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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Stan : A Probabilistic Programming Language

Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the No-U-Turn sampler, an adaptive form of Hamiltonian Monte Carlo sampling. Penalized maximum likelihood estimates are calculated using optimization methods such as the limited memory Broyden-Fletcher-Goldfarb-Shanno algorithm. Stan is also a platform for computing log densities and their gradients and Hessians, which can be used in alternative algorithms such as variational Bayes, expectation propagation, and marginal inference using approximate integration. To this end, Stan is set up so that the densities, gradients, and Hessians, along with intermediate quantities of the algorithm such as acceptance probabilities, are easily accessible. Stan can also be called from the command line using the cmdstan package, through R using the rstan package, and through Python using the pystan package. All three interfaces support sampling and optimization-based inference with diagnostics and posterior analysis. rstan and pystan also provide access to log probabilities, gradients, Hessians, parameter transforms, and specialized plotting.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

DOE Data Days (Q4 FY2021 Report)

During the FY21Q4 the DOE Data Days (D3) leftover funds from D3 2020 were rolled-over to a new project task and project lead was transferred from Stan Ruppert to Rebecca Rodd. This project will be a continuation of previous DOE Data Day Conferences that were funded through the EOS project. The following are high-level accomplishments: Wrote a draft life-cycle plan for FY22 project for continuation of D3, Sought feedback from previous D3 committees to begin selection of FY22 planning committee, and Project management transitioned from Stan Ruppert to Rebecca Rodd in anticipation of Stan’s retirement at the end of FY21.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2018

Adapting to Artificial Intelligence

There is no need to be afraid of the emerging advances in artificial intelligence, says Argonne’s Marius Stan, Program Lead for Intelligent Materials Design. Although artificial intelligence may upend the job market in some ways, he says, it may also create new industries and positions as employees begin to designing and making robots. “It’s the problem and the solution,” Stan says. Meanwhile, artificial intelligence is playing a significant role in defining new research methods that bring us to resolution or discovery more quickly than ever before. Argonne is using or developing many of these technologies as AI extends to new branches of science and technology, sprouting new buds that represent various facets of human function and cognition — from learning to language processing to visual recognition.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Covariance Testing at BNL [Slides]

This presentation discusses testing implemented in FUDGE & ADVANCE in regard to proper ENDF formatting: STAN, STANEF, CHECKR, FUDGE, NJOY, convert to BOXR format, plotting, endfcovreport.py which is an overview of ENDF library’s covariance contents, and covariance Matrix class implements that are the core of all GNDS covariance. Several checks are performed, including symmetric, real, positive definite, condition # of Eigenvalues, and too big uncertainties. The presentation states that it can fix too big and/or small uncertainties and that it can plot matrices. It states that further testing is recommended by CSEWG but has not yet been implemented and suggests methods such as documentation which needs a human to execute, completeness which is partially complete, and reasonableness which has not been started. The presentation concludes by elaborating on reasonableness and states that only cross section is documented, that similar limits on CP reactions cross sections are needed, that maximum limits are needed too which is tricky since ENDF assumes Normal PDFs, and that there may be other observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges

The long atmospheric residence time of CO 2 creates an urgent need to add atmospheric carbon drawdown to CO 2 regulatory strategies. Synthetic and systems biology (SSB), which enables manipulation of cellular phenotypes, offers a powerful approach to amplifying and adding new possibilities to current land management practices aimed at reducing atmospheric carbon. The participants (in attendance: Christina Agapakis, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Charles DeLisi, Dan Drell, Sheldon Glashow, Steve Hamburg, Henry Jacoby, Henry Kelly, Mark Kon, Todd Kuiken, Mary Lidstrom, Mike MacCracken, June Medford, Jerry Melillo, Ron Milo, Pilar Ossorio, Ari Patrinos, Keith Paustian, Kristala Jones Prather, Kent Redford, David Resnik, John Reilly, Richard J. Roberts, Daniel Segre, Susan Solomon, Elizabeth Strychalski, Chris Voigt, Dominic Woolf, Stan Wullschleger, and Xiaohan Yang) identified a range of possibilities by which SSB might help reduce greenhouse gas concentrations and which might also contribute to environmental sustainability and adaptation. These include, among other possibilities, engineering plants to convert CO 2 produced by respiration into a stable carbonate, designing plants with an increased root-to-shoot ratio, and creating plants with the ability to self-fertilize. A number of serious ecological and societal challenges must, however, be confronted and resolved before any such application can be fully assessed, realized, and deployed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

The Case for Artificial Intelligence

The emerging era of artificial intelligence will be beneficial to society and is worth embracing, says Argonne’s Marius Stan, Program Lead for Intelligent Materials Design. Artificial intelligence is playing a significant role in defining new research methods that bring us to resolution or discovery more quickly than ever before. Argonne is using or developing many of these technologies as AI extends to new branches of science and technology, sprouting new buds that represent various facets of human function and cognition — from learning to language processing to visual recognition.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Estimating geographic origins of corn and soybean biomass for biofuel production: A detailed dataset

Sustainable fuel initiatives in the United States such as the Environmental Protection Agency’s Renewable Fuel Stan- dard and the Department of Energy’s Sustainable Aviation Fuel Grand Challenge have increased the production of corn ethanol and soybean biodiesel. However, the lack of precise information regarding biomass sourcing at a localized level has hindered accurate understanding of both biofuel costs and environmental impact of these production pathways. By harnessing the power of geospatial analysis and leveraging United States Department of Agriculture (USDA) crop cen- sus data, this dataset fills this critical knowledge gap. This dataset offers a novel estimation of geospatial biomass sourc- ing for biofuel production in the United States by synthe- sizing 2017 USDA crop census data, biorefinery data from the United States Energy Information Administration, and publicly available information about biomass sourcing for biofuel production. This dataset provides a detailed under- standing of biomass use for first generation biofuel pro- duction, enabling stakeholders to make informed decisions about resource allocation, investment strategies, and infras- tructure development. Furthermore, the county-level gran- ularity of the dataset allows for increased fidelity in the techno-economic assessments and life-cycle analyses of first- generation biofuels in the United States.

09 BIOMASS FUELS↗
DOE OSTI2023

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low–molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration—presumably a coiled coil—held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP—i.e., the long dimension of the pore—and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

MST resistive wall tearing mode simulations

Here, the Madison Symmetric Torus (MST) is a toroidal device that, when operated as a stan dard tokamak, does not have major disruptions. Unlike most tokamaks, the MST plasma is surrounded by a close fitting highly conducting wall, with a resistive wall penetration time two orders of magnitude longer than in JET or DIII-D, and three times longer than in ITER. The MST can operate with edge q a ⩽ 2, unlike standard tokamaks. Simulations presented here indicate that the MST is unstable to resistive wall tearing modes (RWTMs) and resistive wall modes (RWMs). They could in principle cause disruptions, but the predicted thermal quench time is much longer than the experimental pulse time. If the MST thermal quench time were comparable to measurements in JET and DIII-D, theory and simulations predict that disruptions would have been observed in MST. This is consistent with the modeling herein, predicting that disruptions are caused by RWTMs and RWMs. In the low q a ~ 2 regime of MST, the RWTM asymptotically satisfies the RWM dispersion relation. The transition from RWTM to RWM occurs smoothly at q a = m/n, where m, n are poloidal and toroidal mode numbers.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron

Abstract New variants of SARS-CoV-2 show remarkable heterogeneity in their relative fitness over both time and space. In this paper we extend the tools available for estimating the selection strength for new SARS-CoV-2 variants to a hierarchical, mixed-effects, renewal equation model. This formulation allows us to estimate selection effects at the global level while incorporating both measured and unmeasured heterogeneity among countries. Applying this model to the spread of Omicron in forty countries, we find evidence for very strong but very heterogeneous selection effects. To test whether this heterogeneity is explained by differences in the immune landscape, we considered several measures of vaccination rates and recent population-level infection as covariates, finding moderately strong, statistically significant effects. We also found a significant positive correlation between the selection advantage of Delta and Omicron at the country level, suggesting that other region-specific explanatory variables of fitness differences do exist. Our method is implemented in the Stan programming language, can be run on standard consumer-grade computing resources, and will be straightforward to apply to future variants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data

The rapid acceleration of microbial genome sequencing increases opportunities to understand bacterial gene function. Unfortunately, only a small proportion of genes have been studied. Recently, TnSeq has been proposed as a cost-effective, highly reliable approach to predict gene functions as a response to changes in a cell’s fitness before-after genomic changes. However, major questions remain about how to best determine whether an observed quantitative change in fitness represents a meaningful change. To address the limitation, we develop a Gaussian mixture model framework for classifying gene function from TnSeq experiments. In order to implement the mixture model, we present the Expectation-Maximization algorithm and a hierarchical Bayesian model sampled using Stan’s Hamiltonian Monte-Carlo sampler. We compare these implementations against the frequentist method used in current TnSeq literature. From simulations and real data produced by E.coli TnSeq experiments, we show that the Bayesian implementation of the Gaussian mixture framework provides the most consistent classification results.

Li, Kevin↗
DOE OSTI2017

Methodology for assessing the safety of Hydrogen Systems: HyRAM 1.1 technical reference manual

The HyRAM software toolkit provides a basis for conducting quantitative risk assessment and consequence modeling for hydrogen infrastructure and transportation systems. HyRAM is designed to facilitate the use of state-of-the-art science and engineering models to conduct robust, repeatable assessments of hydrogen safety, hazards, and risk. HyRAM is envisioned as a unifying platform combining validated, analytical models of hydrogen behavior, a stan- dardized, transparent QRA approach, and engineering models and generic data for hydrogen installations. HyRAM is being developed at Sandia National Laboratories for the U. S. De- partment of Energy to increase access to technical data about hydrogen safety and to enable the use of that data to support development and revision of national and international codes and standards. This document provides a description of the methodology and models contained in the HyRAM version 1.1. HyRAM 1.1 includes generic probabilities for hydrogen equipment fail- ures, probabilistic models for the impact of heat flux on humans and structures, and computa- tionally and experimentally validated analytical and first order models of hydrogen release and flame physics. HyRAM 1.1 integrates deterministic and probabilistic models for quantifying accident scenarios, predicting physical effects, and characterizing hydrogen hazards (thermal effects from jet fires, overpressure effects from deflagrations), and assessing impact on people and structures. HyRAM is a prototype software in active development and thus the models and data may change. This report will be updated at appropriate developmental intervals.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

The use of multiwavelets for uncertainty estimation in seismic surface wave dispersion.

This report describes a new single-station analysis method to estimate the dispersion and uncer- tainty of seismic surface waves using the multiwavelet transform. Typically, when estimating the dispersion of a surface wave using only a single seismic station, the seismogram is decomposed into a series of narrow-band realizations using a bank of narrow-band filters. By then enveloping and normalizing the filtered seismograms and identifying the maximum power as a function of frequency, the group velocity can be estimated if the source-receiver distance is known. However, using the filter bank method, there is no robust way to estimate uncertainty. In this report, I in- troduce a new method of estimating the group velocity that includes an estimate of uncertainty. The method is similar to the conventional filter bank method, but uses a class of functions, called Slepian wavelets, to compute a series of wavelet transforms of the data. Each wavelet transform is mathematically similar to a filter bank, however, the time-frequency tradeoff is optimized. By taking multiple wavelet transforms, I form a population of dispersion estimates from which stan- dard statistical methods can be used to estimate uncertainty. I demonstrate the utility of this new method by applying it to synthetic data as well as ambient-noise surface-wave cross-correlelograms recorded by the University of Nevada Seismic Network.

58 GEOSCIENCES↗
DOE OSTI2019

On the Development of Godunov Methods and Their Application to Gasdynamics

We are interested in developing the most accurate numeral models to simulate Gadynamics of explosions. But we must first recognize that there is no unique way to discretize the partial differential equations (PDEs) of gas dynamics, and also, there is no unique method to integrate the discretized forms of these equations. This has spawned a variety of numerical methods (religions*) that attempt to solve this conundrum, for example: Artificial Viscosity method created by the American mathematician John von Neumann, Flux-Corrected-Transport (FCT) method invented by Dr. Jay Boris, founder of the Laboratory for Computational Physics (LCP) at NRL, WENO method developed by Professor Stan Osher of UCLA and Professor Bjorn Enquist of U. Texas, and Godunov method by Academician Sergei Konstantinovich Godunov, Professor of the Sobolev Institute of Mathematics, RAS, in Novosibirsk to name just a few.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

University of Hawai‘i, Shallow Geothermal Resources: Energy Technology Innovation Partnership Project (Final Report)

Scientists at Lawrence Berkeley National Laboratory (Berkeley Lab) have teamed up with the University of Hawai‘i at Manoa (UH Manoa) through the U.S. Department of Energy’s Energy Technology Innovation Partnership Project to evaluate the technological and market feasibility of shallow geothermal heat exchanger (GHE) technology. UH requested this analysis to evaluate opportunities in building cooling, energy efficiency, and emissions reduction applications in Hawai‘i. UH has an abundance of geologic and geothermal data and is looking to the national labs’ expertise to execute this analysis. UH is also interested in investigating policy, regulatory, and business conditions advantageous for implementation of a pilot project and more broad deployment of this technology in Hawai‘i. In many locations around the world, the demands for heating and cooling are roughly balanced over the course of the year, so GHEs do not cause significant long-term changes in subsurface temperature. This is not the case in Hawai’i, where the demand for heating is very small, meaning that, over time, GHEs will add heat to the subsurface. If temperatures increase significantly, GHE systems will not work as designed. Regional groundwater flow has the potential to sweep heated water away from boreholes, thereby maintaining the functionality of the GHE system. Significant regional groundwater flow requires two things: a sufficiently large driving hydraulic head gradient (usually closely related to surface topography), and sufficient porosity and permeability to enable groundwater to flow in large enough quantities to enable near-borehole temperatures to be maintained at ambient values. Hawai‘i’s volcanic terrain offers ample surface topographic variation. The lava itself shows an extremely large range of porosity and permeability, so sites with large enough values of these properties must be selected. Numerical modeling of coupled groundwater and heat flow can be used to determine how large is large enough. Primarily, closed-loop systems have been investigated. Other options considered are open-loop systems and using cool seawater as the chilling source. Project work investigated the feasibility of GHE technology at two scales. At the island scale, GIS layers of various attributes relevant for GHE were combined to develop an overall favorability map for employing GHE in Hawai‘i. At the local scale, a hydrogeologic model for the subsurface component of a closed-loop system was developed for the Stan Sheriff Center at the UH Manoa campus. This site is considered promising because the rock below and immediately downgradient of the borefield is highly permeable, consisting of a subsurface karst system (limestone containing high-permeability open channels), which is underlain by a thick, high-permeability fractured basalt. Moreover, the site is near the base of the Ko‘olau Range, providing a large hydraulic head gradient. Thus, groundwater flow through the site is expected to be large, enabling efficient removal of heated groundwater. A full-GHE-system model of the site was also developed, with a simplified representation of the subsurface, in which groundwater flow is not considered and heat transfer is purely by conduction. Using the building cooling load data provided by UH, simulation results show that with groundwater flow present, a GHE can operate successfully for at least 10 years, but with no groundwater flow, the subsurface begins to heat up after only one year of operation, making the GHE unviable within 2-6 years. The team also developed a techno-economic model for this site to compare the cost of cooling using a GHE system with the costs of operating the current air-conditioning system. The GHE system is advantageous economically if favorable tax incentives and interest rates can be obtained.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

An Agnostic Approach to Building Empirical Type Ia Supernova Light Curves: Evidence for Intrinsic Chromatic Flux Variation Using Nearby Supernova Factory Data

We present a new empirical Type Ia supernova (SN Ia) model with three chromatic flux variation templates: one phase dependent and two phase independent. No underlying dust extinction model or patterns of intrinsic variability are assumed. Implemented with Stan and trained using spectrally binned Nearby Supernova Factory spectrophotometry, we examine this model's 2D, phase-independent flux variation space using two motivated basis representations. In both, the first phase-independent template captures variation that appears dust-like, while the second captures a combination of effectively intrinsic variability and second-order dust-like effects. We find that ≈13% of the modeled phase-independent flux variance is not dust-like. Previous empirical SN Ia models either assume an effective dust extinction recipe in their architecture, or only allow for a single mode of phase-independent variation. The presented results demonstrate such an approach may be insufficient, because it could "leak" noticeable intrinsic variation into phase-independent templates.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Integrating New Arctic Plant Functional Types in a Land Surface Model Using Above- and Belowground Field Observations: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication "Integrating New Arctic Plant Functional Types in a Land Surface Model Using Above- and Belowground Field Observations". We used field observations of biomass and leaf traits (Salmon et al., 2019b) across a gradient of plant communities on the Seward Peninsula in northwest Alaska (Breen et al., 2020; Iversen et al., 2017) to replace the original ELM configuration with nine, arctic-specific PFTs. Original arctic PFTs in the model were (1) broadleaf deciduous boreal shrub and (2) C3 arctic grass. New PFTs were (1) lichen, (2) bryophyte, (3) evergreen dwarf shrub, (4) deciduous dwarf shrub, (5) deciduous low shrub, (6) deciduous low to tall shrub, (7) alder shrub, (8) forb, and (9) graminoid. New PFTs were parameterized and evaluated using site-level trait and biomass measurements (Salmon et al., 2019b), root C:N ratios and rooting depth patterns (Salmon et al., 2019c), and root biomass (Salmon et al., 2020). This archive contains forcing data and model output from ELM simulations conducted at the Kougarok Hillslope site (Kougarok Road Mile Marker 64). Simulations were conducted for the Kougarok Hillslope site using meteorological driving data from the Scenarios Network for Alaska and Arctic Planning (SNAP) downscaled climate projection dataset using NCAR-CCSM forcing (Bieniek et al., 2020 dataset; Walsh et al., 2018). The archive includes three versions of model simulations representing a progression from the original model configuration to an Arctic-specific configuration (see Output section below). Simulation 1 used grid cell data from a global E3SM configuration, including the fractional area of E3SM PFTs assigned to the grid cell containing the Kougarok Hillslope site in global simulations. This simulation did not distinguish between different plant communities on the Kougarok Hillslope, but instead used a single point simulation to represent the entire area. Simulation 2 used default E3SM PFT definitions combined with adjusted depth to bedrock for plant communities with shallow rocky layers to represent the role of abiotic soil factors in driving site differences (based on depth measurements of Iversen et al., 2019a), and adjusted the relative areas of the broadleaf deciduous boreal shrub and C3 arctic grass PFTs to reflect the observed spatial coverage of shrub and non-shrub PFTs across Kougarok Hillslope plant communities. Simulation 3 used the new arctic PFT definitions and parameterizations based on the vegetation types present at the site, along with the adjusted soil depths used in Simulation 2. Included are *.pdf, *.nc (NetCDF), *tar.gz, *.py, and *.bash files. We would like to thank Mary's Igloo Native Corporation for allowing us to perform this research on their land and giving us the opportunity to share this research with their community. Thanks to Shawn Serbin and Alistair Rogers for helpful discussions. Holly Vander Stel, Joanne Childs, and Stan Wullschleger helped with collection of field data. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗