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DOE OSTI2019

Exploring a new definition of the green valley and its implications

ABSTRACT The distribution of galaxies on a colour–magnitude diagram reveals a bimodality, featuring a passively evolving red sequence and a star-forming blue cloud. The region between these two, the green valley (GV), represents a fundamental transition where quenching processes operate. We exploit an alternative definition of the GV using the 4000 Å break strength, an indicator that is more resilient than colour to dust attenuation. We compare and contrast our GV definition with the traditional one, based on dust-corrected colour, making use of data from the Sloan Digital Sky Survey. Our GV selection – that does not need a dust correction and thus does not carry the inherent systematics – reveals very similar trends regarding nebular activity (star formation, AGN, quiescence) to the standard dust-corrected 0.1(g − r). By use of high-SNR stacked spectra of the quiescent GV subsample, we derive the simple stellar population (SSP) age difference across the GV, a rough proxy of the quenching time-scale (Δt). We obtain an increasing trend with velocity dispersion (σ), from Δt ∼ 1.5 Gyr at σ = 100 km s−1, up to 3.5 Gyr at σ = 200 km s−1, followed by a rapid decrease in the most massive GV galaxies (Δt ∼ 1 Gyr at σ = 250 km s−1), suggesting two different modes of quenching, or the presence of an additional channel (rejuvenation).

Angthopo, James↗

DOE OSTI2021

Automated Generation of Integrated Digital and Spiking Neuromorphic Machine Learning Accelerators

The growing numbers of application areas for artificial intelligence (AI) methods have led to an explosion of domain-specific accelerators that could support every new machine learning (ML) algorithm advancement, clearly highlighting the need for a capability to quickly and automatically transition from algorithm definition to hardware implementation and explore design space along a variety of SWaP (size, weight and Power). The software defined architectures (SODA) synthesizer implements a compiler-based modular infrastructure for the end-to-end generation of machine learning accelerators from high-level frameworks to hardware description language. At the same time, neuromorphic computing, by mimicking how the brain operates, promises to perform artificial intelligence tasks at efficiencies orders of magnitude higher than the current conventional tensor-processing based accelerators, as demonstrated by a variety of specialized designs leveraging Spiking Neural Networks (SNNs). Nevertheless, the mapping of an artificial neural network (ANN) to solutions supporting SNNs is still a non-trivial and very device-specific task, and completely lack the possibility to design hybrid systems that integrate conventional and spiking neural models. In this paper we discuss the support for such an integrated generation leveraging the SODA Synthesizer framework and its modular structure. In particular, we present a new MLIR dialect (part of the SODA frontend) that allows expressing spiking neural network features (e.g., available resources, spiking sequences, analog signal reading, etc.) and illustrate how it enables mapping to Spiking Neurons and deployment to the related specialized hardware (which, in the digital domain, could be generated through the other existing layers of the SODA Synthesizer). We then discuss the opportunities for even deeper integration afforded by the hardware compilation infrastructure, providing a path towards the generation of complex heterogeneous artificial intelligence systems.

Curzel, Serena↗

DOE OSTI2021

Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation

ABSTRACT Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales) , respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 ( Hypocreales , Ascomycota ) was isolated from the sponge Stelletta normani . A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica . Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica . The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

Stratigraphy of the Descartes region /Apollo 16/ - Implications for the origin of samples

Analysis of terrain in the Apollo 16 Descartes landing region shows a series of features that form a stratigraphic sequence which dominates the history and petrogenesis at the site. An ancient 150-km diam crater centered on the Apollo 16 site is one of the earliest recognizable major structures. Nectaris ejecta was concentrated in a regional low at the base of the back slope of the Nectaris basin to form the Descartes Mountains. Subsequently, a 60-km diam crater formed in the Descartes Mountains centered about 25 km to the west of the site. This crater dominates the geology and petrogenetic history of the site. Stone and Smoky Mountains represent the degraded terraced crater walls, and the dark matrix breccias and metaclastic rocks derived from North and South Ray craters represent floor fallback breccias from this cratering event. The interpretation is developed that the stratigraphy of the Cayley and Descartes, and thus the historical record of the Apollo 16 region, documents the complex interaction of deposits and morphology of local and regional impact cratering events. Large local 60- to 150-km diam craters have had a dramatic and previously unrecognized effect on the history and petrology of the Apollo 16 site.

Head, J. W.↗

NASA NTRS1975

The peculiar object HD 44179 /'The red rectangle'/

A strong infrared source detected in the AFCRL sky survey is confirmed, and is identified with the binary star HD 44179, embedded in a peculiar nebula. UBVRI and broad-band photometry between 2.2 and 27 microns are combined with blue, red, and near-infrared spectra, polarimetry and spectrophotometry of the star, and a range of direct and image-tube photographs of the nebula, to suggest a composite model of the system. In this model, the infrared radiation derives from thermal emission by dust grains contained in a disklike geometry about the central object, which appears to be of spectral type B9-A0 III and which may be in pre-main-sequence evolution. Two infrared emission features are found, peaking at 8.7 and 11.3 microns, the latter corresponding to the feature seen in the spectrum of the planetary nebula NGC 7027. The complex nebular structure is discussed on the basis of photographs through narrow-band continuum and emission-line filters. The polarization data support the suggestion of a disk containing some large particles. No radio continuum emission is detected.

Cohen, M.↗

NASA NTRS1988

A multivariate variational objective analysis-assimilation method. Part 1: Development of the basic model

The variational method of undetermined multipliers is used to derive a multivariate model for objective analysis. The model is intended for the assimilation of 3-D fields of rawinsonde height, temperature and wind, and mean level temperature observed by satellite into a dynamically consistent data set. Relative measurement errors are taken into account. The dynamic equations are the two nonlinear horizontal momentum equations, the hydrostatic equation, and an integrated continuity equation. The model Euler-Lagrange equations are eleven linear and/or nonlinear partial differential and/or algebraic equations. A cyclical solution sequence is described. Other model features include a nonlinear terrain-following vertical coordinate that eliminates truncation error in the pressure gradient terms of the horizontal momentum equations and easily accommodates satellite observed mean layer temperatures in the middle and upper troposphere. A projection of the pressure gradient onto equivalent pressure surfaces removes most of the adverse impacts of the lower coordinate surface on the variational adjustment.

Achtemeier, Gary L.↗

NASA NTRS1990

Radial spreading of viscous-gravity currents with solidifying crust

In the present investigation of solidifying-crust effects on the dynamics and surface morphology of radial viscous-gravity currents, polyethylene glycol inflows into the base of a tank holding a cold sucrose solution are used as analogs. As the radial current advanced away from the inlet, its surface solidified and deformed through a combination of folding anf fracturing. When cooling was sufficiently rapid, solid crust formed and caused the spreading rate to increase; progressively colder experiments revealed a sequence of surface morphologies resembling features of cooling lava flows and lava lakes, including multiarmed rift structures with shear offsets and bulbous lobate forms resembling pillow lavas on the ocean floor.

Fink, Jonathan H.↗

NASA NTRS1990

The substorm event of 28 January 1983 - A detailed global study

A comprehensive timeline of the growth, expansion, and recovery phases of a small isolated substorm with an expansion phase onset at 07:39 U.T. on January 28, 1983 is provided. The data sets examined include those from the electron-plasma, magnetometer, and energetic-particle instruments onboard ISEE-3. In addition to these data sets, a number of other spacecraft and ground-based data is utilized, including the magnetospheric energy-input rates evaluated in the upstream solar wind and imaging sequences used for examining auroral features during growth and expansion phases. Substorm energy-input and -output relationships are estimated quantitatively, and the timing and physical dimensions of the distant tail disturbance implied by global observations available are evaluated.

Baker, D. N.↗

NASA NTRS2004

Internal Structure of the Southern Polar Cap of Mars and Formation Implications

The surfaces of the Martian polar caps have been studied in detail but little is known about their internal structure. Exposures of the cap interior can be seen in the many troughs and scarps which incise them. The layered sequences visible in these topographic features have been known to exist for many years, however first order questions concerning the internal stratigraphy remain. We have identified a prominent bench forming layer near the top of the southern layered deposits. We have mapped its exposure in high-resolution MOC images on the eastern and western scarps. These images have been carefully registered to a MOLA derived DEM so topographic measurements along this bench can be extracted along with the location of each trace. What results are a set of measurements of the top of the bench forming layer in three dimensions. The top of this layer represents a distinct stratigraphic horizon. The prominent bench outcrops on both the eastern and western scarps which bound the highest portion of the southern layered deposits. Confirmation that these are two benches are indeed the same stratigraphic surface comes from the similarity of surrounding (nonbench forming) layers.

Byrne, S.↗

NASA NTRS2002

Distant Cluster Hunting: A Comparison of X-Ray and Optical Cluster Detection Techniques and Catalogs from the ROSAT Optical X-Ray Survey - II

We present and analyze the optical and X-ray catalogs of moderate-redshift cluster candidates from the ROSA TOptical X-Ray Survey, or ROXS. The survey covers the sky area contained in the fields of view of 23 deep archival ROSA T PSPC pointings, 4.8 square degrees. The cross-correlated cluster catalogs were con- structed by comparing two independent catalogs extracted from the optical and X-ray bandpasses, using a matched-filter technique for the optical data and a wavelet technique for the X-ray data. We cross-identified cluster candidates in each catalog. As reported in Paper 1, the matched-filter technique found optical counter- parts for at least 60% (26 out of 43) of the X-ray cluster candidates; the estimated redshifts from the matched filter algorithm agree with at least 7 of 1 1 spectroscopic confirmations (Az 5 0.10). The matched filter technique. with an imaging sensitivity of ml N 23, identified approximately 3 times the number of candidates (155 candidates, 142 with a detection confidence >3 u) found in the X-ray survey of nearly the same area. There are 57 X-ray candidates, 43 of which are unobscured by scattered light or bright stars in the optical images. Twenty-six of these have fairly secure optical counterparts. We find that the matched filter algorithm, when applied to images with galaxy flux sensitivities of mI N 23, is fairly well-matched to discovering z 5 1 clusters detected by wavelets in ROSAT PSPC exposures of 8000-60,000 s. The difference in the spurious fractions between the optical and X-ray (30%) and IO%, respectively) cannot account for the difference in source number. In Paper I, we compared the optical and X-ray cluster luminosity functions and we found that the luminosity functions are consistent if the relationship between X-ray and optical luminosities is steep (Lx o( L&f). Here, in Paper 11, we present the cluster catalogs and a numerical simulation of the ROXS. We also present color-magnitude plots for several of the cluster candidates, and examine the prominence of the red sequence in each. We find that the X-ray clusters in our survey do not all have a prominent red sequence. We conclude that while the red sequence may be a distinct feature in the color-magnitude plots for virialized massive clusters, it may be less distinct in lower mass clusters of galaxies at even moderate redshifts. Multiple, complementary methods of selecting and defining clusters may be essential, particularly at high redshift where all methods start to run into completeness limits, incomplete understanding of physical evolution, and projection effects.

Donahue, Megan↗

NASA NTRS2021

Dual Quaternion Visual Servo Control

This paper focuses on a dual quaternion-based estimation and control approach for position-based visual servoing (PBVS). The pose estimation of the camera is achieved using a dual quaternion-based Extended Kalman Filter (EKF), which estimates the position and orientation of the camera based on feature points acquired through a sequence of camera images. Based on the estimation, a dual quaternion control law is developed to regulate the camera to the desired pose. Leveraging the local exponential stability of the EKF and the global exponential stability of the designed controller, a nonlinear separation principle is used to prove the stability of the joint estimation and control for PBVS. The method is distinguished from other PBVS methods in the sense that a compact representation of dual quaternion is used to represent the pose, and a joint stability of estimator and controller for PBVS in dual quaternion space is presented. The proposed dual quaternion PBVS method is validated using a simulation.

Quaternions↗

NASA NTRS1991

Parallel computation of manipulator inverse dynamics

In this article, parallel computation of manipulator inverse dynamics is investigated. A hierarchical graph-based mapping approach is devised to analyze the inherent parallelism in the Newton-Euler formulation at several computational levels, and to derive the features of an abstract architecture for exploitation of parallelism. At each level, a parallel algorithm represents the application of a parallel model of computation that transforms the computation into a graph whose structure defines the features of an abstract architecture, i.e., number of processors, communication structure, etc. Data-flow analysis is employed to derive the time lower bound in the computation as well as the sequencing of the abstract architecture. The features of the target architecture are defined by optimization of the abstract architecture to exploit maximum parallelism while minimizing architectural complexity. An architecture is designed and implemented that is capable of efficient exploitation of parallelism at several computational levels. The computation time of the Newton-Euler formulation for a 6-degree-of-freedom (dof) general manipulator is measured as 187 microsec. The increase in computation time for each additional dof is 23 microsec, which leads to a computation time of less than 500 microsec, even for a 12-dof redundant arm.

Fijany, Amir↗

NASA NTRS2020

EDL Simulation Results for the Mars 2020 Landing Site Safety Assessment

The Mars 2020 rover is NASA’s next flagship mission, set to explore Mars in search of scientific evidence of past microbial life. Importantly, the rover will also, for the first time, have the ability to collect and cache rock and soil samples for retrieval and return to laboratories here on Earth. A key step in the development of the Mars 2020 mission is the selection of a suitable landing site with the largest likelihood of meeting scientific goals. This decision is a complex and critical one that requires close interaction between the scientific and engineering communities. The chosen landing site must be both scientifically interesting — providing the project with the greatest possible chance of gathering credible and defendable scientific evidence — and also safe enough to attempt a landing in the first place. Thus, arguably one of the most important undertakings of the Entry, Descent, and Landing (EDL) team, is to effectively enumerate, quantify, and communicate the landing risks to all of the stakeholders. The culmination of this effort is the Landing Site Safety Assessment, which is a review commissioned by the project, presided over by the EDL Standing Review Board, and attended by management and science stakeholders, in which the EDL team communicates their assessment of the associated landing risks and the statistical probability of a successful landing at each of the final candidate landing sites. This paper summarizes the results of high-fidelity computer simulations of the Mars 2020 EDL sequence used in this assessment. From an EDL performance perspective, all four candidates offer similar level of robustness, which is in-family with Mars Science Laboratory (MSL). However, two new features of the Mars 2020 EDL sequence – range trigger and Terrain-Relative Navigation (TRN) – dramatically enhance the capability of the EDL system to safely land at landing sites with much more rugged terrain than ever before considered. This has allowed the landing site selection for Mars 2020 to proceed in a manner that has been unprecedentedly weighted more heavily toward scientific interest and less heavily on engineering constraints. With TRN, the overall probability of success is predicted to be approximately 99% for all of the candidates.

David Way↗

DOE OSTI2020

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

Much attention is being paid to conformational biases in the ensembles of intrinsically disordered proteins. However, it is currently unknown whether or how conformational biases within the disordered ensembles of foldable proteins affect function in vivo. Recently, we demonstrated that water can be a good solvent for unfolded polypeptide chains, even those with a hydrophobic and charged sequence composition typical of folded proteins. These results run counter to the generally accepted model that protein folding begins with hydrophobicity-driven chain collapse. Here we investigate what other features, beyond amino acid composition, govern chain collapse. We found that local clustering of hydrophobic and/or charged residues leads to significant collapse of the unfolded ensemble of pertactin, a secreted autotransporter virulence protein from Bordetella pertussis , as measured by small angle X-ray scattering (SAXS). Sequence patterns that lead to collapse also correlate with increased intermolecular polypeptide chain association and aggregation. Crucially, sequence patterns that support an expanded conformational ensemble enhance pertactin secretion to the bacterial cell surface. Similar sequence pattern features are enriched across the large and diverse family of autotransporter virulence proteins, suggesting sequence patterns that favor an expanded conformational ensemble are under selection for efficient autotransporter protein secretion, a necessary prerequisite for virulence. More broadly, we found that sequence patterns that lead to more expanded conformational ensembles are enriched across water-soluble proteins in general, suggesting protein sequences are under selection to regulate collapse and minimize protein aggregation, in addition to their roles in stabilizing folded protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗

DOE OSTI2024

Genomic factors shaping codon usage across the Saccharomycotina subphylum

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. It has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. We characterized codon usage across 1,154 strains from 1,051 species from the fungal subphylum Saccharomycotina to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns. We found a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is distinct between the 12 orders to such a degree that yeasts can be classified with an accuracy >90% using a machine learning algorithm. We also characterized the degree to which codon usage bias is impacted by translational selection. We found it was influenced by a combination of features, including the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that avoidance of the CGN codons is associated with a decline in arginine tRNA function. Consistent with previous findings, codon usage bias within the Saccharomycotina is shaped by genomic features and GC bias. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Vision-based recursive estimation of rotorcraft obstacle locations

The authors address vision-based passive ranging during nap-of-the-earth (NOE) rotorcraft flight. They consider the problem of estimating the relative location of identifiable features on nearby obstacles, assuming a sequence of noisy camera images and imperfect measurements of the camera's translation and rotation. An iterated extended Kalman filter is used to provide recursive range estimation. The correspondence problem is simplified by predicting and tracking each feature's image within the Kalman filter framework. Simulation results are presented which show convergent estimates and generally successful feature point tracking. Estimation performance degrades for features near the optical axis and for accelerating motions. Image tracking is also sensitive to angular rate.

Leblanc, D. J.↗