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At least 1,513 records · Page 84

Integrating biological knowledge for mechanistic inference in the host-associated microbiome

Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.

59 BASIC BIOLOGICAL SCIENCES↗

Multischeme transport with upwinding for Rattlesnake code

This report conclude our efforts at INL to make Rattlesnake, the MOOSE-based radiation multigroup transport application, fully support the multischeme transport capability. Specifically, it details all five types of interface condition with upwinding method for coupling eight available discretization schemes within Rattlesnake. These discretization schemes include SN (discrete ordinates method), PN (spherical harmonics expansion method) and diffusion for angular discretization, and continuous finite element method (CFEM) and discontinuous finite element method (DFEM) for spatial discretization. The other type of method based on Lagrange multipliers for coupling schemes based on CFEM has been studied in the past. Besides simple test problems, a more realistic application of multischeme transport for TREAT (transient reactor test facility) experiment modeling are presented. Several enhancements are reviewed at the end which could potentially be useful in the future.

97 MATHEMATICS AND COMPUTING↗

Computational support of the laminar flow supersonic wind tunnel, CNSFV code development, Maglev, and grid generation

This final report covers the work done on corporate agreement NCC2-616 over a period of 5 1/2 years. It is broken into three segments of approximately 1 1/2 to 2 years each. The report is a summary report and is not intended to be comprehensive of all the work done under this corporate agreement. A more complete coverage of the work done is obtained from the papers and reports listed in the 'Papers' section. Additional reporting of significant work was done through 'Technical Highlights' and 'Research and Technical Summaries'. A listing of copies are given in the 'Technical Highlights and R and T' section. The work was also reported in a series of seminars, conference meetings, branch reviews, workshops, and project reviews. A list of these talks is given in the 'Presentation' section. Also during this time three students ranging from high school to graduate level were supervised. A list of the students and the type of work accomplished is given in the 'Mentoring' section. The report concludes with the 'Appendices' sections which include the three papers produced during the last 1 1/2 years of this corporate agreement.

Klopfer, Goetz H.↗

The long road to ignition: An eyewitness account

This paper reviews the many twists and turns in the long journey that culminated in ignition in late 2022 using the laser heated indirect-drive approach to imploding DT filled targets at the National Ignition Facility (NIF), located at the Lawrence Livermore National Laboratory (LLNL). We describe the early origins of the Laser Program at LLNL and key developments such as the paradigm shifting birth of high energy density physics (HEDP) studies with lasers, changes in choice of laser wavelength, and the development of key diagnostics and computer codes. Fulfilling the requirements of the multi-faceted Nova Technical Contract was a necessary condition for the approval of the NIF, but more importantly, the end of the Cold War and the cessation of nuclear testing were key catalysts in that approval, along with the ready-and-waiting field of HEDP. The inherent flexibility of the field of laser driven inertial confinement fusion played a fundamental role in achieving success at the NIF. We describe how the ultimately successful ignition target design evolved from the original “point design” target, through the lessons of experiment. All key aspects of that original design changed: The capsule's materials and size were changed; the hohlraum's materials, size, laser entrance hole size, and gas fills were also all changed, as were the laser pulse shapes that go along with all those changes. The philosophy to globally optimize performance for stability (by raising the adiabat and thus lowering the implosion convergence) was also key, as was progress in target fabrication, and in increasing NIF's energy output. The persistence of the research staff and the steadfast backing of our supporters were also necessary elements in this success. We gratefully acknowledge seven decades of researcher endeavors and four decades of the dedicated efforts of many hundreds of personnel across the globe who have participated in NIF construction, operation, target fabrication, diagnostic, and theoretical advances that have culminated in ignition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An X-Ray Analysis Database of Photoionization Cross Sections Including Variable Ionization

Results of research efforts in the following areas are discussed: review of the major theoretical and experimental data of subshell photoionization cross sections and ionization edges of atomic ions to assess the accuracy of the data, and to compile the most reliable of these data in our own database; detailed atomic physics calculations to complement the database for all ions of 17 cosmically abundant elements; reconciling the data from various sources and our own calculations; and fitting cross sections with functional approximations and incorporating these functions into a compact computer code.Also, efforts included adapting an ionization equilibrium code, tabulating results, and incorporating them into the overall program and testing the code (both ionization equilibrium and opacity codes) with existing observational data. The background and scientific applications of this work are discussed. Atomic physics cross section models and calculations are described. Calculation results are compared with available experimental data and other theoretical data. The functional approximations used for fitting cross sections are outlined and applications of the database are discussed.

Wang, Ping↗

Validating LES for Jet Aeroacoustics

Engineers charged with making jet aircraft quieter have long dreamed of being able to see exactly how turbulent eddies produce sound and this dream is now coming true with the advent of large eddy simulation (LES). Two obvious challenges remain: validating the LES codes at the resolution required to see the fluid-acoustic coupling, and the interpretation of the massive datasets that are produced. This paper addresses the former, the use of advanced experimental techniques such as particle image velocimetry (PIV) and Raman and Rayleigh scattering, to validate the computer codes and procedures used to create LES solutions. This paper argues that the issue of accuracy of the experimental measurements be addressed by cross-facility and cross-disciplinary examination of modern datasets along with increased reporting of internal quality checks in PIV analysis. Further, it argues that the appropriate validation metrics for aeroacoustic applications are increasingly complicated statistics that have been shown in aeroacoustic theory to be critical to flow-generated sound, such as two-point space-time velocity correlations. A brief review of data sources available is presented along with examples illustrating cross-facility and internal quality checks required of the data before it should be accepted for validation of LES.

Bridges, James↗

Atomic Data for Plasma Spectroscopy: The CHIANTI Database, Improvements and Challenges

CHIANTI is an atomic database and software package for modeling emission lines and continua from hot astrophysical plasmas. It is freely available to all researchers and has been widely used in the Heliophysics and Astrophysics communities for almost 25 years. In this review, we summarize the properties of the current version of the database and give an overview of the relevant atomic processes. We also discuss progress towards a complete implementation of collisional-radiative modeling, simultaneously solving for atomic level and ion populations for individual elements.

A&M databases↗

Data processing techniques used with MST radars: A review

The data processing methods used in high power radar probing of the middle atmosphere are examined. The radar acts as a spatial filter on the small scale refractivity fluctuations in the medium. The characteristics of the received signals are related to the statistical properties of these fluctuations. A functional outline of the components of a radar system is given. Most computation intensive tasks are carried out by the processor. The processor computes a statistical function of the received signals, simultaneously for a large number of ranges. The slow fading of atmospheric signals is used to reduce the data input rate to the processor by coherent integration. The inherent range resolution of the radar experiments can be improved significant with the use of pseudonoise phase codes to modulate the transmitted pulses and a corresponding decoding operation on the received signals. Commutability of the decoding and coherent integration operations is used to obtain a significant reduction in computations. The limitations of the processors are outlined. At the next level of data reduction, the measured function is parameterized by a few spectral moments that can be related to physical processes in the medium. The problems encountered in estimating the spectral moments in the presence of strong ground clutter, external interference, and noise are discussed. The graphical and statistical analysis of the inferred parameters are outlined. The requirements for special purpose processors for MST radars are discussed.

Rastogi, P. K.↗

A review on the state of thermal hydraulics research on air ingress scenarios in High-Temperature Gas-cooled Reactors following a D-LOFC

With the expectation of near-immediate carbon neutrality, widespread implementation of proven High-Temperature Gas-cooled Reactors (HTGRs) embodies a viable solution pathway given their inherent, passive safety features and high thermal efficiency. This study provides an overview of the current state of research involving the thermal hydraulics associated with air ingress from a depressurized loss of forced cooling (D-LOFC) in HTGRs. Accurately characterizing and predicting the physical phenomena underlying air ingress is of paramount concern, as the integrity of the fuel and core graphite support structures are threatened by the presence of oxygen. Broadly speaking, the air ingress scenario can be delineated into three main stages: (1) Depressurization, (2) Density-Driven Flow, and (3) Natural Convection. In tandem with the underlying fundamental theory, this review collates and synthesizes the existing body of contemporary research concerning the air ingress scenario following a D-LOFC. As evinced by this review, our current understanding and predictive abilities have benefited from extensive research, predominantly concentrated on the rate of air ingestion into the core. Here, additional research is necessary to holistically capture the phenomenology of an air ingress scenario following a D-LOFC by considering an additional variable: the oxygen content of the ingressing air. The latter variable requires investigation into the complex interactions of the fully integrated system. Additionally, while numerical tools are evolving domestically through the Nuclear Energy Advanced Modeling and Simulation program, a sufficiently validated code remains absent.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education and training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction data via different types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Strategies for the production of cell wall‐deconstructing enzymes in lignocellulosic biomass and their utilization for biofuel production

Summary Microbial cell wall‐deconstructing enzymes are widely used in the food, wine, pulp and paper, textile, and detergent industries and will be heavily utilized by cellulosic biorefineries in the production of fuels and chemicals. Due to their ability to use freely available solar energy, genetically engineered bioenergy crops provide an attractive alternative to microbial bioreactors for the production of cell wall‐deconstructing enzymes. This review article summarizes the efforts made within the last decade on the production of cell wall‐deconstructing enzymes in planta for use in the deconstruction of lignocellulosic biomass. A number of strategies have been employed to increase enzyme yields and limit negative impacts on plant growth and development including targeting heterologous enzymes into specific subcellular compartments using signal peptides, using tissue‐specific or inducible promoters to limit the expression of enzymes to certain portions of the plant or certain times, and fusion of amplification sequences upstream of the coding region to enhance expression. We also summarize methods that have been used to access and maintain activity of plant‐generated enzymes when used in conjunction with thermochemical pretreatments for the production of lignocellulosic biofuels.

09 BIOMASS FUELS↗

Scoping Analysis of MACCS Modeling Improvements for the Study of Protective Action Recommendations

In late 2004, the U.S. Nuclear Regulatory Commission (NRC) initiated a project to analyze the relative efficacy of alternative protective action strategies in reducing consequences to the public from a spectrum of nuclear power plant core melt accidents. The study is documented in NUREG/CR-6953, “Review of NUREG-0654, Supplement 3, ‘Criteria for Protective Action Recommendations for Severe Accidents,’” Volumes 1, 2, and 3. The Protective Action Recommendations (PAR) study provided a technical basis for enhancing the protective action guidance contained in Supplement 3, “Guidance for Protective Action Strategies,” to NUREG-0654/FEMA-REP-1, Rev. 1, “Criteria for Preparation and Evaluation of Radiological Emergency Response Plans and Preparedness in Support of Nuclear Power Plants, ” dated November 2011. In the time since, a number of important changes and additions have been made to the MACCS code suite, the nuclear accident consequence analysis code used to perform the study. The purpose of this analysis is to determine whether the MACCS results used in the PAR study would be different given recent changes to the MACCS code suite and input parameter guidance. Updated parameters that were analyzed include cohorts, keyhole evacuation, shielding and exposure parameters, compass sector resolution, and a range of source terms from rapidly progressing accidents. Results indicate that using updated modeling assumptions and capabilities may lead to a decrease in predicted health consequences for those within the emergency planning zone compared to the original PAR study.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Controlled flexibility in technical editing - The levels-of-edit concept at JPL

The levels-of-edit concept, which can be used to specify the amount of editorial effort involved in the preparation of a manuscript for publication, is discussed. Nine types of editing are identified and described. These include coordination edit (preparing estimates, gathering cost data, monitoring production processes), policy edit, integrity edit (making sure that parts of a publication match in a physical or numerical sense), screening edit (ensuring that the quality of camera-ready copy is sufficient for external publication), copy clarification edit, format edit, mechanical style edit, language edit, and substantive edit (reviewing the manuscript for content coherence, emphasis, subordination and parallelism). These functions are grouped into five levels of edit. An edit-level number is assigned to each manuscript, providing a quantitative and qualitative indicator of the editing to be done which is clearly understood by authors, managers, and editors alike. In addition, clear boundaries are drawn between normal and extraordinary editing tasks. Individual organizations will group various edits in different ways to reflect their needs and priorities; the essential element of the system is unambiguous definition and coding of the types and amount of work to be done.

Buehler, M. F.↗

Wind-tunnel based definition of the AFE aerothermodynamic environment

The Aeroassist Flight Experiment (AFE), scheduled to be performed in 1994, will serve as a precursor for aeroassisted space transfer vehicles (ASTV's) and is representative of entry concepts being considered for missions to Mars. Rationale for the AFE is reviewed briefly as are the various experiments carried aboard the vehicle. The approach used to determine hypersonic aerodynamic and aerothermodynamic characteristics over a wide range of simulation parameters in ground-based facilities is presented. Facilities, instrumentation and test procedures employed in the establishment of the data base are discussed. Measurements illustrating the effects of hypersonic simulation parameters, particularly normal-shock density ratio (an important parameter for hypersonic blunt bodies), and attitude on aerodynamic and aerothermodynamic characteristics are presented, and predictions from computational fluid dynamic (CFD) computer codes are compared with measurement.

Miller, Charles G.↗

Influence of Coupled Radiation and Ablation on the Aerothermodynamic Environment of Planetary Entry Vehicles

A review of recently published coupled radiation and ablation capabilities involving the simulation of hypersonic flowfields relevant to Earth, Mars, or Venus entry is presented. The three fundamental mechanisms of radiation coupling are identified as radiative cooling, precursor photochemistry, and ablation-radiation interaction. The impact of these mechanisms are shown to be significant for a 3 m radius sphere entering Earth at hypothetical Mars return conditions (approximately 15 km/s). To estimate the influence precursor absorption on the radiative flux for a wide range of conditions, a simplified approach is developed that requires only the non-precursor solution. Details of a developed coupled ablation approach, which is capable of treating both massively ablating flowfields in the sublimation regime and weakly ablating diffusion Climited oxidation cases, are presented. A review of the two primary uncoupled ablation approximations, identified as the blowing correction and film coefficient approximations, is made and their impact for Earth and Mars entries is shown to be significant for recession and convective heating predictions. Fully coupled ablation and radiation simulations are presented for the Mars return sphere throughout its entire trajectory. Applying to the Mars return sphere the Pioneer- Venus heritage carbon phenolic heatshield, which has properties available in the open literature, the differences between steady state ablation and coupling to a material response code are shown to be significant.

Johnston, Christopher O.↗

Assessing Uncertainties and Variability 34 Years of Surface Radiative Fluxes Using GEWEX SRB Release4-IP

The NASA/GEWEX Surface Radiation Budget (SRB) project produces 3-hrly shortwave and longwave surface and top of atmosphere radiative fluxes for the 1983-near present time period. The new Release 4 Integrated Product (IP) uses the newly recalibrated and processed ISCCP HXS product as its primary input for cloud and radiance data, replacing ISCCP DX with a ninefold increase in pixel count (10 km instead of 30 km). This first version retains a 1°x1° resolution enabling intercomparison against previous versions and other data sets such as CERES, but spans 34 years from July 1983 through June 2017 and was announced by Kummerow et al. 2019 (GEWEX News). This new IP product also uses an atmospheric temperature and moisture dataset known as nnHIRS and other parameters such as near surface and skin temperatures from SeaFlux and LandFlux data sets. In addition to the input data improvements, several important algorithm improvements have been made since Release 3. These include recalculated SW atmospheric transmissivities and reflectivities, updated ocean and snow/ice albedos, and variable total solar irradiance consistent with SORCE measurements. The LW code has been updated to improve the optical property treatment for clouds and aerosols are included in this version. Radiative treatment of ice clouds is also improved in the LW. The variable aerosol optical properties for the SW and LW are specified using a detailed aerosol history from the Max Planck Institute Aerosol Climatology (MAC). Here we present an assessment of the LW radiative fluxes and the uncertainty of those fluxes relative to the various inputs to surface SW/LW flux measurements from BSRN and PMEL buoys measurements. We review the validation of the SW and LW fluxes and then in terms of time series and then assess the products in terms of their long-term variability of the surface SW and LW net fluxes compared to multiple other data products including atmospheric reanalysis products. The comparisons of radiative estimates to observations are performed at various temporal scales and aimed at investigation of agreement at longer time averages but accessing potential change in diurnal magnitude and daily variability. Utilizing this uncertainty information, to access long-term variability of surface radiation components at selected region and global scales, considering satellite sampling/calibration “artifacts” as necessary. At the longer time scales, the net SW and net LW the TOA and surface have implications toward closure of the energy budgets at the surface, we assess these compared to other studies on energy budget closure for the same selected global and regional scales.

Paul W Stackhouse↗

Review and analysis of the DNW/Model 360 rotor acoustic data base

A comprehensive model rotor aeroacoustic data base was collected in a large anechoic wind tunnel in 1986. Twenty-six microphones were positioned around the azimuth to collect acoustic data for approximately 150 different test conditions. A dynamically scaled, blade-pressure-instrumented model of the forward rotor of the BH360 helicopter simultaneously provided blade pressures for correlation with the acoustic data. High-speed impulsive noise, blade-vortex interaction noise, low-frequency noise, and broadband noise were all captured in this extensive data base. Trends are presentes for each noise source, with important parametric variations. The purpose of this paper is to introduce this data base and illustrate its potential for predictive code validation.

Zinner, R. A.↗

Partitioned coupling strategies for multi-physically coupled radiative heat transfer problems

This article aims to propose new aspects concerning a partitioned solution strategy for multi-physically coupled fields including the physics of thermal radiation. Particularly, we focus on the partitioned treatment of electro–thermo-mechanical problems with an additional fourth thermal radiation field. One of the main goals is to take advantage of the flexibility of the partitioned approach to enable combinations of different simulation software and solvers. Within the frame of this article, we limit ourselves to the case of nonlinear thermoelasticity at finite strains, using temperature-dependent material parameters. For the thermal radiation field, diffuse radiating surfaces and gray participating media are assumed. Moreover, we present a robust and fast partitioned coupling strategy for the fourth field problem. Stability and efficiency of the implicit coupling algorithm are improved drawing on several methods to stabilize and to accelerate the convergence. To conclude and to review the effectiveness and the advantages of the additional thermal radiation field several numerical examples are considered to study the proposed algorithm. In particular we focus on an industrial application, namely the electro–thermo-mechanical modeling of the field-assisted sintering technology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗