiological scanning data and to make confident and accurate decisions based on the data images. It will challenge the traditional mathematical concept of detection limits for scanning. It will demonstrate that more data, even if the individual datum comprising the dataset is of 'poorer quality' (i.e., has a larger uncertainty and, thus, a larger calculated minimum detection value), is significantly more powerful than a smaller dataset comprised of higher quality measurements. This presentation will cause the open-minded health physicist to rethink how they prescribe, collect, evaluate, and make decisions based upon radiological scan data. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Influence of intermolecular interactions on the infrared complex indices of refraction for binary liquid mixtures

This paper investigates the accuracy of deriving the composite optical constants of binary mixtures from only the complex indices of refraction of the neat materials. These optical constants enable the reflectance spectra of the binary mixtures to be modeled for multiple scenarios (e.g., different substrates, thicknesses, volume ratios), which is important for contact and standoff chemical detection. Using volume fractions, each mixture's complex index of refraction was approximated via three different mixing rules. To explore the impact of intermolecular interactions, these predictions are tested by experimental measurements for two representative sets of binary mixtures: (1) tributyl phosphate combined with n-dodecane, a non-polar medium, to represent mixtures which primarily interact via dispersion forces and (2) tributyl phosphate and 1-butanol to represent mixtures with polar functional groups that can also interact via dipole–dipole interactions, including hydrogen bonding. The residuals and the root-mean-square error between the experimental and calculated index values are computed and demonstrate that for miscible liquids in which the average geometry of the cross-interactions can be considered isotropic (e.g., dispersion), the refractive indices of the mixtures can be modeled using composite n and k values derived from volume fractions of the neat liquids. Conversely, in spectral regions where the geometry of the cross-interactions is more restricted and anisotropic (e.g., hydrogen bonding), the calculated n and k values vary from the measured values. The impact of these interactions on the reflectance spectra are then compared by modeling a thin film of the binary mixtures on an aluminum substrate using both the measured and the mathematically computed indices of refraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Recent advances in theoretical and numerical studies of wire array Z-pinch in the IAPCM

Fast Z-pinch has produced the most powerful X-ray radiation source in laboratory and also shows the possibility to drive inertial confinement fusion (ICF). Recent advances in wire-array Z-pinch researches at the Institute of Applied Physics and Computational Mathematics are presented in this paper. A typical wire array Z-pinch process has three phases: wire plasma formation and ablation, implosion and the MRT instability development, stagnation and radiation. A mass injection model with azimuthal modulation coefficient is used to describe the wire initiation, and the dynamics of ablated plasmas of wire-array Z-pinches in (r, θ) geometry is numerically studied. In the implosion phase, a two-dimensional(r, z) three temperature radiation MHD code MARED has been developed to investigate the development of the Magneto-Rayleigh-Taylor(MRT) instability. We also analyze the implosion modes of nested wire-array and find that the inner wire-array is hardly affected before the impaction of the outer wire-array. While the plasma accelerated to high speed in the implosion stage stagnates on the axis, abundant x-ray radiation is produced. The energy spectrum of the radiation and the production mechanism are investigated. The computational x-ray pulse shows a reasonable agreement with the experimental result. We also suggest that using alloyed wire-arrays can increase multi-keV K-shell yield by decreasing the opacity of K-shell lines. In addition, we use a detailed circuit model to study the energy coupling between the generator and the Z-pinch implosion. Recently, we are concentrating on the problems of Z-pinch driven ICF, such as dynamic hohlraum and capsule implosions. Our numerical investigations on the interaction of wire-array Z-pinches on foam convertors show qualitative agreements with experimental results on the “Qiangguang I” facility. An integrated two-dimensional simulation of dynamic hohlraum driven capsule implosion provides us the physical insights of wire-array plasma acceleration, shock generation and production, hohlraum formation, radiation ablation and fuel compression.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

BBN-simple: How to bake a universe-sized cake

Big Bang Nucleosynthesis (BBN), the process of creation of lightest elements in the early universe, is a highly robust, precise, and ultimately successful theory that forms one of the three pillars of the standard hot-Big-Bang cosmological model. Existing theoretical treatments of BBN and the associated computer codes are accurate and flexible, but are typically highly technical and opaque, and not suitable for pedagogical understanding of the BBN. Here we present BBN-simple - a from-scratch numerical calculation of the lightest element abundances pitched at an advanced undergraduate or beginning graduate level. We review the physics of the early universe relevant for BBN, provide information about the reaction rates, and discuss computational-mathematics background that is essential in setting up a BBN calculation. Here, we calculate the abundances of the principal nuclear species in a standard cosmological model, and find a reasonably good agreement with public precision-level BBN codes.

Big bang nucleosynthesis↗
DOE OSTI2015

Homogeneous-heterogeneous reaction effects in peristalsis through curved geometry

This paper looks at the influence of homogeneous-heterogeneous reactions on the peristaltic transport of non-Newtonian fluid in a curved channel with wall properties. Constitutive relations for thermodynamic third grade material are utilized in the problem development. An electrically conducting fluid in the presence of radial applied magnetic field is considered. The governing flow equations are developed in the presence of viscous heating. Mathematical computations are simplified employing long wavelength and low Reynolds number considerations. The solutions for velocity, temperature, concentration and heat transfer coefficient are obtained and examined. The features of sundry parameters are analyzed by plotting graphs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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 OSTI2013

Deployment and Overview of RAVEN Capabilities for a Probabilistic Risk Assessment Demo for a PWR Station Blackout

Starting in 2012, Idaho National Laboratory (INL) has been engaged to provide tools and methodologies to support a new approach to safety assessment and management of safety related issues for Nuclear Power Plants (NPPs). This activity is placed under the Risk Informed Safety Margin Characterization (RISMC) [2] umbrella that is one of the technical paths of the Department Of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program. RISMC takes a broader approach to risk evaluation by generating more comprehensive information. This information is used to gain a more accurate estimation of risk margins and to highlight feasible improvements that seek the optimal point between risk mitigation and economical viability of the nuclear energy option. This is, of course, done without taking any judgmental approach with respect to risk, which is a regulatory body task, and the economical viability, which is up to the single states and the open electricity market. RISMC is therefore composed of methodologies and tools. The augmented information that RISMC seeks to generate, as enabling decision tool, is not holistic with respect all possible metrics and operational aspects of a power plant; it is rather channeled toward the improvement of safety and the associated economical impact. While these are indeed two very broad metrics, they still allow a focus within the development of the underlying tools that, in a resource constrained environment (DOE founding, computational, mathematical) maximize the benefit of the program to the nuclear industry.

99 GENERAL AND MISCELLANEOUS↗
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↗