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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Comparison of Eulerian Bin and Lagrangian Particle-Based Schemes in Simulations of Pi Chamber Dynamics and Microphysics

This paper presents a comparison of simulations applying either a traditional Eulerian bin microphysics or a novel particle-based Lagrangian approach to represent CCN activation and cloud droplet growth. The Eulerian microphysics solve the evolution equation for the spectral density function, whereas the Lagrangian approach follows computational particles referred to as superdroplets. Each superdroplet represents a multiplicity of natural droplets that makes the Lagrangian approach computationally feasible. The two schemes apply identical representation of CCN activation and use the same droplet growth equation; these make direct comparison between the two schemes practical. The comparison, the first of its kind, applies an idealized simulation setup motivated by laboratory experiments with the Pi Chamber and previous model simulations of the Pi Chamber dynamics and microphysics. The Pi Chamber laboratory apparatus considers interactions between turbulence, CCN activation, and cloud droplet growth in moist Rayleigh–Bénard convection. Simulated steady-state droplet spectra averaged over the entire chamber are similar, with the mean droplet concentration, mean radius, and spectral width close in Eulerian and Lagrangian simulations. Small differences that do exist are explained by the inherent differences between the two schemes and their numerical implementation. The local droplet spectra differ substantially, again in agreement with the inherent limitations of the theoretical foundation behind each approach. There is a general agreement between simulations and Pi Chamber observations, with simplifications of the CCN activation and droplet growth equation used in the simulations likely explaining specific differences.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Drop size distribution broadening mechanisms in a bin microphysics Eulerian model

In this study, processes that broaden drop size distributions (DSDs) in Eulerian models with two-moment bin microphysics are analyzed. Numerous tests are performed to isolate the effects of different physical mechanisms that broaden DSDs in two- and three-dimensional Weather Research and Forecasting model simulations of an idealized ice-free cumulus cloud. Additionally, sensitivity of these effects to modifying horizontal and vertical model grid spacings is also examined. As expected, collision-coalescence is a key process broadening the modeled DSDs. In-cloud droplet activation also contributes substantially to DSD broadening, whereas evaporation has only a minor effect and sedimentation has little effect. Cloud dilution (mixing of cloud-free and cloudy air) also broadens the DSDs considerably, whether or not it is accompanied by evaporation. This mechanism involves the reduction of droplet concentration from dilution along the cloud’s lateral edges, leading to locally high supersaturation and enhanced drop growth when this air is subsequently lifted in the updraft. DSD broadening ensues when the DSDs are mixed with those from the cloud core. Decreasing the horizontal and vertical model grid spacings from 100 m to 30 m has limited impact on the DSDs. However, when these physical broadening mechanisms (in-cloud activation, collision-coalescence, dilution, etc.) are turned off, there is a reduction of DSD width by up to ~20-50% when the vertical grid spacing is decreased from 100 m to 30 m, consistent with effects of artificial broadening from vertical numerical diffusion. Nonetheless, this artificial numerical broadening appears to be relatively unimportant overall for DSD broadening when physically based broadening mechanisms in the model are included for this cumulus case.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A method for achieving complete microbial genomes and improving bins from metagenomics data

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage

Hundreds of target specific peptides are routinely discovered by peptide display platforms. However, due to the high cost of peptide synthesis only a limited number of peptides are chemically made for further analysis. Here we describe an accurate and cost effective method to bin peptides on-phage based on binding region(s), without any requirement for peptide or protein synthesis. This approach, which integrates phage and yeast display platforms, requires display of target and its alanine variants on yeast. Flow cytometry was used to detect binding of peptides on-phage to the target on yeast. Once hits were identified, they were synthesized to confirm their binding region(s) by HDX (Hydrogen deuterium exchange) and crystallography. Moreover, we have successfully shown that this approach can be implemented as part of a panning process to deplete non-functional peptides. This technique can be applied to any target that can be successfully displayed on yeast; it narrows down the number of peptides requiring synthesis; and its utilization during selection results in enrichment of peptide population against defined binding regions on the target.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Glaciation of mixed-phase clouds: insights from bulk model and bin-microphysics large-eddy simulation informed by laboratory experiment

Abstract. Mixed-phase clouds affect precipitation and radiation differently from liquid and ice clouds, posing greater challenges to their representation in numerical simulations. Recent laboratory experiments using the Pi Cloud Chamber explored cloud glaciation conditions based on increased injection of ice-nucleating particles. In this study, we use two approaches to reproduce the results of the laboratory experiments: a bulk scalar mixing model and large-eddy simulation (LES) with bin microphysics. The first approach assumes a well-mixed domain to provide an efficient assessment of the mean cloud properties for a wide range of conditions. The second approach resolves the energy-carrying turbulence, the particle size distribution, and their spatial distribution to provide more details. These modeling approaches enable a separate and detailed examination of liquid and ice properties, which is challenging in the laboratory. Both approaches demonstrate that, with an increased ice number concentration, the flow and microphysical properties exhibit the same changes in trends. Additionally, both approaches show that the ice integral radius reaches the theoretical glaciation threshold when the cloud is subsaturated with respect to liquid water. The main difference between the results of the two approaches is that the bulk model allows for the complete glaciation of the cloud. However, LES reveals that, in a dynamic system, the cloud is not completely glaciated as liquid water droplets are continuously produced near the warm lower boundary and subsequently mixed into the chamber interior. These results highlight the importance of the ice mass fraction in distinguishing the mixed-phase clouds and ice clouds.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1978

Effects of range bin shape and Doppler filter response in a digital SAR data processor

In calibrating the backscatter coefficient obtained with an imaging synthetic aperture radar (SAR) system to determine absolute values of radar cross-section and reflectivity it is common practice to use a target of known radar cross-section placed within the scene. A corner reflector acts as a point target, but the return from it may not be centered in the resolution cell. It is important, for accurate calibration, to perform straddling corrections based on the range bin and Doppler filter response curves.

Griffin, C. R.↗
NASA NTRS1989

Chi-squared and C statistic minimization for low count per bin data

Results are presented from a computer simulation comparing two statistical fitting techniques on data samples with large and small counts per bin; the results are then related specifically to X-ray astronomy. The Marquardt and Powell minimization techniques are compared by using both to minimize the chi-squared statistic. In addition, Cash's C statistic is applied, with Powell's method, and it is shown that the C statistic produces better fits in the low-count regime than chi-squared.

Nousek, John A.↗
NASA NTRS1990

User's guide: Nimbus-7 Earth radiation budget narrow-field-of-view products. Scene radiance tape products, sorting into angular bins products, and maximum likelihood cloud estimation products

The archived Earth radiation budget (ERB) products produced from the Nimbus-7 ERB narrow field-of-view scanner are described. The principal products are broadband outgoing longwave radiation (4.5 to 50 microns), reflected solar radiation (0.2 to 4.8 microns), and the net radiation. Daily and monthly averages are presented on a fixed global equal area (500 sq km), grid for the period May 1979 to May 1980. Two independent algorithms are used to estimate the outgoing fluxes from the observed radiances. The algorithms are described and the results compared. The products are divided into three subsets: the Scene Radiance Tapes (SRT) contain the calibrated radiances; the Sorting into Angular Bins (SAB) tape contains the SAB produced shortwave, longwave, and net radiation products; and the Maximum Likelihood Cloud Estimation (MLCE) tapes contain the MLCE products. The tape formats are described in detail.

Kyle, H. Lee↗
NASA NTRS1993

Converting Gravity-Bin Parameters To Spherical Harmonics

New method of computation of gravitational field of Earth provides for conversion of gravity-bin parameters to coefficients of spherical harmonics. Traditional representation of gravitational field recovered by new method.

Wu, Jiun-Tsong↗
NASA NTRS2012

Evaluation of Cloud Microphysics Simulated using a Meso-Scale Model Coupled with a Spectral Bin Microphysical Scheme through Comparison with Observation Data by Ship-Borne Doppler and Space-Borne W-Band Radars

Equivalent radar reflectivity factors (Ze) measured by W-band radars are directly compared with the corresponding values calculated from a three-dimensional non-hydrostatic meso-scale model coupled with a spectral-bin-microphysical (SBM) scheme for cloud. Three case studies are the objects of this research: one targets a part of ship-borne observation using 95 GHz Doppler radar over the Pacific Ocean near Japan in May 2001; other two are aimed at two short segments of space-borne observation by the cloud profiling radar on CloudSat in November 2006. The numerical weather prediction (NWP) simulations reproduce general features of vertical structures of Ze and Doppler velocity. A main problem in the reproducibility is an overestimation of Ze in ice cloud layers. A frequency analysis shows a strong correlation between ice water contents (IWC) and Ze in the simulation; this characteristic is similar to those shown in prior on-site studies. From comparing with the empirical correlations by the prior studies, the simulated Ze is overestimated than the corresponding values in the studies at the same IWC. Whereas the comparison of Doppler velocities suggests that large-size snowflakes are necessary for producing large velocities under the freezing level and hence rules out the possibility that an overestimation of snow size causes the overestimation of Ze. Based on the results of several sensitivity tests, we conclude that the source of the overestimation is a bias in the microphysical calculation of Ze or an overestimation of IWC. To identify the source of the problems needs further validation research with other follow-up observations.

Iguchi, T.↗
NASA NTRS2019

MOA-bin-29b: A Microlensing Gas-giant Planet Orbiting a Low-mass Host Star

We report the discovery of a gas-giant planet orbiting a low-mass host star in the microlensing event MOA-bin-29 that occurred in 2006. We find five degenerate solutions with the planet/host-star mass ratio of q ∼ 10(exp−2). The Einstein radius crossing time of all models are relatively short (∼4–7 days), which indicates that the mass of host star is likely low. The measured lens-source proper motion is 5–9 mas/yr depending on the models. Since only finite source effects are detected, we conduct a Bayesian analysis in order to obtain the posterior probability distribution of the lens physical properties. As a result, we find the lens system is likely to be a gas-giant orbiting a brown dwarf or a very late M-dwarf in the Galactic bulge. The probability distributions of the physical parameters for the five degenerate models are consistent within the range of error. By combining these probability distributions, we conclude that the lens system is a gas giant with a mass of M(p)= 0.63(sub +1.13, sub 0.39) M(Jup) orbiting a brown dwarf with a mass of M(h)= 0.06 (sup +0.11, sub -0.04) M(ʘ) at a projected star–planet separation of r⊥ = 0.53(sup +0.89, sub -0.18)au . The lens distance is D(L)= 6.89(sup +1.19, sub -1.19) kpc, i.e., likely within the Galactic bulge.

Iona Kondo↗
DOE OSTI2024

On Quantum Rainbows: Density Operator in the Frequency-Bin Representation for Entangled Twin-Photons Generated With Sub-Threshold Microcombs

Kerr optical frequency combs are generated by pumping a high-Q integrated microresonator with a resonant laser. Below threshold, the pump laser field mediates the phenomenon of spontaneous four-wave mixing, where two pump photons are symmetrically up- and down-converted as twin photons that can be entangled across up to tens of eigenmodes in the spectral domain. While these room-temperature integrated photonic circuits are expected to play a central role in quantum technology, their high dimensionality and dissipative nature are a challenge for their theoretical description, therefore hindering the understanding of their properties and potential of performance. In this article, we develop a framework that permits to obtain an explicit solution for the density operator of quantum microcombs below threshold. Furthermore, this self-consistent theoretical description allows for their complete characterization, as well as for the analytical determination of various performance metrics such as fidelity, purity, and entropy.

42 ENGINEERING↗