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At least 1,711 records · Page 95

Advantages and Limits of Metagenomic Assembly and Binning of a Giant Virus

ABSTRACT Giant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here, we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of the major capsid protein indicated the presence of other giant viruses in the sample matrix but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. However, our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics. IMPORTANCE The discovery of large and giant nucleocytoplasmic large DNA viruses (NCLDV) with genomes in the megabase range and equipped with a wide variety of features typically associated with cellular organisms was one of the most unexpected, intriguing, and spectacular breakthroughs in virology. Recent studies suggest that these viruses are highly abundant in the oceans, freshwater, and soil, impact the biology and ecology of their eukaryotic hosts, and ultimately affect global nutrient cycles. Genome-resolved metagenomics is becoming an increasingly popular tool to assess the diversity and coding potential of giant viruses, but this approach is currently lacking validation.

59 BASIC BIOLOGICAL SCIENCES↗

Validation of the SCEPTRE Boltzmann-CSD Solver

A new Boltzmann-CSD solver has been developed within the SCEPTRE radiation-transport code, based on the 1st-order form of the transport equation, using discontinuous finite elements in space and energy and discrete ordinates in angle. The Boltzmann-CSD solver has been validated against experimental data for electron energy deposition distributions and for electron emission spectra. Comparison of the calculated results with experimental data shows excellent agreement for many of the test configurations and reasonable agreement for other test configurations. The tests have also been modeled with the ITS Monte Carlo code, which also shows excellent to reasonable agreement with the SCEPTRE results and experimental data. The SCEPTRE Boltzmann-CSD solver relies on electron cross sections generated by the legacy CEPXS code, which currently is limited to electron-only Boltzmann-CSD cross sections. Performing full electron-photon radiation transport with the Boltzmann-CSD solver will require further development in the cross section generating code. For the energy- deposition calculations, neglecting photon transport results in at most about 5% overprediction of the energy deposition for high-energy electrons on high-Z targets, and relatively insignificant difference for the other test configurations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Preliminary Axial Flow Turbine Design and Off-Design Performance Analysis Methods for Rotary Wing Aircraft Engines: Validation - Part 1

For the preliminary design and the off-design performance analysis of axial flow turbines, a pair of intermediate level-of-fidelity computer codes, TD2-2 (design; reference 1) and AXOD (off-design; reference 2), are being evaluated for use in turbine design and performance prediction of the modern high performance aircraft engines. TD2-2 employs a streamline curvature method for design, while AXOD approaches the flow analysis with an equal radius-height domain decomposition strategy. Both methods resolve only the flows in the annulus region while modeling the impact introduced by the blade rows. The mathematical formulations and derivations involved in both methods are documented in references 3, 4 for TD2-2) and in reference 5 (for AXOD). The focus of this paper is to discuss the fundamental issues of applicability and compatibility of the two codes as a pair of companion pieces, to perform preliminary design and off-design analysis for modern aircraft engine turbines. Two validation cases for the design and the off-design prediction using TD2-2 and AXOD conducted on two existing high efficiency turbines, developed and tested in the NASA/GE Energy Efficient Engine (GE-E3) Program, the High Pressure Turbine (HPT; two stages, air cooled) and the Low Pressure Turbine (LPT; five stages, un-cooled), are provided in support of the analysis and discussion presented in this paper.

Chen, Shu-cheng, S.↗

Small-scale validation tests for MFIX-Exa CFD-DEM

This report describes several bench-scale fluidization experiments that can be used to validate the CFD-DEM method as encapsulated in the MFIX-Exa code. The five cases considered are the cold-flow fluidized beds of Müller et al., Link et al. (spout-fluid), and Goldschmidt et al. (bi-disperse), the hot fluidized bed of Patil et al., and the adsorbing fluidized bed of Li et al. and Janssen. In most cases, MFIX-Exa with “standard” or “typical” CFD-DEM settings, the Gidaspow drag model, and the Gunn heat transfer provide a relatively good prediction of the quantities considered: mean void fraction profiles, mean velocity profiles, fluctuating velocity profiles, mean particle temperature and segregation index. These results, with other verification and validation tests reported elsewhere, contribute to a body of work providing confidence and credibility in CFD predictions from the MFIX-Exa code.

97 MATHEMATICS AND COMPUTING↗

Evaluation of Agency Non-Code Layered Pressure Vessels (LPVs) : Appendices - Volume 2

In coordination with the Office of Safety and Mission Assurance and the respective Center Pressure System Managers (PSMs), the NASA Engineering and Safety Center (NESC) was requested to formulate a consensus draft proposal for the development of additional testing and analysis methods to establish the technical validity, and any limitation thereof, for the continued safe operation of facility non-code layered pressure vessels. The PSMs from each NASA Center were asked to participate as part of the assessment team by providing, collecting, and reviewing data regarding current operations of these vessels. This document contains the appendices to the main report.

Prosser, William H.↗

Nondestructive and destructive assay for forensics characterization of weapons-grade plutonium produced in LEU irradiated in a thermal neutron spectrum

A post-irradiation examination (PIE) of an enriched uranium sample was performed to advance a nuclear forensics methodology, based on intra-elemental nuclide ratios. The PIE was carried out on a few milligrams of low enriched uranium dioxide (LEUO 2 ) sample, irradiated to a burnup of 1 GWd/MTU. The PIE of the LEUO 2 sample provided the concentration of selected plutonium and fission product nuclides ( 239 Pu, 240 Pu, 241 Pu, 91 Y, 95 Zr, 95 Nb, 103 Ru, 133 Cs, 134 Cs, 135 Cs, 137 Cs, 136 Ba, 138 Ba, 140 Ba, 140 La, 141 Ce, 144 Ce, 149 Sm, 150 Sm, 152 Sm, 153 Eu, and 154 Eu). The PIE supported validation of the MCNP (Monte Carlo N-Particle neutronics simulation code) predicted concentration of these nuclides in the irradiated LEUO 2 sample. This study showed that most of the MCNP predicted nuclide concentrations were within 15% and several within 10% compared to the PIE results. Furthermore, gamma and mass spectrometry of nuclides in irradiated LEUO 2 enabled the determination of uranium burnup and time since irradiation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Low-Speed Testing of the 5.2% Semispan CRM-HL in the DNW-NWB Wind Tunnel

In this paper the wind tunnel test of the 5.2% CRM-HL in the DNW-NWB low speed wind tunnel is described. The tunnel test campaign is settled in the DLR project ADaMant, in which it is of interest to generate qualitative data for CFD validation to improve the predictive accuracy, efficiency, and usability of physical modeling in CFD codes at the borders of the flight envelope. Different configurations of the CRM-HL were tested in a closed as well as in an open test section of the wind tunnel. Several measurement techniques were used to generate validation data including forces and moments, pressures, flow visualization with tufts and oil painting, and infrared thermography for boundary layer transition detection. The evaluation of the results focuses on these techniques in the closed test section. The test comprises Mach numbers from 0.15 to 0.23 and Reynolds numbers from 1.2x10 6 to 1.2x10 6 . Some results are also compared to data from the NASA Langley Research Center 14x22 Foot wind tunnel to assess the repeatability of measurements of the same model in different wind tunnels.

DLR↗

Application of New Los Alamos OPLIB Opacities in Solar Modeling Using the Mesa Code

The Sun provides the only local laboratory to test our understanding of stellar physics. The production, then, of valid dynamical models of the Sun is critical to how we think about other stars. Despite improvements in modeling methodologies and abundance measurements, solar models continue to reproduce errors in convection zone depth and surface helium abundance compared to helioseismic observations. Using the 1D stellar evolution code MESAstar, this work first evaluates the effect of changes to timestep resolution and mixing length theory on model outputs. A standard test case is then constructed with both GS98 and AGSS09 abundances using OP and OPAL opacities before implementing the new Los Alamos OPLIB opacities. It is shown that, when using GS98 abundances, OPLIB opacities improve agreement with helioseismic inference of the convection zone base radius, R czb , by 1.68-σ and 1.19-σ compared to OP and OPAL, respectively, while worsening agreement with the inferred envelope helium mass fraction, Y surf , by 0.63-σ and 0.98-σ for OP and OPAL.

14 SOLAR ENERGY↗

CTF Validation and Verification (V.4.2)

Coolant-Boiling in Rod Arrays- Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for Light Water Reactor (LWR) analysis. It uses a two-fluid, three-field (i.e. fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of nine conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and has been used and modified by several institutions over the last several decades. COBRA-TF is also used at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently became the PSU RDFMG version of COBRA-TF (CTF). One part of the improvement process includes validating the methods in CTF. This document seeks to provide a certain level of certainty and confidence in the predictive capabilities of the code for the scenarios it was designed to model-rod bundle geometries with operating conditions that are representative of prototypical Pressurized Water Reactor (PWR)s and Boiling Water Reactor (BWR)s in both normal and accident conditions. This is done by modeling a variety of experiments that simulate these scenarios and then presenting a qualitative and quantitative analysis of the results that demonstrates the accuracy to which CTF is capable of capturing specific quantities of interest.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

An arbitrary grid CFD algorithm for configuration aerodynamics analysis. Volume 1: Theory and validations

This report documents the user input and output data requirements for the FEMNAS finite element Navier-Stokes code for real-gas simulations of external aerodynamics flowfields. This code was developed for the configuration aerodynamics branch of NASA ARC, under SBIR Phase 2 contract NAS2-124568 by Computational Mechanics Corporation (COMCO). This report is in two volumes. Volume 1 contains the theory for the derived finite element algorithm and describes the test cases used to validate the computer program described in the Volume 2 user guide.

Baker, A. J.↗

ASME Code change proposal to implement new universal high temperature constitutive models for Section III, Division 5

This report completes work on a universal high temperature constitutive model suitable for use with the ASME Boiler & Pressure Vessel Code Section III, Division 5 rules for the design by inelastic analysis of Class A nuclear reactor components. The goals of this work are to provide a simple model form that adequately captures the high temperature response of materials and can be applied to any future Code material. Additionally, the report describes an automated process for calibrating a model against test data. The idea is to simplify the effort required to generate a constitutive model for an arbitrary material, provided test data is available. This will accelerate the process of qualifying new Code materials in the future. In addition, the report provides calibrated models and detailed validation comparisons to test data for five currently-qualified or soon-to-be qualified materials: 316H, Grade 91, Alloy 800H, Alloy 617, and Alloy 709. The report surveys the available data for the remaining two ASME Class Materials --- 2.25Cr-1Mo and 304H --- concluding that there is enough data data to generate a model for 2.25Cr-1Mo steel provided some additional sources of non-public data can be included in the test database, but that a dedicated cyclic test campaign would be needed for 304H. Supplemental material includes the full text of an ASME Code change proposal to incorporate the models for the four currently-qualified Class A material, detailed validation comparisons to test data for the five material models, and input files for reference implementations of the constitutive models in the NEML and NEML2 modeling frameworks.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

3D Material Response of the MSL Heatshield Using NuSil-Coated PICA

The Mars Science Laboratory (MSL) was protected during its atmospheric entry by an instrumented heatshield that used NASA's Phenolic Impregnated Carbon Ablator (PICA) material [1]. PICA is a lightweight carbon fiber/polymeric resin material that offers outstanding performance for protecting probes during planetary entry. Data from the Mars Entry Descent and Landing Instrument (MEDLI) suite on MSL offers unique in-flight validation data for models of material response and atmospheric entry. MEDLI recorded, among other things, time-resolved in-depth temperature data of PICA using thermocouple sensors assembled in the MEDLI Integrated Sensor Plugs (MISP) [2]. A space-grade silicone-based coating commercially known as NuSil CV-1144-0 [3] was applied to the entire MSL heatshield, including the MEDLI plugs, to mitigate the spread of dust from PICA. Modeling the thermal response of PICA-NuSil (PICA-N) system is still an open challenge. Ground testing of PICA-N models exhibited surface temperature jumps of the order of 150 K due to oxide scale formation and sub-sequent NuSil burn-off. It is therefore critical to include a validated model for the material response of the coating in engineering codes. A test campaign has been conducted at the NASA’s Langley HyMETS [4] facility to screen the response of PICA-N and gather detailed data on its behavior [5]. A first model of PICA-N thermal response has been developed using the Hy-METS experiments [6]. The objective of this work is to analyze the material response of the latest PICA-N model compared to the engineering model used to simulate the entry of MSL. The environment and material response around the MSL aeroshell during Mars atmospheric entry is simulated using a collection of tools. The Direct Simulation Monte Carlo SPARTA code [7] is used in the rarefied regime, the Data Parallel Line Relaxation (DPLR) code [8] is used in the continuum regime and radiative heating conditions are provided by the Nonequilibrium air radiation (NEQAIR) code [9] to estimate the environmental conditions. The thermal response inside the material is computed using the Porous material Analysis Toolbox based on Open-FOAM (PATO) [10,11,12]. Thermodynamic and chemistry properties are estimated using the Mutation++ library [13]. The approach implemented in PATO as a first cut PICA-N thermal response model is outlined in Figure 1. While the recession is less than the coating thickness, the Surface mass and energy balance Boundary Condition (SBC) uses the NuSil B’ tables. Once the recession removes the coating, the usual PICA B’ tables are used for the SBC. The B’ tables are computed using an equilibrium solver implemented in Mutation++, given the temperature, pressure, blowing rate, composition of the pyrolysis and environment gases, and the condensed species at the surface. Preliminary results of the 3D material response of the MSL heat-shield at the peak heating (80 sec after Entry Interface) are shown in Figure 2. Current NASA’s mission to Mars, Mars 2020, used the spare heatshield of MSL for thermal protection during entry, descent, and landing. In preparation for Mars 2020 post-flight analysis, the PATO high-fidelity material response capability was benchmarked against flight data from MEDLI. This effort represents an important milestone toward the development of validated predictive capabilities for designing thermal protection systems for planetary probes. This bench-marking is awaiting the final release of the MEDLI-2 data.

Aerospace↗

Exploring phage–host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics

Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage–host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.

Bacterial Pathogenesis↗

PICSAR-QED: a Monte Carlo module to simulate strong-field quantum electrodynamics in particle-in-cell codes for exascale architectures

Abstract Physical scenarios where the electromagnetic fields are so strong that quantum electrodynamics (QED) plays a substantial role are one of the frontiers of contemporary plasma physics research. Investigating those scenarios requires state-of-the-art particle-in-cell (PIC) codes able to run on top high-performance computing (HPC) machines and, at the same time, able to simulate strong-field QED processes. This work presents the PICSAR-QED library, an open-source, portable implementation of a Monte Carlo module designed to provide modern PIC codes with the capability to simulate such processes, and optimized for HPC. Detailed tests and benchmarks are carried out to validate the physical models in PICSAR-QED, to study how numerical parameters affect such models, and to demonstrate its capability to run on different architectures (CPUs and GPUs). Its integration with WarpX, a state-of-the-art PIC code designed to deliver scalable performance on upcoming exascale supercomputers, is also discussed and validated against results from the existing literature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

CFD validation of a supersonic laminar flow control concept

A three-dimensional Navier-Stokes code is used in conjunction with a linear compressible stability analysis code to develop a numerical procedure for prediction of laminar flow transition. The procedure is applied to a modified F-16XL fighter with a laminar flow control glove at supersonic speed. Details of boundary layer stability analysis indicate that, computationally, laminar flow could be realized on the highly swept wing in the absence of the leading edge attachment-line contamination. Effects of the three-dimensionality of the flow were shown to be important in the boundary layer stability analysis. The numerically predicted surface pressures compare favorably with the flight test data.

Woan, Chung-Jin↗

CFD activities at NASA. Marshall Space Flight Center (validation)

Computational fluid dynamics objectives are presented for Marshall Space Flight Center. Topics covered include: codes in use, applications to hardware development, and the Center's benchmark plan for the future. All results are presented in viewgraph format.

Schutzenhofer, Luke A.↗

Evaluation of the Land Surface Reflectance Fundamental Climate Data Record

The land surface reflectance is a fundamental climate data record at the basis of the derivation of other climate data records (Albedo, LAI/Fpar, Vegetation indices) and has been recognized as a key parameter in the understanding of the land-surface-climate processes. In this presentation, we present the validation of the Land surface reflectance used for MODIS, VIIRS, Landsat 8 and Sentinel 2 data. This methodology uses the 6SV Code and data from the AERONET network. The overall accuracy clearly reaches the satellite specifications. To understand how to improve the validation, we developed an exhaustive error budget. Results show an impact of the absorption of aerosol and of the fine mode volume concentration.

Atmospheric correction↗

CTF Validation and Verification: Version 4.3

Coolant-Boiling in Rod Arrays- Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for light water reactor (LWR) analysis. It uses a two-fluid, three-field (i.e., fluid film, fluid drops, and vapor) modeling approach. Both subchannel and 3D Cartesian forms of nine conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and has been used and modified by several institutions over the last several decades. COBRA-TF is also used at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently became the CTF. One part of the improvement process includes validating the methods in CTF. This document seeks to provide a certain level of certainty and confidence in the predictive capabilities of the code for the scenarios it was designed to model—rod bundle geometries with operating conditions that are representative of prototypical pressurized water reactor (PWR)s and boiling water reactor (BWR)s in both normal and accident conditions. This is done by modeling a variety of experiments that simulate these scenarios and then presenting a qualitative and quantitative analysis of the results that demonstrates the accuracy to which CTF is capable of capturing specific quantities of interest.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗