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At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
NASA NTRS2002

The Fourier-Kelvin Stellar Interferometer Mission Concept

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging interferometer for the mid-infrared spectral region (5-30 microns). FKSI is conceived as a scientific and technological precursor to TPF as well as Space Infrared Interferometric Telescope (SPIRIT), Submillimeter Probe Evolution of Cosmic Structure (SPECS), and Single Aperture for Infrared Observatory (SAFIR). It will also be a high angular resolution system complementary to Next Generation Space Telescope (NGST). The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We are in the process of studying alternative interferometer architectures and beam combination techniques, and evaluating the relevant science and technology tradeoffs. Some of the technical challenges include the development of the cryocooler systems necessary for the telescopes and focal plane array, light and stiff but well-damped truss systems to support the telescopes, and lightweight and coolable optical telescopes. The goal of the design study is to determine if a mid-infrared interferometry mission can be performed within the cost and schedule requirements of a Discovery class mission. At the present time we envision the FKSI as comprised of five one meter diameter telescopes arranged along a truss structure in a linear non-redundant array, cooled to 35 K. A maximum baseline of 20 meters gives a nominal resolution of 26 mas at 5 microns. Using a Fizeau beam combination technique, a simple focal plane camera could be used to obtain both Fourier and spectral data simultaneously for a given orientation of the array. The spacecraft will be rotated to give sufficient Fourier data to reconstruct complex images of a broad range of astrophysical sources.

Danchi, W. C.↗
NASA NTRS2003

Iterative pass optimization of sequence data

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment-based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure--the iterative improvement method--to create alignments at internal nodes by solving a series of median problems. The combination of a three-sequence direct optimization with iterative improvement and a branch-length-based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

NASA Discipline Evolutionary Biology↗
NASA NTRS2000

Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.

Synechococcus Group/classification/growth & develo↗
NASA NTRS2003

The Fourier-Kelvin Stellar Interferometer (FKSI): A Discovery Class TPF/DARWIN Pathfinder Mission Concept

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging and nulling interferometer for the mid-infrared spectral region (5-30 microns). FKSI is conceived as a scientific and technological pathfinder to TPF/DARWIN as well as SPIRIT, SPECS, and SAFIR. It will also be a high angular resolution system complementary to NGST. The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We have been studying alternative interferometer architectures and beam combination techniques, and evaluating the relevant science and technology tradeoffs. Some of the technical challenges include the development of the cryocooler systems necessary for the telescopes and focal plane array, light and stiff but well-damped truss systems to support the telescopes, and lightweight and coolable optical telescopes. We present results of detailed design studies of the FKSI starting with a design consisting of five one meter diameter telescopes arranged along a truss structure in a linear non-redundant array, cooled to 35 K. A maximum baseline of 20 meters gives a nominal resolution of 26 mas at 5 microns. Using a Fizeau beam combination technique, a simple focal plane camera could be used to obtain both Fourier and spectral data simultaneously for a given orientation of the array. The spacecraft will be rotated to give sufficient Fourier data to reconstruct complex images of a broad range of astrophysical sources. Alternative and simpler three and two telescope designs emphasizing nulling and spectroscopy also have been investigated and will be discussed.

Danchi, W. C.↗
NASA NTRS2005

The Fourier-Kelvin Stellar Interferometer (FKSI): A Progress Report and Preliminary Results from Our Laboratory Testbed

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging and nulling interferometer for the near-infrared to mid-infrared spectral region (3-8 microns). FKSI is conceived as a scientific and technological pathfinder to TPF/DARWIN as well as SPIRIT, SPECS, and SAFIR. It will also be a high angular resolution system complementary to JWST. The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We report additional studies of the imaging capabilities of the FKSI with various configurations of two to five telescopes, studies of the capabilities of FKSI assuming an increase in long wavelength response to 10 or 12 microns (depending on availability of detectors), and preliminary results from our nulling testbed.

Berry, Richard↗
DOE OSTI2021

The APOGEE Data Release 16 Spectral Line List

The updated H-band spectral-line list (from λ15000–17000) adopted by the Apache Point Observatory Galactic Evolution Experiment (APOGEE) for the SDSS-IV Data Release 16 (DR16) is presented in this work. The APOGEE line list is a combination of atomic and molecular lines, with data drawn from laboratory, theoretical, and astrophysical sources. Oscillator strengths and damping constants are adjusted using high signal-to-noise, high-resolution spectra of the Sun, and α Boo (Arcturus), as “standard stars.” Updates to the DR16 line list, as compared to the previous DR14 version, include the addition of molecular H{sub 2}O and FeH lines, as well as a much larger (by a factor of ∼4) atomic line list, including a significantly greater number of transitions with hyperfine splitting. More recent references and line lists for the crucial molecules, CO and OH, as well as for C{sub 2} and SiH, are also included. In contrast to DR14, DR16 contains measurable lines from the heavy neutron-capture elements cerium (as Ce ii), neodymium (as Nd ii), and ytterbium (as Yb ii), as well as one line from rubidium (as Rb i), which may be detectable in a small fraction of APOGEE red giants.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2003

Radioastronomical Searches for Instellar Biomolecules

Impacts of comets and asteroids could have delivered large amounts of organic matter to the early Earth. to retain a significant interstellar signature; observations of recent bright comets indicate that they have a molecular inventory consistent with their ices being largely unmodified interstellar material. Many simple organic molecules with biochemical significance observed in circumstellar envelopes and in molecular clouds, similar to that from which the Solar System formed, may have acted as the precursors of the more complex organics found in meteorites. Therefore, there is potentially a strong link between interstellar organics and prebiotic chemical evolution. Radioastronomical observations, particularly at millimeter wavelengths, allow us to determine the chemical composition and characteristics of the molecular inventory in interstellar space. Here we report some of our recent results from extensive astronomical searches for astrobiologically-important interstellar organics.

Kuan, Y.-J.↗
DOE OSTI2025

Methanol at Water–TiO 2 Interfaces: Free Energies of Water and Methanol Dissociation

Methanol adsorption on TiO 2 surfaces has long been studied due to its role in enhancing photocatalytic hydrogen evolution, yet how it modulates surface chemistry under aqueous conditions remains little understood. Using molecular dynamics with an ab initio-based deep neural network potential, we find that methanol adsorption induces markedly different effects on the aqueous surfaces of anatase and rutile, the two common phases of TiO 2 . In anatase, methanol adsorption significantly enhances water dissociation, which is otherwise rare at the neat water interface. This enhancement arises from an alternative dissociation pathway mediated by surface-bound methoxyl groups. In contrast, methanol adsorption tends to suppress water dissociation on rutile, replacing it with thermodynamically favored methanol dissociation. Overall, methanol adsorption in an aqueous environment alters not only the availability of key reactive intermediates involved in hydrogen evolution but also the hydrogen source, which turns out to be primarily methanol on rutile, whereas both water and methanol are consumed on anatase. These results provide mechanistic insights into the coupled roles of organic adsorbates and water at photocatalytic interfaces, with implications on how methanol enhances the activity of H 2 evolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Molecular gas and star formation in HI-deficient Virgo cluster galaxies

Mapping of the CO emission line in 42 Virgo cluster galaxies reveals that the molecular gas contents and distributions are roughly normal in severaly HI-deficient Virgo spirals. The survival of the molecular component mitigates the impact of the HI-stripping on star formation and subsequent galactic evolution. For spirals which are deficient in HI by a factor of 10, far-infrared, H alpha line, and nonthermal radio continuum luminosities are lower by no more than a factor of 2. The fact that the inner galactic disks are stripped of HI, while CO is normal, suggests that the lifetime of the molecular phase is approximately one billion years in the inner regions of luminous spirals.

Kenney, Jeffrey D.↗
NASA NTRS1991

A simulation of the collapse and fragmentation of cooling molecular clouds

The application of the Smoothed Particle Hydrodynamics method to the fragmentation of rotating cloud and disk systems is described, allowing for molecular cooling due to H2 and CO. A novel approach to solving Poisson's equation for disklike structures which exploits the multigrid algorithm is also described. Numerical studies are presented which investigate the evolution of both rotating clouds and Maclaurin disks, in each case with both an isothermal equation of state and with molecular cooling. The results establish the influence of molecular cooling on the fragmentation of molecular clouds. The isothermal sequences, if they fragment at all, do so into far fewer lumps than the cooling sequences. This is not due to a cooling instability as such, but rather to the reduced thermal support. One of the sequences shows a remarkable similarity to the W49A star-forming region.

Monaghan, Joe J.↗
DOE OSTI2025

Physicochemical and Molecular Insights into the Boundary Layer and Free Troposphere Aerosol Interactions over the Southern Great Plains

Ambient aerosols’ vertical profiles are critical for evaluating the role of aerosols in atmospheric chemistry and radiative transfer, but limited data on these profiles hinders our ability to fully assess their impact on the Earth's radiative balance. Here, in this study, we investigated the size-, time-, and altitude resolved composition of individual particles and bulk molecular composition of particle samples collected by an uncrewed aerial system–ArcticShark over the Southern Great Plains. Single particle microanalysis shows that, the free tropospheric (FT) samples are dominated (56-66%) by carbonaceous sulfate particles, while boundary layer (BL) samples are dominated (57-74%) by carbonaceous particles. Back trajectory simulations suggest that FT particles are likely influenced by long-range transport and have undergone aqueous-phase processing. Conversely, in-situ size distribution data shows evidence of particle growth in the upper BL and just below the FT. This observation may indicate vertical transport of particles from an elevated aerosol layer in the FT, possibly linked to a new particle formation event. This observation is further supported by high resolution molecular composition data, which reveals particle volatility increasing with increasing size, which aligns with the growth event. This study aids in fundamental understanding of the compositional and molecular specificity of vertically resolved organic aerosols to provide insights into particle size evolution for future atmospheric models.

ArcticShark↗
DOE OSTI2026

Convergent evolution of aerobic fermentation through divergent mechanisms acting on key shared glycolytic genes

As the tree of life becomes increasingly accessible to molecular investigations, describing mechanisms underlying evolutionary convergence and constraint will be crucial to understanding diversification. The lineage including the model yeast Saccharomyces cerevisiae evolved aerobic fermentation in part through an ancient whole genome duplication and retention of glycolytic genes. To evaluate glycolytic rates across diverse yeasts, we developed and deployed an extracellular acidification rates (ECAR) assay on 299 species that span more than 400 million years of evolution and identified a clade in the genus Saturnispora that convergently evolved aerobic fermentation. Through comparative genomics and transcriptomics, we found that several glycolytic genes had higher expression and novel cis-regulatory elements in aerobically fermenting Saturnispora species. When the transcription factor required for their activation was deleted in Saturnispora dispora, the mutants had reduced glycolytic rates and increased respiration. Intriguingly, many of the upregulated genes are orthologous to duplicated glycolytic genes in S. cerevisiae. These divergent genetic mechanisms affecting the same set of genes suggest that there are strong evolutionary constraints on how aerobic fermentation can arise.

Horianopoulos, Linda C. [Great Lakes Bioenergy Res↗
NASA NTRS1996

Evidence for the Evolution of Grain Properties in the NGC 2024 Star Forming Ridge

High-resolution images of the NGC 2024 molecular ridge in CS(2-1) and 3 mm continuum emission have been obtained using the Owens Valley millimeter array. The data are used to determine the temperature and dynamics of the ridge, and to ascertain the evolutionary state of the embedded protostars FIR2-7. Dust continuum emission is detected from all six FIR sources. The CS(2-1) follows the ridge closely, but does not always coincide with the FIR sources. Direct comparison of column density estimates derived from the CS and the dust emission in the ridge shows that for all FIR sources except FIR5 both methods are in agreement to within a factor of two, assuming a dust opacity k(sub 3 mm) = 0.01 cm(exp 2)/g. However, away from the FIR sources strong CS(1-0) emission is observed in several compact clumps which, with the above dust opacity, should have been detected in 3 mm dust continuum. The brightness temperature of the CS, approx. 40 K, rules out the possibility that the high line-to-continuum ratio is due to low gas temperatures; the discrepancy can be resolved if k(sub 3 mm) is a factor of 10 lower away from the FIR sources. A new high-resolution image of the 450-micron dust continuum emission obtained using the James Clerk Maxwell Telescope supports this hypothesis. These results suggest an evolution in the physical properties of the dust grains, possibly grain size, between quiescent regions in the ridge and the sites of active star formation.

Chandler, C. J.↗
DOE OSTI2023

Ploidy evolution in a wild yeast is linked to an interaction between cell type and metabolism

Ploidy is an evolutionarily labile trait, and its variation across the tree of life has profound impacts on evolutionary trajectories and life histories. The immediate consequences and molecular causes of ploidy variation on organismal fitness are frequently less clear, although extreme mating type skews in some fungi hint at links between cell type and adaptive traits. Here, we report an unusual recurrent ploidy reduction in replicate populations of the budding yeast Saccharomyces eubayanus experimentally evolved for improvement of a key metabolic trait, the ability to use maltose as a carbon source. We find that haploids have a substantial, but conditional, fitness advantage in the absence of other genetic variation. Using engineered genotypes that decouple the effects of ploidy and cell type, we show that increased fitness is primarily due to the distinct transcriptional program deployed by haploid-like cell types, with a significant but smaller contribution from absolute ploidy. The link between cell-type specification and the carbon metabolism adaptation can be traced to the noncanonical regulation of a maltose transporter by a haploid-specific gene. This study provides novel mechanistic insight into the molecular basis of an environment–cell type fitness interaction and illustrates how selection on traits unexpectedly linked to ploidy states or cell types can drive karyotypic evolution in fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

In vitro continuous protein evolution empowered by machine learning and automation

Directed evolution has become one of the most successful and powerful tools for protein engineering. However, the efforts required for designing, constructing, and screening a large library of variants can be laborious, time-consuming, and costly. With the recent advent of machine learning (ML) in the directed evolution of proteins, researchers can now evaluate variants in silico and guide a more efficient directed evolution campaign. Furthermore, recent advancements in laboratory automation have enabled the rapid execution of long, complex experiments for high-throughput data acquisition in both industrial and academic settings, thus providing the means to collect a large quantity of data required to develop ML models for protein engineering. In this perspective, here we propose a closed-loop in vitro continuous protein evolution framework that leverages the best of both worlds, ML and automation, and provide a brief overview of the recent developments in the field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural plasticity enables evolution and innovation of RuBisCO assemblies

Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
NASA NTRS2024

Analysis of Ryugu Fluid Inclusions: An Update

The most direct and convincing evidence for the presence of water and organic molecules on protoplanetary bodies is provided by fluid inclusions trapped in secondary minerals. Our previous work has demonstrated that early solar system fluids have survived as fluid inclusions in a Ryugu pyrrhotite crystal [2]. We hypothesize that the bulk molecular and isotopic composition of individual Ryugu fluid inclusions can be measured to provide ground truth for exploring and thermochemical modeling of the compositional and isotopic evolution of fluids in protoplanetary bodies including asteroids, comets and icy moons. This presentation is an update on our efforts to make measurements of elemental, molecular and, in particular, isotopic compositions of individual aqueous fluid inclusions in Ryugu samples. The measurements we plan will permit us to (1) understand elemental composition of the aqueous fluids present on Ryugu’s progenitor body, (2) track changes in the chemical and stable isotopic composition of altering fluids in small bodies over time, (3) verify the presence of organics in Ryugu fluids, (4) verify the reported significant CO 2 in Ryugu fluids, (5) measure O and H isotopes in preserved Ryugu fluids, (6) provide constraints on temperature range calculations for the mineralizing reactions being performed by other groups using mineral pairs, (7) measure sulfur/chloride and chloride/phosphorus ratios of Ryugu fluids. We note here that recent results from Enceladus reveal the importance of phosphorus in small body aqueous brines, indicating that our proposed research will benefit studies of all current ocean worlds.

Andrei Dolocan↗