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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

HSW-V v1.0: localized injections of interactive volcanic aerosols and their climate impacts in a simple general circulation model

Abstract. A new set of standalone parameterizations is presented for simulating the injection, evolution, and radiative forcing by stratospheric volcanic aerosols against an idealized Held–Suarez–Williamson (HSW) atmospheric background in the Energy Exascale Earth System Model version 2 (E3SMv2). In this model configuration (HSW with enabled volcanism, HSW-V), sulfur dioxide (SO2) and ash are injected into the atmosphere with a specified profile in the vertical, and they proceed to follow a simple exponential decay. The SO2 decay is modeled as a perfect conversion to a long-living sulfate aerosol which persists in the stratosphere. All three species are implemented as tracers in the model framework and are transported by the dynamical core's advection algorithm. The aerosols contribute simultaneously to local heating of the stratosphere and cooling of the surface by a simple plane-parallel Beer–Lambert law applied on two zonally symmetric radiation broadbands in the longwave and shortwave ranges. It is shown that the implementation parameters can be tuned to produce realistic temperature anomaly signatures of large volcanic events. In particular, results are shown for an ensemble of runs that mimic the volcanic eruption of Mt. Pinatubo in 1991. The design requires no coupling to microphysical subgrid-scale parameterizations and thus approaches the computational affordability of prescribed aerosol forcing strategies. The idealized simulations contain a single isolated volcanic event against a statistically uniform climate, where no background aerosols or other sources of externally forced variability are present. HSW-V represents a simpler-to-understand tool for the development of climate source-to-impact attribution methods.

Hollowed, Joseph P. (ORCID:0000000286581672)↗
NASA NTRS1977

Kinetics data for diffusion of outgas species from RTV 560

A detailed analytical and experimental study was made of the outgassing behavior of RTV 560 silicone rubber. The four outgas species which predominate in the temperature range of 285 K to 425 K were separately identified. The initial concentration of these species in the parent material and their bulk volatilities were determined. The diffusion coefficients and activation energy for diffusion of the two major species were deduced from outgassing rate data. It is shown that by using these data in a diffusion theory model, the outgassing rates of these major species can be predicted for arbitrary geometry and any temperature within the range studied.

Liu, C. K.↗
NASA NTRS2016

Advancements in Afterbody Radiative Heating Simulations for Earth Entry

Four advancements to the simulation of backshell radiative heating for Earth entry are presented. The first of these is the development of a flow field model that treats electronic levels of the dominant backshell radiator, N, as individual species. This is shown to allow improvements in the modeling of electron-ion recombination and two-temperature modeling, which are shown to increase backshell radiative heating by 10 to 40%. By computing the electronic state populations of N within the flow field solver, instead of through the quasi-steady state approximation in the radiation code, the coupling of radiative transition rates to the species continuity equations for the levels of N, including the impact of non-local absorption, becomes feasible. Implementation of this additional level of coupling between the flow field and radiation codes represents the second advancement presented in this work, which is shown to increase the backshell radiation by another 10 to 50%. The impact of radiative transition rates due to non-local absorption indicates the importance of accurate radiation transport in the relatively complex flow geometry of the backshell. This motivates the third advancement, which is the development of a ray-tracing radiation transport approach to compute the radiative transition rates and divergence of the radiative flux at every point for coupling to the flow field, therefore allowing the accuracy of the commonly applied tangent-slab approximation to be assessed for radiative source terms. For the sphere considered at lunar-return conditions, the tangent-slab approximation is shown to provide a sufficient level of accuracy for the radiative source terms, even for backshell cases. This is in contrast to the agreement between the two approaches for computing the radiative flux to the surface, which differ by up to 40%. The final advancement presented is the development of a nonequilibrium model for NO radiation, which provides significant backshell radiation at velocities below 10 km/s. The developed model reduces the nonequilibrium NO radiation by 50% relative to the previous model.

Johnston, Christopher O.↗
DOE OSTI2024

Statistical data analysis of x-ray spectroscopy data enabled by neural network accelerated Bayesian inference

Bayesian inference applied to x-ray spectroscopy data analysis enables uncertainty quantification necessary to rigorously test theoretical models. However, when comparing to data, detailed atomic physics and radiation transfer calculations of x-ray emission from non-uniform plasma conditions are typically too slow to be performed in line with statistical sampling methods, such as Markov Chain Monte Carlo sampling. Furthermore, differences in transition energies and x-ray opacities often make direct comparisons between simulated and measured spectra unreliable. Here, we present a spectral decomposition method that allows for corrections to line positions and bound–bound opacities to best fit experimental data, with the goal of providing quantitative feedback to improve the underlying theoretical models and guide future experiments. In this work, we use a neural network (NN) surrogate model to replace spectral calculations of isobaric hot-spots created in Kr-doped implosions at the National Ignition Facility. The NN was trained on calculations of x-ray spectra using an isobaric hot-spot model post-processed with Cretin, a multi-species atomic kinetics and radiation code. The speedup provided by the NN model to generate x-ray emission spectra enables statistical analysis of parameterized models with sufficient detail to accurately represent the physical system and extract the plasma parameters of interest.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Predicting Antimicrobial Resistance Using Partial Genome Alignments

Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and predict AMR phenotypes can help to mitigate the spread of AMR by informing clinical decision making and appropriate mitigation strategies. Many bioinformatic methods have been developed for predicting AMR phenotypes from whole-genome sequences and AMR genes, but recent studies have indicated that predictions can be made from incomplete genome sequence data. In order to more systematically understand this, we built random forest-based machine learning classifiers for predicting susceptible and resistant phenotypes for Klebsiella pneumoniae (1,640 strains), Mycobacterium tuberculosis (2,497 strains), and Salmonella enterica (1,981 strains). We started by building models from alignments that were based on a reference chromosome for each species. We then subsampled each chromosomal alignment and built models for the resulting subalignments, finding that very small regions, representing approximately 0.1 to 0.2% of the chromosome, are predictive. In K. pneumoniae, M. tuberculosis, and S. enterica, the subalignments are able to predict multiple AMR phenotypes with at least 70% accuracy, even though most do not encode an AMR-related function. We used these models to identify regions of the chromosome with high and low predictive signals. Finally, subalignments that retain high accuracy across larger phylogenetic distances were examined in greater detail, revealing genes and intergenic regions with potential links to AMR, virulence, transport, and survival under stress conditions. IMPORTANCE Antimicrobial resistance causes thousands of deaths annually worldwide. Understanding the regions of the genome that are involved in antimicrobial resistance is important for developing mitigation strategies and preventing transmission. Machine learning models are capable of predicting antimicrobial resistance phenotypes from bacterial genome sequence data by identifying resistance genes, mutations, and other correlated features. They are also capable of implicating regions of the genome that have not been previously characterized as being involved in resistance. In this study, we generated global chromosomal alignments for Klebsiella pneumoniae, Mycobacterium tuberculosis, and Salmonella enterica and systematically searched them for small conserved regions of the genome that enable the prediction of antimicrobial resistance phenotypes. In addition to known antimicrobial resistance genes, this analysis identified genes involved in virulence and transport functions, as well as many genes with no previous implication in antimicrobial resistance.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1981

Simultaneous spectroscopic determination of the latitudinal, seasonal, and diurnal variability of stratospheric N2O, NO, NO2, and HNO3

A program for the measurement of latitudinal, seasonal, and diurnal variations in stratospheric N2O, NO, NO2 and HNO3 is described, which uses airborne Fourier transform absorption spectroscopy to simultaneously determine columns, above 12 km, of the four molecules. The data may prove useful for comparison with two-dimensional models of stratospheric chemistry, since simultaneous measurement of several species with the same technique provides an inherently more reliable set for model comparisons, by eliminating uncorrelated atmospheric variability and reducing differences in instrumental biases.

Coffey, M. T.↗
NASA NTRS1995

Nitrogen and Oxygen Photochemistry following SL9

The collision of Shoemaker Levy 9 (SL9) with Jupiter caused many new molecular species to be deposited in the Jovian stratosphere. We use a photochemical model to follow the evolution of the impact derived species. Our results regarding the nitrogen and oxygen compounds are presented here. NH3 photolysis initiates the nitrogen photochemistry. Much of the nitrogen ends up in N2, nitrogen-sulfur compounds, and HCN, but NH3 and nitriles such as C2H3CN may also exist in observable quantities for a year or so after the impacts. Oxygen species survive for a long time in the Jovian stratosphere. The only major oxygen containing compounds that exhibit dramatic changes in the lower stratosphere in the first year following the impacts are SO, SO2, and OCS - H2O, CO2, and CO are comparatively stable. We discuss the important photochemical processes operating on the nitrogen and oxygen species in the Jovian stratosphere, make prediction concerning the temporal variation of the major species, and identify molecules that might act as good tracers for atmospheric dynamics.

Moses, Julianne I.↗
NASA NTRS2021

Influence of the Saharan Air Layer on Hurricane Nadine (2012). Part I: Observations from the Hurricane and Severe Storm Sentinel (HS3) Investigation and Modeling Results

This study uses a model with aerosol–cloud–radiation coupling to examine the impact of Saharan dust and other aerosols on Hurricane Nadine (2012). To study aerosol direct (radiation) and indirect (cloud microphysics) effects from individual, as well as all aerosol species, eight different NU-WRF Model simulations were conducted. In several simulations, aerosols led to storm strengthening, followed by weakening relative to the control simulation. This variability of the aerosol impact may be related to whether aerosols are ingested into clouds within the outer rainbands or the eyewall. Upper-tropospheric aerosol concentrations indicate vertical transport of all aerosol types in the outer bands but only vertical transport of sea salt in the inner core. The results suggest that aerosols, particularly sea salt, may have contributed to a stronger initial intensification but that aerosol ingestion into the outer bands at later times may have weakened the storm in the longer term. In most aerosol experiments, aerosols led to a reduction in cloud and precipitation hydrometeors, the exception being the dust-only case that produced periods of enhanced hydrometeor growth. The Saharan air layer (SAL) also impacted Nadine by causing a region of strong easterlies impinging on the eastern side of the storm. At the leading edge of these easterlies, cool and dry air near the top of the SAL was being ingested into the outer-band convection. This midlevel low-equivalent-potential-temperature air gradually lowered toward the surface and eventually contributed to significant cold-pool activity in the eastern rainband and in the northeast quadrant of the storm. Such enhanced downdraft activity could have led to weakening of the storm, but it is not presently possible to quantify this impact.

Jainn J. Shi↗
DOE OSTI2022

Vaccine-Associated Enhanced Respiratory Disease following Influenza Virus Infection in Ferrets Recapitulates the Model in Pigs

Influenza A virus (IAV) causes respiratory disease in swine and humans. Vaccines are used to prevent influenza illness in both populations but must be frequently updated due to rapidly evolving strains. Mismatch between the circulating strains and the strains contained in vaccines may cause loss of efficacy. Whole inactivated virus (WIV) vaccines with adjuvant, utilized by the swine industry, are effective against antigenically similar viruses; however, vaccine-associated enhanced respiratory disease (VAERD) may happen when the WIV is antigenically mismatched with the infecting virus. VAERD is a repeatable model in pigs, but had yet to be experimentally demonstrated in other mammalian species. We recapitulated VAERD in ferrets, a standard benchmark animal model for studying human influenza infection, in a direct comparison to VAERD in pigs. Both species were vaccinated with WIV with oil-in-water adjuvant containing a d -1 H1N2 (1B.2.2) derived from the pre-2009 human seasonal lineage, then challenged with a 2009 pandemic H1N1 (H1N1pdm09, 1A.3.3.2) 5 weeks after vaccination. Nonvaccinated and challenged groups showed typical signs of influenza disease, but the mismatched vaccinated and challenged pigs and ferrets showed elevated clinical signs, despite similar viral loads. VAERD-affected pigs exhibited a 2-fold increase in lung lesions, while VAERDaffected ferrets showed a 4-fold increase. Similar to pigs, antibodies from VAERD-affected ferrets preferentially bound to the HA2 domain of the H1N1pdm09 challenge strain. These results indicate that VAERD is not limited to pigs, as demonstrated here in ferrets, and the need to consider VAERD when evaluating new vaccine platforms and strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Regularized machine learning on molecular graph model explains systematic error in DFT enthalpies

Abstract A major goal of materials research is the discovery of novel and efficient heterogeneous catalysts for various chemical processes. In such studies, the candidate catalyst material is modeled using tens to thousands of chemical species and elementary reactions. Density Functional Theory (DFT) is widely used to calculate the thermochemistry of these species which might be surface species or gas-phase molecules. The use of an approximate exchange correlation functional in the DFT framework introduces an important source of error in such models. This is especially true in the calculation of gas phase molecules whose thermochemistry is calculated using the same planewave basis set as the rest of the surface mechanism. Unfortunately, the nature and magnitude of these errors is unknown for most practical molecules. Here, we investigate the error in the enthalpy of formation for 1676 gaseous species using two different DFT levels of theory and the ‘ground truth values’ obtained from the NIST database. We featurize molecules using graph theory. We use a regularized algorithm to discover a sparse model of the error and identify important molecular fragments that drive this error. The model is robust to rigorous statistical tests and is used to correct DFT thermochemistry, achieving more than an order of magnitude improvement.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Assessment of Bird Strike Likelihood to Refine Bird Strike Risk Models

In its most basic form, bird strike risk is comprised of a frequency component that reflects the likelihood of a collision and a severity component that reflects the cost (monetary or otherwise) of the incident. The bird strike risk model currently used by United State Department of Agriculture (USDA) Wildlife Services to evaluate the risk posed by individual bird species at airports and establish priorities for management was developed in 2018. The model uses airport-specific data on the number of reported strikes for a species recorded in the Federal Aviation Administration (FAA)’s National Wildlife Strike Database as a measure of frequency and the species’ relative hazard score as a measure of severity. The model was tested against independent data, found to perform well overall, and is being implemented widely across the United States. However, the model has limitations, including that species known to pose risk to aircraft locally, but not present in the strike record database, are not reflected as a major component of risk. Standard bird survey methodology commonly used at airports (e.g. point counts or transects) potentially can be used to complement wildlife strike records to calculate frequency or relative abundance of species. However, these methods generally focus on airport-wide population estimation and often ignore vital information that contributes to the true likelihood of a strike, such as use of runway protection zones and other critical areas, and spatial and temporal overlap with departing or approaching aircraft. As such, a more detailed understanding of space use by birds across landcovers and population fluctuations across the year is needed to accurately estimate the likelihood of bird strikes at airports. In this manuscript, we will review the extant risk model, including a discussion on its limitations. We then discuss approaches for refining our understanding of strike likelihood and briefly touch on needs for estimating probability of strike severity (cost).

bird strike, aircraft collision, damage by wildlif↗
NASA NTRS1988

Simulation of the transport of halogen species from the equatorial and mid-latitude stratosphere to the polar stratosphere in a two-dimensional model

The bulk of O sub 3 destruction in the Antarctic stratosphere takes place in the lower stratosphere between 15 and 25 km. Both O sub 3 and the halogen reservoir species have their origins in the higher altitude region (20 to 30 km) in the equatorial and mid-latitude stratosphere. Using the Caltech-JPL two-dimensional residual circulation model, researchers investigate the growth of stratospheric halogen due to the increase of CFCl sub 3 and CF sub 2 Cl sub 2.

Yung, Yuk L.↗
DOE OSTI2024

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Efficient generation of bone morphogenetic protein 15-edited Yorkshire pigs using CRISPR/Cas9†

Abstract Bone morphogenetic protein 15 (BMP15), a member of the transforming growth factor beta (TGF-β) superfamily, plays an essential role in ovarian follicular development in mono-ovulatory mammalian species. Studies using a biallelic knockout mouse model revealed BMP15 potentially has just a minimal impact on female fertility and ovarian follicular development in poly-ovulatory species. In contrast, our previous study demonstrated that in vivo knockdown of BMP15 significantly affected porcine female fertility, as evidenced by the dysplastic ovaries containing significantly decreased numbers of follicles and an increased number of abnormal follicles. This finding implied that BMP15 plays an important role in the regulation of female fertility and ovarian follicular development in poly-ovulatory species. To further investigate the regulatory role of BMP15 in porcine ovarian and follicular development, here, we describe the efficient generation of BMP15-edited Yorkshire pigs using CRISPR/Cas9. Using artificial insemination experiments, we found that the biallelically edited gilts were all infertile, regardless of different genotypes. One monoallelically edited gilt #4 (Δ66 bp/WT) was fertile and could deliver offspring with a litter size comparable to that of wild-type gilts. Further analysis established that the infertility of biallelically edited gilts was caused by the arrest of follicular development at pre-antral stages, with formation of numerus structurally abnormal follicles, resulting in streaky ovaries and the absence of obvious estrous cycles. Our results strongly suggest that the role of BMP15 in non-rodent poly-ovulatory species may be as important as that in mono-ovulatory species.

Shi, Xuan↗
DOE OSTI2025

Investigating late-stage particle production in pp collisions with balance functions

Balance functions have been regarded in the past as a method of investigating the late-stage hadronization found in the presence of a strongly-coupled medium. They are also used to constrain mechanisms of particle production in large and small collision systems. Charge balance functions for inclusive and identified particle pairs are reported as a function of charged particle multiplicity in proton–proton collisions simulated with the PYTHIA8 and the EPOS4 models. The charge balance functions of inclusive, pion, kaon, and proton pairs exhibit amplitudes and shapes that depend on particle species and differ significantly in the two models due to the different particle production mechanisms implemented in PYTHIA and EPOS. The shapes and amplitudes also evolve with multiplicity in both models. In addition, the evolution of the longitudinal rms width and that of balance functions integrals with multiplicity (and average transverse momentum) feature significant differences in the two models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1989

Three-dimensional calculation of supersonic reacting flows using an LU scheme

A new three-dimensional numerical program incorporated with comprehensive real gas property models was developed to simulate supersonic reacting flows. The code employs an implicit finite volume, Lower-Upper (LU) time-marching method to solve the complete Navier-Stokes and species equations in a fully-coupled and very efficient manner. A chemistry model with nine species and eighteen reaction steps are adopted in the program to represent the chemical reaction of H2 and air. To demonstrate the capability of the program, flow fields of underexpanded hydrogen jets transversely injected into supersonic air stream inside the combustors of scramjets are calculated. Results clearly depict the flow characteristics, including the shock structure, separated flow regions around the injector, and the distribution of the combustion products.

Yu, Sheng-Tao↗
NASA NTRS1989

Three-dimensional calculation of supersonic reacting flows using an LU scheme

A new three-dimensional numerical program incorporated with comprehensive real gas property models has been developed to simulate supersonic reacting flows. The code employs an implicit finite volume, Lower-Upper (LU) time-marching method to solve the complete Navier-Stokes and species equations in a fully-coupled and very efficient manner. A chemistry model with nine species and eighteen reaction steps are adopted in the program to represent the chemical reaction of H2 and air. To demonstrate the capability of the program, flow fields of underexpanded hydrogen jets transversely injected into supersonic air stream inside the combustors of scramjets are calculated. Results clearly depict the flow characteristics, including the shock structure, separated flow regions around the injector, and the distribution of the combustion products.

Yu, Sheng-Tao↗
DOE OSTI2025

PERCEPTIVE: an R shiny $\underline{p}$ipelin$\underline{e}$ for the p$\underline{r}$edi$\underline{c}$tion of $\underline{ep}$igenetic modula$\underline{t}$ors $\underline{i}$n no$\underline{v}$el sp$\underline{e}$cies

Epigenetic processes are central to regulating gene expression, genome stability, and metabolic function across the tree of life; yet, their roles remain underexplored in microalgae, especially as new species continue to be identified and characterized. This is likely due to the cumbersome nature and species-dependent attributes of epigenetic wet-lab methodologies, which preclude the rapid identification of epigenetic modifications and modulators. However, there is high conservation of epigenetic processes from budding yeast to humans; in many cases, one may infer how behavior and function are epigenetically regulated in novel species by identifying epigenetic modulators, or the proteins responsible for conferring epigenetic modifications. Here, to this end, we have developed a graphical software package, titled PERCEPTIVE (pipeline for the prediction of epigenetic modulators in novel species). This platform solely uses the genomic sequence of an algal species, and preexisting information from other model organisms, to predict the epigenetic modulators and associated modifications in algae. Predictions are presented to the user in a graphical interface, which provides literature-based interpretation of results, enabling users to quickly understand potential epigenetic processes in their algal species of interest and plan follow-up experiments. To test PERCEPTIVE, we predicted epigenetic modulators in several feedstock candidate algae species. To validate these predictions, wet-lab studies were performed, including mass spectrometry; these results underscore the high accuracy of PERCEPTIVE predictions. Overall, PERCEPTIVE represents a powerful in silico tool for the research and manipulation of algal species, which does not require a priori knowledge of epigenetics and is accessible to a broad set of investigators.

59 BASIC BIOLOGICAL SCIENCES↗