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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 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution

When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that generate the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Both cis- and trans-acting regulatory divergence can be hastened by directional selection through adaptation, sexual selection, and inter-sexual conflict, in addition to cryptic evolution under stabilizing selection. Dysfunctional sex-biased gene expression, in particular, may provide an important source of sexually-dimorphic genetic incompatibilities. Here, we characterize and compare male and female/hermaphrodite transcriptome profiles for sibling nematode species Caenorhabditis briggsae and C. nigoni, along with allele-specific expression in their F 1 hybrids, to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, misexpression of sex-biased genes pervades F 1 hybrids of both sexes. This finding implicates greater fragility of male genetic networks to produce dysfunctional organismal phenotypes. Spermatogenesis genes are especially prone to high divergence in both expression and coding sequences, consistent with a “faster male” model for Haldane’s rule and elevated sterility of hybrid males. Moreover, underdominant expression pervades male-biased genes compared to female-biased and sex-neutral genes and an excess of cis-trans compensatory regulatory divergence for X-linked genes underscores a “large-X effect” for hybrid male expression dysfunction. Extensive regulatory divergence in sex determination pathway genes likely contributes to demasculinization of XX hybrids. The evolution of genetic incompatibilities due to regulatory versus coding sequence divergence, however, are expected to arise in an uncorrelated fashion. This study identifies important differences between the sexes in how regulatory networks diverge to contribute to sex-biases in how genetic incompatibilities manifest during the speciation process.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

Critical evaluation of Jet-A spray combustion using propane chemical kinetics in gas turbine combustion simulated by KIVA-2

Jet-A spray combustion has been evaluated in gas turbine combustion with the use of propane chemical kinetics as the first approximation for the chemical reactions. Here, the numerical solutions are obtained by using the KIVA-2 computer code. The KIVA-2 code is the most developed of the available multidimensional combustion computer programs for application of the in-cylinder combustion dynamics of internal combustion engines. The released version of KIVA-2 assumes that 12 chemical species are present; the code uses an Arrhenius kinetic-controlled combustion model governed by a four-step global chemical reaction and six equilibrium reactions. Researchers efforts involve the addition of Jet-A thermophysical properties and the implementation of detailed reaction mechanisms for propane oxidation. Three different detailed reaction mechanism models are considered. The first model consists of 131 reactions and 45 species. This is considered as the full mechanism which is developed through the study of chemical kinetics of propane combustion in an enclosed chamber. The full mechanism is evaluated by comparing calculated ignition delay times with available shock tube data. However, these detailed reactions occupy too much computer memory and CPU time for the computation. Therefore, it only serves as a benchmark case by which to evaluate other simplified models. Two possible simplified models were tested in the existing computer code KIVA-2 for the same conditions as used with the full mechanism. One model is obtained through a sensitivity analysis using LSENS, the general kinetics and sensitivity analysis program code of D. A. Bittker and K. Radhakrishnan. This model consists of 45 chemical reactions and 27 species. The other model is based on the work published by C. K. Westbrook and F. L. Dryer.

Nguyen, H. L.↗
NASA NTRS2022

VESIcal: An Open-source Thermodynamic Model Engine for Mixed Volatile (H2O-CO2) Solubility in Silicate Melts

Modeling the solubility of volatiles in silicate melts is fundamental to the interpretation of volcanic systems and has implications for magma dynamics, eruption style, and material transport between the mantle, crust, and atmosphere. Recent advancements in computational capabilities and access to computing tools has outpaced the functionality and extensibility of previously available modeling platforms. Here we present VESIcal (Volatile Equilibria and Saturation Index calculator), the first comprehensive modeling tool for H2O, CO2, and mixed (H2O-CO2) solubility in silicate melts that: a) allows users access to seven popular models, with easy inter-comparison between models; b) provides universal functionality for all models (e.g., functions for calculating saturation pressures, degassing paths, etc.); c) can process large datasets (1,000’s of samples) automatically; d) can output computed data into an Excel spreadsheet or CSV file for post-modeling analysis; e) integrates plotting capabilities directly within the tool; and f) provides all of this within the framework of a python library, making the tool extensible by the user and allowing any of the model functions to be incorporated into any other code capable of calling python.Here we will provide a demonstration of VESIcal and its capabilities with applications to various volcanic processes affected by volatiles. VESIcal represents the first tool capable of directly comparing multiple solubility models and equations of state. We find that commonly used models predict surprisingly different volatile solubilities, particularly for pure CO2 or mixed CO2-H2O fluids. Even for melt compositions that are well represented in the calibration datasets of multiple models (e.g., MORBs), calculated solubilities for pure CO2 and pure H2O can deviate from one another by factors of >2 leading to 2x deviations in calculated saturation pressures (e.g., 5 to 10 kbar). The solubility of CO2 predicted by different rhyolitic models also differs substantially, overwhelming other sources of uncertainty such as analytical errors on measurements of volatile contents or uncertainties in crustal density profiles. This highlights the importance of model choice when drawing geological conclusions based on volatiles in magmas.

Kayla Iacovino↗
NASA NTRS2024

Shallow Soil Polychlorinated Biphenyl Site Assessment Report

This report presents a summary of the shallow soil polychlorinated biphenyl (PCB) site assessment activities that occurred from December 2020 through July 2022 at General Services Administration Reclamation Yard, Solid Waste Management Unit (SWMU) 010, located at the John F. Kennedy Space Center (KSC), Florida. The site is monitored under KSC’s Resource Conservation and Recovery Act Corrective Action Program, which also meets the requirements of Chapter 62-780, Florida Administrative Code. For the purposes of this report, three separate shallow soil plumes, known as the Northeast Shallow Soil PCB Plume, Southeast Shallow Soil PCB Plume, and West Shallow Soil PCB Plume, were identified for this site. The activities presented in this report include seven field events conducted between December 2020 and July 2022, which include shallow soil sample collection in the Northeast, Southeast, and West Shallow Soil PCB Plumes. AECOM Technical Services, Inc., personnel collected 330 soil samples from 118 boring locations. The samples were collected at 0.5-foot depth intervals to various depths based on analytical results and depth to groundwater. The soil samples were submitted to a fixed-based laboratory for analysis by United States Environmental Protection Agency Method 8082A for total PCBs. Several soil samples had PCB concentrations above the State of Florida Direct Exposure Residential and Industrial Soil Cleanup Target Levels (SCTLs), and two soil samples had PCB concentrations above the State of Florida Leachability for Groundwater. No soil borings were located beneath impervious surfaces, such as concrete or asphalt. The current Land Use Control Implementation Plan (LUCIP) covers PCBs in soils above the residential SCTL, which includes the paved areas.

PCBs↗
NASA NTRS2024

Soil Interim Measures Implementation Report Q6 Radar Station – Solid Waste Management Unit 112 Locations of Concern 3 and 10 Kennedy Space Center, Florida

This report presents a summary of the soil interim measures (IM) implementation activities that occurred from January 23 through June 6, 2023, at the Q6 Radar Station (Q6RS) Solid Waste Management Unit (SWMU) 112, located at the John F. Kennedy Space Center (KSC), Florida. The site is monitored under KSC’s Resource Conservation and Recovery Act Corrective Action Program, which also meets the requirements of Chapter 62-780, Florida Administrative Code. Assessment activities have previously been performed at 10 Q6RS Locations of Concern (LOCs), identified during a SWMU assessment in 2013 (NASA 2013). Since the SWMU assessment, further confirmatory sampling and assessment was conducted for each LOC, and based on the data collected during these assessments, it was determined that Resource Conservation and Recovery Act Facility Investigation to further evaluate soil and groundwater was to be conducted at two LOCs: LOC 1 – Former Underground Storage Tanks (groundwater) and LOC 3 – Radar Antenna Refurbishment Area (soil). The LOC 1 groundwater assessment is ongoing, and the results will be presented under a separate cover. It was also determined that soil IM would be completed at two of the LOCs, LOC 3 and LOC 10 – Compressor Building Condensate Discharge. A Soil IM Work Plan was prepared and submitted in October 2021 (NASA 2021). The plan proposed excavation and disposal of barium and copper impacted soil in the LOC 3 and 10 areas. This report presents a summary and results of the soil IM implementation activities conducted at LOCs 3 and 10. The site contaminates of concern for this soil IM are barium and copper. The activities presented in this report includes soil IM implementation and groundwater sampling. From January 23 through March 24, 2023, AECOM Technical Services, Inc. (AECOM) field personnel conducted IM implementation activities in the LOC 3 and 10 areas. As presented in the IM Work Plan, shallow soils, impacted with metals, were excavated to a depth of 2 feet below land surface in the central area of the site around the radar antenna and associated equipment. AECOM personnel excavated 77.43 tons of soil using hand tools and, when able, heavy equipment. The soils were placed into lined roll-off containers, which were covered and transported under manifest to the Cedar Trail Landfill in Bartow, Florida. The site was restored to original condition using certified clean backfill material (sand), with filter fabric, and gravel. Areas outside of the excavation were restored with grass seed. On June 6, 2023, AECOM field personnel conducted groundwater sampling activities within the soil IM excavation area. AECOM personnel collected one groundwater sample from monitoring well Q6RS-MW0003. The sample was submitted to a fixed-based laboratory for analysis by United States Environmental Protection Agency Method 6020B for metals (barium and copper). Barium and copper were detected at 18 micrograms per liter (µg/L) and 14 µg/L, respectively, and were below the State of Florida Groundwater Cleanup Target Levels (GCTLs) for barium at 2,000 µg/L and copper at 1,000 µg/L.

Chadwick Sloan Lee↗
NASA NTRS2024

Shallow Soil Polychlorinated Biphenyl Site Assessment Report: General Services Administration Reclamation Yard Solid Waste Management Unit 010

This report presents a summary of the shallow soil polychlorinated biphenyl (PCB) site assessment activities that occurred from December 2020 through July 2022 at General Services Administration Reclamation Yard, Solid Waste Management Unit (SWMU) 010, located at the John F. Kennedy Space Center (KSC), Florida. The site is monitored under KSC’s Resource Conservation and Recovery Act Corrective Action Program, which also meets the requirements of Chapter 62-780, Florida Administrative Code. For the purposes of this report, three separate shallow soil plumes, known as the Northeast Shallow Soil PCB Plume, Southeast Shallow Soil PCB Plume, and West Shallow Soil PCB Plume, were identified for this site. The activities presented in this report include seven field events conducted between December 2020 and July 2022, which include shallow soil sample collection in the Northeast, Southeast, and West Shallow Soil PCB Plumes. AECOM Technical Services, Inc., personnel collected 330 soil samples from 118 boring locations. The samples were collected at 0.5-foot depth intervals to various depths based on analytical results and depth to groundwater. The soil samples were submitted to a fixed-based laboratory for analysis by United States Environmental Protection Agency Method 8082A for total PCBs. Several soil samples had PCB concentrations above the State of Florida Direct Exposure Residential and Industrial Soil Cleanup Target Levels (SCTLs), and two soil samples had PCB concentrations above the State of Florida Leachability for Groundwater. No soil borings were located beneath impervious surfaces, such as concrete or asphalt. The current Land Use Control Implementation Plan (LUCIP) covers PCBs in soils above the residential SCTL, which includes the paved areas.

soil assessment↗
DOE OSTI2020

Analytical formula for pellet fuel source density in toroidal plasma configurations based on an areal deposition model

An analytical formula for the fuel source density η F (Ψ) over a magnetic flux surface Ψ following pellet injection is derived. During pellet motion the ablated and ionized fuel will be initially deposited nearby the pellet, prior to subsequent homogenization within the magnetic flux surfaces. Here in our research, it is assumed that the deposition area projected normal to the magnetic field is on the order of the cross-sectional area of the ionized ablation column whose axis is aligned with the magnetic field. Previous pellet deposition codes [1] employed a point source deposition approximation, which overpredicts the surface-averaged density, particularly when the obliquity between the pellet trajectory and the flux surface normal approaches 90 degrees. A key finding of this study is that as the obliquity approaches 90 degrees, grazing trajectory, the areal model predicts a well behaved η F and removes the unphysical divergence stemming from the point model. To illustrate the difference exhibited between areal and point models for near grazing trajectories, we considered vertical pellet injection into a CFETR-like tokamak with a negative triangularity plasma cross section using a pellet ablation/deposition module.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2020

The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

Abstract Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic and synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility and histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.

Azodi, Christina B.↗
DOE OSTI2020

Electron transport in gaseous detectors with a Python-based Monte Carlo simulation code

Understanding electron drift and diffusion in gases and gas mixtures is a topic of central importance for the development of modern particle detection instrumentation. The industry-standard MagBoltz code has become an invaluable tool during its 20 years of development, providing capability to solve for electron transport (‘swarm’) properties based on a growing encyclopedia of built-in collision cross sections. We have made a refactorization of this code from FORTRAN into Cython, and studied a range of gas mixtures of interest in high energy and nuclear physics. The results from the new open source PyBoltz package match the outputs from the original MagBoltz code, with comparable simulation speed. An extension to the capabilities of the original code is demonstrated, in implementation of a new Modified Effective Range Theory interface. We hope that the versatility afforded by the new Python code-base will encourage continued use and development of the MagBoltz tools by the particle physics community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Charge breeders: Development of diagnostic tools to probe the underlying physics

Charge breeders were developed more than 20 years ago in the context of radioactive ion beam (RIB) production. The main goal is to boost the charge state of a singly charged RIB to a higher value matching the A/Q of a post-accelerator. In that way, the RIB produced at some tens of keV can efficiently be accelerated to energies in a range of few MeV/u up to several tens of MeV/u, which is of interest for nuclear structure and nuclear astrophysics experiments. Two families of charge breeders have been developed: one based on Electron Cyclotron Resonance Ion Sources (ECRISs) suitable for Continuous Wave (CW) operation and another built around Electron Beam Ion Sources (EBISs) used for pulsed post-accelerators. For many years, experimental studies have been carried out to enhance the charge breeding process and improve the extracted beam quality, i.e., purity, intensity, emittance, and time structure. The evolution of the charge breeders is also closely related to the emergence of new facilities delivering even more exotic beams. Diagnostic tools, such as Faraday cups, beam profile monitors, and emittance scanners, are mandatory to tune the machines and evaluate their performances. However, to go beyond that, a better understanding of plasma physics (in ECRIS) and electron-ion interactions (in EBIS), as well as the 1+ beam characteristics, for instance, energy spread transverse emittance, is needed. Therefore, simulation codes modeling the physics phenomena in both type of charge breeders were developed to support the understanding of experimental outputs and to gain insights into non-observable parameters. Nevertheless, more sophisticated diagnostic tools are required to improve the charge breeding performance and to extend the potential applications toward new RIB facilities. This Review will present the two kinds of charge breeders and their technical evolutions. It will review the diagnostic tools and simulation codes employed for operation and evaluation of the internal physics processes.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Modeling of advanced accelerator concepts

Computer modeling is essential to research on Advanced Accelerator Concepts (AAC), as well as to their design and operation. This paper summarizes the current status and future needs of AAC systems and reports on several key aspects of (i) high-performance computing (including performance, portability, scalability, advanced algorithms, scalable I/Os and In-Situ analysis), (ii) the benefits of ecosystems with integrated workflows based on standardized input and output and with integrated frameworks developed as a community, and (iii) sustainability and reliability (including code robustness and usability).

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Opacities of singly and doubly ionized neodymium and uranium for kilonova emission modeling

ABSTRACT Even though the electromagnetic counterpart AT2017gfo to the binary neutron star merger GW170817 is powered by the radioactive decay of r-process nuclei, only few tentative identifications of light r-process elements have been made so far. One of the major limitations for the identification of heavy nuclei is incomplete or missing atomic data. While substantial progress has been made on lanthanide atomic data over the last few years, for actinides there has been less emphasis, with the first complete set of opacity data only recently published. We perform atomic structure calculations of neodymium (Z = 60) as well as the corresponding actinide uranium (Z = 92). Using two different codes [flexible atomic code (fac) and hartree–fock-relativistic (hfr)] for the calculation of the atomic data, we investigate the accuracy of the calculated data (energy levels and electric dipole transitions) and their effect on kilonova opacities. For the fac calculations, we optimize the local central potential and the number of included configurations and use a dedicated calibration technique to improve the agreement between theoretical and available experimental atomic energy levels (AELs). For ions with vast amounts of experimental data available, the presented opacities agree quite well with previous estimations. On the other hand, the optimization and calibration method cannot be used for ions with only few available AELs. For these cases, where no experimental nor benchmarked calculations are available, a large spread in the opacities estimated from the atomic data obtained with the various atomic structure codes is observed. We find that the opacity of uranium is almost double the neodymium opacity.

Flörs, A. (ORCID:0000000320242819)↗
DOE OSTI2022

PETSc/TAO Users Manual: Revision 3.18

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

PETSc/TAO Users Manual (Rev. 3.20)

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

PETSc/TAO Users Manual Revision 3.22

This manual describes the use of the Portable, Extensible Toolkit for Scientific Computation (PETSc) and the Toolkit for Advanced Optimization (TAO) for the numerical solution of partial differential equations (PDEs) and related problems on high-performance computers. PETSc/TAO is a suite of data structures and routines that provide the building blocks for implementing large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all distributed memory communication.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Propagation of radio frequency waves through turbulent plasmas

The practical and economic viability of tokamak fusion reactors depends, in a significant way, on the efficiency of radio frequency (RF) waves to deliver energy and momentum to the plasma in the core of the reactor. The RF electromagnetic waves, excited by antenna structures placed near the wall of a tokamak, have to propagate through the turbulent edge plasma along their path to the core of the fusion device. In present day experiments, the radial width of the edge region and scrape-off layer is of the order of a few centimeters. In ITER, and in future fusion reactors, this width will be of the order of tens of centimeters. Any effects on RF waves due to plasma turbulence have to be properly understood in order to optimize the delivery of RF energy and momentum into the core. This paper is on a multi-pronged, theoretical and computational, approach that is being pursued to quantify the effect of edge plasma turbulence on the propagation of RF waves. The theoretical and analytical models are based on solutions of the Faraday-Ampere equation in a magnetized plasma and on the Kirchhoff tangent plane approximation. An effective medium approach has been developed so as to approximate the permittivity of a turbulent plasma by analytical expressions. The computations are being carried out with a newly developed code ScaRF that is based on the finite difference finite domain technique for solving Maxwell's equations. The plasma permittivity can be assigned as desired. The code is being used to validate the analytical and theoretical models and to evaluate their limitations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗